https://teaching.healthtech.dtu.dk/22145/api.php?action=feedcontributions&feedformat=atom&user=Carol 2026-09-07T08:40:09Z User contributions MediaWiki 1.41.0 https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=133 2026-08-27T12:37:03Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in the written exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — TBD.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 '''EXAM'''<br /> : 11-12 '''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=132 2026-08-27T12:34:02Z

<p>Carol: /* Wednesday, 28 October 2026 — B-cell epitope prediction */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — TBD.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 '''EXAM'''<br /> : 11-12 '''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=131 2026-08-26T22:30:33Z

<p>Carol: /* Wednesday, 16 September 2026 — MHC binding prediction, Part 2 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 '''EXAM'''<br /> : 11-12 '''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=130 2026-08-26T22:29:21Z

<p>Carol: /* Wednesday, 11 November 2026 — Written EXAM */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 '''EXAM'''<br /> : 11-12 '''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=129 2026-08-26T22:29:04Z

<p>Carol: /* Wednesday, 11 November 2026 — Written EXAM */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 '''EXAM'''<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=128 2026-08-26T22:28:11Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> In order to get access to the written exam you should submit first all the exercises<br /> <br /> The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=127 2026-08-26T22:23:56Z

<p>Carol: /* Wednesday, 25 November 2026 — Project work */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=126 2026-08-26T22:23:47Z

<p>Carol: /* Wednesday, 18 November 2026 — Project work */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=125 2026-08-26T22:22:53Z

<p>Carol: /* Wednesday, 28 October 2026 — B-cell epitope prediction */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=124 2026-08-26T22:22:27Z

<p>Carol: /* Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=123 2026-08-26T22:21:33Z

<p>Carol: /* Wednesday, 21 October 2026 — BCR and TCR structure prediction */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=122 2026-08-26T22:20:49Z

<p>Carol: /* Wednesday, 14 October 2026 — Autumn break */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=121 2026-08-26T22:20:07Z

<p>Carol: /* Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises: To be updated'''<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=120 2026-08-26T22:19:12Z

<p>Carol: /* Wednesday, 7 October 2026 — Vaccine design */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=119 2026-08-26T22:13:49Z

<p>Carol: /* Wednesday, 23 September 2026 — Antigen processing and presentation */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: To be updated'''<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=118 2026-08-26T22:11:55Z

<p>Carol: /* Wednesday, 16 September 2026 — MHC binding prediction, Part 2 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=117 2026-08-26T22:10:43Z

<p>Carol: /* Wednesday, 16 September 2026 — MHC binding prediction, Part 2 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''<br /> <br /> &lt;!--<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=116 2026-08-26T22:10:23Z

<p>Carol: /* Wednesday, 16 September 2026 — MHC binding prediction, Part 2 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2'''<br /> <br /> &lt;!--<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=115 2026-08-26T22:07:08Z

<p>Carol: /* Wednesday, 16 September 2026 — MHC binding prediction, Part 2 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=114 2026-08-26T22:05:20Z

<p>Carol: /* Wednesday, 2 September 2026 — Introduction and databases */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=113 2026-08-26T22:05:02Z

<p>Carol: /* Wednesday, 2 September 2026 — Introduction and databases */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=112 2026-08-26T22:04:41Z

<p>Carol: /* Wednesday, 9 September 2026 — MHC binding prediction, Part 1 */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:'''<br /> :* ''[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=111 2026-08-26T22:00:09Z

<p>Carol: /* Wednesday, 2 September 2026 — Introduction and databases */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material:''' <br /> :* ''Video: Immunology Recap''<br /> :* ''Video: Adaptive Immunity''<br /> :* ''Book chapter: The adaptive Immune system''<br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> :'''Exercise:'''<br /> :* ''[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]''<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=110 2026-08-26T21:54:00Z

<p>Carol: /* Wednesday, 2 September 2026 — Introduction and databases */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Preparation material: Videos and a book chapter''' <br /> <br /> :'''Lectures: We start at 9am'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' <br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=109 2026-08-26T20:59:54Z

<p>Carol: /* General information */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=108 2026-08-26T20:58:41Z

<p>Carol: /* DTU Learn link */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=107 2026-08-26T20:57:41Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=106 2026-08-26T20:51:30Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in DTU guidelines.<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=105 2026-08-26T20:50:29Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in DTU guidelines.<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's [https://www.inside.dtu.dk/en/research/good-scientific-conduct code of honour] and Principles for good scientific conduct.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=104 2026-08-26T20:49:06Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> <br /> All aids are permitted during the written exam, including books, papers, and notes. <br /> '''Internet is not allowed in written the exam''' <br /> You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in DTU guidelines.<br /> <br /> Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built. <br /> <br /> Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected. <br /> <br /> You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and Principles for good scientific conduct.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=103 2026-08-26T20:33:28Z

<p>Carol: /* Teachers */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=102 2026-08-26T20:31:34Z

<p>Carol: /* Course content */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course co-responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=101 2026-08-26T20:29:58Z

<p>Carol: /* Teachers */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course co-responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=100 2026-08-12T15:01:18Z

<p>Carol: /* Hand-ins */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=99 2026-08-12T15:00:06Z

<p>Carol: /* Course content */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a &quot;in class&quot; written exam on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=98 2026-08-12T14:59:29Z

<p>Carol: /* Course content */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts: <br /> * Part 1 consists of lectures and group-based exercises. Part 1 ends with a in class written exam without internet on November 11th.<br /> * Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=97 2026-08-12T14:40:39Z

<p>Carol: /* Where and when */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=96 2026-08-12T14:39:09Z

<p>Carol: /* Lecture and exercise plan */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===<br /> <br /> <br /> :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Written EXAM ===<br /> <br /> : 9-11 EXAM<br /> : 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=95 2026-08-06T10:40:30Z

<p>Carol: /* Exam */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — Written Exam ===<br /> <br /> &lt;!--<br /> :'''Lecture:''' ''TCR interaction models'' — To be announced.<br /> :'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=94 2026-08-06T10:37:44Z

<p>Carol: /* Wednesday, 4 November 2026 — TCR interaction models */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — Written Exam ===<br /> <br /> &lt;!--<br /> :'''Lecture:''' ''TCR interaction models'' — To be announced.<br /> :'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> <br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> === Friday, 18 December 2026 ===<br /> <br /> '''Provisional winter exam (E5-A, 2026):''' Go to https://eksamen.dtu.dk/ and search for course 22145. Please confirm the official date and time in the DTU exam system.<br /> <br /> &lt;!--<br /> === Link collection ===<br /> A quick overview of the websites used in the course: [[Link collection]].<br /> <br /> === FAQ ===<br /> Questions received and answered: [[FAQ]].<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=93 2026-08-06T10:34:53Z

<p>Carol: /* Lecture and exercise plan */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> <br /> === Wednesday, 23 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — TCR interaction models ===<br /> <br /> :'''Lecture:''' ''TCR interaction models'' — To be announced.<br /> :'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> === Friday, 18 December 2026 ===<br /> <br /> '''Provisional winter exam (E5-A, 2026):''' Go to https://eksamen.dtu.dk/ and search for course 22145. Please confirm the official date and time in the DTU exam system.<br /> <br /> &lt;!--<br /> === Link collection ===<br /> A quick overview of the websites used in the course: [[Link collection]].<br /> <br /> === FAQ ===<br /> Questions received and answered: [[FAQ]].<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=92 2026-08-06T10:28:55Z

<p>Carol: /* Where and when */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. <br /> <br /> The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to change.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 23 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — TCR interaction models ===<br /> <br /> :'''Lecture:''' ''TCR interaction models'' — To be announced.<br /> :'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> === Friday, 18 December 2026 ===<br /> <br /> '''Provisional winter exam (E5-A, 2026):''' Go to https://eksamen.dtu.dk/ and search for course 22145. Please confirm the official date and time in the DTU exam system.<br /> <br /> &lt;!--<br /> === Link collection ===<br /> A quick overview of the websites used in the course: [[Link collection]].<br /> <br /> === FAQ ===<br /> Questions received and answered: [[FAQ]].<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=91 2026-08-06T10:27:05Z

<p>Carol: </p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Classes are held on Wednesdays from 09:00 to 12:00 in '''Building 208, teaching room 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''. Unless otherwise specified, classes begin at 09:00.<br /> <br /> The first hour of each class is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn.<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.<br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] — Professor and course coordinator.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.<br /> <br /> === Course content ===<br /> <br /> The course introduces students to state-of-the-art methods in computational immunology.<br /> <br /> The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 consists of lectures and group-based exercises. Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course.<br /> <br /> See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.<br /> <br /> Group submissions are permitted and recommended.<br /> <br /> ''The hand-ins do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.<br /> <br /> === Exam ===<br /> <br /> The assessment consists of two parts: a group oral project presentation with individual questions at the end of the course, and a final two-hour written exam. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.<br /> <br /> The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''<br /> <br /> All aids are permitted during the exam, including books, papers, and notes. You will have '''open access to the internet''', including all materials and websites used during the course. You may also search for information using ChatGPT, Google, Wikipedia, and similar resources. However, you are ''not'' permitted to communicate with other people through email, social media, chat services, or file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.<br /> <br /> AI tools are permitted, but you must clearly state where and how you used them in your answers. Please use generative AI carefully: it may produce overly general answers and could cost you valuable exam time.<br /> <br /> === DTU Learn link ===<br /> <br /> * DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> <br /> We welcome comments, suggestions, criticism, and praise throughout the semester. You can:<br /> <br /> * email the teachers; or<br /> * post under &quot;General feedback&quot; in the &quot;Discussion&quot; area on DTU Learn.<br /> <br /> You may comment on messages posted in the discussion area. When you agree with a comment, please reply with &quot;Agree!&quot; so that the teaching team can see that the feedback is shared by more than one person.<br /> <br /> A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].<br /> <br /> == Lecture and exercise plan ==<br /> <br /> '''Note:''' This is a ''preliminary'' plan and may be subject to change.<br /> <br /> === Wednesday, 2 September 2026 — Introduction and databases ===<br /> <br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select &quot;Test of prior knowledge&quot; under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[Plain text files and Geany]]<br /> :# [[Taxonomy databases]]<br /> :'''Extra material:'''<br /> :* &quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — encyclopedia entry from 2009.<br /> :* &quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 9 September 2026 — Antigen processing and presentation ===<br /> <br /> :'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise for on-screen viewing] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :# [[ExGenbank-new|Using the GenBank database]]<br /> :'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF].<br /> <br /> :'''Background material (assumed knowledge):'''<br /> :* [[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:'''<br /> :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).<br /> :* [https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> --&gt;<br /> <br /> === Wednesday, 16 September 2026 — MHC binding prediction, Part 1 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> === Wednesday, 23 September 2026 — MHC binding prediction, Part 2 ===<br /> <br /> :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :[[ExPairwiseAlignment|Pairwise alignment]]<br /> --&gt;<br /> <br /> === Wednesday, 30 September 2026 — Vaccine design ===<br /> <br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Exercise:''' [[Exercise:_BLAST2|BLAST]].<br /> :'''Extra material:'''<br /> :: [[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' An introduction to NCBI's web interface and expect values is available on [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel].<br /> --&gt;<br /> <br /> === Wednesday, 7 October 2026 — Allergenicity and immunogenicity prediction ===<br /> <br /> :'''Lectures:'''<br /> :* ''Allergenicity prediction'' — Carolina Barra Quaglia.<br /> :* ''Immunogenicity prediction'' — Carolina Barra Quaglia.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).<br /> --&gt;<br /> <br /> :'''Slides:''' Available on DTU Learn.<br /> <br /> &lt;!--<br /> :'''Related advanced course:'''<br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Software to install:''' [https://pymol.org/2/ PyMOL].<br /> ::'''Note:''' You will need the licence file available under this week's topic on DTU Learn. The licence is valid for a limited period. For later educational use, you can register as a student at https://pymol.org/edu/index.php to obtain a personal licence file. If you do not receive an email after registering, contact help@schrodinger.com. A commercial licence is required when PyMOL is used to prepare figures for scientific publications.<br /> --&gt;<br /> <br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.<br /> :# [[Protein Structure and Visualization]].<br /> --&gt;<br /> <br /> &lt;!--<br /> :'''Extra material:'''<br /> :* [https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the 2023 annual database issue of ''Nucleic Acids Research''.<br /> :* [[PyMOL]] — tips and tricks.<br /> :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).<br /> --&gt;<br /> <br /> === Wednesday, 14 October 2026 — Autumn break ===<br /> <br /> :'''No teaching.'''<br /> <br /> === Wednesday, 21 October 2026 — BCR and TCR structure prediction ===<br /> <br /> :'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''GitHub link:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select &quot;Mid-term evaluation&quot; under course 22111. [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:'''<br /> --&gt;<br /> <br /> === Wednesday, 28 October 2026 — B-cell epitope prediction ===<br /> <br /> :'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercise:'''<br /> <br /> &lt;!--<br /> :'''Curriculum:'''<br /> :# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).<br /> :# Pages 1–8 of the &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).<br /> :#* Read the appendix on logarithms, especially log&lt;sub&gt;2&lt;/sub&gt;, if needed.<br /> :'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).<br /> :'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].<br /> --&gt;<br /> <br /> === Wednesday, 4 November 2026 — TCR interaction models ===<br /> <br /> :'''Lecture:''' ''TCR interaction models'' — To be announced.<br /> :'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.<br /> :'''Slides:''' Available on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--<br /> :'''Handouts:'''<br /> :'''Exercises:'''<br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].<br /> :'''Related advanced course:'''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].<br /> --&gt;<br /> <br /> === Wednesday, 11 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> === Wednesday, 18 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].<br /> --&gt;<br /> <br /> === Wednesday, 25 November 2026 — Project work ===<br /> <br /> :'''Lecture:''' No lecture.<br /> <br /> &lt;!--<br /> :'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.<br /> --&gt;<br /> <br /> === Wednesday, 2 December 2026 — Poster session ===<br /> <br /> :Poster presentations will begin at '''08:00'''.<br /> <br /> :'''Poster presentation agenda:''' To be announced.<br /> <br /> == Exam ==<br /> <br /> === Friday, 18 December 2026 ===<br /> <br /> '''Provisional winter exam (E5-A, 2026):''' Go to https://eksamen.dtu.dk/ and search for course 22145. Please confirm the official date and time in the DTU exam system.<br /> <br /> &lt;!--<br /> === Link collection ===<br /> A quick overview of the websites used in the course: [[Link collection]].<br /> <br /> === FAQ ===<br /> Questions received and answered: [[FAQ]].<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=90 2026-08-06T09:54:45Z

<p>Carol: /* Teaching assistant */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Wednesday from 9 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 3 at 9:00'''. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material provided on DTU Learn<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] &amp;mdash; Associate professor, course responsible.<br /> <br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] &amp;mdash; Professor, course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] &amp;mdash; PhD student<br /> <br /> === Course content ===<br /> <br /> The course aims to introduce the students to state-of-the-art methods within computational immunology.<br /> <br /> There is a strong focus on introducing the methods in context with immunology as a domain-specific knowledge area. Furthermore, an introduction to the theory of the methods will be followed by practical exercises, enabling the student to independently perform analyses. The course covers immunological bioinformatics and computational vaccinology with an outlook on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 covers lectures and group-based exercises, and part 2 will cover a group-based research project with the output being a poster presentation on the last day of the course. <br /> <br /> See also [http://kurser.dtu.dk/course/22145 the course base about 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no formal textbook. The curricula consist of lectures and exercises performed in class, supplemented with various papers and book chapters which will be made available on DTU Learn. Please note that ''all'' exercise guides are mandatory curriculum — including the ''answers'' to the exercises which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.<br /> <br /> It is possible (and recommended) to hand in as a group.<br /> <br /> ''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.<br /> <br /> === Exam ===<br /> <br /> The exam consists of a group oral project presentation with individual questions at the end of the course, and a final 2-hour written exam. The grade is based on an overall assessment of both parts of the exam. It is a requirement that the oral presentation is completed, and the written exam is passed, to pass the entire course. The questions will be made available as a PDF file on the DTU online exam system. ''' The only accepted hand-in format is PDF'''. <br /> <br /> All aids are allowed at the exam; you can bring any books, papers, or notes. You will have '''open access to the internet''' which includes all the materials and websites we have used during the course. You are also allowed to search for information on ChatGPT, Google, Wikipedia, etc., but you are ''not'' allowed to communicate with others through e-mail, Facebook, chat, or file-sharing websites. The internet traffic will be logged during the exam to ensure that these restrictions are kept.<br /> <br /> AI bots are allowed but you should state in your answer where and how you have used them. A word of wisdom here: AI generative models will give very general answers which might make you loose precious time of the exam, so be careful on their use.<br /> <br /> === DTU Learn Link ===<br /> * Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can:<br /> * send them by email to the teachers, or <br /> * write them under &quot;General feedback&quot; in &quot;Discussion&quot; in DTU Learn.<br /> If somebody writes a message in &quot;Discussion&quot;, you can comment on it. If you see a message you agree with, please comment &quot;Agree!&quot; so that we can see that it is not just one person's opinion. <br /> <br /> In addition, we will conduct a mid-term evaluation just after the autumn break in [https://evaluering.dtu.dk/ DTU evaluation].<br /> <br /> == Lecture &amp; exercise plan ==<br /> <br /> Note: This is a ''preliminary'' plan, changes may occur!<br /> <br /> === Wednesday, Sep 3 — Introduction &amp; databases ===<br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click &quot;Test of prior knowledge&quot; under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.<br /> --&gt;<br /> :'''Exercise:'''<br /> &lt;!--:# [[Plain text files and Geany]] <br /> :# [[Taxonomy databases]] <br /> :'''Extra material''' <br /> :*&quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — Encyclopedia entry from 2009.<br /> :*&quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the annual database issue of Nucleic Acids Research, 2023<br /> --&gt;<br /> <br /> === Wednesday, Sep 10 — Antigen Processing and Presentation ===<br /> :'''Lecture:''' ''Antigen Processing and Presentation'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise (for printing)] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise (version for on-screen viewing)] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:''' <br /> &lt;!--:# [[ExGenbank-new|Using the GenBank database]] <br /> :'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF] <br /> <br /> :'''Background material''' (supposedly known): <br /> :*[[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:''' <br /> :*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)<br /> :*[https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> --&gt;<br /> <br /> === Wednesday, Sep 17 — MHC binding predictions part 1 ===<br /> :'''Lecture:''' ''MHC binding predictions Part 1'' — Morten Nielsen<br /> :'''Slides:''' on DTU Learn.<br /> <br /> :'''Exercises:'''<br /> <br /> === Wednesday, Sep 24 — MHC binding predictions part 2 ===<br /> :'''Lecture:''' ''MHC binding predictions part 2'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).<br /> :'''Handout''' for the<br /> lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--[[ExPairwiseAlignment|Pairwise alignment]] <br /> --&gt;<br /> <br /> === Wednesday, Oct 1 — Vaccine design ===<br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).<br /> --&gt; <br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:<br /> &lt;!--<br /> :'''Exercise: [[Exercise:_BLAST2|BLAST]]''' <br /> :'''Extra material:''' <br /> ::[[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' (Video introduction to NCBI's web interface and Expect Values) [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel]<br /> --&gt;<br /> <br /> === Wednesday, Oct 8 — Allergenicity prediction ===<br /> <br /> :'''Lecture:''' ''Allergenicity prediction'' — Carolina Barra Quaglia<br /> :'''Lecture:''' ''Immunogenicity prediction'' — Carolina Barra Quaglia<br /> &lt;!--:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Link to advanced course:''' <br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]<br /> --&gt;<br /> &lt;!--:'''Software''' for installation: [https://pymol.org/2/ PyMOL] <br /> ::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.<br /> --&gt;<br /> :'''Exercises:''' <br /> &lt;!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.<br /> :#[[Protein Structure and Visualization]] <br /> --&gt;<br /> <br /> &lt;!--:'''Extra material:''' <br /> :*[https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> :*[[PyMOL]] — some tips and tricks.<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)<br /> --&gt;<br /> <br /> ------<br /> &lt;div align=&quot;center&quot;&gt;<br /> '''Autumn holiday''' <br /> &lt;/div&gt;<br /> ------<br /> <br /> === Wednesday, Oct 22 — BCR and TCR structure predictions ===<br /> :'''Workshop:''' ''BCR and TCR structure predictions'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> :''' GitHub link:''' <br /> &lt;!--<br /> :'''Curriculum:''' <br /> '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click &quot;Mid-term evaluation&quot; under 22111 [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:''' <br /> --&gt;<br /> <br /> === Wednesday, Oct 29 — B Cell epitope predictions ===<br /> :'''Lecture:''' ''B Cell epitope predictions'' — Paolo Marcatili<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--:'''Curriculum:''' <br /> :# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). <br /> :# Pages 1-8 of &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])<br /> :#* Read also the appendix on logarithms (especially log&lt;sub&gt;2&lt;/sub&gt;) if needed!<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)<br /> :'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]<br /> --&gt;<br /> <br /> === Wednesday, Nov 5 — TCR interaction models ===<br /> :'''Lecture:''' ''TCR interaction models'' — TBD<br /> : ''Short introduction to project work'' — Carolina Barra<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--:'''Handouts''' for the lecture: <br /> :'''Exercises:''' <br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]] <br /> :'''Link to advanced course: '''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]<br /> --&gt;<br /> <br /> === Wednesday, Nov 12 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> <br /> === Wednesday, Nov 19 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]] <br /> --&gt;<br /> <br /> === Wednesday, Nov 26 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson --&gt;<br /> <br /> <br /> === Wednesday, Dec 3 — Poster session === <br /> <br /> :Poster presentations will be '''starting at 8:00am'''<br /> <br /> :'''Agenda for the poster presentations:''' TBD<br /> <br /> == Exam ==<br /> <br /> === Wednesday, Dec 18 ===<br /> '''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145. <br /> <br /> <br /> &lt;!-- === Link collection ===<br /> A quick overview of the websites we have used in the course: [[Link collection]]<br /> <br /> === FAQ ===<br /> Questions we have received and answered: [[FAQ]]<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=89 2026-08-06T09:53:13Z

<p>Carol: /* Where and when */</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Wednesday from 9 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 3 at 9:00'''. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material provided on DTU Learn<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] &amp;mdash; Associate professor, course responsible.<br /> <br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] &amp;mdash; Professor, course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://www.dtu.dk/english/person/sebastian-nymann-deleuran?id=117549&amp;entity=profile Sebastian Nymann Deleuran] &amp;mdash; PhD student<br /> <br /> === Course content ===<br /> <br /> The course aims to introduce the students to state-of-the-art methods within computational immunology.<br /> <br /> There is a strong focus on introducing the methods in context with immunology as a domain-specific knowledge area. Furthermore, an introduction to the theory of the methods will be followed by practical exercises, enabling the student to independently perform analyses. The course covers immunological bioinformatics and computational vaccinology with an outlook on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 covers lectures and group-based exercises, and part 2 will cover a group-based research project with the output being a poster presentation on the last day of the course. <br /> <br /> See also [http://kurser.dtu.dk/course/22145 the course base about 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no formal textbook. The curricula consist of lectures and exercises performed in class, supplemented with various papers and book chapters which will be made available on DTU Learn. Please note that ''all'' exercise guides are mandatory curriculum — including the ''answers'' to the exercises which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.<br /> <br /> It is possible (and recommended) to hand in as a group.<br /> <br /> ''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.<br /> <br /> === Exam ===<br /> <br /> The exam consists of a group oral project presentation with individual questions at the end of the course, and a final 2-hour written exam. The grade is based on an overall assessment of both parts of the exam. It is a requirement that the oral presentation is completed, and the written exam is passed, to pass the entire course. The questions will be made available as a PDF file on the DTU online exam system. ''' The only accepted hand-in format is PDF'''. <br /> <br /> All aids are allowed at the exam; you can bring any books, papers, or notes. You will have '''open access to the internet''' which includes all the materials and websites we have used during the course. You are also allowed to search for information on ChatGPT, Google, Wikipedia, etc., but you are ''not'' allowed to communicate with others through e-mail, Facebook, chat, or file-sharing websites. The internet traffic will be logged during the exam to ensure that these restrictions are kept.<br /> <br /> AI bots are allowed but you should state in your answer where and how you have used them. A word of wisdom here: AI generative models will give very general answers which might make you loose precious time of the exam, so be careful on their use.<br /> <br /> === DTU Learn Link ===<br /> * Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can:<br /> * send them by email to the teachers, or <br /> * write them under &quot;General feedback&quot; in &quot;Discussion&quot; in DTU Learn.<br /> If somebody writes a message in &quot;Discussion&quot;, you can comment on it. If you see a message you agree with, please comment &quot;Agree!&quot; so that we can see that it is not just one person's opinion. <br /> <br /> In addition, we will conduct a mid-term evaluation just after the autumn break in [https://evaluering.dtu.dk/ DTU evaluation].<br /> <br /> == Lecture &amp; exercise plan ==<br /> <br /> Note: This is a ''preliminary'' plan, changes may occur!<br /> <br /> === Wednesday, Sep 3 — Introduction &amp; databases ===<br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click &quot;Test of prior knowledge&quot; under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.<br /> --&gt;<br /> :'''Exercise:'''<br /> &lt;!--:# [[Plain text files and Geany]] <br /> :# [[Taxonomy databases]] <br /> :'''Extra material''' <br /> :*&quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — Encyclopedia entry from 2009.<br /> :*&quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the annual database issue of Nucleic Acids Research, 2023<br /> --&gt;<br /> <br /> === Wednesday, Sep 10 — Antigen Processing and Presentation ===<br /> :'''Lecture:''' ''Antigen Processing and Presentation'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise (for printing)] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise (version for on-screen viewing)] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:''' <br /> &lt;!--:# [[ExGenbank-new|Using the GenBank database]] <br /> :'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF] <br /> <br /> :'''Background material''' (supposedly known): <br /> :*[[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:''' <br /> :*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)<br /> :*[https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> --&gt;<br /> <br /> === Wednesday, Sep 17 — MHC binding predictions part 1 ===<br /> :'''Lecture:''' ''MHC binding predictions Part 1'' — Morten Nielsen<br /> :'''Slides:''' on DTU Learn.<br /> <br /> :'''Exercises:'''<br /> <br /> === Wednesday, Sep 24 — MHC binding predictions part 2 ===<br /> :'''Lecture:''' ''MHC binding predictions part 2'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).<br /> :'''Handout''' for the<br /> lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--[[ExPairwiseAlignment|Pairwise alignment]] <br /> --&gt;<br /> <br /> === Wednesday, Oct 1 — Vaccine design ===<br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).<br /> --&gt; <br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:<br /> &lt;!--<br /> :'''Exercise: [[Exercise:_BLAST2|BLAST]]''' <br /> :'''Extra material:''' <br /> ::[[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' (Video introduction to NCBI's web interface and Expect Values) [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel]<br /> --&gt;<br /> <br /> === Wednesday, Oct 8 — Allergenicity prediction ===<br /> <br /> :'''Lecture:''' ''Allergenicity prediction'' — Carolina Barra Quaglia<br /> :'''Lecture:''' ''Immunogenicity prediction'' — Carolina Barra Quaglia<br /> &lt;!--:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Link to advanced course:''' <br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]<br /> --&gt;<br /> &lt;!--:'''Software''' for installation: [https://pymol.org/2/ PyMOL] <br /> ::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.<br /> --&gt;<br /> :'''Exercises:''' <br /> &lt;!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.<br /> :#[[Protein Structure and Visualization]] <br /> --&gt;<br /> <br /> &lt;!--:'''Extra material:''' <br /> :*[https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> :*[[PyMOL]] — some tips and tricks.<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)<br /> --&gt;<br /> <br /> ------<br /> &lt;div align=&quot;center&quot;&gt;<br /> '''Autumn holiday''' <br /> &lt;/div&gt;<br /> ------<br /> <br /> === Wednesday, Oct 22 — BCR and TCR structure predictions ===<br /> :'''Workshop:''' ''BCR and TCR structure predictions'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> :''' GitHub link:''' <br /> &lt;!--<br /> :'''Curriculum:''' <br /> '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click &quot;Mid-term evaluation&quot; under 22111 [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:''' <br /> --&gt;<br /> <br /> === Wednesday, Oct 29 — B Cell epitope predictions ===<br /> :'''Lecture:''' ''B Cell epitope predictions'' — Paolo Marcatili<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--:'''Curriculum:''' <br /> :# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). <br /> :# Pages 1-8 of &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])<br /> :#* Read also the appendix on logarithms (especially log&lt;sub&gt;2&lt;/sub&gt;) if needed!<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)<br /> :'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]<br /> --&gt;<br /> <br /> === Wednesday, Nov 5 — TCR interaction models ===<br /> :'''Lecture:''' ''TCR interaction models'' — TBD<br /> : ''Short introduction to project work'' — Carolina Barra<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--:'''Handouts''' for the lecture: <br /> :'''Exercises:''' <br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]] <br /> :'''Link to advanced course: '''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]<br /> --&gt;<br /> <br /> === Wednesday, Nov 12 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> <br /> === Wednesday, Nov 19 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]] <br /> --&gt;<br /> <br /> === Wednesday, Nov 26 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson --&gt;<br /> <br /> <br /> === Wednesday, Dec 3 — Poster session === <br /> <br /> :Poster presentations will be '''starting at 8:00am'''<br /> <br /> :'''Agenda for the poster presentations:''' TBD<br /> <br /> == Exam ==<br /> <br /> === Wednesday, Dec 18 ===<br /> '''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145. <br /> <br /> <br /> &lt;!-- === Link collection ===<br /> A quick overview of the websites we have used in the course: [[Link collection]]<br /> <br /> === FAQ ===<br /> Questions we have received and answered: [[FAQ]]<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=22145_Immunological_Bioinformatics_Course_Programme_Fall_2026&diff=88 2026-08-06T09:47:57Z

<p>Carol: Created page with &quot;== General information == === Where and when === Wednesday from 9 to 12 in &#039;&#039;&#039;building 208, holdlokale 3/065&#039;&#039;&#039;, starting on &#039;&#039;&#039;Wednesday, Sep 3 at 9:00&#039;&#039;&#039;. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material === Teachers === * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] &amp;mdash; Associate professor, course responsible. *...&quot;</p> <hr /> <div>== General information ==<br /> <br /> === Where and when ===<br /> <br /> Wednesday from 9 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 3 at 9:00'''. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material<br /> <br /> === Teachers ===<br /> <br /> * [https://www.dtu.dk/Person/cwis?id=142840&amp;entity=profile Carolina Barra Quaglia] &amp;mdash; Associate professor, course responsible.<br /> <br /> * [https://www.dtu.dk/person/morten-nielsen?id=5973&amp;entity=profile Morten Nielsen] &amp;mdash; Professor, course responsible.<br /> <br /> === Teaching assistant ===<br /> <br /> * [https://www.dtu.dk/english/person/sebastian-nymann-deleuran?id=117549&amp;entity=profile Sebastian Nymann Deleuran] &amp;mdash; PhD student<br /> <br /> === Course content ===<br /> <br /> The course aims to introduce the students to state-of-the-art methods within computational immunology.<br /> <br /> There is a strong focus on introducing the methods in context with immunology as a domain-specific knowledge area. Furthermore, an introduction to the theory of the methods will be followed by practical exercises, enabling the student to independently perform analyses. The course covers immunological bioinformatics and computational vaccinology with an outlook on infectious diseases, cancer immunotherapy, and autoimmunity.<br /> <br /> The course is taught in two parts. Part 1 covers lectures and group-based exercises, and part 2 will cover a group-based research project with the output being a poster presentation on the last day of the course. <br /> <br /> See also [http://kurser.dtu.dk/course/22145 the course base about 22145].<br /> <br /> === Curriculum ===<br /> <br /> There is no formal textbook. The curricula consist of lectures and exercises performed in class, supplemented with various papers and book chapters which will be made available on DTU Learn. Please note that ''all'' exercise guides are mandatory curriculum — including the ''answers'' to the exercises which will be made available on DTU Learn after each exercise.<br /> <br /> === Hand-ins ===<br /> <br /> Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.<br /> <br /> It is possible (and recommended) to hand in as a group.<br /> <br /> ''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.<br /> <br /> === Exam ===<br /> <br /> The exam consists of a group oral project presentation with individual questions at the end of the course, and a final 2-hour written exam. The grade is based on an overall assessment of both parts of the exam. It is a requirement that the oral presentation is completed, and the written exam is passed, to pass the entire course. The questions will be made available as a PDF file on the DTU online exam system. ''' The only accepted hand-in format is PDF'''. <br /> <br /> All aids are allowed at the exam; you can bring any books, papers, or notes. You will have '''open access to the internet''' which includes all the materials and websites we have used during the course. You are also allowed to search for information on ChatGPT, Google, Wikipedia, etc., but you are ''not'' allowed to communicate with others through e-mail, Facebook, chat, or file-sharing websites. The internet traffic will be logged during the exam to ensure that these restrictions are kept.<br /> <br /> AI bots are allowed but you should state in your answer where and how you have used them. A word of wisdom here: AI generative models will give very general answers which might make you loose precious time of the exam, so be careful on their use.<br /> <br /> === DTU Learn Link ===<br /> * Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397<br /> <br /> === Evaluation and feedback ===<br /> We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can:<br /> * send them by email to the teachers, or <br /> * write them under &quot;General feedback&quot; in &quot;Discussion&quot; in DTU Learn.<br /> If somebody writes a message in &quot;Discussion&quot;, you can comment on it. If you see a message you agree with, please comment &quot;Agree!&quot; so that we can see that it is not just one person's opinion. <br /> <br /> In addition, we will conduct a mid-term evaluation just after the autumn break in [https://evaluering.dtu.dk/ DTU evaluation].<br /> <br /> == Lecture &amp; exercise plan ==<br /> <br /> Note: This is a ''preliminary'' plan, changes may occur!<br /> <br /> === Wednesday, Sep 3 — Introduction &amp; databases ===<br /> :'''Lectures:'''<br /> :* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.<br /> :* ''Databases'' — Carolina Barra Quaglia.<br /> :'''Slides:''' All slides will be made available on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.<br /> :'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click &quot;Test of prior knowledge&quot; under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.<br /> --&gt;<br /> :'''Exercise:'''<br /> &lt;!--:# [[Plain text files and Geany]] <br /> :# [[Taxonomy databases]] <br /> :'''Extra material''' <br /> :*&quot;[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]&quot; — Encyclopedia entry from 2009.<br /> :*&quot;[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]&quot; — article from the annual database issue of Nucleic Acids Research, 2023<br /> --&gt;<br /> <br /> === Wednesday, Sep 10 — Antigen Processing and Presentation ===<br /> :'''Lecture:''' ''Antigen Processing and Presentation'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf &quot;Base-calling&quot; exercise (for printing)] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf &quot;Base-calling&quot; exercise (version for on-screen viewing)] [PDF].<br /> --&gt;<br /> <br /> :'''Exercise:''' <br /> &lt;!--:# [[ExGenbank-new|Using the GenBank database]] <br /> :'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF] <br /> <br /> :'''Background material''' (supposedly known): <br /> :*[[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).<br /> <br /> :'''Extra material:''' <br /> :*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)<br /> :*[https://doi.org/10.1093/nar/gkac1012 &quot;GenBank 2023 update&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> --&gt;<br /> <br /> === Wednesday, Sep 17 — MHC binding predictions part 1 ===<br /> :'''Lecture:''' ''MHC binding predictions Part 1'' — Morten Nielsen<br /> :'''Slides:''' on DTU Learn.<br /> <br /> :'''Exercises:'''<br /> <br /> === Wednesday, Sep 24 — MHC binding predictions part 2 ===<br /> :'''Lecture:''' ''MHC binding predictions part 2'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).<br /> :'''Handout''' for the<br /> lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--[[ExPairwiseAlignment|Pairwise alignment]] <br /> --&gt;<br /> <br /> === Wednesday, Oct 1 — Vaccine design ===<br /> :'''Lecture:''' ''Vaccine design'' — Morten Nielsen.<br /> &lt;!--:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).<br /> --&gt; <br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:<br /> &lt;!--<br /> :'''Exercise: [[Exercise:_BLAST2|BLAST]]''' <br /> :'''Extra material:''' <br /> ::[[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' (Video introduction to NCBI's web interface and Expect Values) [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel]<br /> --&gt;<br /> <br /> === Wednesday, Oct 8 — Allergenicity prediction ===<br /> <br /> :'''Lecture:''' ''Allergenicity prediction'' — Carolina Barra Quaglia<br /> :'''Lecture:''' ''Immunogenicity prediction'' — Carolina Barra Quaglia<br /> &lt;!--:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]<br /> --&gt;<br /> :'''Slides:''' on DTU Learn.<br /> &lt;!--:'''Link to advanced course:''' <br /> ::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]<br /> --&gt;<br /> &lt;!--:'''Software''' for installation: [https://pymol.org/2/ PyMOL] <br /> ::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.<br /> --&gt;<br /> :'''Exercises:''' <br /> &lt;!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.<br /> :#[[Protein Structure and Visualization]] <br /> --&gt;<br /> <br /> &lt;!--:'''Extra material:''' <br /> :*[https://doi.org/10.1093/nar/gkac1077 &quot;RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning&quot;] — article from the annual database issue of Nucleic Acids Research, 2023.<br /> :*[[PyMOL]] — some tips and tricks.<br /> :*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)<br /> --&gt;<br /> <br /> ------<br /> &lt;div align=&quot;center&quot;&gt;<br /> '''Autumn holiday''' <br /> &lt;/div&gt;<br /> ------<br /> <br /> === Wednesday, Oct 22 — BCR and TCR structure predictions ===<br /> :'''Workshop:''' ''BCR and TCR structure predictions'' — Carolina Barra Quaglia<br /> :'''Slides:''' on DTU Learn.<br /> :''' GitHub link:''' <br /> &lt;!--<br /> :'''Curriculum:''' <br /> '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click &quot;Mid-term evaluation&quot; under 22111 [[Image:Emblem-important_tiny.png‎]]<br /> :'''Exercise:''' <br /> --&gt;<br /> <br /> === Wednesday, Oct 29 — B Cell epitope predictions ===<br /> :'''Lecture:''' ''B Cell epitope predictions'' — Paolo Marcatili<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercise:''' <br /> &lt;!--:'''Curriculum:''' <br /> :# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). <br /> :# Pages 1-8 of &quot;''Information theory primer''&quot; ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])<br /> :#* Read also the appendix on logarithms (especially log&lt;sub&gt;2&lt;/sub&gt;) if needed!<br /> :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)<br /> :'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]<br /> --&gt;<br /> <br /> === Wednesday, Nov 5 — TCR interaction models ===<br /> :'''Lecture:''' ''TCR interaction models'' — TBD<br /> : ''Short introduction to project work'' — Carolina Barra<br /> :'''Slides:''' on DTU Learn.<br /> :'''Exercises:'''<br /> <br /> &lt;!--:'''Handouts''' for the lecture: <br /> :'''Exercises:''' <br /> :# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.<br /> :# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]] <br /> :'''Link to advanced course: '''<br /> :: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]<br /> --&gt;<br /> <br /> === Wednesday, Nov 12 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> <br /> === Wednesday, Nov 19 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])<br /> :'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]] <br /> --&gt;<br /> <br /> === Wednesday, Nov 26 — Project work ===<br /> :'''Lecture:''' No LECTURE<br /> &lt;!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson --&gt;<br /> <br /> <br /> === Wednesday, Dec 3 — Poster session === <br /> <br /> :Poster presentations will be '''starting at 8:00am'''<br /> <br /> :'''Agenda for the poster presentations:''' TBD<br /> <br /> == Exam ==<br /> <br /> === Wednesday, Dec 18 ===<br /> '''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145. <br /> <br /> <br /> &lt;!-- === Link collection ===<br /> A quick overview of the websites we have used in the course: [[Link collection]]<br /> <br /> === FAQ ===<br /> Questions we have received and answered: [[FAQ]]<br /> --&gt;</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=Bcell_Epitope_prediction_answers&diff=87 2025-11-04T17:30:24Z

<p>Carol: Created page with &quot;&#039;&#039;&#039;B-cell epitope prediction — Why do some flu vaccines miss? Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart? &#039;&#039;&#039;Part A, Get your bearings in PyMOL (find the ground truth...&quot;</p> <hr /> <div>'''B-cell epitope prediction — Why do some flu vaccines miss?<br /> <br /> Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart?<br /> <br /> '''Part A, Get your bearings in PyMOL (find the ground truth epitope)'''<br /> <br /> Go to the pdb homepage and look for the pdb entries 4FQI and 7K39. It is hemagglutinin protein from Inlfuenza complexed with two different antibodies. Fetch and inspect structures. You can color the different chains in different colors<br /> <br /> * Open 4FQI in PyMOL (fetch 4fqi) and identify chains for HA (HA1/HA2) and Fab (H/L). For ilustrative purposes we will call HA1 the head and HA2 the stem of hemagglutinin.<br /> <br /> * Open 7K39 (fetch 7k39) and similarly identify HA vs antibody chains.<br /> <br /> hint: you can find this information in the structure web-page, in the PDB file itself (you can open it with a text editor and search for COMPND)<br /> <br /> '''Q1.''' List chain IDs for antigen vs antibody in each complex.<br /> <br /> Open 4FQI.pdb with a text editor. Here you will find the list of chains included in the structure.<br /> <br /> &lt;div style=&quot;background-color: lavender; border: solid thin grey;&quot;&gt;<br /> :HEADER VIRAL PROTEIN/IMMUNE SYSTEM 25-JUN-12 4FQI <br /> :TITLE CRYSTAL STRUCTURE OF FAB CR9114 IN COMPLEX WITH A H5N1 INFLUENZA VIRUS<br /> :TITLE 2 HEMAGGLUTININ <br /> :COMPND MOL_ID: 1; <br /> :COMPND 2 MOLECULE: HEMAGGLUTININ HA1; <br /> :COMPND 3 CHAIN: A; <br /> :COMPND 4 FRAGMENT: UNP RESIDUES 17-346; <br /> :COMPND 5 SYNONYM: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1; <br /> :COMPND 6 ENGINEERED: YES; <br /> :COMPND 7 MOL_ID: 2; <br /> :COMPND 8 MOLECULE: HEMAGGLUTININ HA2; <br /> :COMPND 9 CHAIN: B; <br /> :COMPND 10 FRAGMENT: UNP RESIDUES 347-520; <br /> :COMPND 11 SYNONYM: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2; <br /> :COMPND 12 ENGINEERED: YES; <br /> :COMPND 13 MOL_ID: 3; <br /> :COMPND 14 MOLECULE: ANTIBODY CR9114 HEAVY CHAIN; <br /> :COMPND 15 CHAIN: H; <br /> :COMPND 16 FRAGMENT: FAB; <br /> :COMPND 17 ENGINEERED: YES; <br /> :COMPND 18 MOL_ID: 4; <br /> :COMPND 19 MOLECULE: ANTIBODY CR9114 LIGHT CHAIN; <br /> :COMPND 20 CHAIN: L; <br /> :COMPND 21 FRAGMENT: FAB LAMBDA; <br /> :COMPND 22 ENGINEERED: YES <br /> &lt;/div&gt;<br /> <br /> On PyMol<br /> <br /> <br /> <br /> <br /> <br /> :COMPND MOL_ID: 1; <br /> :COMPND 2 MOLECULE: HEMAGGLUTININ HA1; <br /> :COMPND 3 CHAIN: A; <br /> :COMPND 4 FRAGMENT: UNP RESIDUES 17-346; <br /> :COMPND 5 SYNONYM: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1; <br /> :COMPND 6 ENGINEERED: YES; <br /> :COMPND 7 MOL_ID: 2; <br /> :COMPND 8 MOLECULE: HEMAGGLUTININ HA2; <br /> :COMPND 9 CHAIN: B; <br /> :COMPND 10 FRAGMENT: UNP RESIDUES 347-520; <br /> :COMPND 11 SYNONYM: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2; <br /> :COMPND 12 ENGINEERED: YES; <br /> :COMPND 13 MOL_ID: 3; <br /> :COMPND 14 MOLECULE: ANTIBODY CR9114 HEAVY CHAIN; <br /> :COMPND 15 CHAIN: H; <br /> :COMPND 16 FRAGMENT: FAB; <br /> :COMPND 17 ENGINEERED: YES; <br /> :COMPND 18 MOL_ID: 4; <br /> :COMPND 19 MOLECULE: ANTIBODY CR9114 LIGHT CHAIN; <br /> :COMPND 20 CHAIN: L; <br /> :COMPND 21 FRAGMENT: FAB LAMBDA; <br /> :COMPND 22 ENGINEERED: YES <br /> <br /> <br /> Define the real epitope. For each complex, remove waters (remove solvent). Create an epitope selection on HA as all residues within 5 Å of any antibody atom and color it in red.<br /> <br /> ''Hint of PyMOL.'' select epitope, br.(antibody around 5)<br /> ''Hint2'' In one of the complexes you have several antibody H and L chains. You might want to work with one antibody only!<br /> <br /> '''Q2.''' Provide screenshots of the epitopes for the different protein complexes and the sequence panel with chain letters visible. How many epitope residues are there in head vs stem complexes? Are they mostly loops, helices, or strands (qualitatively)? <br /> <br /> <br /> '''Q3.''' Can you identify which residues are part of the epitope? Is the epitope linear? Does it have a linear core? Are the two complexes targeting the same chain?<br /> <br /> Make antigen-only files<br /> <br /> Using pymol, identify the antibody in the structure, select and remove it (action -&gt; remove atoms). Save the resulting molecule as antigen.pdb<br /> If the structure contain several antigen chains that are not part of the epitope, you can remove them.<br /> <br /> You can save using the GUI (remember to select PDB as option) as well as typing &quot;save antigen.pdb&quot; in the command line<br /> <br /> You can also save the fasta sequence of the antigen with the following command:<br /> <br /> save /path/to/folder/XXXX.fasta, all, format=fasta<br /> (remember to change the path and the XXs, name of the PDB complex)<br /> <br /> '''Part B. Sequence-based prediction (BepiPred-2.0 &amp; 3.0)'''<br /> <br /> <br /> Go to the BepiPred2 website and upload the sequences of the stem and the head of hemagglutinin. Leave the default parameters and submit the job. Don't close the window because we will need it again!<br /> <br /> '''Q4.''' does the BepiPred predictions overlap with the actual epitopes?<br /> <br /> Be careful: pdb file numbering does not always start from 1! Compare the numbering of the pdb with the one returned by BepiPred.<br /> <br /> Repeat the prediction now using BepiPred3. <br /> <br /> '''Q5.''' Does the prediction overlap with our epitope now?<br /> <br /> '''Q6.''' What is different in BepiPred 2 compared to Bepipred 3?<br /> <br /> <br /> '''Part C. Structure-based prediction (DiscoTope-2.0 &amp; 3.0)'''<br /> <br /> <br /> Load the antigen.pdb file and submit the prediction in Discotope-2. Save the output as discotope2.pdb<br /> <br /> Once again, the prediction is in the b-factor field (but you can download it in other formats as well)<br /> Load it in pymol and colour according to the b-factor.<br /> <br /> '''Q7:''' Does the prediction overlap with our epitope?<br /> <br /> '''Q8.''' Which prediction best matches our epitope?<br /> <br /> '''Q9.''' Use Discotope to predict the epitopes in the simian HIV GP120 homolog (pdb code 3FUS). If you want to save time, use this pre-cleaned PDB. Compare the results. Try and explain the differences. According to you is it a meaningful result or not? Please note that some bugs might occur, according to which file you use. If some strange results appear, report it in your answer :)<br /> <br /> '''Q10.''' Compare the results obtained in Discotope 2 and 3<br /> <br /> '''Part D. Antigenic drift vs conservation'''<br /> <br /> Compare another HA<br /> Fetch an HA from a different subtype/strain (e.g., another H5N1, H1N1, or the C05-bound head example). For convenience, you can use 4FQI as reference.<br /> <br /> Align HA chains (align) and map your epitope residues from the first antigen onto the second by position.<br /> <br /> '''Q11.''' Which epitope class (head vs stem) is more conserved by sequence identity at the interface? <br /> <br /> '''Part E. Now suppose that we found a good neutralising antibody against Influenza, we isolate the antibody and have a sequence'''<br /> <br /> '''Q12.''' Are there any tools to help us predicting where the antibody will bind in the antigen???</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=Bcell_Epitope_prediction&diff=86 2025-10-28T13:30:16Z

<p>Carol: </p> <hr /> <div>'''B-cell epitope prediction — Why do some flu vaccines miss?<br /> <br /> Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart?<br /> <br /> '''Part A, Get your bearings in PyMOL (find the ground truth epitope)'''<br /> <br /> Go to the pdb homepage and look for the pdb entries 4FQI and 7K39. It is hemagglutinin protein from Inlfuenza complexed with two different antibodies. Fetch and inspect structures. You can color the different chains in different colors<br /> <br /> * Open 4FQI in PyMOL (fetch 4fqi) and identify chains for HA (HA1/HA2) and Fab (H/L). For ilustrative purposes we will call HA1 the head and HA2 the stem of hemagglutinin.<br /> <br /> * Open 7K39 (fetch 7k39) and similarly identify HA vs antibody chains.<br /> <br /> hint: you can find this information in the structure web-page, in the PDB file itself (you can open it with a text editor and search for COMPND)<br /> <br /> &lt;div style=&quot;background-color: lavender; border: solid thin grey;&quot;&gt;<br /> :COMPND MOL_ID: 1; <br /> :COMPND 2 MOLECULE: HEMAGGLUTININ HA1; <br /> :COMPND 3 CHAIN: A; <br /> :COMPND 4 FRAGMENT: UNP RESIDUES 17-346; <br /> :COMPND 5 SYNONYM: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1; <br /> :COMPND 6 ENGINEERED: YES; <br /> :COMPND 7 MOL_ID: 2; <br /> :COMPND 8 MOLECULE: HEMAGGLUTININ HA2; <br /> :COMPND 9 CHAIN: B; <br /> :COMPND 10 FRAGMENT: UNP RESIDUES 347-520; <br /> :COMPND 11 SYNONYM: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2; <br /> :COMPND 12 ENGINEERED: YES; <br /> :COMPND 13 MOL_ID: 3; <br /> :COMPND 14 MOLECULE: ANTIBODY CR9114 HEAVY CHAIN; <br /> :COMPND 15 CHAIN: H; <br /> :COMPND 16 FRAGMENT: FAB; <br /> :COMPND 17 ENGINEERED: YES; <br /> :COMPND 18 MOL_ID: 4; <br /> :COMPND 19 MOLECULE: ANTIBODY CR9114 LIGHT CHAIN; <br /> :COMPND 20 CHAIN: L; <br /> :COMPND 21 FRAGMENT: FAB LAMBDA; <br /> :COMPND 22 ENGINEERED: YES<br /> &lt;/div&gt;<br /> <br /> <br /> '''Q1.''' List chain IDs for antigen vs antibody in each complex.<br /> <br /> Define the real epitope. For each complex, remove waters (remove solvent). Create an epitope selection on HA as all residues within 5 Å of any antibody atom and color it in red.<br /> <br /> ''Hint of PyMOL.'' select epitope, br.(antibody around 5)<br /> ''Hint2'' In one of the complexes you have several antibody H and L chains. You might want to work with one antibody only!<br /> <br /> '''Q2.''' Provide screenshots of the epitopes for the different protein complexes and the sequence panel with chain letters visible. How many epitope residues are there in head vs stem complexes? Are they mostly loops, helices, or strands (qualitatively)? <br /> <br /> <br /> '''Q3.''' Can you identify which residues are part of the epitope? Is the epitope linear? Does it have a linear core? Are the two complexes targeting the same chain?<br /> <br /> Make antigen-only files<br /> <br /> Using pymol, identify the antibody in the structure, select and remove it (action -&gt; remove atoms). Save the resulting molecule as antigen.pdb<br /> If the structure contain several antigen chains that are not part of the epitope, you can remove them.<br /> <br /> You can save using the GUI (remember to select PDB as option) as well as typing &quot;save antigen.pdb&quot; in the command line<br /> <br /> You can also save the fasta sequence of the antigen with the following command:<br /> <br /> save /path/to/folder/XXXX.fasta, all, format=fasta<br /> (remember to change the path and the XXs, name of the PDB complex)<br /> <br /> '''Part B. Sequence-based prediction (BepiPred-2.0 &amp; 3.0)'''<br /> <br /> <br /> Go to the BepiPred2 website and upload the sequences of the stem and the head of hemagglutinin. Leave the default parameters and submit the job. Don't close the window because we will need it again!<br /> <br /> '''Q4.''' does the BepiPred predictions overlap with the actual epitopes?<br /> <br /> Be careful: pdb file numbering does not always start from 1! Compare the numbering of the pdb with the one returned by BepiPred.<br /> <br /> Repeat the prediction now using BepiPred3. <br /> <br /> '''Q5.''' Does the prediction overlap with our epitope now?<br /> <br /> '''Q6.''' What is different in BepiPred 2 compared to Bepipred 3?<br /> <br /> <br /> '''Part C. Structure-based prediction (DiscoTope-2.0 &amp; 3.0)'''<br /> <br /> <br /> Load the antigen.pdb file and submit the prediction in Discotope-2. Save the output as discotope2.pdb<br /> <br /> Once again, the prediction is in the b-factor field (but you can download it in other formats as well)<br /> Load it in pymol and colour according to the b-factor.<br /> <br /> '''Q7:''' Does the prediction overlap with our epitope?<br /> <br /> '''Q8.''' Which prediction best matches our epitope?<br /> <br /> '''Q9.''' Use Discotope to predict the epitopes in the simian HIV GP120 homolog (pdb code 3FUS). If you want to save time, use this pre-cleaned PDB. Compare the results. Try and explain the differences. According to you is it a meaningful result or not? Please note that some bugs might occur, according to which file you use. If some strange results appear, report it in your answer :)<br /> <br /> '''Q10.''' Compare the results obtained in Discotope 2 and 3<br /> <br /> '''Part D. Antigenic drift vs conservation'''<br /> <br /> Compare another HA<br /> Fetch an HA from a different subtype/strain (e.g., another H5N1, H1N1, or the C05-bound head example). For convenience, you can use 4FQI as reference.<br /> <br /> Align HA chains (align) and map your epitope residues from the first antigen onto the second by position.<br /> <br /> '''Q11.''' Which epitope class (head vs stem) is more conserved by sequence identity at the interface? <br /> <br /> '''Part E. Now suppose that we found a good neutralising antibody against Influenza, we isolate the antibody and have a sequence'''<br /> <br /> '''Q12.''' Are there any tools to help us predicting where the antibody will bind in the antigen???</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=Bcell_Epitope_prediction&diff=85 2025-10-28T13:29:59Z

<p>Carol: </p> <hr /> <div>'''B-cell epitope prediction — Why do some flu vaccines miss?<br /> <br /> Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart?<br /> <br /> '''Part A, Get your bearings in PyMOL (find the ground truth epitope)'''<br /> <br /> Go to the pdb homepage and look for the pdb entries 4FQI and 7K39. It is hemagglutinin protein from Inlfuenza complexed with two different antibodies. Fetch and inspect structures. You can color the different chains in different colors<br /> <br /> * Open 4FQI in PyMOL (fetch 4fqi) and identify chains for HA (HA1/HA2) and Fab (H/L). For ilustrative purposes we will call HA1 the head and HA2 the stem of hemagglutinin.<br /> <br /> * Open 7K39 (fetch 7k39) and similarly identify HA vs antibody chains.<br /> <br /> hint: you can find this information in the structure web-page, in the PDB file itself (you can open it with a text editor and search for COMPND)<br /> <br /> &lt;div style=&quot;background-color: lavender; border: solid thin grey;&quot;&gt;<br /> :COMPND MOL_ID: 1; <br /> :COMPND 2 MOLECULE: HEMAGGLUTININ HA1; <br /> :COMPND 3 CHAIN: A; <br /> :COMPND 4 FRAGMENT: UNP RESIDUES 17-346; <br /> :COMPND 5 SYNONYM: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1; <br /> :COMPND 6 ENGINEERED: YES; <br /> :COMPND 7 MOL_ID: 2; <br /> :COMPND 8 MOLECULE: HEMAGGLUTININ HA2; <br /> :COMPND 9 CHAIN: B; <br /> :COMPND 10 FRAGMENT: UNP RESIDUES 347-520; <br /> :COMPND 11 SYNONYM: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2; <br /> :COMPND 12 ENGINEERED: YES; <br /> :COMPND 13 MOL_ID: 3; <br /> :COMPND 14 MOLECULE: ANTIBODY CR9114 HEAVY CHAIN; <br /> :COMPND 15 CHAIN: H; <br /> :COMPND 16 FRAGMENT: FAB; <br /> :COMPND 17 ENGINEERED: YES; <br /> :COMPND 18 MOL_ID: 4; <br /> :COMPND 19 MOLECULE: ANTIBODY CR9114 LIGHT CHAIN; <br /> :COMPND 20 CHAIN: L; <br /> :COMPND 21 FRAGMENT: FAB LAMBDA; <br /> :COMPND 22 ENGINEERED: YES<br /> &lt;div&gt;<br /> <br /> <br /> '''Q1.''' List chain IDs for antigen vs antibody in each complex.<br /> <br /> Define the real epitope. For each complex, remove waters (remove solvent). Create an epitope selection on HA as all residues within 5 Å of any antibody atom and color it in red.<br /> <br /> ''Hint of PyMOL.'' select epitope, br.(antibody around 5)<br /> ''Hint2'' In one of the complexes you have several antibody H and L chains. You might want to work with one antibody only!<br /> <br /> '''Q2.''' Provide screenshots of the epitopes for the different protein complexes and the sequence panel with chain letters visible. How many epitope residues are there in head vs stem complexes? Are they mostly loops, helices, or strands (qualitatively)? <br /> <br /> <br /> '''Q3.''' Can you identify which residues are part of the epitope? Is the epitope linear? Does it have a linear core? Are the two complexes targeting the same chain?<br /> <br /> Make antigen-only files<br /> <br /> Using pymol, identify the antibody in the structure, select and remove it (action -&gt; remove atoms). Save the resulting molecule as antigen.pdb<br /> If the structure contain several antigen chains that are not part of the epitope, you can remove them.<br /> <br /> You can save using the GUI (remember to select PDB as option) as well as typing &quot;save antigen.pdb&quot; in the command line<br /> <br /> You can also save the fasta sequence of the antigen with the following command:<br /> <br /> save /path/to/folder/XXXX.fasta, all, format=fasta<br /> (remember to change the path and the XXs, name of the PDB complex)<br /> <br /> '''Part B. Sequence-based prediction (BepiPred-2.0 &amp; 3.0)'''<br /> <br /> <br /> Go to the BepiPred2 website and upload the sequences of the stem and the head of hemagglutinin. Leave the default parameters and submit the job. Don't close the window because we will need it again!<br /> <br /> '''Q4.''' does the BepiPred predictions overlap with the actual epitopes?<br /> <br /> Be careful: pdb file numbering does not always start from 1! Compare the numbering of the pdb with the one returned by BepiPred.<br /> <br /> Repeat the prediction now using BepiPred3. <br /> <br /> '''Q5.''' Does the prediction overlap with our epitope now?<br /> <br /> '''Q6.''' What is different in BepiPred 2 compared to Bepipred 3?<br /> <br /> <br /> '''Part C. Structure-based prediction (DiscoTope-2.0 &amp; 3.0)'''<br /> <br /> <br /> Load the antigen.pdb file and submit the prediction in Discotope-2. Save the output as discotope2.pdb<br /> <br /> Once again, the prediction is in the b-factor field (but you can download it in other formats as well)<br /> Load it in pymol and colour according to the b-factor.<br /> <br /> '''Q7:''' Does the prediction overlap with our epitope?<br /> <br /> '''Q8.''' Which prediction best matches our epitope?<br /> <br /> '''Q9.''' Use Discotope to predict the epitopes in the simian HIV GP120 homolog (pdb code 3FUS). If you want to save time, use this pre-cleaned PDB. Compare the results. Try and explain the differences. According to you is it a meaningful result or not? Please note that some bugs might occur, according to which file you use. If some strange results appear, report it in your answer :)<br /> <br /> '''Q10.''' Compare the results obtained in Discotope 2 and 3<br /> <br /> '''Part D. Antigenic drift vs conservation'''<br /> <br /> Compare another HA<br /> Fetch an HA from a different subtype/strain (e.g., another H5N1, H1N1, or the C05-bound head example). For convenience, you can use 4FQI as reference.<br /> <br /> Align HA chains (align) and map your epitope residues from the first antigen onto the second by position.<br /> <br /> '''Q11.''' Which epitope class (head vs stem) is more conserved by sequence identity at the interface? <br /> <br /> '''Part E. Now suppose that we found a good neutralising antibody against Influenza, we isolate the antibody and have a sequence'''<br /> <br /> '''Q12.''' Are there any tools to help us predicting where the antibody will bind in the antigen???</div>

Carol https://teaching.healthtech.dtu.dk/22145/index.php?title=Bcell_Epitope_prediction&diff=84 2025-10-28T13:29:21Z

<p>Carol: </p> <hr /> <div>'''B-cell epitope prediction — Why do some flu vaccines miss?<br /> <br /> Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart?<br /> <br /> '''Part A, Get your bearings in PyMOL (find the ground truth epitope)'''<br /> <br /> Go to the pdb homepage and look for the pdb entries 4FQI and 7K39. It is hemagglutinin protein from Inlfuenza complexed with two different antibodies. Fetch and inspect structures. You can color the different chains in different colors<br /> <br /> * Open 4FQI in PyMOL (fetch 4fqi) and identify chains for HA (HA1/HA2) and Fab (H/L). For ilustrative purposes we will call HA1 the head and HA2 the stem of hemagglutinin.<br /> <br /> * Open 7K39 (fetch 7k39) and similarly identify HA vs antibody chains.<br /> <br /> hint: you can find this information in the structure web-page, in the PDB file itself (you can open it with a text editor and search for COMPND)<br /> <br /> :COMPND MOL_ID: 1; <br /> :COMPND 2 MOLECULE: HEMAGGLUTININ HA1; <br /> :COMPND 3 CHAIN: A; <br /> :COMPND 4 FRAGMENT: UNP RESIDUES 17-346; <br /> :COMPND 5 SYNONYM: HEMAGGLUTININ RECEPTOR BINDING SUBUNIT HA1; <br /> :COMPND 6 ENGINEERED: YES; <br /> :COMPND 7 MOL_ID: 2; <br /> :COMPND 8 MOLECULE: HEMAGGLUTININ HA2; <br /> :COMPND 9 CHAIN: B; <br /> :COMPND 10 FRAGMENT: UNP RESIDUES 347-520; <br /> :COMPND 11 SYNONYM: HEMAGGLUTININ MEMBRANE FUSION SUBUNIT HA2; <br /> :COMPND 12 ENGINEERED: YES; <br /> :COMPND 13 MOL_ID: 3; <br /> :COMPND 14 MOLECULE: ANTIBODY CR9114 HEAVY CHAIN; <br /> :COMPND 15 CHAIN: H; <br /> :COMPND 16 FRAGMENT: FAB; <br /> :COMPND 17 ENGINEERED: YES; <br /> :COMPND 18 MOL_ID: 4; <br /> :COMPND 19 MOLECULE: ANTIBODY CR9114 LIGHT CHAIN; <br /> :COMPND 20 CHAIN: L; <br /> :COMPND 21 FRAGMENT: FAB LAMBDA; <br /> :COMPND 22 ENGINEERED: YES<br /> <br /> &amp;nbsp;<br /> <br /> '''Q1.''' List chain IDs for antigen vs antibody in each complex.<br /> <br /> Define the real epitope. For each complex, remove waters (remove solvent). Create an epitope selection on HA as all residues within 5 Å of any antibody atom and color it in red.<br /> <br /> ''Hint of PyMOL.'' select epitope, br.(antibody around 5)<br /> ''Hint2'' In one of the complexes you have several antibody H and L chains. You might want to work with one antibody only!<br /> <br /> '''Q2.''' Provide screenshots of the epitopes for the different protein complexes and the sequence panel with chain letters visible. How many epitope residues are there in head vs stem complexes? Are they mostly loops, helices, or strands (qualitatively)? <br /> <br /> <br /> '''Q3.''' Can you identify which residues are part of the epitope? Is the epitope linear? Does it have a linear core? Are the two complexes targeting the same chain?<br /> <br /> Make antigen-only files<br /> <br /> Using pymol, identify the antibody in the structure, select and remove it (action -&gt; remove atoms). Save the resulting molecule as antigen.pdb<br /> If the structure contain several antigen chains that are not part of the epitope, you can remove them.<br /> <br /> You can save using the GUI (remember to select PDB as option) as well as typing &quot;save antigen.pdb&quot; in the command line<br /> <br /> You can also save the fasta sequence of the antigen with the following command:<br /> <br /> save /path/to/folder/XXXX.fasta, all, format=fasta<br /> (remember to change the path and the XXs, name of the PDB complex)<br /> <br /> '''Part B. Sequence-based prediction (BepiPred-2.0 &amp; 3.0)'''<br /> <br /> <br /> Go to the BepiPred2 website and upload the sequences of the stem and the head of hemagglutinin. Leave the default parameters and submit the job. Don't close the window because we will need it again!<br /> <br /> '''Q4.''' does the BepiPred predictions overlap with the actual epitopes?<br /> <br /> Be careful: pdb file numbering does not always start from 1! Compare the numbering of the pdb with the one returned by BepiPred.<br /> <br /> Repeat the prediction now using BepiPred3. <br /> <br /> '''Q5.''' Does the prediction overlap with our epitope now?<br /> <br /> '''Q6.''' What is different in BepiPred 2 compared to Bepipred 3?<br /> <br /> <br /> '''Part C. Structure-based prediction (DiscoTope-2.0 &amp; 3.0)'''<br /> <br /> <br /> Load the antigen.pdb file and submit the prediction in Discotope-2. Save the output as discotope2.pdb<br /> <br /> Once again, the prediction is in the b-factor field (but you can download it in other formats as well)<br /> Load it in pymol and colour according to the b-factor.<br /> <br /> '''Q7:''' Does the prediction overlap with our epitope?<br /> <br /> '''Q8.''' Which prediction best matches our epitope?<br /> <br /> '''Q9.''' Use Discotope to predict the epitopes in the simian HIV GP120 homolog (pdb code 3FUS). If you want to save time, use this pre-cleaned PDB. Compare the results. Try and explain the differences. According to you is it a meaningful result or not? Please note that some bugs might occur, according to which file you use. If some strange results appear, report it in your answer :)<br /> <br /> '''Q10.''' Compare the results obtained in Discotope 2 and 3<br /> <br /> '''Part D. Antigenic drift vs conservation'''<br /> <br /> Compare another HA<br /> Fetch an HA from a different subtype/strain (e.g., another H5N1, H1N1, or the C05-bound head example). For convenience, you can use 4FQI as reference.<br /> <br /> Align HA chains (align) and map your epitope residues from the first antigen onto the second by position.<br /> <br /> '''Q11.''' Which epitope class (head vs stem) is more conserved by sequence identity at the interface? <br /> <br /> '''Part E. Now suppose that we found a good neutralising antibody against Influenza, we isolate the antibody and have a sequence'''<br /> <br /> '''Q12.''' Are there any tools to help us predicting where the antibody will bind in the antigen???</div>

Carol