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.
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.
| 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 |
| 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 |
| Smith, Lucian Paul; Hucka, Michael; Hoops, Stefan et al. (2015) SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. J Integr Bioinform 12:268 |
Showing the most recent 10 out of 34 publications
