Bioinformatics 3

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

Exam:

Friday, Februar 20, 10:00 am - 12:00 pm, E2 1, Raum 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.

Content:

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) 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)

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

Language

This course is taught in English language.

Lectures:

Lecture 1, October 24 pdf ppt Assign1 Suppl1
Lecture 2, October 27 pdf ppt    
Lecture 3, October 31 pdf ppt Assign2 Suppl2
Lecture 4, November 3 pdf ppt    
Lecture 5, November 7 pdf ppt Assign3 Suppl3 (fixed)
Lecture 6, November 10 Minitest 1
pdf
ppt   ExampleTest
Lecture 7, November 14 pdf ppt Assign4  
Lecture 8, November 17 pdf ppt    
Lecture 9, November 21 pdf ppt Assign5  
Lecture 10, November 24 pdf ppt    
Lecture 11, November 28 pdf ppt Assign6 Suppl6
Lecture 12, December 1 Minitest 2
pdf
ppt    
Lecture 13, December 5 pdf ppt Assign7  
Lecture 14, December 8 pdf ppt    
December 12 no lecture      
December 15 no lecture      
Lecture 15, December 19 pdf ppt    
Lecture 16, January 5 pdf ppt    
Lecture 17, January 9 pdf ppt Assign8  
Lecture 18, January 12 Minitest 3
pdf
ppt    
Lecture 19, January 16 pdf ppt Assign9 Suppl9
Lecture 20, January 19 pdf ppt    
January 23 no lecture      
Lecture 21, January 26 pdf ppt    
Lecture 22, January 30 pdf ppt Assign10 Suppl10
Lecture 23, February 2 pdf ppt    
Lecture 24, February 6 Minitest 4