Computational Systems Biology
Sauro Lab
University of Washington
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What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
 
 
 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 

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This site intoduces the Systems Biology Workbench (SBW), an open source framework connecting heterogeneous software applications. SBW is made up of two kinds of components:

  • Modules: These are the applications that a user would use. We have a wide collection of model editing, model simulation and model analysis tools.
  • Framework: The software framework that allows developers to cross programming language boundaries and connect application modules to form new applications.

Getting Started

We constantly strive to improve the SBW modules we distribute with the framework. The ChangeLog details bug fixes and improvements we make to the modules, the framework and online services. If you have any problems or questions please file a Bug Report or post a question to the Forum. There also is a sparsly populated but growing SBW FAQ.

LINKS:

Download SBW
Documentation
Download SBWMatlab Interface
Download SBWOptimizers
Download SBW BioSPICE Interface

Third-party Groups that use SBW:

cellDesigner (Visual Design)
Dizzy (Stochastic Simulator)
BioSPICE
BioUML

About the Systems Biology Workbench Project

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. 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 easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.

At the last count, there were over 75 different packages for simulating cellular networks (see www.sbml.org ). This proliferation of tools has resulted in a variety of capabilities and interfaces. Though welcome in many respects, this proliferation has resulted in two unwelcome side effects:

  1. Each tool uses its own format, often undocumented, to store models. The result is that a model saved in one tool cannot be loaded into another. This obviously hinders the free exchange of models from one tool to another.
  2. The second problem is that many of the tools duplicate each other's capabilities. Writing simulation tools takes time, and many of the projects are short-lived, which means that the authors are unable to develop the tools very far. As a result, many of the tools provide similar functionality. Unlike other software development communities, there is little tradition of code reuse in the system biology community. As a result, the community has seen much duplicated effort.

Model Interchange The first problem, that of model exchange, has been addressed by introducing a standard format for all tool writers to employ. This standard is called Systems Biology Markup Language (SBML)  Along with CellML (www.cellml.org), the introduction of a standard format is beginning to make a significant impact on tools writers, and the majority of the most widely used tools now employ SBML as a means to exchange models.

Code Reuse The second issue is more difficult to address, that is how to encourage code reuse in the community. Our attempt to resolve this has been to develop a software framework called the System Biology Workbench. The workbench allows different tools to expose programmatic functionality to other tools. This means that a developer can now build on previous work without having to understand in detail the often intricate internal workings of other tools. All a developer need know is the interface that the tool exposes. Thus, a particular tool may expose a time-dependent simulation interface from a simulation tool, another tool developer-rather than invent another simulation tool-can exploit this capability and develop a new tool that can carry out additional functions. The workload for the second developer is greatly reduced, and they can instead concentrate on novel functionality.

 

This work is currently supported through the generous support of NIH/NIGMS

 

The SBW Team

The senior developer for SBW is:

Frank Bergmann. Frank is responsible for the bulk of SBW software development, including the messaging systems, binding libraries, .NET development, Mac and Linux portability, releases (sometimes in collaboration with Sri), distributed SBW development. He is also engaged in a number of other projects which will see the light of day in the near future.

A second key developer is

Sri Paladugu. Sri is responsible for Metatool integration, NOM, the Matlab Translator and a new tool to be released early next year.

Another important developer is

Ravi Rao. Ravi is currently writing a set of new SBML translators to be released in late January 2005. He is also responsible for writing portable versions of the optimizers modules.

Finally, a new comer to SBW is

Klaus Maier. Klaus is developing a suite of new solvers for Langevin systems, frequency analysis tools for deterministic systems and a new high speed Java simulator.

What you get when you download SBW:

  1. SBW Broker: This small program permits the different modules in SBW to communicate
  2. Binding libraries to the most common languages: C/C++, Java, Delphi, Python, Perl, Matlab, .NET
  3. NOM: SBML Support module. This modules provides basic SBML support services and is based on Ben Bornstein's libSBML.
  4. Jarnac: A fast simulator of reaction networks. This is one of the main modules in SBW, it provides may computational services, includes time course simulation (ODE or stochastic), steady state analysis, basic structural properties of networks, dynamic properties like the Jacobian, elasticities, sensitivities, eigenvalues etc. It also supports a scripting language that allows experienced users to directly interact with the computational engine.
  5. JDesigner: This is a friendly GUI front end to an SBW compatible simulator. It allows users to 'draw' networks on screen and simulate them. JDesigner uses Jarnac as it's current simulation backend.
  6. A series of SBML translators, including Matlab and FORTRAN
  7. Metatool: A SBW wrapping around Stefan Schuster's Metatool program which can be used to compute elementary modes.
  8. Optional downloads: Time course optimizers  by Vijay Chickarmane.
  9. There are currently six additional modules which we hope to release before the end of the year.

Collaboration

SBW is a collaboration between a number of individuals and communities. Of particular importance is Mike Hucka and Andrew Finney who were instrumental in the early stages of development. The original project home was at Caltech, with managerial and enthusiastic support from Hamid Bolouri, Hiroaki Kitano and John Doyle.

Detailed documentation and additional information is available here

All our software products are freely available under the terms of the BSD license. We hope other interested parties will join us in this effort and work with us towards these common goals.

Acknowledgments

The Systems Biology Workbench Project was originally funded by a generous grant from the Japan Science and Technology Corporation through the ERATO Kitano Systems Biology Project. Currently support comes from the NIH/NIHMS for which we an extremely grateful. The orignal authors of the SBW included Andrew Finney, Mike Hucka and Herbert Sauro with Hamid Bolouri, John Doyle and Hiroaki Kitano acting as principal investigators.

A detailed description of SBW can be found in our paper published in " Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration." OMICS. 2003 Winter;7(4):355-72. Sauro, Hucka, Finney, Wellock, Bolouri, Doyle, Kitano.

 


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