Bioinformatics 3 WS 12/13

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Nadine Schaadt, Christian Spaniol, Ruslan Akulenko

Lecture: Monday, 2:15 pm – 4:00 pm and Friday, 1:15 pm – 3:00 pm, building E2 1, room 007
Tutorial: Monday, 12:00 pm – 14:00 pm, E2 1, room 007

Requirements: familiarity with contents of Bioinformatik I and II. The students will have to complete programming assignments with Python. This course can be taken as part of the Master program Bioinformatics.

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) buy term papers including epigenetic processes and micro RNAs
  • dynamic simulation of cellular processes (differential equation solvers, stochastic simulations)
  • metabolic networks (linear algebra)

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 (mostly) 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 Friday´s lecture.  In addition each student has to solve one of these problems on the blackboard.

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

Date of the examination: Friday, February 1, 2013, 1:00 pm – 3:00 pm, E2 1, room 007


9 (4 V + 2 Ü)

This course is taught in English language.



Lecture 1, October 15
pdf ppt Assignment Supplement
Lecture 2, October 19
pdf ppt
Lecture 3, October 22
pdf ppt
Lecture 4, October 26
pdf ppt
Lecture 5, October 29
pdf ppt
Lecture 6, November 2
pdf ppt
Lecture 7, November 5
pdf ppt
Lecture 8, November 9
pdf ppt
Lecture 9, November 12
pdf ppt
Lecture 10, November 16
pdf ppt Lecture from 2:15 pm – 3:15 pm
Lecture 11, November 19
Lecture 12, November 23
pdf ppt
Lecture 13, November 26
pdf ppt
Lecture 14, November 30
pdf ppt no tutorial on December 3
Lecture 15, December 10
pdf ppt
Lecture 16, December 14
pdf ppt
Lecture 17, December 17
pdf ppt
Lecture 18a, January 7
Lecture 18b, January 11
pdf ppt
Lecture 19, January 14
pdf ppt
Lecture 20, January 18
pdf ppt
Lecture 21, January 21
pdf ppt
Lecture 22, January 25
January 28 no lecture
Lecture 23, February 1
Final exam