Software Infrastructure for Effective Communication and Reuse of Computational Models
Until recently, the majority of computational models in biology were implemented in custom programs and published as statements of the underlying mathematics. However, to be useful as formal embodiments of our understanding of biological systems, computational models must be put into a consistent form that can be communicated more directly between the software tools used to work with them. In this chapter, we describe the Systems Biology Markup Language (SBML), a format for representing models in a way that can be used by different software systems to communicate and exchange those models. By supporting SBML as an input and output format, different software tools can all operate on an identical representation of a model, removing opportunities for errors in translation and assuring a common starting point for analyses and simulations. We also take this opportunity to discuss some of the resources available for working with SBML as well as ongoing efforts in SBML's continuing evolution.
Additional Information© 2006 MIT Press. 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 organizing 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 email@example.com international mailing list and the DARPA Bio-SPICE project Model Definition Language task force. 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).
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