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Bioinformatics 3 WS 15/16

General Information

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Daria Gaidar, Maryam Nazarieh, Duy Nguyen, Thorsten Will

Lecture: Monday, 2:15 pm - 4:00 pm and Friday, 1:15 pm - 3:00 pm, building E2 1, room 007
Tutorial: Monday, 12 pm - 2 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: Students need to pass the written final exam that will be scheduled near the end of the winter semester or the re-exam that will be scheduled at the beginning of the following summer semester.

Condition for the participation in the final exam: 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, March 7th, 10:00 am - 01:00 pm, building E1 3, lecture hall 001 - see slide 2 of lecture V24

Please find the results of the exam here

 

Please find the results of the re-exam from Friday, April 22nd here!


Leistungspunkte/Credits:

9 (4 V + 2 Ü)

This course is taught in English language.

 

Lectures:
Lecture 1, October 23
pdf
pptx
Assignment 1
Supplement 1
Lecture 2, October 26
pdf
ppt


Lecture 3, October 30
pdf
ppt
Assignment 2
Supplement 2
November 2


no lecture

Lecture 4, November 6
pdf
ppt
Assignment 3
Supplement 3
Lecture 5, November 9
pdf
ppt


Lecture 6, November 13
pdf
ppt
Assignment 4
Supplement 4
Lecture 7, November 16
pdf
ppt


Lecture 8, November 20
pdf
ppt
Assignment 5
Supplement 5
Lecture 9, November 23
pdf
ppt


Lecture 10, November 27
pdf
ppt
Assignment 6

Lecture 11, November 30
pdf
ppt


Lecture 12, December 4
pdf
ppt
Assignment 7
Supplement 7
Lecture 13, December 7
pdf
ppt


Lecture 14, December 11
pdf
ppt
Assignment 8

Lecture 15,  December 14
pdf
ppt


Lecture 16, December 18
pdf
ppt
no assignment

Lecture 17, January 4
pdf
ppt
Assignment 9
(due Jan. 15)

Lecture 18, January 8
pdf
ppt


Lecture 19, January 11
pdf
ppt


Lecture 20, January 15
pdf
ppt
Assignment 10
Supplement 10
Lecture 21, January 18
pdf
ppt


Lecture 22, January 22
pdf
ppt


Lecture 23, January 25
pdf
ppt


Lecture 24, January 29
pdf
ppt
see slide 2 for
content of
final exam

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