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Bioinformatics 3 WS 11/12

General Information

Lecturer: Prof. Dr. Volkhard Helms, Dr. Tihamér Geyer

Tutors: Nadine Schaadt, Christian Spaniol

Lecture: Tuesday, 10:15 am - 12:00 am and Friday, 1:15 pm - 3:00 pm, building E2 1, room 007.
Tutorial: Wednesday, 12:30 am - 02:00 pm, building E2 1. room 007, starting on November 2

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)
  • 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 (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: Tuesday, February 7, 10 am - 12 am

Second chance exam: Friday, April 20, 2:00 pm - 4:00 pm, in E2 1, room 007

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

This course is taught in English language.

 

 

Lectures:

Lecture 1, October 18
V1-Intro


Lecture 2, October 21
V2-Dijkstra-Layout
Assignment 1
Supplements_A1
Lecture 3, October 25
V3-ExperimentalData


Lecture 4, October 28
V4-BayesCommunities
Assigment 2
Supplements A2
Lecture 5, November 4
V5-RobustnessModules
Assignment 3
Supplements A3
Lecture 6, November 8
V6-nonSF
Short Test #1
Lecture 7, November 11
V7-FunctionAnnotation
Assignment 4

Lecture 8, November 15
V8-GeneRegulation


Lecture 9, November 18
V9-PetriBool
Assignment 5
Supplements A5
Lecture 10, November 22
V10-GRN


Lecture 11, November 25
V11-Graph-Connectivity
Assignment 6

Lecture 12, November 29
V12-Menger
Short Test #2

Lecture 13, December 2
V13-NetworkFlow


Lecture 14, December 6
V14-Flow-Metabol-Net


Lecture 15, December 9
V15-FBA-Extreme-Path
Assignment 7
Supplements A7
Lecture 16, December 13
V16-EFM-MCS


Lecture 17, December 16
V17-DD-Method
Assignment 8

Lecture 18, December 20
V18 (only test #3)
Short Test #3

Lecture 19, January 10
V19-PPComplexDensityFitting


Lecture 20, January 13
V20-ProteinComplexConnectivity
Assignment 9
 Supplements A9
Lecture 21, January 17
V21-kinetic-Motifs


Lecture 22, January 20
V22-IntegrationSchemes
Assignment 10

Lecture 23, January 24
V23-DynamicsExamples


Lecture 24, January 27
V24-PhotosynthesisSysBio


Lecture 25, January 31

Short Test #4

February 3



February 7
Exam


February 10



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