SS 2012
Bioinformatics 3 WS 10/11
General Information
Lecturer: Prof. Dr. Volkhard Helms, Dr. Tihamér Geyer
Tutors: Nadine Schaadt, Christian Spaniol
Lecture: Monday, 2:00 pm - 4:00 pm and Friday, 12:30 pm - 2:00 pm, building E2 1, room 007.
The first lecture will take place on Friday, Oct 22.
Tutorial: Wednesday, 10:00 am - 12:00 am, 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 course (SPO 2006).
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)
- dynamic simulation of cellular processes (differential equation solvers, stochastic simulations)
- metabolic networks (linear algebra)
- and modern applications in synthetic biology
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 7, 2:00 pm - 4:00 pm, rooms 003 and 007. RESULTS
Date of the second chance exam:
Wednesday, April 13, 10:00 am - 12:00 am, E2 1, room 007 RESULTS RE-EXAM
Leistungspunkte/Credits:
9 (4 V + 2 Ü)
This course is taught in English language.
Lectures:
| Lecture 1, October 22 |
V1-Intro.pdf |
Assignment 1 |
Supplements 1 |
| Lecture 2, October 25 |
V2-Dijkstra-Layout.pdf |
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| Lecture 3, October 29 |
V3-BuildingNetworks.pdf |
Assignment 2 |
Supplements 2 |
| Lecture 4, November 5 |
V4-BayesCommunities.pdf |
Assignment 3 |
Supplements 3 |
| Lecture 5, November 8 |
V5-RobustnessModules.pdf |
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| Lecture 6, November 12 |
V6-notSF.pdf |
Assignment 4 |
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| Lecture 7, November 15 |
V7-FunctionAnnotation.pdf |
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| Lecture 8, November 19 |
V8-GeneRegulation.pdf |
Assignment 5 |
Supplements 5 |
| Lecture 9, November 22 |
V9-PetriBool.pdf |
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| Lecture 10, November 26 |
V10-Graph-Connectivity.pdf |
Assignment 6 |
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| Lecture 11, November 29 |
V11-Menger.pdf |
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| Lecture 12, December 3 |
V12-NetworkFlow.pdf |
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| Lecture 13, December 6 |
V13-Metabolism.pdf |
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| Lecture 14, December 10 |
V14-FBA-EP.pdf |
Assignment 7 |
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| Lecture 15, December 13 |
V15-EM-MCS.pdf |
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| Lecture 16, December 17 |
V16-DoubleDescrMethod.pdf |
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| Lecture 17, January 3 |
V17-RateEquations.pdf |
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| Lecture 18, January 7 |
V18-KineticMotifs.pdf |
Assignment 8 |
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| January 10 |
test 3, rooms 003 and 007 |
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| Lecture 19, January 14 |
V19-Stochastics.pdf |
Assignment 9 |
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| Lecture 20, January 17 |
V20-Photosynthesis.pdf |
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| Lecture 21, January 21 |
V21-DensityFitting.pdf |
Assignment 10 |
Supplements 10 |
| Lecture 22, January 24 |
V22-ConnectivityAssembly.pdf |
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| January 28 |
test 4, rooms 003 and 007 |
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| January 31 |
research in Helms group |
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| February 7 | FINAL EXAM | ||
