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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:

  • 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 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

RESULTS of the exam of February 2

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
pdf


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
pdf
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
pdf

 
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
pdf


23rd Lecture, January 26
pdf


24th Lecture, January 28
pdf


25th Lecture, February 2
Final exam


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