Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration
Abstract
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.
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.Attached Files
Published - Sauro_2003p355.pdf
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Additional details
- Eprint ID
- 35134
- Resolver ID
- CaltechAUTHORS:20121026-183338290
- Japan Science and Technology Corporation ERATO Kitano Symbiotic Systems Project
- Keck Graduate Institute
- Defense Advanced Research Projects Agency (DARPA)
- MIPR 03-M296-01
- Created
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2012-10-30Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field