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Created page with "== General information == === 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/service/telefonbog/person?id=18103&tab=2&qt=dtupublicationquery Rasmus Wernersson] — External associate professor, course responsible. * [http://www.dtu.dk/service/telefonbog/person?id=34983&tab=2&qt=dtupublicationquery Paolo Marcatili] &md..."

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== General information ==

=== 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/service/telefonbog/person?id=18103&tab=2&qt=dtupublicationquery Rasmus Wernersson] — External associate professor, course responsible.
* [http://www.dtu.dk/service/telefonbog/person?id=34983&tab=2&qt=dtupublicationquery Paolo Marcatili] — Associate professor, guest lecturer. Topic: Protein structure.
* [http://www.dtu.dk/service/telefonbog/person?id=5118&tab=2&qt=dtupublicationquery Anders Gorm Pedersen] — Professor, guest lecturer. Topic: Phylogenetic trees.
* Rasmus Weisel Jensen — PhD student (University of Copenhagen), guest lecturer. Topic: Malaria vaccines.

=== Teaching assistants ===
* [https://www.dtu.dk/service/telefonbog/person?id=149708 Amelie Fritz] — PhD student
* [https://www.dtu.dk/service/telefonbog/person?id=140521 Anna-Lisa Schaap-Johansen] — PhD student
* [https://www.dtu.dk/service/telefonbog/person?id=88268 Camilla Koldbæk Lemvigh] — PhD student
* [https://www.dtu.dk/service/telefonbog/person?id=88645 Helle Rus Povlsen] — PhD student
* [https://www.inside.dtu.dk/en/dtuinside/generelt/telefonbog/person?id=59520 Jesper Vang] — 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 Inside. Please note that ''all'' exercise guides are mandatory curriculum — including the ''answers'' to the exercises which will be made available on this homepage after each exercise.

=== Computers ===
'''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], Safari for Mac or Edge for Windows). '''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.
# '''Java''' runtime engine is needed for running some of the software we use in the course, including jEdit (see below). If it is not already installed on your computer, there are two options for downloading it:
## Oracle java can be downloaded from http://www.java.com. '''Note:''' it is not truly free anymore; if you want to use it for any commercial activities, you need to pay a license fee.
## A truly free alternative is AdoptOpenJDK which can be downloaded from https://adoptopenjdk.net/. '''Windows users:''' Choose "OpenJDK 8" and "HotSpot", and remember to ''enable all subfeatures'' when installing, otherwise it will not work with the software we are going to use. '''Mac users:''' we currently don't recommend this solution for Mac, since jEdit (see below) for Mac does not play nice with AdoptOpenJDK.
# A plain text editor for working with, e.g., sequence files. We recommend '''jEdit''', which you can download for free from http://www.jedit.org. If you experience unsolvable problems installing or running jEdit, there are alternatives, e.g. [http://geany.org/ Geany].
Other software will be installed during the exercises.

=== Where and when ===
Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Feb 4'''. Lectures will be from 13:00 to approx. 14 in '''building 208, auditorium 53''', and the exercises will then take place in '''building 210, rooms 142+148+118'''.

=== 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 Inside (Course 22111 → Assignments).

'''NB:''' It is possible to hand in as a group. We would ''much'' rather receive a 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. 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'''. MacOS X and Windows 10 have built-in functions for converting any printable file to PDF. Users of earlier versions of Windows must install a separate program. Several free alternatives exist, e.g. [http://www.primopdf.com/ PrimoPDF]. (It can be a good idea to install PrimoPDF even for Windows 10 users, it provides some extra options and the resulting files take up less space).

'''Please do ''not'' copy the questions''' from the exercise guide to your logbook. The hand-in module on DTU Inside 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 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 DTU Inside. Hand-in also takes place on DTU Inside, and the procedure is the same as in the exercises. 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.

When you hand in the exam assignment in DTU Inside, you get a '''hand-in code''' that must be written on the hand-in envelope. '''It is ''very'' important that the code is handed in correctly''', otherwise your answer cannot be assessed. The code serves as a control that the hand-in has not been modified since you left the examination room.

=== DTU Inside ===
Link to this year's DTU Inside group: https://cn.inside.dtu.dk/cnnet/element/612495/

=== Evaluation and feedback ===
We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can send these by email to the teachers or write them on "Forum" in the DTU Inside group. If somebody writes a message on the Forum, 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 DTU Inside.

== Lecture & exercise plan ==

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

=== Tuesday Feb 4 — Introduction & taxonomy ===
:'''Lectures:'''
:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen.
:* ''Evolution and taxonomy'' — Rasmus Wernersson.
:'''Slides:''' will be made available on DTU Inside File sharing.
:'''Curriculum:''' [http://www.cbs.dtu.dk/dtucourse/27611spring2011/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 jEdit]] — ([[ExJEdit-Answers|Answers]])
:# [[Taxonomy databases]] — ([[ExTaxonomy-Answers|Answers]])
:'''Extra material'''
::"[[Media:ELS_bioinformatics.pdf|Bioinformatics]]" — Encyclopedia entry from 2009.

=== Tuesday Feb 11 — GenBank ===
:'''Lecture:''' ''DNA as Biological Information'' — Rasmus Wernersson
:'''Curriculum:''' [[Media:DNA_SequencingTutorial.pdf|DNA sequencing tutorial]] — source: IDT Tech Vault
:'''Handout''' for the lecture: [[Media:HandoutEx_BaseCalling_Simple.pdf‎|"Base-calling" exercise (for printing)]] [PDF] - [[Media:BaseCalling_on_screen_version.pdf|"Base-calling exercise (version for on-screen viewing)]] [PDF] (NEW, Feb 2020).
:'''Slides:''' on DTU Inside File sharing.


:'''Exercise:''' [[ExGenbank-new|Using the GenBank database]] — ([[ExGenbank-new-answers|Answers]])
:'''Reference material''' for the exercise: [[Media:GenBank+FASTA_handout_revised.pdf|GenBank + FASTA format]] [PDF] (UPDATED, Feb 11th 2020)

:'''Background material''' (supposedly known):
::[[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).
::[[Media:GeneStructure.pdf|Overview of eukaryotic gene structure]] (PDF).

:'''Extra material:'''
::[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)
::[https://academic.oup.com/nar/article/47/D1/D94/5144964 "GenBank"] — article from the annual database issue of Nucleic Acids Research, 2019.
::[https://academic.oup.com/nar/article/48/D1/D84/5608994 "GenBank"] — article from the annual database issue of Nucleic Acids Research, 2020.

=== Tuesday Feb 18 — Translation & UniProt ===
:'''Lecture:''' ''Protein databases'' — Henrik Nielsen
:'''Curriculum:''' [[Media:VirtualRibosome.pdf|Virtual Ribosome]] — software article (PDF).
:'''Slides:''' on DTU Inside File sharing.

:'''Exercises:'''
:#[[Exercise: Translation - Virtual Ribosome]] — ([[ExTranslation-answers|Answers]])
:#[[Exercise: The protein database UniProt]] — ([[ExUniProt-answers|Answers]])

:'''Background material''' (supposedly known):
::[http://www.cbs.dtu.dk/dtucourse/27611spring2011/PDF/protein_handout.pdf Levels of protein structure] [PDF]
::[[Media:GeneStructure.pdf|Overview of eukaryotic gene structure]] (PDF).

:'''Extra material:'''
::[https://academic.oup.com/nar/article/47/D1/D506/5160987 "UniProt: a worldwide hub of protein knowledge"] — article from the annual database issue of Nucleic Acids Research, 2019.

=== Tuesday Feb 25 — Pairwise alignment ===
:'''Lecture:''' ''Pairwise alignment'' — Henrik Nielsen.
:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Inside File sharing → Textbook excerpt).
:'''Handout''' for the lecture: [[Media:New_handout_alignscores.pdf|Alignment scores]]
:'''Slides:''' on DTU Inside File sharing.
:'''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment]] — ([[ExPairwiseAlignment-AnswersEng|Answers]])


=== Tuesday Mar 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'' — Paolo Marcatili
:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]
:'''Slides:''' on DTU Inside File sharing.

:'''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 the file sharing under this week's folder.
:'''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://academic.oup.com/nar/article/47/D1/D520/5144142 "Protein Data Bank: the single global archive for 3D macromolecular structure data"] — article from the annual database issue of Nucleic Acids Research, 2019.
:*[[PyMOL]] — some tips and tricks.
:*[http://www.cbs.dtu.dk/~blicher/Courses/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)

=== Tuesday Mar 10 — 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 Inside File sharing → Textbook excerpt).
:'''Slides:''' on DTU Inside File sharing.
:'''[[Exercise: 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 Mar 17 — Case: Malaria vaccine ===
:'''Lecture:''' ''Malaria and vaccines'' — Rasmus Weisel Jensen (KU).
:'''Curriculum:''' [http://www.cdc.gov/dpdx/malaria/ Malaria — Causal Agents / Life Cycle]
:'''Slides:''' on DTU Inside File sharing.
:'''Exercise:''' [[Exercise:Malaria Vaccine|Malaria vaccine]] — ([[Answers:Malaria Vaccine|Answers]])

=== Tuesday Mar 24 — Sequence information & logo-plots ===
:'''Lecture:''' ''Sequence information & logo-plots'' — Rasmus Wernersson
:'''Curriculum:'''
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Inside File sharing → Textbook excerpt).
:# Pages 1-8 of "''Information theory primer''" ([http://www.cbs.dtu.dk/courses/27040/teachingmaterials/informationtheory_primer.pdf PDF])
:#* Read also the appendix on logarithms (especially Log<sub>2</sub>) if needed!
:'''Slides:''' on DTU Inside File sharing.
:'''Handout''' for the lecture: [[Media: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]] — ([[ExSeqLogosAnswers|Answers]])

=== Tuesday Mar 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 Inside File sharing.
:'''Handouts''' for the lecture: [[Media:Estimationofpseudocounts_new+examples.pdf|How to estimate pseudo frequencies]] ([[Media:Estimationofpseudocounts_answer_brief.pdf|Answer]]) 
:'''[[Exercise: Construction of sequence logos and weight matrices]]''' - ([[ExLogo+Matrix-answers|Answers]])
:'''Link to advanced course: '''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]

------
<div align="center">
[[Image:Easter-egg-free-to-use-cliparts.png|25px]] '''Easter holidays''' [[Image:Easter-egg-free-to-use-cliparts.png|25px]]
</div>
------

=== Tuesday Apr 14 — PSI-BLAST ===
:'''Lecture:''' ''PSI-BLAST'' — Rasmus Wernersson
:'''Curriculum:'''
:'''Slides:''' on DTU Inside File sharing.
:'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]] — ([[ExPSIBLAST_answer|Answers]])

=== Tuesday Apr 21 — Multiple alignments ===
:'''Lecture:''' ''Multiple alignment'' — Henrik Nielsen
:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
:'''Slides:''' on DTU Inside File sharing.
:'''Exercise:''' [[Exercise: Multiple Alignments (English version)|Multiple Alignments]] — ([[ExMulAlign-Answers-English|Answers]])


=== Tuesday Apr 28 — Phylogenetic trees ===
:'''Lecture:''' ''Phylogenetic Reconstruction: Distance Matrix Methods'' — Anders Gorm Pedersen
:'''Curriculum:'''
:# ''Introduction to Tree Building'', PDF on Inside File sharing → 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'', [http://www.cbs.dtu.dk/courses/27615/pdf/understanding_evo_trees.pdf PDF].
:'''Slides:''' on DTU Inside File sharing.
:'''Handout''' for lecture: [http://www.cbs.dtu.dk/dtucourse/27611spring2008/Ex09_Phylo/handout_distance.pdf Reconstructing a distance tree] ([[Media:handout_distance_answers.pdf|Answer]])
:'''Software''' for installation: [http://tree.bio.ed.ac.uk/software/figtree/ FigTree tree-viewer]
:'''[[Exercise: Phylogeny]]''' — ([[Exercise:_Phylogeny-Answers|Answers]])
:'''Link to advanced course:'''
::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]

=== Tuesday May 5 — Bioinformatics in practice + old exam questions ===
:'''Lecture:''' "Real life case": ''Bioinformatics and Systems Biology in precision medicine'' - Rasmus Wernersson
:'''Curriculum:''' (None - lean back and enjoy)
:'''Slides:''' on DTU Inside File sharing.
:'''Exercise:''' We train on the old exam set from '''2017''' - available on the file share.

== Exam ==

=== Tuesday May 26 ===
'''Summer exam 2020:''' Go to http://onlineeksamen.dtu.dk/ and find 22111.


The assignment will be accessible from '''9:00''' on Tuesday May 26.

=== 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:Course plan spring 2020 - Revision history