BioSysBio:workshopA1

Modeling with the Systems Biology Workbench

Author(s): Herbert Sauro
Affiliations: University of Washington
Contact: hsauro@u.washington.edu
Keywords: SBW

Abstract

Modeling biochemical systems requires a wide range of modeling approaches and analysis techniques. In this workshop the approach taken by the Systems Biology Workbench (SBW) will be discussed through examples taken from the modeling of signaling pathways and gene networks. Different modeling approaches will be illustrated including deterministic and stochastic modeling (Gillespie and Langevin). In addition, a range of analysis methods will be employed, such as bifurcation and sensitivity analysis. The SBW is based on the idea of linking disparate tools together, possibly written in different languages so that tools can exploit each others capabilities. The model interchange language used by SBW is the Systems Biology Markup Language (SBML). Some simple examples of how additional tools can be added to SBW will be discussed.

For those wishing to follow some of the demonstrations, we recommend you download the latest SBW from either

http://public.kgi.edu/~fbergman (latest version prior to upload to sourceforge)

or

http://www.sys-bio.org

You will of course need to bring along a Windows based laptop to install the Windows version of SBW. An autoinstaller for the Mac version is still under development and the Linux version requires technical expertise on how to compile and install Linux applications (For further details of the Mac/Linux version contact fbergman@kgi.edu).

A growing body of documentation can be found at our Wiki:

http://www.sys-bio.org/sbwWiki/

Power point presentation used in the tutorial:

Media:Tutorial2007.ppt

Note: openwetware seems to think this file is a word doc and will save it on your hard drive as Tutorial2007.ppt.doc. To get the powerpoint slide, remove the .doc extension.