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
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.
Read more...
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.
Read more
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:
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.
Funding Provided by:
Visitor Map
This map displays the last 20 visitors to the site, starting September 22nd, 2007.
Last updated:
October 25, 2007