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Bioinformatics 3 WS 13/14

General Information

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

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