What is the Systems Biology ?
The Systems Biology
(SBW) is a modular, broker-based,
message-passing framework for simplified application
intercommunications. Features include:
- Bindings for C, C++, Delphi, Java, Perl, Python
- Support for Windows and Linux (with MacOS X planned)
- Distributed operation via SSH
- Bidirectional CORBA-SBW gateway
- Collection of modules provided with the base
- Simple stochastic simulator
- An SBML-to-MATLAB ODE and Simulink file translator
- An SBML reader module
- A "clipboard" module for exchanging SBML models
- A Browser that outputs module interface definitions
- A simple plotting module for time-series data
- A generic simulation-control GUI interface
Many third-party, SBW-enabled modules exist (see the download page for
- Jarnac, a biochemical simulation package for Windows
- JDesigner, a visual biochemical network layout tool
- MetaToolSBW, a network analysis tool
- Pasadena Twain, a simple interactive ODE solver
- GillespieService, a module
implementing a stochastic simulator
- A bifurcation analysis module
- An optimization module
- An SBML Validator for checking the syntax of an SBML file
- A simple Windows TrayTool utility
- An Inspector that lists running modules and their services
What is the Systems Biology Markup Language?
Molecular biotechnology now makes it possible to build
elaborate systems models, but the systems biology community
needs agreed-upon information standards if models are to be
shared, evaluated and developed cooperatively. We propose
the Systems Biology
Markup Language (SBML) as a common representation
language for storing biochemical models. SBML is based on XML, and contains structures
for representing compartments, species and reactions, as well
as optional unit definitions, parameters and rules
We have kept the
base definition of the language as simple as possible, so that
simulator developers will not find it too difficult to implement
support for SBML in their tools.
Tau Leap module
(Dec 20, 2002) A new module, TauLeapService, is now available from the download page.
(Dec 11, 2002) We will hold a tutorial on SBW during ICSB 2002.
(Dec 8, 2002) A release of SBW, 1.0.3, is now available from the download page.
New mailing list
(Oct 1, 2002) A new SBW developer's mailing list is available on SourceForge.