The Systems Biology Markup Language (SBML) is a popular, machine-readable, model representation format allowing computational models of biochemical networks to be exchanged between software tools such as editing programs, simulators, and databases. It is supported not only by open-source and commercial developers of systems biology software, but also by major journals such as Nature. Our group continues to lead and guide the evolution of SBML and related infrastructure, and as a result, we also keenly feel some of the limitations and challenges that have become apparent only as a result of SBML's exploding success. One such challenge is ensuring a high degree of conformance to the SBML specification by the steadily growing number of tools. We have come to realize that simply providing a definition of SBML, holding workshops and discussions, and so forth, are not enough to ensure consistent interpretation and behavior by different software systems. There need to be concrete and objective mechanisms for validating SBML implementations. In preliminary work over the past year, we developed a self-contained """"""""SBML Semantic Test Suite"""""""" allowing software developers and users to test the behavior of simulation tools against SBML benchmark models ranging in complexity from basic to advanced, covering a majority of the features defined in the language. In this proposal, we aim to (1) extend and refine this preliminary effort into a comprehensive SBML Test Suite, and (2) develop a web-based system allowing anyone to upload test results, assess them independently, and optionally compare them to the results of other software tools. The overall goal is to provide objective facilities for validating different software tools' coverage and conformance to the definition of SBML, and thereby help ensure the highest level of consistency possible across SBML- aware software systems. This is something that is crucial for users to have confidence in SBML as a standard model representation format for simulation and analysis in biomedical research. ? ? ? ?
| Hucka, Michael; Bergmann, Frank T; Dräger, Andreas et al. (2015) Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform 12:271 |
| 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 |
| Bornstein, Benjamin J; Keating, Sarah M; Jouraku, Akiya et al. (2008) LibSBML: an API library for SBML. Bioinformatics 24:880-1 |
