Modelling and Simulation Tools in Systems Biology - ICSB 2016

Educators:
- Ron Henkel, Andreas Weidemann: HITS (Heidelberg, Germany; NBI.SysBio)
- Akira Funahashi, Noriko Hiroi: Keio University (Yokohama, Japan)
- Martin Golebiewski, Olga Krebs: HITS (Heidelberg, Germany)
- Ursula Kummer, Frank Bergmann, Jürgen Pahle, Sven Sahle: Univ of Heidelberg (Germany)
- Nicolas Le Novère: Babraham Institute (Cambridge, UK)
- Jacky Snoep: Stellenbosch University (South Africa)
- Natalie Stanford: University of Manchester (UK)

Date:
16 September, 2016 (8:30 - 13:30)

Location:
The venue for satellite meetings will be the lecture halls of the Universitat Pompeu Fabra (UPF), next to the Parc de Recerca Biomèdica de Barcelona (PRBB) Barcelona, Spain

Contents:
- Model setup using different software tools and systems biology platforms
- Using experimental data for setting up quantitative models
- Parameter estimation, optimization and model fitting
- Simulation, analysis and visualization of biochemical models
- Database supported modelling: integrated data management and model databases
- Community standards and formats for systems biology models

Learning goals:
Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic dat and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats.

Prerequisites:
Laptop

Keywords:
Modelling, models, simulation, database, metabolic, signalling, networks, Biology, Biochemistry, Systems Biology

Tools covered:
BioModels database: http://www.ebi.ac.uk/biomodels-main/
CellDesigner: http://www.celldesigner.org/
COPASI: http://www.copasi.org
JWS Online: http://jjj.biochem.sun.ac.za/
SABIO-RK: http://sabio.h-its.org/
SEEK: http://fair-dom.org/platform/seek/

Contact:
Name: Andreas Weidemann
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Name: Martin Golebiewski
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

http://co.mbine.org/events/tutorial2016