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. ? ? ?
| Neal, Maxwell Lewis; König, Matthias; Nickerson, David et al. (2018) Harmonizing semantic annotations for computational models in biology. Brief Bioinform : |
| Hucka, Michael (2017) SBMLPkgSpec: a LaTeX style file for SBML package specification documents. BMC Res Notes 10:451 |
| Waltemath, Dagmar; Karr, Jonathan R; Bergmann, Frank T et al. (2016) Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans Biomed Eng 63:2007-14 |
| Schreiber, Falk; Bader, Gary D; Gleeson, Padraig et al. (2016) Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J Integr Bioinform 13:289 |
| Hucka, Michael; Smith, Lucian P (2016) SBML Level 3 package: Groups, Version 1 Release 1. J Integr Bioinform 13:290 |
| Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero et al. (2016) The systems biology format converter. BMC Bioinformatics 17:154 |
| Bergmann, Frank T; Sahle, Sven; Zimmer, Christoph (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586-8 |
| Rodriguez, Nicolas; Thomas, Alex; Watanabe, Leandro et al. (2015) JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics 31:3383-6 |
| 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 |
| 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 |
Showing the most recent 10 out of 34 publications
