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 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. SBML is supported by over 280 systems today, employed in model generation pipelines, accepted by hundreds of journals, used by large collaborative model construction efforts, described in textbooks, used in courses, and encouraged by NIH and other funding bodies. It is clear that SBML is central to a growing ecology of standards that collectively cover the whole life cycle of computational models. The modeling community at large is currently engaged in ?nalizing and applying recently-developed SBML extensions (known as SBML Level 3 packages) that provide additional constructs in SBML for the use of modeling formalisms such as ?ux balance analysis, qualitative models, rule-based models, spatial processes, and more. In this proposal for renewed funding, our focus is on resources that will enable the community to ful?ll the promise of SBML Level 3 as an exchange format for a wide range of biological research applications. We propose to (1) continue supporting, extending and generalizing crucial SBML software, including libraries such as libSBML and JSBML, and infrastructure such as SBML.org; (2) update and extend numerous software tools to support interoperability between SBML and other formats and systems that include MATLAB, Cytoscape, BioPAX and more; and (3) develop instructional materials for SBML, focusing especially on its use in different biological modeling scenarios as well as its relationships to other contemporary formats. This project will thus continue support for crucial SBML software and resources needed by developers and users alike; it will also derive new software libraries that other standardization efforts can reuse, develop tools that help bridge SBML with other formats and resources, and generate materials that will help everyone make more effective use of SBML for years to come.
Computation modeling is increasingly a crucial aspect of biomedical research, and SBML (the Systems Biology Markup Language) has become the de facto standard open format for exchanging models between software tools in computational systems biology. Software developers and researchers who write modeling software bene?t from the availability of open-source SBML software resources, such as software libraries (e.g., libSBML and JSBML), that provide starting points for incorporating SBML support in their software. The goals of this project are to continue support and enhancement of numerous software resources that have proven to be essential for the SBML-using community, develop software to improve interoperability between SBML and other formats, and develop instructional materials for all facets of SBML, especially recently-developed SBML enhancements and their use in the context of different real-life modeling approaches.
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| Hucka, Michael (2017) SBMLPkgSpec: a LaTeX style file for SBML package specification documents. BMC Res Notes 10:451 |
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| Hucka, Michael; Bergmann, Frank T; Hoops, Stefan et al. (2015) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J Integr Bioinform 12:266 |
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