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About the Systems Biology Workbench Project

One of the problems faced by computational biologists is that simulation models and results often cannot be compared, shared or re-used directly because the tools developed by different researchers often are not compatible with each other. Unfortunately, no single package currently answers all the needs of the emerging systems biology community, despite an emphasis by many developers to continue adding more features to their software tools. Nor is such a scenario likely: the range of tools needed is vast, and new techniques requiring new tools are emerging far more rapidly than the rate at which any single package may be developed. For the foreseeable future, then, systems biology researchers are likely to continue using multiple packages to carry out their work. The best we can do is to develop ways to ease sharing and communication between such packages.

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Available Modules

Collaboration

SBW is a collaboaration between a number of individuals and communities. Of particular importance is Mike Hucka and Andrew Finney who were intrumental in the early stages of development. They continue to provide support. The original project home was at Caltech under the generous tutelage of Hamid Bolouri, Hiroaki Kitano and John Dolye.

Approach

The current inability to exchange models between simulation/analysis tools has its roots in the lack of a common format for describing models. We sought to address this problem from the very beginning of the project by developing an open, extensible, model representation language. This is the Systems Biology Markup Language (SBML).

The software aspect of our work involves the development of a framework, the Systems Biology Workbench (SBW), enabling different tools to interact with each other. This framework supports tools written in different programming languages and potentially running on different platforms and different physical machines. We aim to facilitate collaboration among developers of systems biology software by creating a framework simple enough that developers find it easier to build an SBW interface than to recreate functionality available in other tools. Developers can then concentrate on developing best-of-breed solutions in the areas where they have special expertise.

SBW was originally developed in collaboration with the groups developing the simulation packages BioSpice, Cellerator, DBsolve, E-CELL, Gepasi, Jarnac, ProMoT/DIVA, StochSim and Virtual Cell.

All our software products are freely available under the terms of the GNU LGPL. 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 DARPA BioSPICE and Department of Energy GTL programs 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.