Bioinformatics 3 WS 13/14

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Ruslan Akulenko, Mohamed Hamed, Duy Nguyen, Christian Spaniol

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) 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: Monday, February 3, at 2:15 pm in E2 1, 007

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

This course is taught in English language.

 

Lectures:

Lecture 1, October 18 pdf ppt Assignment 1 Supplementary 1
Lecture 2, October 21 pdf ppt    
Lecture 3, October 25 pdf ppt Assignment 2 Supplementary 2
Lecture 4, October 28 pdf ppt    
Lecture 5, November 4 pdf ppt    
Lecture 6, November 8 pdf ppt Assignment 3 Supplementary 3
Lecture 7, November 11 Minitest 1
pdf
ppt    
Lecture 8, November 15 pdf ppt Assignment 4  
Lecture 9, November 18 pdf ppt    
Lecture 10, November 22 pdf ppt Assignment 5  
Lecture 11, November 25 pdf ppt    
Lecture 12, November 29 Minitest 2
pdf
ppt    
Lecture 13, December 2 pdf ppt Assignment 6 Supplementary 6
Lecture 14, December 6 pdf ppt    
Lecture 15, December 9 pdf ppt    
Lecture 16, December 13 pdf ppt Assignment 7  
Lecture 17, December 16 Minitest 3
(no proofs
from V13 + V14)
pdf
ppt    
Lecture 18, January 6 pdf ppt    
Lecture 19, January 10 pdf ppt    
Lecture 20, January 13 pdf ppt Assignment 8
 
Lecture 21, January 17 pdf ppt    
Lecture 22, January 20 pdf ppt    
Lecture 23, January 24 Minitest 4
(only V18-V22, not
slides 1-21 from V22)
 

Assignment 9

Supplementary 9
Lecture 24, February 3 final exam (about
assignments)
  last tutorial: January 31 at 3:00 pm