	Jun 12 2008: SBW Tutorial at ICSB 2008 The SBW team is holding a tutorial on the use of SBW at the ICSB 2008 Friday August 22nd, 10-13. For more information and registration see our tutorials page.
	Feb 05 2008: Simulator Comparison Updated We updated the simulation results page to accomodate new results submitted by BioUML,SBToolBox2 and VCell. We also updated the results generated by COPASI and roadRunner. Read more
	Dec 19 2007: NIH Award (2007) NIH Award (2007): We are pleased to announce a three year NIH award to continue development of our systems biology software. Highlights include collaborating with the SBGN community to implement the SBGN standard and investigating the modular frameworks that have been proposed by the SBML community (cf. Stefan Hoops).

Version 2.7.8 of SBW Released August 2008

We are pleased to announce a release of the Systems Biology Workbench 2.7.8 ,available

DOWNLOAD the Systems Biology Workbench

ICSB Tutorial coming up

The SBW Team will be giving a tutorial at the ICSB 2008. More information is available on the tutorial wiki page.

Standards and Specifications in Synthetic Biology

Workshop Logo On April 26-27, 2008 we organized a Workshop on Standards and Specifications in Synthetic Biology at the Talaris Conference Center in Seattle, Washington. The conference was a success and participants from various countries presented and discussed:

experimental standards,
organization/storage/sharing of biological parts,
computer languages for modeling synthetic biology and
software tools for synthetic biology.

A proposed data model for Biobricks was created to describe the minimal amount of information needed to specify a Biobrick and how to classify Biobricks into families. A report of the workshop will be published in IET Synthetic Biology.

Systems and Synthetic Biology Course 498: Spring 2008

This course will cover the basics of cellular network dynamics, control and function. Genetic, protein signaling and metabolic pathways will be discussed in relation to their properties and enginering. A special section on practical aspects of synthetic biology will be given with possible hands-on experience in the lab in using basic molecular biology techniques (Web page).

Comparing Simulation Results

Comparing Simulation Results among SBML capable simulators has always been of interest to us. Not knowing the correct result of an SBML simulation, we figured that it would be best to compare what sort of results common simulators would give on a set of curated SBML files.

ICSB Tutorial coming up

The SBW Team will be giving a tutorial at the ICSB 2007. More information is available on the tutorial wiki page.

Version 2.7.7 of SBW Released April 2008

We are pleased to announce a release of the Systems Biology Workbench 2.7.7 ,available

DOWNLOAD the Systems Biology Workbench

CompuCell3D and SBW

CompuCell3D is a tissue and organ simulator based on the Cellular Potts Model. In collaboration with the CompuCell3D team at Indiana University (Glazier et al.) we have demonstrated a combined tool, linking CompuCell3D with SBW. The demonstration illustrates the use of Python as a flexible scripting glue that combines the Cellular Potts Model with the portable reaction based simulator (roadRunner) that is available with the Systems Biology Workbench. The movie available here demonstrates a 2D tissue made up of 115 cells, in each cell there is a simple reaction network that generates an oscillatory signal. This signal is used to modify the properties of the cell membrane which in turn influences the movement of cells through the tissue. The movie itself was generated from one of ComputeCell3D's tools. All simulations were run on Linux but could easily have been generated on Windows or the Mac OS X.

Online Services started

As of Nov. 17th 2005 several Web Applications are available on sys-bio org. Including:

SBML Layout Viewer: This application displays/creates a layout for SBML models
SBML Validation: This application validates SBML models
SBML Simulation: This application simulates SBML models using various simulators
SBML Translator: This application translates SBML to Fortran/Java/Matlab/XPP/...
Web Service creation: Create a web service for a installed SBW Module for use in other programs
Model Repository: Repository of evolved networks exhibiting oscillatory / switching behavior.

For BioSPICE users, download the SBW Analyzers here
Version 1.2 is compatible with BioSPICE 6.0

NEW BIOMODELS: We are very pleased to announce that we are a contributor to the first formal database of computational models for Systems Biology. This is a joint venture between EBI, Caltech, Sys Bio Institute, Japan, KGI and Stellenbosch, S. Africa. The database infrastructure was developed by Marco Donizelli and Nicolas Le Novère at EBI. KGI will be providing curation expertise (Harish Dharuri). Download models from BIOMODELS and simulate then under a large number of simulators including the Systems Biology Workbench.

This site is devoted to computational aspects of biochemical networks, their dynamics, function and evolution, be they metabolic, signal or gene networks. Various labels have been used to describe the study of such networks, including 'Systems Biology', 'Computational Biology' or even perhaps Molecular Physiology. We will use the label Computational Systems Biology to cover an area of research concerned with how chemical networks within living systems behave.

Computational Biology

Funding Provided by:

Visitor Map

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Last updated: October 25, 2007