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Bioinformatics 3 WS 14/15

General Information

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Ruslan Akulenko, Thorsten Will, Duy Nguyen, Maryam Nazarieh

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: Friday, Februar 20, 10:00 am - 12:00 pm, E2 1, Raum 007

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

This course is taught in English language.

 

Lectures:
Lecture 1, October 24
pdf
ppt
Assign1
Suppl1
Lecture 2, October 27
pdf
ppt


Lecture 3, October 31
pdf
ppt
Assign2
Suppl2
Lecture 4, November 3
pdf
ppt


Lecture 5, November 7
pdf
ppt
Assign3 Suppl3 (fixed)
Lecture 6, November 10
Minitest 1
pdf
ppt

ExampleTest
Lecture 7, November 14
pdf
ppt
Assign4
Lecture 8, November 17
pdf
ppt


Lecture 9, November 21
pdf
ppt
Assign5

Lecture 10, November 24
pdf
ppt


Lecture 11, November 28
pdf
ppt
Assign6
Suppl6
Lecture 12, December 1
Minitest 2
pdf
ppt


Lecture 13, December 5
pdf
ppt
Assign7

Lecture 14, December 8
pdf
ppt


December 12
no lecture



December 15
no lecture



Lecture 15, December 19
pdf ppt

Lecture 16, January 5
pdf
ppt


Lecture 17, January 9
pdf
ppt
Assign8

Lecture 18, January 12
Minitest 3
pdf
ppt


Lecture 19, January 16
pdf
ppt
Assign9
Suppl9
Lecture 20, January 19
pdf
ppt


January 23
no lecture



Lecture 21, January 26
pdf
ppt


Lecture 22, January 30
pdf
ppt
Assign10
Suppl10
Lecture 23, February 2
pdf
ppt


Lecture 24, February 6
Minitest 4



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