22145 Immunological Bioinformatics Course Programme Fall 2024
General information
Where and when
Lectures and exercises will take place every Wednesday morning from 8 to 12 in Holdlokale 3/065, building 208, starting on Wednesday, Sep 4 at 8:00.
Teachers
- Carolina Barra Quaglia — Associate professor, course responsible.
- Morten Nielsen — Professor, course responsible.
Teaching assistant
- Astrid Brix Saksager — PhD student
Course content
The course aims to introduce the students to state-of-the-art methods within 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 course is taught in two parts. Part 1 covers lectures and group-based exercises and part 2 will cover group-based project work aiming at creating a full project workflow.
See also the course base about 22145.
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.
Hand-ins
Regardless of your choice of writing software, the result ' must be handed in as a PDF file. LibreOffice and Google Docs can make PDFs directly. MacOS and Windows 10/11 have built-in functions for converting any printable file to PDF.
NB: It is possible to hand in as a group. We would much rather receive one group hand-in than several identical logbooks.
NB: 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.
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.
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.
Chatbots are allowed but you should state in your answer that you have used them.
DTU Learn Link
- Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/215856
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 DTU evaluation.
Lecture & exercise plan
Note: This is a preliminary plan, changes may occur!
Wednesday, Sep 4 — Introduction & databases
- Lectures:
- Introduction to immunological bioinformatics — Carolina Barra Quaglia.
- Databases — Carolina Barra Quaglia.
- Slides: All slides will be made available on DTU Learn.
- Exercises:
Wednesday, Sep 11 — B cell epitopes
- Lecture: B cell receptors and B cell epitopes — Carolina Barra Quaglia
- Slides: on DTU Learn.
- Exercise:
Wednesday, Sep 18 — Allergenicity prediction
- Lecture: Allergens — Carolina Barra Quglia
- Curriculum: Virtual Ribosome — software article (PDF).
- Slides: on DTU Learn.
- Exercises:
Wednesday, Sep 25 — MHC binding predictions
- Lecture: MHC binding predictions part 1 — Morten Nielsen.
- Slides: on DTU Learn.
- Exercise:
Wednesday, Oct 2 — MHC binding predictions
- Lecture: MHC binding predictions part 2 — Morten Nielsen.
- Slides: on DTU Learn.
- Exercise: BLAST
Wednesday, Oct 9 — Antigen Processing and Immunogenicity
- Lecture: Antigen Processing — Carolina Barra Quaglia
- Lecture: Immunogenicity prediction — Carolina Barra Quaglia
- Slides: on DTU Learn.
- Software for installation: 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.
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- Exercises:
- PyMol tutorial (PDF) — basic usage of PyMOL.
- Protein Structure and Visualization
Autumn holiday
Tuesday Oct 22 — Case: Malaria vaccine
- Lecture: Malaria and vaccines — Thomas Lavstsen, Associate Professor, University of Copenhagen
- Curriculum: Malaria — Causal Agents / Life Cycle
- Slides: on DTU Learn.
- File:Emblem-important tiny.png Mid-term evaluation: Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 File:Emblem-important tiny.png
- Exercise: Malaria vaccine
Tuesday Oct 29 — Sequence information & logo-plots
- Lecture: Sequence information & logo-plots — Rasmus Wernersson
- Curriculum:
- Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
- Pages 1-8 of "Information theory primer" (PDF)
- Read also the appendix on logarithms (especially log2) if needed!
- Slides: on DTU Learn.
- Handout for the lecture: How to construct sequence logos (PDF)
- Exercise: DNA and Peptide Logos
Tuesday Nov 5 — Weight matrices and other prediction methods
- Lecture: Introduction to prediction methods, especially Weight Matrices — Henrik Nielsen
- Curriculum: Same as last week!
- Slides: on DTU Learn.
- Exercises:
- 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.
- Construction of weight matrices
- Link to advanced course:
Tuesday Nov 12 — PSI-BLAST
- Lecture: PSI-BLAST — Rasmus Wernersson
- Curriculum:
- Slides: on DTU Learn.
- Exercise: PSI-BLAST
Tuesday Nov 19 — Multiple alignments
- Lecture: Multiple alignment — Henrik Nielsen
- Curriculum: RevTrans (article)
- Slides: on DTU Learn.
- Exercise: Multiple Alignments
Tuesday Nov 26 — Phylogenetic trees
- Lecture: Phylogenetic Reconstruction: Distance Matrix Methods — Henrik Nielsen
- Curriculum:
- Introduction to Tree Building, PDF on Learn
- Evolutionary trees (minus the section "How to reconstruct an evolutionary tree")
- Understanding Evolutionary Trees, PDF.
- Slides: on DTU Learn.
- Handout for lecture: Reconstructing a distance tree
- Exercise: Phylogeny
- Link to advanced course:
Tuesday Dec 3 — Bioinformatics in practice + old exam questions
- Lecture: AI, phage discovery and rainforest genomics — Bent Petersen, KU.
- Curriculum: (None - lean back and enjoy)
- Slides: on DTU Learn.
- Exercise: We train on the old exam set from spring 2022 - available on DTU Learn. Note that there is no hand-in. The answers will become available 17:00 on Tuesday Dec 3.
Exam
Monday Dec 16
Winter exam 2024: Go to https://eksamen.dtu.dk/ and find 22111.
Here is a guide to the Digital Exam interface (in Danish and English).
The assignment will be accessible from XXX on Dec 16.
Checklist for computers
Check here whether your computer has all the software needed for the exam: Checklist for computers
Link collection
A quick overview of the websites we have used in the course: Link collection
FAQ
Questions we have received and answered: FAQ