Continued Support of Essential SBML Software and Community Resources

California Institute Of Technology, Pasadena CA

Investigators

Linked publications & trials

Abstract

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 SBML.org 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.