The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology

M. Hucka, A. Finney, H. Sauro, H. Bolouri, J. Doyle, H. Kitano

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    60 Citations (Scopus)
    88 Downloads (Pure)

    Abstract

    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
    Original languageEnglish
    Title of host publicationProcs Pacific Symposium on Biocomputing
    Pages450-461
    Volume7
    Publication statusPublished - 2002

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