The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology
Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and 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. We describe the SBW architecture and the current set of modules, as well as alternative implementation technologies.
Additional Information© 2002 World Scientific Press. This work has been funded by the Japan Science and Technology Corporation under the ERATO Kitano Systems Biology Project. The Systems Biology Workbench has benefitted from the input of many people. We wish to acknowledge in particular the authors of BioSpice, DBsolve, Cellerator, E-Cell, Gepasi, ProMoT /DIVA, StochSim, and Virtual Cell, and the members of the sysbio mailing list. We also thank Mark Borisuk, Mineo Morohashi and TauMu Yi for support, comments and advice.
Submitted - hucka_2002.pdf