The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology

Over the years, a variety of biochemical network modeling packages have been developed and used by researchers in biology. No single package currently answers all the needs of the biology community; nor is one likely to do so in the near future, because the range of tools needed is vast and new techniques are emerging too rapidly. It seems unavoidable that, for the foreseeable future, systems biology researchers are likely to continue using multiple packages to carry out their work. In this chapter, we describe the ERATO Systems Biology Workbench (SBW) and the Systems Biology Markup Language (SBML), two related efforts directed at the problems of software package interoperability. The goal of the SBW project is to create an integrated, easy-to-use software environment that enables sharing of models and resources between simulation and analysis tools for systems biology. SBW uses a modular, plug-in architecture that permits easy introduction of new components. SBML is a proposed standard XML-based language for representing models communicated between software packages; it is used as the format of models communicated between components in SBW