Lecturer:
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
Re-exam
The results are available in LSF; exam review: Monday – Thursday, 9:00 am – 2:00 pm, E2 1, room 314
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 | ppt | |||
| Lecture 2, April 13 | ppt | Assignment 1 | Supplement 1 | |
| Lecture 3, April 17 | ppt | |||
| no lecture on April 20 | Assignment 2 | Supplement 2 (+RandomNetwork) | ||
| Lecture 4, April 24 | ppt | |||
| Lecture 5, April 27 | ppt | Assignment 3 | Supplement 3 | |
| Lecture 6, May 4 | ppt | Assignment 4 | Supplement 4 | |
| Lecture 7, May 8 | ppt | |||
| Lecture 8, May 11 | ppt | Assignment 5 | Supplement 1, part 2, part 3 | |
| Lecture 9, May 15 | ppt | |||
| Lecture 10, May 18 | ppt | |||
| Lecture 11, May 22 | ppt | |||
| no lecture on May 25 | ||||
| Lecture 12, May 29 | ppt | Assignment 6 | Supplement 6 | |
| Lecture 13, June 1 | ppt | |||
| Lecture 14, June 5 | ppt | Assignment 7 | Supplement 7 | |
| Lecture 15, June 8 | ppt | |||
| Lecture 16, June 12 | ppt | Assignment 8 | Supplement 8 | |
| Lecture 17, June 15 | ppt | |||
| Lecture 18, June 19 | ppt | Assignment 9 | Task 1: Please assume exchange fluxes to be unconstrained (follow the solution engaging the T(E ). | |
| Lecture 19, June 22 | ppt | Tutorial on June 22nd, 3:15 pm, E2 1, room 007 | ||
| Lecture 20, June 26 | ppt | |||
| Lecture 21, June 29 | ppt | |||
| Lecture 22, July 3 | ppt | Assignment 10 | Tutorial for assignment 10: Tuesday, July 24th, 12.30 – 2:00 pm, E2 1, room 007 | |
| Lecture 23, July 6 | ppt | |||
| Lecture 24, July 10 | ppt | |||
| Lecture 25, July 13 | ppt | |||
| Lecture 26, July 17 | ppt |