Willkommen zum Wiki des Praxisseminars:
Rechnergestützte Systembiologie SS 2017

Aktuelles

Vorbesprechung findet am 19.04. um 10:15 in 017/A6 statt.

Allgemeine Informationen

SWS: 4, ECTS: 5
Dozentin: Heike Siebert
Tutorin:
Sprache: Deutsch/Englisch

Termine

Praxisseminar

Mi 10-14 h

Arnimallee 6 SR 017 (Bioinformatik-Pool)

Content:

The course focuses on the modeling of molecular networks using discrete/logical approaches. The theoretical framework will be introduced and software tools presented. On the basis of suitable research articles, the participants will conduct their own modeling project in small groups.

Final presentation

Each group should prepare a 30-minutes talk presenting the key findings of their modeling project, touching on biological background, model construction and analysis, results and conclusions. Each group member should do about half of the presentation. The talk will be followed by a discussion.

Additionally a rough documentation of the modeling project should be handed in, including bullet points on reasoning and references for model construction, list of validation and analysis steps and an overview of the respective results.

Zeitplan

Datum	Thema	Todo
19.04.	Vorbesprechung
26.04.	Intro Systembiologie	Karlebach/Shamir paper
03.05.	Structural Analysis	Network Software - short presentation
10.05.	Network Software, Boolean modeling I
17.05.	Boolean modeling II
24.05.	Perturbation analysis, multi-valued modeling, project
31.05.	Software Tutorial BoolNet, Model checking
07.06.	Software Tutorial GINsim, experimental data	starting point network
14.06.	Softare Tutorial PyBoolNet, experimental data	data questions
21.06.	Software Tutorial EpiLog	informal status report
28.06.	Uncertainty analysis, Project
05.07.	Project	informal status report
12.07.	Synthetic Biology, Project
19.07.	Final presentations	documentation

Material

• Modeling survey: Karlebach and Shamir, 2008
• slides about SBML
• Structural analysis: Albert 2005, slides
• Cytoscape, NetworkX
• Slides boolean modeling: part 1, part 2
• Boolean modeling tutorial Saadatpour and Albert, 2012
• Sea Urchin, Davidson, 2007
• Slides multi-valued modeling here, Drosophila example
• Slides model checking
• Slides data and paper
• Slides Uncertainty
• Slides SynthBio

Modeling Project

Cell fate decisions
Laslo et al., 2008

Apoptosis regulation
Igney, Krammer, 2002
Zou et al., 2002

Segmentation clock
Aulehla et al., 2003
Rida et al., 2004

C. elegans endoderm development
Maduro et al., 2002

p53 Mdm2 network
Shi et al., 2012
Wade et al., 2010

Software tutorials

GINsim
Website with tutorials and models
Papers:background, application

BoolNet
Website
Papers: background, application

PyBoolNet
Website with tutorial and models
Papers:background, application

EpiLog
Website with tutorial and models
Papers: Cellular Automata, application

Deliverables

• Presentation modeling project
• Documentation modeling project
• Softwaretutorial