Continued Support and Development of SBML and Essential SBML Infrastructure

California Institute Of Technology, Pasadena CA

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Abstract

DESCRIPTION (provided by applicant): The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. It provides a means of representing quantitative models of biochemical reaction networks in a tool-independent fashion. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. It is the most successful effort in this area to date, with over 100 software systems supporting SBML today and more SBML-compatible tools being announced monthly. The broad acceptance of a common, open format for exchanging models between software tools is a crucial step towards wider use of quantitative modeling in biology, because it allows researchers to publish and build upon each other's work with greater ease and accuracy. This proposal is a competing continuation application to the three-year grant (NIGMS GM070923) that has provided the major source of funding for SBML development since 2004. We propose to undertake a series of efforts aimed at supporting and enhancing SBML and critical SBML software infrastructure, developing an SBML testing framework, and supporting the SBML community. Our specific aims are: (1) continue development and evolution of the SBML language (including the completion of remaining SBML Level 3 work, organizing SBML workshops and other educational events, and applying SBML to modeling problems in synthetic biology);(2) develop interfaces between SBML and two recent complimentary efforts, BioPAX and SBGN;(3) continue developing and supporting libSBML, the most popular open-source application programming interface (API) library for reading, writing and manipulating SBML files and data streams;(4) develop a reference implementation of SBML Level 3 in an integrated software environment;and (5) develop a comprehensive test suite and associated facilities for testing the completeness and quality of SBML implementations in different software tools.