Bioinformatics 3 – SS 2018

Lecturer:

Prof. Dr. Volkhard Helms

Tutors

Duy Nguyen, Thorsten Will, Daria Gaidar, Markus Hollander

Lecture:

Tuesday, 10:15 am – 11:45 am and Friday, 1:15 pm – 3:00 pm, building E2 1, room 007

Tutorial:

Tuesday, 12.30  – 2 pm, E2 1, room 007

Please regard:  The tutorial for assignment 10 will take place on Tuesday, July 24th, 12:30 – 2:00 pm, in E2 1, room 007!

Exam:

Friday, July 27th, 10:00 am – 1:00 pm, building E1 3, lecture hall 002

Please find the results of the exam here.

Re-exam

Friday, October 19th, 2:00 pm – 5:00 pm, building 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.

Content:

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)

Schein/Certification:

Students need to pass the written final exam that will be scheduled near the end of the summer semester or the re-exam that will be scheduled at the beginning of the following winter semester.

Condition for 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)

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

Language

This course is taught in English language.

Lectures:

Lecture Slides (pdf) Slides (ppt) Assignments Supplements
Lecture 1, April 10 pdf ppt
Lecture 2, April 13 pdf ppt  Assignment 1 Supplement 1 
Lecture 3, April 17 pdf ppt
no lecture on April 20  Assignment 2 Supplement 2 (+RandomNetwork)
Lecture 4, April 24 pdf ppt
Lecture 5, April 27 pdf  ppt Assignment 3 Supplement 3
Lecture 6, May 4 pdf ppt Assignment 4  Supplement 4 
Lecture 7, May 8 pdf ppt
Lecture 8, May 11 pdf ppt Assignment 5 Supplement 1part 2part 3
Lecture 9, May 15 pdf ppt
Lecture 10, May 18 pdf ppt
Lecture 11, May 22 pdf ppt
no lecture on May 25
Lecture 12, May 29 pdf ppt Assignment 6  Supplement 6
Lecture 13, June 1 pdf ppt
Lecture 14, June 5 pdf ppt  Assignment 7  Supplement 7
Lecture 15, June 8 pdf ppt
Lecture 16, June 12 pdf ppt  Assignment 8  Supplement 8
Lecture 17, June 15 pdf ppt
Lecture 18, June 19 pdf ppt  Assignment 9  Task 1: Please assume exchange fluxes to be unconstrained (follow the solution engaging the T(E ).
Lecture 19, June 22 pdf ppt  Tutorial on June 22nd, 3:15 pm, E2 1,  room 007
Lecture 20, June 26 pdf ppt
Lecture 21, June 29 pdf ppt
Lecture 22, July 3 pdf  ppt  Assignment 10  Tutorial for assignment 10: Tuesday, July 24th, 12.30 – 2:00 pm, E2 1, room 007
Lecture 23, July 6 pdf ppt
Lecture 24, July 10 pdf ppt
Lecture 25, July 13 pdf ppt
Lecture 26, July 17 pdf ppt