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The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology

Hucka, Michael and Finney, Andrew and Sauro, Herbert M. and Bolouri, Hamid and Doyle, John C. and Kitano, Hiroaki (2002) The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology. In: Pacific Symposium on Biocomputing 2002. World Scientific Press , River Edge, NJ, pp. 450-461. ISBN 9789812799623. https://resolver.caltech.edu/CaltechAUTHORS:20130108-142104885

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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.


Item Type:Book Section
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Doyle, John C.0000-0002-1828-2486
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.
Funders:
Funding AgencyGrant Number
Japan Science and Technology Corporation ERATO Kitano Symbiotic Systems ProjectUNSPECIFIED
Record Number:CaltechAUTHORS:20130108-142104885
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130108-142104885
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36246
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:09 Jan 2013 17:56
Last Modified:26 Nov 2019 11:15

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