	May 10 2010: SBW 2.8.0 Released We are pleased to announce a release of the Systems Biology Workbench 2.8.0, available from: This release is about improving performance and making it easier to simulate models. We have improved Roadrunners' performance and stability again (Including support for simultaneous discrete events!). It now correctly handles all SBML features except for delay differential equations and algebraic rules. Perhaps more significantly, we have updated the 'Simulation Tool' as the primar…
	Dec 21 2009: Synthetic Biology Design Platform TinkerCell: a modular CAD tool for synthetic biology. Journal of Biological Engineering 2009, 3:19doi:10.1186/1754-1611-3-19. TinkerCell is a an example of a computer aided design application specifically geared towards synthetic biology. See www.tinkercell.com for more details and downloads.
	Oct 16 2009: Antimony v1.3 released Version 1.3 of antimony has been released at antimony.sourceforge.net The latest version includes small changes to the Antimony language (most notably, the ability to set the display name of elements), and larger enhancements to the QTAntimony editor. Various stability issues have been finally tracked down and fixed, and new features have been added such as a more robust error message handling, the ability to convert SBML to different levels and versions, an…
	Aug 20 2009: Network Enumeration Database Our network enumeration page was hard to find. It now has a dedicated link in the Research Page. The enumeration page gives download links to roughly 300 million mass-action reaction networks stored in a compact format. The page also gives details and downloads for command line utilities and online tools for working with the networks. Funded by NSF FIBR.
	Aug 19 2009: SBW 2.7.10 Released We are pleased to announce the a release of the Systems Biology Workbench 2.7.10, available from: The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms - to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, open-source software infrastructure which is eas…

Version 2.8.1 of SBW Released July 2010

We are pleased to announce the release 2.8.1 of the Systems Biology Workbench.

DOWNLOAD the Systems Biology Workbench

Announcing the UW JSim/SBW Course August 2010

Part of this course will focus on the use of SBW in relation to metabolic modeling. A text book, models and notes will be provided. For more information see our Workshop Page

Announcing the Joint SBW & CompuCell3D Workshop 2010

We are pleased to announce Joint User-Training Workshop "Developing Multi-Scale,Multi-Cell Developmental and Biomedical Simulations with CompuCell3D and SBW". It will focus on teaching the basics of multi-cell, multi-scale modeling using the open-source packages CompuCell3D and SBW. For more information see our Workshop Page

SBW Paper Published

If SBW is used to generate research results or a citation is required in a review, please use the following citation:

Frank T. Bergmann, Herbert M. Sauro. SBW - a modular framework for systems biology. Frank T. Bergmann, Herbert M. Sauro December 2006 Proceedings of the 37th conference on Winter simulation WSC '06 Publisher: Winter Simulation Conference Pages: 1637 - 1645 BibTex link

ICSB Tutorial coming up

The SBW Team will be giving a tutorial at the ICSB 2009. 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:

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