View source for 22111:Course plan autumn 2023

== General information ==

=== Where and when ===
Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Aug 29 at 13:00'''. 

Lectures will be from 13:00 to approx. 14 in '''building 306, auditorium 33''', and the exercises will then take place in '''building 210, rooms 142+148+162+168'''.

=== Teachers ===

* [http://www.dtu.dk/service/telefonbog/person?id=25617&cpid=257116&tab=2&qt=dtupublicationquery Henrik Nielsen] &mdash; Associate professor, course responsible.
* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] &mdash; Assistant professor, course responsible.
* [https://www.dtu.dk/service/telefonbog/person?id=18103&tab=2&qt=dtupublicationquery Rasmus Wernersson] &mdash; External associate professor.
<!-- * [http://www.dtu.dk/service/telefonbog/person?id=5118&tab=2&qt=dtupublicationquery Anders Gorm Pedersen] &mdash; Professor, guest lecturer. Topic: Phylogenetic trees. -->

=== Teaching assistants ===

* [https://www.dtu.dk/person/astrid-brix-saksager?id=118546 Astrid Brix Saksager] — PhD student
* [https://www.dtu.dk/person/louis-maximilian-kraft?id=183582 Louis Kraft] — PhD student
* [https://www.dtu.dk/person/joakim-noeddeskov-clifford?id=117839 Joakim Clifford] — PhD student, stand-in for Louis Aug 29 and for Astrid Nov 21.
* [https://www.dtu.dk/person/kristine-fredlund-degn?id=68467 Kristine Degn] — PhD student, stand-in for Astrid Oct 3
* [https://www.dtu.dk/person/sebastian-nymann-deleuran?id=117549 Sebastian Deleuran] — PhD student, stand-in for Louis Sep 12

=== 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 M1 or M2 CPUs) 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_(English_version)|multiple alignments]].
* The website [https://itol.embl.de/ iTOL] has 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:''' It is possible to hand in as a group. We would ''much'' rather receive one group hand-in than a number of identical logbooks. 

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.
<!-- For Windows users, however, we recommend the free program [http://getgreenshot.org/ Greenshot] which can not only take screenshots and copy them to the clipboard, but also make simple edits and annotations in the screenshots. -->

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.

'''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. 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 information on 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.
-->

Just like in the weekly hand-ins, we kindly ask you: ''Please don't copy the questions in your answer document'' — that might result in the answer being flagged as plagiarism.

=== DTU Learn & Inside ===
Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/167348

Link to this year's DTU Inside group: https://cn.inside.dtu.dk/cnnet/element/682925/

=== 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 Aug 29 — Introduction & taxonomy ===
:'''Lectures:'''
:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen.
:* ''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.
:'''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:'''
:# [[Plain text files and Geany]] <!--  — ([[ExJEdit-Answers|Answers]])  -->
:# [[Taxonomy databases]] <!--  — ([[ExTaxonomy-Answers|Answers]]) -->
:'''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 annual database issue of Nucleic Acids Research, 2023

=== Tuesday Sep 5 — 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.

<!--
:'''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.
-->
:'''Exercise:''' [[ExGenbank-new|Using the GenBank database]] <!-- — ([[ExGenbank-new-answers|Answers]]) -->
:'''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/gkac1012 "GenBank 2023 update"] — article from the annual database issue of Nucleic Acids Research, 2023.

=== Tuesday Sep 12 — Translation & UniProt ===
:'''Lecture:''' ''Protein databases'' — Henrik Nielsen
:'''Curriculum:''' [[Media:VirtualRibosome.pdf|Virtual Ribosome]] — software article (PDF).
:'''Slides:''' on DTU Learn.

:'''Exercises:''' 
:#[[Exercise: Translation - Virtual Ribosome]] <!-- — ([[ExTranslation-answers|Answers]]) -->
:#[[Exercise: The protein database UniProt]] <!-- — ([[ExUniProt-answers|Answers]]) -->
:'''Background material''' (supposedly known): 
:*[https://teaching.healthtech.dtu.dk/material/36611/PDF/protein_handout.pdf Levels of protein structure] [PDF]
:*[[Media:GeneStructure.pdf|Overview of eukaryotic gene structure]] (PDF).

:'''Extra material:''' 
:*[https://doi.org/10.1093/nar/gkac1052 "UniProt: the Universal Protein Knowledgebase in 2023"] — article from the annual database issue of Nucleic Acids Research, 2023.
<!--
:*[[Media:uniprotkb_quickguide.pdf|"A Quick Guide to UniProtKB"]] — nice printable overview.
-->

=== Tuesday Sep 19 — 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: [[Media:New_handout_alignscores.pdf|Alignment scores]] 
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment]] <!-- — ([[ExPairwiseAlignment-AnswersEng|Answers]]) -->

=== Tuesday Sep 26 — BLAST ===
:'''Lecture:''' ''Introduction to BLAST'' — Rasmus Wernersson.
:'''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:_BLAST2|BLAST]]''' <!-- — ([[ExBlast-Answers|Answers]]) -->
<!--
:'''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]
-->

=== Tuesday Oct 3 — 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://teaching.healthtech.dtu.dk/36617/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]

:'''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.
:'''Exercises:''' 
:#[[Media:PyMol_tutorial2017_v4.pdf|PyMol tutorial]] (PDF) — basic usage of PyMOL.
:#[[Protein Structure and Visualization]] <!-- — ([[Protein_Structure_and_Visualization_Answers|Answers]]; NB: the last section labelled "PyMOL magic" is NOT curriculum, just a tip!) -->
:'''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 annual database issue of Nucleic Acids Research, 2023.
:*[[PyMOL]] — some tips and tricks.
:*[https://teaching.healthtech.dtu.dk/material/36611/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)

=== Tuesday Oct 10 — 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.
:[[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:''' [[Exercise:Malaria Vaccine|Malaria vaccine]] <!-- — ([[Answers:Malaria Vaccine|Answers]]) -->

------
<div align="center">
 '''Autumn holiday''' 
</div>
------

=== Tuesday Oct 24 — Sequence information & logo-plots ===
:'''Lecture:''' ''Sequence information & logo-plots'' — Carolina Barra Quaglia
:'''Curriculum:''' 
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). 
:# Pages 1-8 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/36611/PDF/informationtheory_primer.pdf PDF])
:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!
:'''Slides:''' on DTU Learn.
:'''Handout''' for the lecture: [[Media:logo_exercise.pdf|How to construct sequence logos]] (PDF)
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]] <!-- — ([[ExSeqLogosAnswers|Answers]]) -->

=== Tuesday Oct 31 — 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.
<!--:'''Handouts''' for the lecture: -->
:'''Exercises:''' 
:# [[Media:Estimationofpseudocounts_new+examples.pdf|How to estimate pseudo frequencies]]  <!-- ([[Media:Estimationofpseudocounts_answer_brief.pdf|Answer]]) --> '''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]] <!-- - ([[ExLogo+Matrix-answers|Answers]]) -->
:'''Link to advanced course: '''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]

=== Tuesday Nov 7 — PSI-BLAST ===
:'''Lecture:''' ''PSI-BLAST'' — Rasmus Wernersson 
:'''Curriculum:''' 
:'''Slides:''' on DTU Learn.
:'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]] <!-- — ([[ExPSIBLAST_answer|Answers]]) -->

=== Tuesday Nov 14 — 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]] <!-- — ([[ExMulAlign-Answers-English|Answers]]) -->

=== Tuesday Nov 21 — Phylogenetic trees ===
:'''Lecture:''' ''Phylogenetic Reconstruction: Distance Matrix Methods'' — Henrik Nielsen
<!-- :'''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/36611/PDF/understanding_evo_trees.pdf PDF].
:'''Slides:''' on DTU Learn.
:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/36611/PDF/handout_distance.pdf Reconstructing a distance tree] <!-- ([[Media:handout_distance_answers.pdf|Answer]]) -->
<!-- :'''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]]''' <!-- — ([[Exercise:_Phylogeny-Answers|Answers]]) -->
:'''Link to advanced course:''' 
::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]

=== Tuesday Nov 28 — Bioinformatics in practice + old exam questions ===
:'''Lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson <!--"Real life case": ''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 Nov 28.

== Exam ==

=== Thursday Dec 14 ===
'''Winter exam 2023:''' Go to https://eksamen.dtu.dk/ and find 22111. 

[[Media:Vejledning-til-digital-eksamen-DE-DKENG_0322.pdf|Here is a guide]] to the Digital Exam interface (in Danish and English).

The assignment will be accessible from '''15:00''' on Thursday Dec 14.

=== 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]]