Willkommen zum Wiki des Praxisseminars:
Rechnergestützte Systembiologie SS 2015

Aktuelles

The Praxisseminar starts at 9:00.

1. Termin/Vorbesprechung am Donnerstag 16.04.2015, 9:30 (nicht 8:30!), in Arnimallee 6, SR 017.

Allgemeine Informationen

SWS: 4, ECTS: 5
Dozente/in: Heike Siebert, Susanna Röblitz
Tutorin:
Sprache: Deutsch/Englisch

Termine

Praxisseminar

Do 9:00-12h

Arnimallee 6 SR 017 (Bioinformatik-Pool)

Inhalt

Im Praxisseminar geht es um die Modellierung molekularer Netzwerke mittels diskreter/logischer Methoden sowie Differentialgleichungen. Im Laufe das Semesters werden theoretische Grundlagen erarbeitet, Tools vorgestellt und in Gruppen eigenständig Modelle ausgesuchter Systeme auf Basis von Fachartikeln konstruiert und analysiert.

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 a third of the presentation. The talk will be followed by a 15-minute 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
16.04.	Vorbesprechung
23.04.	modeling formalisms and resources	Karlebach/Shamir paper
30.04.	Boolean modeling I
07.05.	Boolean modeling II
21.05.	BoolNet, Modeling project
28.05.	Cell Collcetive, Modeling project	first model, ideas for validation
04.06.	Modeling project	short (10 minutes) presentation
11.06.	CellDesigner, ODE modeling I
18.06.	Copasi, ODE modeling II
25.06.	Modeling project
02.07.	Modeling project
09.07.	Project presentations, signal transduction pathways
16.07.	Project presentations, gene networks

Material

• Modeling survey: Karlebach and Shamir, 2008
• slides about SBML
• Slides boolean modeling: part 1, part 2
• Boolean modeling tutorial Saadatpour and Albert, 2012
• Sea urchin development Smith et al., 2007
• BoolNet stuff: presentation, tutorial file
• xml-files for signal-response curves: linear, hyperbolic, sigmoidal

Modeling Project

Cell fate decisions
Laslo et al., 2008

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

Circadian rhythm in cyanobacteria
Nishiwaki et al., 2007

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

Hormonal regulation of human cycle
Chabbert et al., 1998

Excel data sheets

Example Copasi model file

Example Copasi data file

Software tutorials
Cell Collective
Website with tutorials and models (account required to access models)
Papers:The Cell Collective, Bio-Logic Builder, application

BoolNet
Website
Papers: background and application