22145 Immunological Bioinformatics Course Programme Fall 2024: Difference between revisions

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(Created page with "== 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 === * [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. * [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course...")
 
 
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=== Where and when ===
=== 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'''.  
Wednesday from 8 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 4 at 8:00'''.


=== Teachers ===
=== Teachers ===
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=== Hand-ins ===
=== 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.  
Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.


'''NB:''' It is possible to hand in as a group. We would ''much'' rather receive one group hand-in than several identical logbooks.  
It is possible (and recommended) to hand in as a group.


 
''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.
'''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 ===
=== Exam ===
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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.
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.  
Chatbots are allowed but you should state in your answer that you have used them.


=== DTU Learn Link ===
=== DTU Learn Link ===
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:'''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.
:'''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.
-->
-->
:'''Exercises:'''
:'''Exercise:'''
:# [[Plain text files and Geany]]  
<!--:# [[Plain text files and Geany]]  
:# [[Taxonomy databases]]  
:# [[Taxonomy databases]]  
<!--:'''Extra material'''  
:'''Extra material'''  
:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.
:*"[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 annual database issue of Nucleic Acids Research, 2023
:*"[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
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=== Wednesday, Sep 18 — Allergenicity prediction ===
=== Wednesday, Sep 18 — Allergenicity prediction ===
:'''Lecture:''' ''Allergens'' — Carolina Barra Quglia
:'''Lecture:''' ''Allergens'' — Carolina Barra Quglia
:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/VirtualRibosome.pdf Virtual Ribosome] — software article (PDF).
:'''Slides:''' on DTU Learn.
:'''Slides:''' on DTU Learn.


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-->  
-->  
:'''Slides:''' on DTU Learn.
:'''Slides:''' on DTU Learn.
:'''Exercise:
<!--
:'''Exercise: [[Exercise:_BLAST2|BLAST]]'''  
:'''Exercise: [[Exercise:_BLAST2|BLAST]]'''  
<!--
:'''Extra material:'''  
:'''Extra material:'''  
::[[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]
::[[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]
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::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]
::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]
-->
-->
:'''Software''' for installation: [https://pymol.org/2/ PyMOL]  
<!--:'''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.
::'''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.
-->
-->
:'''Exercises:'''  
:'''Exercises:'''  
:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.
<!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.
:#[[Protein Structure and Visualization]]  
:#[[Protein Structure and Visualization]]  
-->


<!--:'''Extra material:'''  
<!--:'''Extra material:'''  
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------
------


=== Tuesday Oct 22 — Case: Malaria vaccine ===
=== Wednesday, Oct 23 — TCR interaction models and TCR repertoires ===
:'''Lecture:''' ''Malaria and vaccines'' — [https://cmp.ku.dk/staff/?pure=en/persons/226923 Thomas Lavstsen], Associate Professor, University of Copenhagen
:'''Workshop:''' ''TCR interaction models and TCR repertoires'' — Leon Eyrich Jessen
:'''Curriculum:''' [http://www.cdc.gov/dpdx/malaria/ Malaria — Causal Agents / Life Cycle]
:'''Slides:''' on DTU Learn.
:'''Slides:''' on DTU Learn.
:[[Image:Emblem-important_tiny.png‎]] '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]
:''' GitHub link:'''
:'''Exercise:''' [[Exercise:Malaria Vaccine|Malaria vaccine]]
<!--
:'''Curriculum:'''
'''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]
:'''Exercise:'''  
-->


=== Tuesday Oct 29 — Sequence information & logo-plots ===
=== Wednesday, Oct 30 — Vaccine design ===
:'''Lecture:''' ''Sequence information & logo-plots'' — Rasmus Wernersson
:'''Lecture:''' ''Vaccine design'' — Morten Nielsen
:'''Curriculum:'''  
:'''Slides:''' on DTU Learn.
:'''Exercise:'''
<!--:'''Curriculum:'''  
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).  
:# 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])
:# 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!
:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!
:'''Slides:''' on DTU Learn.
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)
:'''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]]
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]
-->


=== Tuesday Nov 5 — Weight matrices and other prediction methods ===
 
:'''Lecture:''' ''Introduction to prediction methods, especially Weight Matrices'' — Henrik Nielsen
=== Wednesday, Nov 6 — Predictions  in Autoimmunity ===
:'''Curriculum:''' Same as last week!
:'''Lecture:''' ''Case study: Autoimmunity'' — Carolina Barra
:'''Slides:''' on DTU Learn.
:'''Slides:''' on DTU Learn.
<!--:'''Handouts''' for the lecture: -->
:'''Exercises:'''
 
<!--:'''Handouts''' for the lecture:  
:'''Exercises:'''  
:'''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.
:# [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.
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:'''Link to advanced course: '''
:'''Link to advanced course: '''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]
-->


=== Tuesday Nov 12 — PSI-BLAST ===
=== Wednesday, Nov 13 — Beginning Project work ===
:'''Lecture:''' ''PSI-BLAST'' — Rasmus Wernersson
:'''Lecture:''' ''Short introduction to project work'' — Carolina Barra
:'''Curriculum:'''
:'''Slides:''' on DTU Learn.
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]]
:'''Exercise:'''


=== Tuesday Nov 19 — Multiple alignments ===
=== Wednesday, Nov 20 — Project work ===
:'''Lecture:''' ''Multiple alignment'' — Henrik Nielsen
:'''Lecture:''' No LECTURE
:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
<!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]  
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]  
-->


=== Tuesday Nov 26 — Phylogenetic trees ===
=== Wednesday, Nov 27 — Project work ===
:'''Lecture:''' ''Phylogenetic Reconstruction: Distance Matrix Methods'' — Henrik Nielsen
:'''Lecture:''' No LECTURE
<!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson -->
<!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson -->
:'''Curriculum:'''
:# ''Introduction to Tree Building'', PDF on Learn <!-- XXX WHERE? → Slides etc → Lecture12 -->
:# ''[http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 Evolutionary trees]'' (minus the section "How to reconstruct an evolutionary tree")
:# ''Understanding Evolutionary Trees'', [https://teaching.healthtech.dtu.dk/material/22111/PDF/understanding_evo_trees.pdf PDF].
:'''Slides:''' on DTU Learn.
:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/22111/PDF/handout_distance.pdf Reconstructing a distance tree]
<!-- :'''Software''' for installation: [https://github.com/rambaut/figtree/releases FigTree tree-viewer]
::'''IMPORTANT NOTE''' for Windows users: Download the <tt>.zip</tt> file (FigTree.v1.4.4.zip) and unpack it. Then, go to the "lib" subfolder and double-click the <tt>.jar</tt> file. The <tt>.exe</tt> file may not work.
:'''TEST''' of the internal webserver we are going to use during the exercise: Please go to https://services.healthtech.dtu.dk/service.php?TreeHugger and click "View <u>example alignment files</u>". Then, copy either the "Sample DNA alignment" or the "Sample peptide dataset" and paste it in the TreeHugger input field. Click <u>Submit query</u> when instructed by the lecturer.
-->
:'''Exercise: [[Exercise: Phylogeny (Seaview version)|Phylogeny]]'''
:'''Link to advanced course:'''
::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]


=== Tuesday Dec 3 — Bioinformatics in practice + old exam questions ===
 
:'''Lecture:''' ''AI, phage discovery and rainforest genomics'' — Bent Petersen, KU.
=== Wednesday, Dec 4 — Project work poster session ===  
:'''Curriculum:''' (None - lean back and enjoy)
:'''Agenda for the poster presentations:''' TBD
:'''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 ==
== Exam ==


=== Monday Dec 16 ===
=== Wednesday, Dec 18 ===
'''Winter exam 2024:''' Go to https://eksamen.dtu.dk/ and find 22111.  
'''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145.  


[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).


The assignment will be accessible from '''XXX''' on Dec 16.
<!-- === Link collection ===
 
=== 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]]
A quick overview of the websites we have used in the course: [[Link collection]]


=== FAQ ===
=== FAQ ===
Questions we have received and answered: [[FAQ]]
Questions we have received and answered: [[FAQ]]
-->

Latest revision as of 18:57, 27 August 2024

General information

Where and when

Wednesday from 8 to 12 in building 208, holdlokale 3/065, starting on Wednesday, Sep 4 at 8:00.

Teachers

Teaching assistant

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.

It is possible (and recommended) to hand in as a group.

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

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.
Exercise:

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
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:

Wednesday, Oct 9 — Antigen Processing and Immunogenicity

Lecture: Antigen Processing — Carolina Barra Quaglia
Lecture: Immunogenicity prediction — Carolina Barra Quaglia
Slides: on DTU Learn.
Exercises:


Autumn holiday

Wednesday, Oct 23 — TCR interaction models and TCR repertoires

Workshop: TCR interaction models and TCR repertoires — Leon Eyrich Jessen
Slides: on DTU Learn.
GitHub link:

Wednesday, Oct 30 — Vaccine design

Lecture: Vaccine design — Morten Nielsen
Slides: on DTU Learn.
Exercise:


Wednesday, Nov 6 — Predictions in Autoimmunity

Lecture: Case study: Autoimmunity — Carolina Barra
Slides: on DTU Learn.
Exercises:


Wednesday, Nov 13 — Beginning Project work

Lecture: Short introduction to project work — Carolina Barra
Slides: on DTU Learn.
Exercise:

Wednesday, Nov 20 — Project work

Lecture: No LECTURE

Wednesday, Nov 27 — Project work

Lecture: No LECTURE


Wednesday, Dec 4 — Project work poster session

Agenda for the poster presentations: TBD

Exam

Wednesday, Dec 18

Winter exam E5-A 2024: Go to https://eksamen.dtu.dk/ and find 22145.


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