Bioinformatics 3 WS 09/10
General Information
Lecturer: Dr. Tihamér Geyer
Tutors: Nadine Schaadt, Christian Spaniol
Lecture: Tuesday and Thursday, 2:00 pm  4:00 pm, building E2 1, room 001 E1 3, room 0.16
Tutorial: Friday, 12:00 am  2:00 pm, building E1 4 (MPI), room 0.23
The first tutorial will be on October 30
Requirements: familiarity with contents of Bioinformatik I and II. This course can be taken as part of the Master course (SPO 2006).
Contents: the course will cover methodological aspects of integrated biology and systems biology:
 proteinprotein 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 45minutes 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 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 Thursday´s lecture or until 11 am at room 1.05 building C 7.1. 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: Thursday, February 4, Tuesday, February 2, 2010, 2:00 pm  4:00 pm, E2 1, room 007
The second chance exam (oral) takes place on Wednesday, April 14. Please contact Dr. Geyer to fix a date.
Final Grades
Leistungspunkte/Credits: 9 (4 V + 2 Ü)
This course is taught in English language.
Lectures:
1st Lecture, October 13  pdf 

2nd Lecture, October 15  pdf 
Assignment 1 
Supplementary 
3rd Lecture, October 20  pdf 


4th Lecture, October 22  pdf 
Assignment 2 
Supplementary 2 
October 27 
no lecture 

October 29  no lecture 

5th Lecture, November 3  pdf 
Assignment 3 
Supplementary 3 
6th Lecture, November 5  Test 1: Results 

7th Lecture, November 10  pdf 
Assignment 4 

8th Lecture, November 12  pdf 

November 17  no lecture 

November 19  no lecture 

9th Lecture, November 24 
pdf 
Assignment 5 
Supplementary 5 
10th Lecture, November 26 
pdf 

11th Lecture, December 1  Test 2: Results 
Assignment 6 

12th Lecture, December 3  article link 

13th Lecture, December 8  pdf 
Assignment 7 

14th Lecture, December 10  pdf 

15th Lecture, December 15 
pdf 


16th Lecture, December 17 
Test 3: Results 

17th Lecture, January 5  pdf 
Assignment 8 

18th Lecture, January 7 
pdf 

19th Lecture, January 12  pdf 
Assignment 9 

20th Lecture, January 14  pdf 

21st Lecture, January 19 
pdf 
Assignment 10 
New version: Supplementary 10 
22nd Lecture, January 21 
Test 4 Results 

23rd Lecture, January 26 
pdf 

24th Lecture, January 28 
pdf 

25th Lecture, February 2 
Final exam 