Computational Systems Biology
Sauro Lab
University of Washington
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maintained by Frank Bergmann

ICSB 2008 Tutorial

The SBW team is holding a tutorial on the use of SBW at the ICSB 2008 Friday August 22nd, 10-13.


This tutorial aims to familiarize participants with the tools provided in the Systems Biology Workbench for building and analyzing deterministic and stochastic models. Using SBW and integrated 3rd party software, we will introduce modeling, time course and steady state concepts, parameter sensitivity (MCA) and bifurcation analysis.

At the level of single cells, biochemical processes can involve molecules in low abundance. Such systems, given the probabilistic nature of chemistry at the molecular level, have been investigated by introducing stochastic processes and many interesting phenomena have been explained. This tutorial will provide hands-on modeling experience for stochastic gene expression, stochastic focusing (sensitivity increase due to stochastic fluctuations), cell fate decision based on stochastic single events, and stochastic switching/chatter models.

Online tutorial description

Tutorial Materials

Jarnac Models

The following Jarnac files will be used during the tutorial.

Updated Jarnac Files


In order to follow the hands-on-exercises, participants should bring along their computers, running a Windows operating system. In order to run the software the following pre-requisites have to be installed on the machine (chances are, that you already have them):

The main tool to install is the Systems Biology Workbench, which includes almost all you need for the tutorial. You may optionally install Oscill8 if you wish to try and draw bifurcation diagrams.

No prior knowledge about how to use the software will be expected.

More Information

We placed additional tutorials here:

If you would like to see what we have done at a past ICSB Tutorial look here:

tutorials/icsb2008.txt · Last modified: 2008/08/21 22:55 by fbergman

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