22145 Immunological Bioinformatics Course Programme Fall 2026: Difference between revisions
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=== Where and when === | === Where and when === | ||
Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, | 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'''. | ||
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. | 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. | ||
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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. | 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. | ||
The course is taught in two parts | The course is taught in two parts: | ||
* Part 1 consists of lectures and group-based exercises. Part 1 ends with a "in class" written exam on November 11th. | |||
* Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd. | |||
See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145]. | See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145]. | ||
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Group submissions are permitted and recommended. | Group submissions are permitted and recommended. | ||
''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. | ''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. | ||
=== Exam === | === Exam === | ||
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== Lecture and exercise plan == | == Lecture and exercise plan == | ||
'''Note:''' This is a ''preliminary'' plan and may be subject to | '''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates. | ||
=== Wednesday, 2 September 2026 — Introduction and databases === | === Wednesday, 2 September 2026 — Introduction and databases === | ||
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=== Wednesday, 9 | === Wednesday, 9 September 2026 — MHC binding prediction, Part 1 === | ||
:'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen. | :'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen. | ||
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:'''Exercises:''' | :'''Exercises:''' | ||
=== Wednesday, | === Wednesday, 16 September 2026 — MHC binding prediction, Part 2 === | ||
:'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen. | :'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen. | ||
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:'''Lecture:''' '' | === Wednesday, 23 September 2026 — Antigen processing and presentation === | ||
:'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia. | |||
:'''Slides:''' Available on DTU Learn. | |||
<!-- | <!-- | ||
:'''Curriculum:''' | :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault. | ||
:'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf "Base-calling" exercise for printing] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf "Base-calling" exercise for on-screen viewing] [PDF]. | |||
--> | --> | ||
:'''Exercise:''' | :'''Exercise:''' | ||
<!-- | <!-- | ||
:''' | :# [[ExGenbank-new|Using the GenBank database]] | ||
:'''Reference material:''' [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank and FASTA formats] [PDF]. | |||
:'''Background material (assumed knowledge):''' | |||
:* [[File:Phone_34.gif]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube). | |||
:* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF). | |||
:'''Extra material:''' | :'''Extra material:''' | ||
: | :* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI). | ||
:* [https://doi.org/10.1093/nar/gkac1012 "GenBank 2023 update"] — article from the 2023 annual database issue of ''Nucleic Acids Research''. | |||
--> | --> | ||
=== Wednesday, | === Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction === | ||
:'''Lectures:''' | :'''Lectures:''' | ||
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:* [[PyMOL]] — tips and tricks. | :* [[PyMOL]] — tips and tricks. | ||
:* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise). | :* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise). | ||
--> | |||
=== Wednesday, 7 October 2026 — Vaccine design === | |||
:'''Lecture:''' ''Vaccine design'' — Morten Nielsen. | |||
<!-- | |||
:'''Curriculum:''' Sections 3.2.5–3.3 (pages 47–52) of ''Immunological Bioinformatics'' (PDF available on DTU Learn). | |||
--> | |||
:'''Slides:''' Available on DTU Learn. | |||
:'''Exercise:''' | |||
<!-- | |||
:'''Exercise:''' [[Exercise:_BLAST2|BLAST]]. | |||
:'''Extra material:''' | |||
:: [[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]. | |||
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=== Wednesday, 4 November 2026 — | === Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions === | ||
:'''Lecture:''' ''TCR interaction models'' — | :'''Lecture:''' ''TCR interaction models'' — Morten Nielsen | ||
:'''Slides:''' Available on DTU Learn. | :'''Slides:''' Available on DTU Learn. | ||
:'''Exercises:''' | :'''Exercises:''' | ||
<!-- | <!-- | ||
:'''Handouts:''' | :'''Handouts:''' | ||
:'''Exercises:''' | :'''Exercises:''' | ||
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=== Wednesday, 11 November 2026 — | === Wednesday, 11 November 2026 — Written EXAM === | ||
:''' | : 9-11 EXAM | ||
: 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia. | |||
=== Wednesday, 18 November 2026 — Project work === | === Wednesday, 18 November 2026 — Project work === | ||
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== Exam == | == Exam == | ||
The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd''' | |||
''' | |||
Latest revision as of 17:01, 12 August 2026
General information
Where and when
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.
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.
Teachers
- Carolina Barra Quaglia — Associate Professor and course coordinator.
- Morten Nielsen — Professor and course coordinator.
Teaching assistant
- Eric Bautista Farrerons — PhD student.
Course content
The course introduces students to state-of-the-art methods in computational immunology.
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.
The course is taught in two parts:
- Part 1 consists of lectures and group-based exercises. Part 1 ends with a "in class" written exam on November 11th.
- Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.
See also the DTU course description for course 22145.
Curriculum
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.
Hand-ins
Regardless of the software used to prepare your work, all submissions must be handed in as PDF files.
Group submissions are permitted and recommended.
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.
Exam
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.
The written exam questions will be provided as a PDF through the DTU online exam system. PDF is the only accepted submission format.
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.
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.
DTU Learn link
- DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397
Evaluation and feedback
We welcome comments, suggestions, criticism, and praise throughout the semester. You can:
- email the teachers; or
- post under "General feedback" in the "Discussion" area on DTU Learn.
You may comment on messages posted in the discussion area. When you agree with a comment, please reply with "Agree!" so that the teaching team can see that the feedback is shared by more than one person.
A midterm evaluation will also be conducted shortly after the autumn break through DTU Evaluation.
Lecture and exercise plan
Note: This is a preliminary plan and may be subject to changes. Check the page regularly for updates.
Wednesday, 2 September 2026 — Introduction and databases
- Lectures:
- Introduction to immunological bioinformatics — Carolina Barra Quaglia.
- Databases — Carolina Barra Quaglia.
- Slides: All slides will be made available on DTU Learn.
- Exercise:
Wednesday, 9 September 2026 — MHC binding prediction, Part 1
- Lecture: MHC binding prediction, Part 1 — Morten Nielsen.
- Slides: Available on DTU Learn.
- Exercises:
Wednesday, 16 September 2026 — MHC binding prediction, Part 2
- Lecture: MHC binding prediction, Part 2 — Morten Nielsen.
- Slides: Available on DTU Learn.
- Exercise:
Wednesday, 23 September 2026 — Antigen processing and presentation
- Lecture: Antigen processing and presentation — Carolina Barra Quaglia.
- Slides: Available on DTU Learn.
- Exercise:
Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction
- Lectures:
- Allergenicity prediction — Carolina Barra Quaglia.
- Immunogenicity prediction — Carolina Barra Quaglia.
- Slides: Available on DTU Learn.
- Exercises:
Wednesday, 7 October 2026 — Vaccine design
- Lecture: Vaccine design — Morten Nielsen.
- Slides: Available on DTU Learn.
- Exercise:
Wednesday, 14 October 2026 — Autumn break
- No teaching.
Wednesday, 21 October 2026 — BCR and TCR structure prediction
- Workshop: BCR and TCR structure prediction — Carolina Barra Quaglia.
- Slides: Available on DTU Learn.
- GitHub link:
Wednesday, 28 October 2026 — B-cell epitope prediction
- Lecture: B-cell epitope prediction — Paolo Marcatili.
- Slides: Available on DTU Learn.
- Exercise:
Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions
- Lecture: TCR interaction models — Morten Nielsen
- Slides: Available on DTU Learn.
- Exercises:
Wednesday, 11 November 2026 — Written EXAM
- 9-11 EXAM
- 11-12Introduction: Short introduction to project work — Carolina Barra Quaglia.
Wednesday, 18 November 2026 — Project work
- Lecture: No lecture.
Wednesday, 25 November 2026 — Project work
- Lecture: No lecture.
Wednesday, 2 December 2026 — Poster session
- Poster presentations will begin at 08:00.
- Poster presentation agenda: To be announced.
Exam
The exam has two parts: A 2hs written exam on November 4th and an oral presentation of the group project on December 2nd