AG 3: Teaching

Computational Biology / Bioinformatics II (SS 2005)

Teacher: Thomas Lengauer

Tutor: Christoph Bock

Language: English

Time and location:

Course:	Tuesday and Thursday, 14-16 h, Building 46, Room 024 (MPI Building). Starting Thursday, April 14, 2005. Last lecture Tuesday, July 12, 2005.
Tutorials:	Wednesday, 9-11 h, Building 46, Room 021 or Wednesday, 16-18 h, Building 46, Room 021 (identical content - please choose one) starting April 20, 2005.
Exam:	Date of first exam: Thursday, July 14 2005, 13-16 h Location of first exam: building 23.2 (corrected), ground floor, room 21 Results of first exam: click here Date of second exam: Tuesday, November 8 2005, 13-16 h Location of second exam: chemistry lecture hall, building 23.2, ground floor, room 21 Results of second exam: click here
Office hours:	Thomas Lengauer: Thursday, 13:30-14:00h, Building 46 (MPI Building), Room 501 and after each lecture in the lecture hall Christoph Bock: Tuesday, 16-17 h, Building 46 (MPI Building), Room 522.

Prerequisites:

The course is obligatory for bioinformatics students and is targeted towards students in the 4th semester. The course is the sequel to the course 'Bioinformatik I' given by Hans-Peter Lenhof last semester. Students who did not take that course will have to work up on their own some of the basic material on sequence alignment and phylogeny.

Requirements for the course certificate:

Homework assignments will be made available every Thursday on this page. Please return your solutions within one week, the DEADLINE is the following Thursday 15:00 h. All students who achieve at least 50% of possible points in the assignments qualify for the written exam. It is permitted to submit solutions in groups of up to two persons.

The standard proceeding for the assignment submissions is as follows:

• The complete solution (incl. source code & command line syntax, if necessary) must be submitted in written form to the postbox in front of room 502 on the 5th floor of Building 46 (MPI Building).
• In addition, for all programming exercises a runnable version of the program must be sent to bio2_tutorial@bioproject.de.
• We strongly encourage that you submit computer printed solutions. In case you plan to hand in hand-written text please observe that we can only grade neat and easily readable sheets.
• Please read the assignment sheets carefully - there may be deviations from these rules for some assignments.

Overview:

The course concentrates on "downstream" problems in computational biology, i.e. those problems that arise after the basic genome and protein sequence has been analyzed. Problems that are covered include protein structure comparison, protein structure prediction, protein domain and protein family analysis, protein function analysis, analysis of protein interactions (docking), drug comparison and drug screening, analysis of mRNA expression data, analysis of metabolic and regulatory networks, analysis of genetic variations, analysis of resistance patterns in infectious diseases.

Material:

restricted access