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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 distribution:
    • 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 links):

  • 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 (constraints). 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.
Project news
Tau Leap module
(Dec 20, 2002) A new module, TauLeapService, is now available from the download page.
SBW Tutorial
(Dec 11, 2002) We will hold a tutorial on SBW during ICSB 2002.
SBW 1.0.3
(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.