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Studying Bioinformatics in Saarbrücken
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Zellsimulationen

Summer Semester 2005


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

Tutors: Dr. Tihamér Geyer, Thomas Binsl

Lecture: Friday, 9:00 am - 11:00 am, building 45, HS 001

Tutorial:

Audience: Special lecture in bioinformatics for B.Sc. and M.Sc. students of bioinformatics and for interested students from other disciplines.

Requirements: Contents of lecture "Bioinformatics III" is recommended.

Contents:

  1. Introduction of numerical techniques to solve systems of kinetic rate equations.
    1. Application to simple biological circuits.

  2. Metabolic Flux Analysis: numerical basics
    1. How does Flux Analyzer compute elementary modes?
    2. Which functions of Matlab are used?
    3. Application: we are going to use the program
      "Flux Analyzer" that is based on Matlab to study a small model system.

  3. Graph networks
    1. We will search genome sequences for proline-rich extensions and potential ligands and construct an interaction network between them.
    2. This application will make use of the package Cytoscape.

  4. Introduction to numerical techniques to solve the partial differential equation of diffusion.
    1. Application: apply the software package Virtual Cell to diffusional processes inside photosyntetic vesicles of Rhodobacter sphaeroides.

Condition for certification: Oral examination

Condition for the participation in the examination: At least half of the points of the 4 - 5 assignments.

Leistungspunkte/Credits: 5 (2 V + 1 Ü)

This course is taught in English language.
1st Lecture, April 15: pdf
2nd Lecture, April 22: pdf
3rd Lecture, April 29: pdf Assign. 1 Solution 1
4th Lecture, May 13: ppt pdf Suggested Reading
5th Lecture, May 20: ppt pdf Suggested Reading
6th Lecture, June 3: ppt pdf Assign. 2 Suggested Reading
7th Lecture, June 10: pdf Assign. 3 Solution 3
8th Lecture, June 17: ppt pdf Suggested Reading
9th Lecture, June 24: ppt pdf
10th Lecture, July 1: ppt pdf Suggested Reading
11th Lecture, July 8: pdf Assign. 4
12th Lecture, July 15: pdf