22145 Immunological Bioinformatics Course Programme Fall 2026: Difference between revisions

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(Created page with "== General information == === Where and when === 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 === Teachers === * [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. *...")
 
 
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=== Where and when ===
=== Where and when ===


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
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 ===
=== Teachers ===


* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible.
* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate Professor and course coordinator.
 
* [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor and course coordinator.
* [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsible.


=== Teaching assistant ===
=== Teaching assistant ===


* [https://www.dtu.dk/english/person/sebastian-nymann-deleuran?id=117549&entity=profile Sebastian Nymann Deleuran] — PhD student
* [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.


=== Course content ===
=== Course content ===


The course aims to introduce the students to state-of-the-art methods within computational immunology.
The course introduces students to state-of-the-art methods in computational immunology.


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.
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 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.  
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 course base about 22145].
See also [http://kurser.dtu.dk/course/22145 the DTU course description for course 22145].


=== Curriculum ===
=== Curriculum ===


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.
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 ===
=== Hand-ins ===


Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.
Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.


It is possible (and recommended) to hand in as a group.
Group submissions are permitted and recommended.


''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.
''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 ===


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'''.  
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.


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.
The written exam questions will be provided as a PDF through the DTU online exam system. '''PDF is the only accepted submission format.'''


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.
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.


=== DTU Learn Link ===
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.
* Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397
 
=== DTU Learn link ===
 
* DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397


=== Evaluation and feedback ===
=== Evaluation and feedback ===
We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can:
* send them by email to the teachers, or
* write them under "General feedback" in "Discussion" in DTU Learn.
If somebody writes a message in "Discussion", you can comment on it. If you see a message you agree with, please comment "Agree!" so that we can see that it is not just one person's opinion.


In addition, we will conduct a mid-term evaluation just after the autumn break in [https://evaluering.dtu.dk/ DTU evaluation].
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.


== Lecture & exercise plan ==
A midterm evaluation will also be conducted shortly after the autumn break through [https://evaluering.dtu.dk/ DTU Evaluation].


Note: This is a ''preliminary'' plan, changes may occur!
== 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 ===


=== Wednesday, Sep 3 — Introduction &  databases ===
:'''Lectures:'''
:'''Lectures:'''
:* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.
:* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.
:* ''Databases'' — Carolina Barra Quaglia.
:* ''Databases'' — Carolina Barra Quaglia.
:'''Slides:''' All slides will be made available on DTU Learn.
:'''Slides:''' All slides will be made available on DTU Learn.
<!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.
 
:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.
<!--
:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — written by Anders Gorm Pedersen.
:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, select "Test of prior knowledge" under course 22111, and complete the anonymous form. Please spend no more than 10 minutes on it.
-->
-->
:'''Exercise:'''
:'''Exercise:'''
<!--:# [[Plain text files and Geany]]  
 
:# [[Taxonomy databases]]  
<!--
:'''Extra material'''  
:# [[Plain text files and Geany]]
:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.
:# [[Taxonomy databases]]
:*"[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]" — article from the annual database issue of Nucleic Acids Research, 2023
:'''Extra material:'''
:* "[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — encyclopedia entry from 2009.
:* "[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]" — article from the 2023 annual database issue of ''Nucleic Acids Research''.
-->
 
=== 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.
 
<!--
:'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).
:'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].
-->
-->


=== Wednesday, Sep 10 — Antigen Processing and Presentation ===
:'''Slides:''' Available on DTU Learn.
:'''Lecture:''' ''Antigen Processing and Presentation'' — Carolina Barra Quaglia
:'''Exercise:'''
:'''Slides:''' on DTU Learn.
 
<!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault
<!--
:'''Handout''' for the lecture: [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 (version for on-screen viewing)] [PDF].
:[[ExPairwiseAlignment|Pairwise alignment]]
-->
-->


:'''Exercise:'''
<!--:# [[ExGenbank-new|Using the GenBank database]]
:'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF]


:'''Background material''' (supposedly known):
=== Wednesday, 23 September 2026 — Antigen processing and presentation ===
:*[[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).
:'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.
:'''Slides:''' Available on DTU Learn.


:'''Extra material:'''  
<!--
:*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)
:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault.
:*[https://doi.org/10.1093/nar/gkac1012 "GenBank 2023 update"] — article from the annual database issue of Nucleic Acids Research, 2023.
:'''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].
-->
-->


=== Wednesday, Sep 17 — MHC binding predictions part 1 ===
:'''Exercise:'''
:'''Lecture:''' ''MHC binding predictions Part 1'' — Morten Nielsen
:'''Slides:''' on DTU Learn.


:'''Exercises:'''
<!--
:# [[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).


=== Wednesday, Sep 24 — MHC binding predictions part 2 ===
:'''Extra material:'''
:'''Lecture:''' ''MHC binding predictions part 2'' — Morten Nielsen.
:* [http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI).
<!--:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).
:* [https://doi.org/10.1093/nar/gkac1012 "GenBank 2023 update"] — article from the 2023 annual database issue of ''Nucleic Acids Research''.
:'''Handout''' for the
lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]
-->
-->
:'''Slides:''' on DTU Learn.
 
:'''Exercise:'''  
=== Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===
<!--[[ExPairwiseAlignment|Pairwise alignment]]  
 
:'''Lectures:'''
:* ''Allergenicity prediction'' — Carolina Barra Quaglia.
:* ''Immunogenicity prediction'' — Carolina Barra Quaglia.
 
<!--
:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein structure] (Wikipedia).
-->
 
:'''Slides:''' Available on DTU Learn.
 
<!--
:'''Related advanced course:'''
::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology].
-->
-->


=== Wednesday, Oct 1 — Vaccine design ===
:'''Lecture:''' ''Vaccine design'' — Morten Nielsen.
<!--:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).
-->
:'''Slides:''' on DTU Learn.
:'''Exercise:
<!--
<!--
:'''Exercise: [[Exercise:_BLAST2|BLAST]]'''  
:'''Software to install:''' [https://pymol.org/2/ PyMOL].
:'''Extra material:'''
::'''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.
::[[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]
-->
-->


=== Wednesday, Oct 8 — Allergenicity prediction  ===
:'''Exercises:'''


:'''Lecture:''' ''Allergenicity prediction'' — Carolina Barra Quaglia
<!--
:'''Lecture:''' ''Immunogenicity prediction'' — Carolina Barra Quaglia
:# [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMOL tutorial] (PDF) — basic use of PyMOL.
<!--:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]
:# [[Protein Structure and Visualization]].
-->
-->
:'''Slides:''' on DTU Learn.
 
<!--:'''Link to advanced course:'''  
<!--
::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]
:'''Extra material:'''
:* [https://doi.org/10.1093/nar/gkac1077 "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"] — article from the 2023 annual database issue of ''Nucleic Acids Research''.
:* [[PyMOL]] — tips and tricks.
:* [https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise).
-->
-->
<!--:'''Software''' for installation: [https://pymol.org/2/ PyMOL]
 
::'''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.
=== 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).
-->
-->
:'''Exercises:'''  
 
<!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.
:'''Slides:''' Available on DTU Learn.
:#[[Protein Structure and Visualization]]  
:'''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].
-->
-->


<!--:'''Extra material:'''  
=== Wednesday, 14 October 2026 — Autumn break ===
:*[https://doi.org/10.1093/nar/gkac1077 "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"] — article from the annual database issue of Nucleic Acids Research, 2023.
 
:*[[PyMOL]] — some tips and tricks.
:'''No teaching.'''
:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)
 
=== 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:'''
 
<!--
:'''Curriculum:'''
:'''Midterm evaluation:''' Go to https://evaluering.dtu.dk/ and select "Mid-term evaluation" under course 22111. [[Image:Emblem-important_tiny.png‎]]
:'''Exercise:'''
-->
-->


------
=== Wednesday, 28 October 2026 — B-cell epitope prediction ===
<div align="center">
 
'''Autumn holiday'''  
:'''Lecture:''' ''B-cell epitope prediction'' — Paolo Marcatili.
</div>
:'''Slides:''' Available on DTU Learn.
------
:'''Exercise:'''


=== Wednesday, Oct 22 — BCR and TCR structure predictions ===
:'''Workshop:''' ''BCR and TCR structure predictions'' — Carolina Barra Quaglia
:'''Slides:''' on DTU Learn.
:''' GitHub link:'''
<!--
<!--
:'''Curriculum:'''  
:'''Curriculum:'''
'''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]
:# Pages 68–80 of ''Immunological Bioinformatics'' (PDF available on DTU Learn).
:'''Exercise:'''  
:# Pages 1–8 of the "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]).
:#* Read the appendix on logarithms, especially log<sub>2</sub>, if needed.
:'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF).
:'''Exercise:''' [[ExSeqLogos|DNA and peptide logos]].
-->
-->


=== Wednesday, Oct 29 — B Cell epitope predictions ===
=== Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===
:'''Lecture:''' ''B Cell epitope predictions'' — Paolo Marcatili
 
:'''Slides:''' on DTU Learn.
:'''Exercise:'''
<!--:'''Curriculum:'''
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
:# Pages 1-8 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])
:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]
-->


=== Wednesday, Nov 5 — TCR interaction models ===
:'''Lecture:''' ''TCR interaction models'' — Morten Nielsen
:'''Lecture:''' ''TCR interaction models'' — TBD
:'''Slides:''' Available on DTU Learn.
: ''Short introduction to project work'' — Carolina Barra
:'''Slides:''' on DTU Learn.
:'''Exercises:'''
:'''Exercises:'''


<!--:'''Handouts''' for the lecture:
<!--
:'''Exercises:'''  
 
:# [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.
:'''Handouts:'''
:# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]]  
:'''Exercises:'''
:'''Link to advanced course: '''
:# [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.
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]
:# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].
:'''Related advanced course:'''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].
-->
-->


=== Wednesday, Nov 12 — Project work ===
=== Wednesday, 11 November 2026 — Written EXAM ===
:'''Lecture:''' No LECTURE


=== Wednesday, Nov 19 — Project work ===
: 9-11 EXAM
:'''Lecture:''' No LECTURE
: 11-12'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.
<!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]
-->


=== Wednesday, Nov 26 — Project work ===
=== Wednesday, 18 November 2026 — Project work ===
:'''Lecture:''' No LECTURE
<!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson -->


:'''Lecture:''' No lecture.


=== Wednesday, Dec 3 — Poster session ===
<!--
:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article]).
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple alignments]].
-->


:Poster presentations will be '''starting at 8:00am'''
=== Wednesday, 25 November 2026 — Project work ===


:'''Agenda for the poster presentations:''' TBD
:'''Lecture:''' No lecture.


== Exam ==
<!--
:'''Extra lecture:''' ''Bioinformatics and systems biology in precision medicine'' — Rasmus Wernersson.
-->
 
=== Wednesday, 2 December 2026 — Poster session ===


=== Wednesday, Dec 18 ===
:Poster presentations will begin at '''08:00'''.
'''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145.  


:'''Poster presentation agenda:''' To be announced.


<!-- === Link collection ===
== Exam ==
A quick overview of the websites we have used in the course: [[Link collection]]


=== FAQ ===
The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''
Questions we have received and answered: [[FAQ]]
-->

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

Teaching assistant

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

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

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