22111:Course plan autumn 2026

Henni — Mon, 03 Aug 2026 14:45:49 GMT

Created page with "== General information == === Where and when === Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 2 at 13:00'''. Lectures will be from 13:00 to approx. 14 in '''Aud. 54, building 208''', and the exercises will then take place in '''the group rooms ALC1 (001), ALC2 (011), ALC4 (012), and "Touch Down" (024) also in building 208'''. === Teachers === * [http://www.dtu.dk/service/telefonbog/person?id=..."

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== General information ==

=== Where and when ===
Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 2 at 13:00'''.

Lectures will be from 13:00 to approx. 14 in '''Aud. 54, building 208''', and the exercises will then take place in '''the group rooms ALC1 (001), ALC2 (011), ALC4 (012), and "Touch Down" (024) also in building 208'''.

=== Teachers ===

* [http://www.dtu.dk/service/telefonbog/person?id=25617&cpid=257116&tab=2&qt=dtupublicationquery Henrik Nielsen] — Associate professor, course responsible.
* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible.
* [https://www.dtu.dk/service/telefonbog/person?id=18103&tab=2&qt=dtupublicationquery Rasmus Wernersson] — Affiliated professor.


=== Teaching assistants ===

* [https://www.dtu.dk/person/mads-vodder-hartmann?id=137701&entity=profile Mads Vodder Hartmann] — PhD student
* [https://www.dtu.dk/person/david-lokjaer-faurdal?id=98246&entity=profile David Lokjær Faurdal] — PhD student

=== Course content ===
In this course, a large emphasis is placed on the practical usage of bioinformatics databases and tools. A typical lecture will present the theoretical aspects of the topics of the day — sometimes including a small group exercise using pen and paper — and last about an hour. The rest of the time will be spent on practical computer exercises, where the teachers and teaching assistants will be ready to help.

See also [http://kurser.dtu.dk/course/22111 the course base about 22111].

=== Curriculum ===
There is no formal textbook. The curriculum consists of the exercise guides, supplemented with various papers and chapters which will be made available on this homepage or 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.

=== Computers ===
====Hardware====
'''You must bring your own laptop''' to the exercises, and it must be able to connect to DTU's wireless network. The type of computer / operating system is not important; Windows, Mac or Linux will all work fine. An iPad or an Android tablet, on the other hand, will not be good enough. A Chromebook will also not be enough (unless you have succeeded in installing a Linux distribution on it, but in that case we assume you know what you're doing).

In some of the exercises ("PDB/PyMOL", "Malaria vaccine", and "Old exam questions"), you will work with the molecular visualization program PyMOL. This is rather difficult to control by a touchpad, so please remember to '''bring a mouse'''. The mouse should have two buttons plus a scroll-wheel.

====Software====
# Most importantly: an updated '''internet browser''' (e.g. [http://www.google.com/chrome Google Chrome], [http://www.mozilla.com/ FireFox], [http://www.opera.com/ Opera], [https://www.microsoft.com/edge Edge], or Safari for Mac only). '''NB:''' You must have more than one browser installed; Safari for Mac or Edge for Windows may have glitches with some bioinformatics websites, and in those cases it is important to be able to switch to an alternative browser.
# A plain text editor for working with, e.g., sequence files. We recommend '''Geany''', which you can download for free from https://geany.org/. You will find some tips and installation instructions in [[Plain_text_files_and_Geany|the first exercise]].
Other software will be installed during the exercises.

'''Note:''' Previously in the course, we have used some java-based software; but it is our experience that new Macs (with M-series CPUs, a.k.a. ARM chips) often have problems with java. Therefore, we have replaced these programs with other options:
* [https://geany.org/ Geany] has replaced [http://jedit.org/ jEdit], see the exercise in [[Plain_text_files_and_Geany|plain text files]].
* [https://doua.prabi.fr/software/seaview SeaView] has replaced [https://www.jalview.org/ Jalview], see the exercise in [[Exercise:_Multiple_Alignments_(Seaview_version)|multiple alignments]].
* [https://doua.prabi.fr/software/seaview SeaView] (and to some degree the website [https://itol.embl.de/ iTOL]) has also replaced the software [https://github.com/rambaut/figtree/releases FigTree], see the exercise in [[Exercise: Phylogeny|phylogenetic trees]].
Be aware that if you are working on old exam sets, they may refer to the old software.

=== Hand-ins ===
As preparation for the computer-based exam, each participant or group must write a "'''logbook'''" with answers to the questions posed in the exercise guides. After the exercise, you should upload the logbook to DTU Learn.

'''NB:''' All hand-ins are per definition group hand-ins. If you work alone, you must form a "group" of one person.


You decide which software you prefer for writing the logbook — e.g. Microsoft Word, [http://www.libreoffice.org/ LibreOffice] (free), [http://www.openoffice.org/ Apache OpenOffice] (free), Pages for Mac, [https://docs.google.com/ Google Docs] or similar. You should be able to insert '''screenshots''' in the logbooks for documentation purposes. Microsoft Word has a built-in screenshot tool. Both Windows 10/11 and Mac OS also have dedicated screenshot tools.


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.

'''Please do ''not'' copy the questions''' from the exercise guide to your logbook. The hand-in module on DTU Learn has a system for plagiarism detection, which will raise an alarm if significant portions of your hand-in are identical to documents found on the internet — and that includes the exercise guides.

In case you don't finish the exercises Tuesday afternoon, there is still a chance to hand in — the deadline for handing in at Learn is '''Thursday at 13:00''' each week. The '''answers to the exercises''' will become visible at the same moment (Thursday at 13:00). You should read the answers carefully and compare with your own answers.

We do not offer individual feedback on the hand-ins, but we will give a collective feedback before the lecture the next Tuesday, where we address any common mistakes there may have been.

'''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 22111 exam is electronic; i.e. you must bring your own computer, and you will ''not'' get a paper copy of the questions.

This year, the exam questions will be Multiple Choice.




=== DTU Learn & Inside ===
* Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271404
* Link to this year's Campusnet group: https://campusnet.dtu.dk/cnnet/element/805277

=== 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 on, 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 in [https://evaluering.dtu.dk/ DTU evaluation].

== Lecture & exercise plan ==

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

=== Tuesday Sep 2 — Introduction & taxonomy ===
:'''Lectures:'''
:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen.
:* ''Test of prior knowledge'' — a Vevox session.
:* ''Evolution and taxonomy'' — Rasmus Wernersson.
:'''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.

:'''Exercises:'''
:# [[Plain text files and Geany]]
:# [[Taxonomy databases]]
:'''Extra material'''
:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.
:*"[https://doi.org/10.1093/nar/gkae979 Database resources of the National Center for Biotechnology Information in 2025]" — article from the annual database issue of Nucleic Acids Research, 2025

=== Tuesday Sep 9 — GenBank ===
:'''Lecture:''' ''DNA as Biological Information'' — Rasmus Wernersson
:'''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].
:'''Slides:''' on DTU Learn.


:'''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):
:*[[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/gkae1114 "GenBank 2025 update"] — article from the annual database issue of Nucleic Acids Research, 2025.

=== Tuesday Sep 16 — Translation & UniProt ===
:'''Lecture:''' ''Protein databases'' — Henrik Nielsen
:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/VirtualRibosome.pdf Virtual Ribosome] — software article (PDF).
:'''Slides:''' on DTU Learn.

:'''Exercises:'''
:#[[Exercise: Translation - Virtual Ribosome]]
:#[[Exercise: The protein database UniProt]]
:'''Background material''' (supposedly known):
:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/protein_handout.pdf Levels of protein structure] [PDF]
:*[https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).

:'''Extra material:'''
:*[https://doi.org/10.1093/nar/gkae1010 "UniProt: the Universal Protein Knowledgebase in 2025"] — article from the annual database issue of Nucleic Acids Research, 2025.


=== Tuesday Sep 23 — Pairwise alignment ===
:'''Lecture:''' ''Pairwise alignment'' — Henrik Nielsen.
:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment]]

=== Tuesday Sep 30 — BLAST ===
:'''Lecture:''' ''Introduction to BLAST'' — Carolina Barra Quaglia.
:'''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:_BLAST3|BLAST]]'''


=== Tuesday Oct 7 — Protein structure, PDB & PyMOL ===
:'''Remember to bring a mouse for this day's exercise.''' The mouse should have two buttons and a scroll wheel.
:'''Lecture:''' ''Protein 3D structure'' — Carolina Barra Quaglia
:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]
:'''Slides:''' on DTU Learn.

:'''Link to advanced course:'''
::* [http://kurser.dtu.dk/course/22117 22117 Protein Structure and Computational Biology]

:'''Software''' for installation: [https://pymol.org/ PyMOL] (choose the newest version)
::'''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:'''
:#[[Media:PyMOL_tutorial.pdf|PyMol tutorial]] (PDF) — basic usage of PyMOL.
:#[https://teaching.healthtech.dtu.dk/22111/index.php/Protein_Structure Protein Structure exercise]
:'''Extra material:'''
:*[https://doi.org/10.1093/nar/gkae1091 "Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank"] — article from the annual database issue of Nucleic Acids Research, 2025.
:*[[PyMOL]] — some tips and tricks.
:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)

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'''Autumn holiday'''
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=== Tuesday Oct 21 — Sequence information & logo-plots ===
:'''Lecture:''' ''Sequence information & logo-plots'' — Rasmus Wernersson
:'''Curriculum:'''
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
:# Pages 1-9 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/primer-2.72.pdf PDF])
:#* 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)
:[[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]]
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]

=== Tuesday Oct 28 — Case: Malaria vaccine ===
:'''Lecture:''' ''Malaria and vaccines'' — [https://cmp.ku.dk/staff/?pure=en/persons/226923 Thomas Lavstsen], Associate Professor, University of Copenhagen
:'''Curriculum:''' [http://www.cdc.gov/dpdx/malaria/ Malaria — Causal Agents / Life Cycle]
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[Exercise:Malaria Vaccine|Malaria vaccine]]

=== Tuesday Nov 4 — Weight matrices and other prediction methods ===
:'''Lecture:''' ''Introduction to prediction methods, especially Weight Matrices'' — Henrik Nielsen
:'''Curriculum:''' Same as Oct 21!
:'''Slides:''' on DTU Learn.

:'''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.
:# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]]
:'''Link to advanced course: '''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]

=== Tuesday Nov 11 — PSI-BLAST ===
:'''Lecture:''' ''PSI-BLAST'' — Rasmus Wernersson
:'''Curriculum:'''
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]]

=== Tuesday Nov 18 — Multiple alignments ===
:'''Lecture:''' ''Multiple alignment'' — Henrik Nielsen
:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]

=== Tuesday Nov 25 — Phylogenetic trees ===
:'''Lecture:''' ''Phylogenetic Reconstruction: Distance Matrix Methods'' — Henrik Nielsen

:'''Curriculum:'''
:# ''Introduction to Tree Building'', PDF on Learn 
:# ''[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]

:'''Exercise: [[Exercise: Phylogeny (Seaview version)|Phylogeny]]'''
:'''Link to advanced course:'''
::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]

=== Tuesday Dec 2 — Bioinformatics in practice + old exam questions ===
:'''Lecture:''' ''AI, phage discovery and supercomputing'' — [https://globe.ku.dk/staff-list/?pure=en/persons/271131 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 2.

== Exam ==

=== Tuesday Dec 16 ===
'''Winter exam 2025:''' Go to https://eksamen.dtu.dk/ and find 22111.

[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 '''XX:00''' 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]]

22111 - Recent changes [en]

22111:Course plan autumn 2026

22111:Course plan autumn 2026