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

• Henrik Nielsen — Associate professor, course responsible.
• Carolina Barra Quaglia — Assistant professor, course responsible.
• Rasmus Wernersson — External associate professor.

Teaching assistants

• Astrid Brix Saksager — PhD student
• Louis Kraft — PhD student
• Joakim Clifford — PhD student, stand-in for Louis Aug 29 and for Astrid Nov 21.
• Kristine Degn — PhD student, stand-in for Astrid Oct 3
• 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 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

1. Most importantly: an updated internet browser (e.g. Google Chrome, FireFox, Opera, 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.
2. 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 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:

• Geany has replaced jEdit, see the exercise in plain text files.
• SeaView has replaced Jalview, see the exercise in multiple alignments.
• The website iTOL has replaced the software FigTree, see the exercise in 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, LibreOffice (free), Apache OpenOffice (free), Pages for Mac, 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.

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.

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 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: 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:

1. Plain text files and Geany
2. Taxonomy databases

Extra material

• "Bioinformatics" — Encyclopedia entry from 2009.
• "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: DNA sequencing tutorial — source: IDT Tech Vault

Handout for the lecture: [1] [PDF] / "Base-calling" exercise (version for on-screen viewing) [PDF].

Slides: on DTU Learn.

‎ Base-calling exercise (for printing)

Exercise: Using the GenBank database

Reference material for the exercise: GenBank + FASTA format [PDF]

Background material (supposedly known):

• mRNA splicing (YouTube).
• Overview of eukaryotic gene structure (PDF).

Extra material:

• Entrez Sequences Quick Start (NCBI)
• "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: Virtual Ribosome — software article (PDF).

Slides: on DTU Learn.

Exercises:

1. Exercise: Translation - Virtual Ribosome
2. Exercise: The protein database UniProt

Background material (supposedly known):

• Levels of protein structure [PDF]
• Overview of eukaryotic gene structure (PDF).

Extra material:

• "UniProt: the Universal Protein Knowledgebase in 2023" — article from the annual database issue of Nucleic Acids Research, 2023.

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: Alignment scores

Slides: on DTU Learn.

Exercise: Pairwise alignment

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: BLAST

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: Protein Structure (Wikipedia)

Slides: on DTU Learn.

Link to advanced course:

• 22117 Protein Structure and Computational Biology

Software for installation: 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:

1. PyMol tutorial (PDF) — basic usage of PyMOL.
2. Protein Structure and Visualization

Extra material:

• "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.
• PyMOL basics — a small example (optional extra exercise)

Tuesday Oct 10 — Case: Malaria vaccine

Lecture: Malaria and vaccines — Thomas Lavstsen, Associate Professor, University of Copenhagen

Curriculum: Malaria — Causal Agents / Life Cycle

Slides: on DTU Learn.

Mid-term evaluation: Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111

Exercise: Malaria vaccine

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Autumn holiday 

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Tuesday Oct 24 — Sequence information & logo-plots

Lecture: Sequence information & logo-plots — Carolina Barra Quaglia

Curriculum:

1. Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
2. Pages 1-8 of "Information theory primer" (PDF)
   • Read also the appendix on logarithms (especially log₂) if needed!

Slides: on DTU Learn.

Handout for the lecture: How to construct sequence logos (PDF)

Exercise: DNA and Peptide Logos

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.

Exercises:

1. 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.
2. Construction of weight matrices

Link to advanced course:

22125: Algorithms in bioinformatics

Tuesday Nov 7 — PSI-BLAST

Lecture: PSI-BLAST — Rasmus Wernersson

Curriculum:

Slides: on DTU Learn.

Exercise: PSI-BLAST

Tuesday Nov 14 — Multiple alignments

Lecture: Multiple alignment — Henrik Nielsen

Curriculum: RevTrans (article)

Slides: on DTU Learn.

Exercise: Multiple Alignments

Tuesday Nov 21 — Phylogenetic trees

Lecture: Phylogenetic Reconstruction: Distance Matrix Methods — Henrik Nielsen

Curriculum:

1. Introduction to Tree Building, PDF on Learn
2. Evolutionary trees (minus the section "How to reconstruct an evolutionary tree")
3. Understanding Evolutionary Trees, PDF.

Slides: on DTU Learn.

Handout for lecture: Reconstructing a distance tree

Exercise: Phylogeny

Link to advanced course:

• 22115 Computational Molecular Evolution

Tuesday Nov 28 — Bioinformatics in practice + old exam questions

Lecture: Bioinformatics and Systems Biology in precision medicine — Rasmus Wernersson

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.

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