ICSB/COMBINE Tutorial 2012

Modelling and Simulation of Quantitative Biological Models

Date: Sunday, August 19, 2012, 9:00 am - 2:30 pm
Venue: Donnelly Centre for Cellular and Biomolecular Research (CCBR)

In this tutorial participants will learn setting-up quantitative computer models of biological networks using experimental kinetic data and simulating them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills to enable them to access experimental kinetics data from available resources, assembling computer models with these data and finally simulating the models within different tools. Attendees are expected to bring their own computer.

Target audience

Modellers and experimentalists with some basic experience in modelling and simulation of biological networks

Agenda

09:10 - 09:30 Introduction
09:30 - 10:20 Accessing biochemical reaction kinetics data via the SABIO-RK database
10:20 - 11:20 Creating mathematical models in CellDesigner (please download CellDesigner4.3beta from this page)
11:20 - 11:40 Break
11:40 - 12:40 Setting up and simulating quantitative models in Virtual Cell (VCell) (please install VCell 5.1 beta from here)
12:40 - 13:00 Lunch break
13:00 - 13:45 Simulating models in COPASI (please download the latest version (Build 35) from www.copasi.org)
13:45 - 14:15 Simulating models with JWS Online and setting up models with OneStop
14:15 - 14:20 Integrated handling of data, models and processes via SEEK and setting up models online using SYCAMORE
14:20 - 14:30 Discussions


Registration

The participation is free of charge.
Tutorial registration

Venue

The tutorial location is:
Donnelly Centre for Cellular and Biomolecular Research (CCBR)
Red Room
University of Toronto
160 College Street
Toronto M5S 3E1
Canada


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Tutors

Frank Bergmann: BIOQUANT, University of Heidelberg (Germany) / California Institute of Technology, Pasadena (USA)
Received Ph.D. degree in computational and systems biology from CGU, USA in 2010. He is involved in the development of modeling and simulation software for the Systems Biology Workbench since 2004.

Michael Blinov: Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT (USA).
Mathematician by training, working on modeling and algorithms development in signal transduction. He is one of the developers of rule-based modeling and BioNetGen software, currently working on rule-based and data-driven modeling in VCell.

Akira Funahashi: Dept. of Biosciences and Informatics, Keio University, Yokohama (Japan)
Received Ph.D. degree in computer science from Keio University, Japan, in 2000. He is involved in the development of CellDesigner for 10 years.

Martin Golebiewski: Heidelberg Institute for Theoretical Studies, Heidelberg (Germany)
Biochemist by training, involved in the development and population of the reaction kinetics database SABIO-RK for 7 years. Since 2010 he is also involved in implementation and coordination of the data management for the Virtual Liver Systems Biology initiative.

Noriko Hiroi: Dept. of Biosciences and Informatics, Keio University, Yokohama (Japan)
Received Ph.D. degree in medical science from the University of Tokyo, Japan, in 2002. She has participated in the test-and-feedback work for prerelease versions of CellDesigner for 9 years, also involved in the development of a Plugin software.

Stefan Hoops: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA (USA)

Ion Moraru: Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT (USA)
Cell biologist by training, working on experimental and modeling studies of signal transduction. He has been involved in the development of the VCell platform for more than 10 years.

Franco du Preez: Manchester Institute of Biotechnology (MIB), The University of Manchester (UK).
Received Ph.D. degree in biochemistry from Stellenbosch University, South Africa in 2009. Involved in model curation and development of the JWS Online repository and member of the SysMO-DB team.

Sven Sahle: BIOQUANT, University of Heidelberg (Germany)
He has been working on modeling biochemical reaction networks (and developing computational methods and tools) for more than 10 years and is one of the authors of COPASI. Originally trained as a physicist, Ph.D. in theoretical chemistry.

Tutorial coordinator

Martin Golebiewski
HITS gGmbH
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg, Germany
Phone: +49-6221-533-281 / Mobile: +49-15209825809 / FAX: +49-6221-533-298

Detailed Information

COPASI

COPASI is a software tool for handling, simulating, and analysing kinetic models of biochemical reaction networks. It is intended for biologists who are not experts in numerical algorithms or programming languages. The tutorial will give an overview over the features of COPASI, such as deterministic and stochastic simulation, parameter scans, sensitivities and control analysis. It will then focus on parameter estimation. We will provide model files for download in this space, so if you want to follow along the presentation on your own computer, please download the latest COPASI version (Build 35) from the website www.copasi.org and install it on your computer.

Model archive for the tutorial Download