The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an inpuUoutput 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. Previous work on GM070923 helped make SBML widely supported as a de facto standard;as of October, 2012, over 250 software systems (both open-source and commercial) are known to support it worldwide. The experiences of the past three years make the present competing renewal application simultaneously easier and more difficult to write. It is easier because we know what needs to happen to support the current generation of SBML (Level 3);it is more difficult because the landscapes of both biological modeling and software technologies are changing rapidly, and while it is clear that SBML must evolve somehow, we cannot forecast or prescribe the details because the changes in SBML must be driven bottom-up by the modeling community. Our proposed solution to this dilema is to create resources that will enable the community to collectively define the shape of SBML to come, while continuing to provide support for important software resources for the SBML community. More specifically, we will (1) support and enhance SBML infrastructure, notably libSBML, JSBML, the Online SBML Validator, the SBML Test Suite, the Online SBML Test Suite and database, and the SBML Demonstrator;(2) encourage and guide the user community to develop still-unfinished SBML Level 3 packages;and (3) provide resources to help the community evolve SBML through (a) a redesigned website with a new question- oriented discussion system, (b) a software code generator and prototyping (DEVISER, for "Design Explorer and Viewer for Iterative SBML Enhancement of Representations"), and (c) the development of RDF Schemas for SBML Level 3 and SBML Level 3 packages. We will use the products of Aim 3 to help engage the community in investigating how SBML should evolve, exploring different alternatives and questions in a way that minimizes impact on existing software tools.

Public Health Relevance

Computation modeling is increasingly becoming a crucial aspect of biological research, and SBML (the Systems Biology Markup Language) has become the de facto standard open format for exchanging models between software tools in systems biology. Software developers and researchers who write modeling software benefit from the availability of open-source SBML software resources, such as software libraries (libSBML and JSBML), that provide starting points for incorporating SBML support in their software. The goals of this project are to support and enhance a number of such software resources that have proven to be essential for the SBML- using community, as well as develop new tools to help the community evolve SBML in the coming years.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Biodata Management and Analysis Study Section (BDMA)
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Lyster, Peter
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California Institute of Technology
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