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Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

Hucka, M. and Finney, A. and Bornstein, B. J. and Keating, S. M. and Shapiro, B. E. and Matthews, J. and Kovitz, B. L. and Schilstra, M. J. and Funahashi, A. and Doyle, J. C. and Kitano, H. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Systems Biology, 1 (1). pp. 41-53. ISSN 1741-2471. doi:10.1049/sb:20045008.

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Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon informationstandards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Item Type:Article
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Hucka, M.0000-0001-9105-5960
Keating, S. M.0000-0002-3356-3542
Doyle, J. C.0000-0002-1828-2486
Additional Information:© IEE 2004. Reprinted with permission. Received 24 March 2004; revised 24 May 2004. We thank Herbert Sauro for his fundamental work on SBML Level 1 as well as crucial discussions and software development work. We also thank Hamid Bolouri for organising and leading the SBML effort during its first two and-a-half years, and we thank the SBML development community for their continuing enthusiasm, participation, feedback and support. The SBML community includes the members of the international mailing list and the BioSPICE model definition language task force. We thank Linda Taddeo for bibliographic and editorial help in preparing this manuscript. Finally, we thank the following agencies and institutions for their generous support. The development of SBML was originally funded by the Japan Science and Technology Corporation (JST) under the ERATO Kitano Symbiotic Systems Project. Support for the continued development of SBML and associated software, meetings and activities today comes from the following sources: the National Human Genome Research Institute (USA); the National Institute of General Medical Sciences (USA); the International Joint Research Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of Education, Culture, Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the DARPA IPTO Bio-Computation Program (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 AgencyUNSPECIFIED
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
Air Force Office of Scientific Research (AFOSR)UNSPECIFIED
University of HertfordshireUNSPECIFIED
Molecular Sciences InstituteUNSPECIFIED
Systems Biology Institute (Japan)UNSPECIFIED
Subject Keywords:lingua franca; software infrastructure; computational systems biology; Systems Biology Markup Language; computational modelling; biochemical reactions; regulatory networks; overview
Issue or Number:1
Record Number:CaltechAUTHORS:HUCieesb04
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:2099
Deposited By: Tony Diaz
Deposited On:09 Mar 2006
Last Modified:08 Nov 2021 19:45

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