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Bioinformatik 3 WS 08/09

General Information

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Sikander Hayat, Peter Walter

Lecture: Tuesday and Thursday, 2:00 pm - 4:00 pm, building E1 3, room 0.16

Tutorial: Monday, 2:00 pm - 4:00 pm, building E1 3, room 0.15
The first tutorial will be on Tuesday, Oct. 30 at 2:00 pm in building E1 3, room 0.16 (instead of lecture). On Monday, Nov. 3 there will be lecture.

Requirements: familiarity with contents of Bioinformatik I and II. This course can be taken as part of the Master course (SPO 2006).

Contents: the course will cover methodological aspects of integrated biology and systems biology:

  • protein-protein interaction networks (mathematical graphs, Bayesian networks)
  • analysis of protein complexes (density fitting, Fourier transformation)
  • transcriptional regulatory networks (Boolean networks)
  • dynamic simulation of cellular processes (differential equation solvers, stochastic simulations)
  • metabolic networks (linear algebra)
  • and modern applications in synthetic biology

Condition for certification: There will be four 45-minutes tests on different parts of the lecture. An averaged score will be computed from the best three results of the four tests. This score will count 50% for the grade of certification ("Schein"). The other 50% are taken from the mark in the final exam (120 min) that will cover the material of the assignments.

Condition for the participation in the final exam: (a) successful participation in 3 out of the 4 tests, (b) at least half of the points of the assignments. Solutions have to be returned at the beginning of the following Thursday´s lecture or until 11 am at room 1.05 building C 7.1.  In addition each student has to solve one of these problems on the blackboard.
Points after assignment 1-9 -> All exercise groups passed the limit for the participation in the final exam.

OVERVIEW admissions to the exam here!
Hints and solutions for assignments 1-9 are available here! Update for hints for assignment 1; hints for assignment 10

Textbook: V. Helms, Principles of Computational Cell Biology, Wiley (2008) 

Date of the examination: Tuesday, February 24, 10:00 am - 12:00 am, building E1 3, room 0.15

RESULTS of the exam of February 24



Leistungspunkte/Credits: 9 (4 V + 2 Ü)

This course is taught in English language.


1st Lecture, October 21 ppt pdf   Assignment 1
2nd Lecture, October 23 ppt pdf
3rd Lecture, October 28 ppt pdf  
4th Lecture, October 30 ppt pdf  Assignment 2, supplement
5th Lecture, November 4 ppt pdf  
6th Lecture, November 6 ppt pdf   
7th Lecture, November 11 results test 1 pdf Assignment 3
8th Lecture, November 13 ppt pdf
9th Lecture, November 18 ppt pdf  
10th Lecture, November 20 ppt pdf Assignment 4, supplement
11th Lecture, November 25 ppt pdf   
12th Lecture, November 27 ppt pdf  
13th Lecture, December 2 ppt pdf
14th Lecture, December 4 results test 2/ppt pdf   
15th Lecture, December 9 ppt pdf   Assignment 5, supplement
16th Lecture, December 11 ppt pdf   
17th Lecture, December 16 ppt    
December 18



18th Lecture, January 6 ppt pdf    Assignment 6
19th Lecture, January 8 ppt pdf  
20th Lecture, January 13 results test 3/ ppt pdf
Assignment 7, supplement
Program for force directed layout of graphs
January 15 no lecture
21st Lecture, January 20 ppt
22nd Lecture, January 22 ppt pdf
 Assignment 8
23rd Lecture, January 27 ppt pdf  
24th Lecture, January 29 ppt pdf   Assigment 9
25th Lecture, February 3
ppt pdf

26th Lecture, February 5 ppt pdf    
27th Lecture, February 10 ppt
 test 4
no lecture on February 12 results test 4 pdf
Assignment 10, supplement
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