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Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration

Sauro, Herbert M. and Hucka, Michael and Finney, Andrew and Wellock, Cameron and Bolouri, Hamid and Doyle, John and Kitano, Hiroaki (2003) Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. OMICS: A Journal of Integrative Biology, 7 (4). pp. 355-372. ISSN 1536-2310. doi:10.1089/153623103322637670.

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Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components—written in diverse programming languages and running on different platforms—to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW 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 in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.

Item Type:Article
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URLURL TypeDescription
Hucka, Michael0000-0001-9105-5960
Doyle, John0000-0002-1828-2486
Additional Information:© 2003 Mary Ann Liebert, Inc. publishers. This work was initially funded by the Japan Science and Technology Corporation under the ERATO Kitano Systems Biology Project. The development of JDesigner and Jarnac were partially funded by ERATO and the Keck Graduate Institute. More recent support for H.M.S. and C.W. was received via a grant awarded from the DARPA/IPTO BioCOMP program, contract number MIPR 03-M296-01. We wish to acknowledge Mark Borisuk, Mineo Morohashi, and Tau-Mu Yi for support, comments, and advice, and the BioSPICE team at SRI and Berkeley for their invaluable assistance in enabling BioSPICE/SBW integration.
Funding AgencyGrant Number
Japan Science and Technology Corporation ERATO Kitano Symbiotic Systems ProjectUNSPECIFIED
Keck Graduate InstituteUNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)MIPR 03-M296-01
Issue or Number:4
Record Number:CaltechAUTHORS:20121026-183338290
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Official Citation:Herbert M. Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano. OMICS: A Journal of Integrative Biology. December 2003, 7(4): 355-372. doi:10.1089/153623103322637670
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:35134
Deposited By: Linda Taddeo
Deposited On:30 Oct 2012 21:01
Last Modified:09 Nov 2021 23:12

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