22145 Immunological Bioinformatics Course Programme Fall 2026 - Revision history

Carol: /* Hand-ins */

2026-08-12T15:01:18Z

Hand-ins

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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 ===

Carol: /* Course content */

2026-08-12T15:00:06Z

Course content

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	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 ~~without internet~~ on November 11th.		* 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.		* Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.

Carol: /* Course content */

2026-08-12T14:59:29Z

Course content

← Older revision		Revision as of 16:59, 12 August 2026
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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. 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.		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 without internet 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].

Carol: /* Where and when */

2026-08-12T14:40:39Z

Where and when

← Older revision		Revision as of 16:40, 12 August 2026
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	=== Where and when ===		=== Where and when ===

	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'''.		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.

Carol: /* Lecture and exercise plan */

2026-08-12T14:39:09Z

Lecture and exercise plan

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	-->		-->

	=== Wednesday, 4 November 2026 — ~~Written Exam~~ ===		=== Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===

	~~<!--~~
	:'''Lecture:''' ''TCR interaction models'' — ~~To be announced.~~		:'''Lecture:''' ''TCR interaction models'' — Morten Nielsen
	~~:'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.~~
	:'''Slides:''' Available on DTU Learn.		:'''Slides:''' Available on DTU Learn.
	:'''Exercises:'''		:'''Exercises:'''

			<!--

	:'''Handouts:'''		:'''Handouts:'''
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	-->		-->

	=== Wednesday, 11 November 2026 — ~~Project work~~ ===		=== Wednesday, 11 November 2026 — Written EXAM ===

	:'''~~Lecture~~:''' ~~No lecture~~.		: 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 ===

Carol: /* Exam */

2026-08-06T10:40:30Z

Exam

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	== Exam ==		== Exam ==

	~~=== Friday, 18 December 2026 ===~~		The exam has two parts: A 2hs written exam on '''November 4th''' and an oral presentation of the group project on '''December 2nd'''

	'''~~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.~~

	~~<!--~~
	~~=== Link collection ===~~
	~~A quick overview~~ of the ~~websites used in the course: [[Link collection]].~~

	~~=== FAQ ===~~
	~~Questions received and answered: [[FAQ]].~~
	~~-->~~

Carol: /* Wednesday, 4 November 2026 — TCR interaction models */

2026-08-06T10:37:44Z

Wednesday, 4 November 2026 — TCR interaction models

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	-->		-->

	=== Wednesday, 4 November 2026 — ~~TCR interaction models~~ ===		=== Wednesday, 4 November 2026 — Written Exam ===

			<!--
	:'''Lecture:''' ''TCR interaction models'' — To be announced.		:'''Lecture:''' ''TCR interaction models'' — To be announced.
	:'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.		:'''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.
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	:'''Exercises:'''		:'''Exercises:'''

	~~<!--~~
	:'''Handouts:'''		:'''Handouts:'''
	:'''Exercises:'''		:'''Exercises:'''

Carol: /* Lecture and exercise plan */

2026-08-06T10:34:53Z

Lecture and exercise plan

← Older revision		Revision as of 12:34, 6 August 2026
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	== Lecture and exercise plan ==		== Lecture and exercise plan ==

	'''Note:''' This is a ''preliminary'' plan and may be subject to ~~change~~.		'''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 ~~September 2026 — Antigen processing and presentation ===~~		=== Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===

	~~:'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.~~
	~~:'''Slides:''' Available on DTU Learn.~~

	~~<!--~~
	~~:'''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:'''~~

	~~<!--~~
	~~:# [[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:'''~~
	~~:* [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, 16~~ 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, 23 September 2026 — MHC binding prediction, Part 2 ===		=== 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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	-->		-->

	~~=== Wednesday, 30 September 2026 — Vaccine design ===~~

	:'''Lecture:''' ''~~Vaccine design~~'' — ~~Morten Nielsen~~.		=== Wednesday, 23 September 2026 — Antigen processing and presentation ===

			:'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.
			:'''Slides:''' Available on DTU Learn.

	<!--		<!--
	:'''Curriculum:''' ~~Sections 3~~.2.~~5–3~~.~~3 (pages 47–52) of~~ ''~~Immunological Bioinformatics~~'' (PDF ~~available~~ on ~~DTU Learn)~~.		:'''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].
	-->		-->

	~~:'''Slides:''' Available on DTU Learn.~~
	:'''Exercise:'''		:'''Exercise:'''

	<!--		<!--
	:'''~~Exercise~~:''' [[~~Exercise~~:~~_BLAST2\|BLAST~~]].		:# [[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:'''
	:: [~~[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]~~.		:* [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, ~~7 October~~ 2026 — Allergenicity and immunogenicity prediction ===		=== 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].
	-->		-->

Carol: /* Where and when */

2026-08-06T10:28:55Z

Where and when

← Older revision		Revision as of 12:28, 6 August 2026
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	=== Where and when ===		=== Where and when ===

	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~~.		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'''.

	The first hour of each class is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn.		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 ===

Carol at 10:27, 6 August 2026

2026-08-06T10:27:05Z

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