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SBML Models and MathSBML

Shapiro, Bruce E. and Finney, Andrew and Hucka, Michael and Bornstein, Benjamin and Funahashi, Akira and Jouraku, Akiya and Keating, Sarah M. and Le Novère, Nicolas and Matthews, Joanne and Schilstra, Maria J. (2007) SBML Models and MathSBML. In: Introduction to Systems Biology. Humana Press , Totowa, NJ, pp. 395-421. ISBN 9781597455312.

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MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral, computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation.

Item Type:Book Section
Hucka, Michael0000-0001-9105-5960
Keating, Sarah M.0000-0002-3356-3542
Le Novère, Nicolas0000-0002-6309-7327
Additional Information:© 2007 Humana Press. SBML was initially funded by a generous grant from the Japan Science and Technology Agency under the ERA TO Kitano Symbiotic Systems Project. Additional support for the continued development of SBML and associated software and activities has come from the National Human Genome Research Institute (USA), the National Institute of General Medical Sciences (USA), the International Joint Research Program of NEDO (Japan), the ERATO-SORST Program of the Japan Science and Technology Agency (Japan), the Ministry of Agriculture (Japan), the Ministry of Education, Culture, Sports, Science and Technology (Japan), the BBSRC e-Science Initiative (UK), the DARPA IPTO Bio-Computation Program (USA), the Army Research Office's Institute for Collaborative Biotechnologies (USA), and the Air Force Office of Scientific Research (USA). Additional support is provided by the California Institute of Technology (USA), the University of Hertfordshire (UK), the Molecular Sciences Institute (USA), and the Systems Biology Institute (Japan).
Funding AgencyGrant Number
Japan Science and Technology Agency ERATO Kitano Symbiotic Systems ProjectUNSPECIFIED
National Human Genome Research InstituteUNSPECIFIED
National Institute of General Medical SciencesUNSPECIFIED
International Joint Research Program of NEDO (Japan)UNSPECIFIED
Japan Science and Technology Agency (ERATO-SORST)UNSPECIFIED
Ministry of Agriculture (Japan)UNSPECIFIED
Ministry of Education, Culture, Sports, Science and Technology (MEXT)UNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)UNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Army Research Office (ARO)UNSPECIFIED
Air Force Office of Scientific Research (AFOSR)UNSPECIFIED
University of HertfordshireUNSPECIFIED
Molecular Sciences InstituteUNSPECIFIED
Systems Biology Institute (Japan)UNSPECIFIED
Subject Keywords:SBML, libSBML, MathSBML, Systems Biology, XML, Biomodels
Record Number:CaltechAUTHORS:20130107-155707023
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36217
Deposited By: Linda Taddeo
Deposited On:10 Jan 2013 21:59
Last Modified:09 Mar 2020 13:18

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