Bioinformatics for Human Biologists October 2012

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Bioinformatics for Human Biologists - October 2012

In 2012 the course runs Monday to Friday, October 1st-5th.

Course homepage: Bioinformatics for Human Biologists

General Information


October 1st - 5th, 2012.


The course unfortunately does not have a single venue but takes place in four different locations. The venues are listed below:

  • Monday + Tuesday:
Panum: Room 42.0.01 in the pavilion (next to the Panum building entrance at Nørre Allé).
  • Wednesday:
Panum: Store Mødesal, room 5.1.14.
  • Thursday:
Panum: Mini auditorium 2, room 29.1.32.
  • Friday:
Teilum building: Auditorium B. A map of Rigshospitalet can be found here. Search for Teilum in the search field on the left.


The curriculum consists of hand-out notes and the computer exercises. There is no formal text-book; all reading material will be available online, linked directly from this page. The material can be read on a day-to-day basis.


The course is pass/fail based on participation (both lectures and exercises).

Hardware / Software used

First and foremost: YOU MUST BRING YOUR OWN LAPTOP TO THE COURSE. For the PyMOL-based exercises Tuesday and Wednesday, please bring a 3-button / scrollwheel mouse as well.

The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. FireFox, Safari or a recent version of Internet Explorer - a browser which supports tabs is recommended) and Java installed.

Java is used in some exercises to run visualization software. Link:

We recommend the JEdit text editor for use on sequence files, since it is well suited for this purpose and is platform independent. Link:

For the protein structure exercise the PyMOL software (also cross-platform) will be used. Main link:

Free Student's version:


Each group has to keep a "logbook" with answers to the questions from the exercises. After completing an exercise, mail the report to Thomas Holberg Blicher. IMPORTANT: Make sure to put [Humanbio] + exercise date in the mail header.

The logbook should be kept as minimalistic as possible - the important thing here is to simply focus on giving a nice and simple overview of your answers and not to spend a lot of time on fancy formatting. For example:

Answers to the Multiple Alignment exercise
Report by: Rasmus Wernersson (v18103) 

Question 1
Fasta format file: 


Question 2
2a): xxxx yyyy zzzz
2b): ddd jjj uuu

Please note: We collect these answers for two purposes:

  1. Assessing participation in the exercises.
  2. As a means to improve our teaching, since we get a chance to learn what questions are typically difficult to answer or understand.

Exercise hand-ins

Table of exercise reports that has been mailed in: (Last updated on:)

Lecture plan

Monday (Oct 1st)

9.15 - 12.00
Lecture: Introduction to course (Thomas Holberg Blicher, CPR)
Lecture: Pairwise alignment (Anders Gorm Pedersen, CBS)
Slides: Pairwise alignment
Exercise: Pairwise alignment using EBI resources
13.00 - 16.30
Lecture: BLAST - sequence based database searching (Sune Pletscher-Frankild, CPR)
Handouts: handout_alignscores.pdf
Exercise: Using BLAST - statistics & results

Tuesday (Oct 2nd)

9.15 - 12.00/12.30
Lecture: Multiple alignments (Anders Gorm Pedersen, CBS)
Lecture: Pylogenetic trees (Anders Gorm Pedersen, CBS)
Software: Download FigTree from here:
Handout: Multiple alignment by hand
Exercises: 1) Multiple alignment, 2) Phylogenetic trees
13.00 - 16.30
Lecture: Protein structure analysis (Thomas Holberg Blicher, CPR)
Slides: Protein structure analysis
Exercise: Visualizing protein structures in PyMOL. Only exercise 1.

Wednesday (Oct 3rd)

9.15 - 12.00
Lecture: Protein structure modelling (Thomas Holberg Blicher, CPR)
Slides: Protein structure modelling
Exercise: Homology modelling.
13.00 - 16.30
Lecture: Prediction methods in immunological bioinformatics (Claus Lundegaard/Ole Lund, CBS)
Exercise: [1]

Thursday (Oct 4th)

9.15 - 12.00
Lecture: Protein properties, modifications and localization (Thomas Holberg Blicher, CPR)
Slides: Sequence predictions
Exercise: Structure predictions from sequence features. Page 1-5 (i.e. skip the last page regarding fold recognition).
13.00 - 16.30
Lecture: Systems Biology (Lars Juhl Jensen, CPR)
Slides: Systems biology
Exercise: During presentation!

Friday (Oct 5th)

9.15 - 12.00
Lecture: Medical informatics (Peter Bjødstrup Jensen, CPR)
Readings: "Mining electronic health records: towards better research applications and clinical care."
Exercise: Text mining data: For Excel, for Open Office.
13.00 - 16.30
Lecture: Bioinformatics in the real world (Rasmus Wernersson, Intomics A/S)
Readings: None.
Slides: Bioinformatics in Biomedical Research
Exercise: Catch up on missing exercises.

Supplementary reading material


Future projects: Contact information

We very much welcome master thesis projects from students at the human biology study line (and Ph.D. projects as well). Such projects are coordinated with the research group in question: