22111:Course plan autumn 2024: Difference between revisions
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Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 3 at 13:00'''. | Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting '''Tuesday Sep 3 at 13:00'''. | ||
Lectures will be from 13:00 to approx. 14 in ''' | 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, and ALC3/002, also in building 208'''. | ||
=== Teachers === | === Teachers === | ||
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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. | 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. | '''NB:''' All hand-ins are per definition group hand-ins. If you work alone, you must form a "group" of one person. | ||
<!-- 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. | 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. | ||
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'''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. | '''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. | '''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. | ||
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:'''Lectures:''' | :'''Lectures:''' | ||
:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen. | :* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen. | ||
:* ''Evolution and taxonomy'' — | :* ''Evolution and taxonomy'' — Carolina Barra Quaglia. | ||
:'''Slides:''' will be made available on DTU Learn. | :'''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. | :'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen. | ||
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:'''Extra material''' | :'''Extra material''' | ||
:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009. | :*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009. | ||
:*"[https://doi.org/10.1093/nar/ | :*"[https://doi.org/10.1093/nar/gkad1044 Database resources of the National Center for Biotechnology Information]" — article from the annual database issue of Nucleic Acids Research, 2024 | ||
=== Tuesday Sep 10 — GenBank === | === Tuesday Sep 10 — GenBank === | ||
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:'''Extra material:''' | :'''Extra material:''' | ||
:*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI) | :*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI) | ||
:*[https://doi.org/10.1093/nar/ | :*[https://doi.org/10.1093/nar/gkad903 "GenBank 2024 update"] — article from the annual database issue of Nucleic Acids Research, 2024. | ||
=== Tuesday Sep 17 — Translation & UniProt === | === Tuesday Sep 17 — Translation & UniProt === | ||
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:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn). | :'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn). | ||
:'''Slides:''' on DTU Learn. | :'''Slides:''' on DTU Learn. | ||
:'''Exercise: [[Exercise: | :'''Exercise: [[Exercise:_BLAST3|BLAST]]''' | ||
<!-- | <!-- | ||
:'''Extra material:''' | :'''Extra material:''' | ||
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:'''Link to advanced course:''' | :'''Link to advanced course:''' | ||
::* [ | ::* [http://kurser.dtu.dk/course/22117 22117 Protein Structure and Computational Biology] | ||
:'''Software''' for installation: [https://pymol.org | :'''Software''' for installation: [https://pymol.org/ 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. | ::'''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:''' | :'''Exercises:''' | ||
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=== Tuesday Oct 29 — Sequence information & logo-plots === | === Tuesday Oct 29 — Sequence information & logo-plots === | ||
:'''Lecture:''' ''Sequence information & logo-plots'' — | :'''Lecture:''' ''Sequence information & logo-plots'' — Rasmus Wernersson | ||
:'''Curriculum:''' | :'''Curriculum:''' | ||
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). | :# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn). | ||
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:'''Slides:''' on DTU Learn. | :'''Slides:''' on DTU Learn. | ||
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF) | :'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF) | ||
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]] | :'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]] | ||
=== Tuesday Nov 5 — Weight matrices and other prediction methods === | === Tuesday Nov 5 — Weight matrices and other prediction methods === | ||
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=== Tuesday Dec 3 — Bioinformatics in practice + old exam questions === | === Tuesday Dec 3 — Bioinformatics in practice + old exam questions === | ||
:'''Lecture:''' | :'''Lecture:''' ''AI, phage discovery and rainforest genomics'' — Bent Petersen, KU. | ||
:'''Curriculum:''' (None - lean back and enjoy) | :'''Curriculum:''' (None - lean back and enjoy) | ||
:'''Slides:''' on DTU Learn. | :'''Slides:''' on DTU Learn. | ||
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=== Monday Dec 16 === | === Monday Dec 16 === | ||
'''Winter exam | '''Winter exam 2024:''' 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). | [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). | ||
Latest revision as of 14:30, 15 November 2024
General information
Where and when
Lectures plus subsequent exercises will take place every Tuesday afternoon during the semester, starting Tuesday Sep 3 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, and ALC3/002, also in building 208.
Teachers
- Henrik Nielsen — Associate professor, course responsible.
- Carolina Barra Quaglia — Associate professor, course responsible.
- Rasmus Wernersson — External associate professor.
Teaching assistants
- Hanxi Li — PhD student
- Myeonghyun Yoou — Industrial 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 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. 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.
- 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: 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, 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.
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. 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/215668
- Link to this year's DTU Inside group: https://campusnet.dtu.dk/cnnet/element/739577
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 Sep 3 — Introduction & taxonomy
- Lectures:
- Introduction to the course, bioinformatics, and computers — Henrik Nielsen.
- Evolution and taxonomy — Carolina Barra Quaglia.
- 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:
- Extra material
- "Bioinformatics" — Encyclopedia entry from 2009.
- "Database resources of the National Center for Biotechnology Information" — article from the annual database issue of Nucleic Acids Research, 2024
Tuesday Sep 10 — GenBank
- Lecture: DNA as Biological Information — Rasmus Wernersson
- Curriculum: DNA sequencing tutorial — source: IDT Tech Vault
- Handout for the lecture: "Base-calling" exercise (for printing) [PDF] / "Base-calling" exercise (version for on-screen viewing) [PDF].
- Slides: on DTU Learn.
- 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 2024 update" — article from the annual database issue of Nucleic Acids Research, 2024.
Tuesday Sep 17 — Translation & UniProt
- Lecture: Protein databases — Henrik Nielsen
- Curriculum: Virtual Ribosome — software article (PDF).
- Slides: on DTU Learn.
- Exercises:
- Background material (supposedly known):
- Extra material:
- "UniProt: the Universal Protein Knowledgebase in 2023" — article from the annual database issue of Nucleic Acids Research, 2023.
Tuesday Sep 24 — 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 Oct 1 — 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: BLAST
Tuesday Oct 8 — 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:
- 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:
- PyMol tutorial (PDF) — basic usage of PyMOL.
- 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)
Autumn holiday
Tuesday Oct 22 — 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
Tuesday Oct 29 — Sequence information & logo-plots
- Lecture: Sequence information & logo-plots — Rasmus Wernersson
- Curriculum:
- Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
- 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 Nov 5 — 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:
- 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.
- Construction of weight matrices
- Link to advanced course:
Tuesday Nov 12 — PSI-BLAST
- Lecture: PSI-BLAST — Rasmus Wernersson
- Curriculum:
- Slides: on DTU Learn.
- Exercise: PSI-BLAST
Tuesday Nov 19 — Multiple alignments
- Lecture: Multiple alignment — Henrik Nielsen
- Curriculum: RevTrans (article)
- Slides: on DTU Learn.
- Exercise: Multiple Alignments
Tuesday Nov 26 — Phylogenetic trees
- Lecture: Phylogenetic Reconstruction: Distance Matrix Methods — Henrik Nielsen
- Curriculum:
- Introduction to Tree Building, PDF on Learn
- Evolutionary trees (minus the section "How to reconstruct an evolutionary tree")
- Understanding Evolutionary Trees, PDF.
- Slides: on DTU Learn.
- Handout for lecture: Reconstructing a distance tree
- Exercise: Phylogeny
- Link to advanced course:
Tuesday Dec 3 — Bioinformatics in practice + old exam questions
- Lecture: 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 Dec 3.
Exam
Monday Dec 16
Winter exam 2024: 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 XXX 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