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. Previous work on GM070923 helped make SBML widely supported as a de facto standard;as of October, 2009, over 175 software systems (both open-source and commercial) are known to support it worldwide. Today, there are a number of international groups working on supporting the next generation of SBML and defining new modular packages to extend the features of SBML Level 3. It has become difficult to mandate or even predict the direction in which specific SBML features are de- veloped by the community. What the systems biology modeling community needs for the next few years is leeway to explore solutions at the timescales they deem appropriate. However, at the same time, it not yet possible to leave certain aspects of core software development and maintenance entirely to the rest of the community as self-sustaining open-source software projects. Consequently, this application is a renewal proposal for GM070923 with a narrow scope focused on SBML software only. We wish to perform additional software development and support of certain crucial software resources for the benefit of the SBML commu- nity for three more years. The software goals include maintaining and continuing to enhance libSBML, the SBML Test Suite, the SBML Demonstrator, SBMLeditor, and the online SBML validator;in addition, we will continue to develop plug-in extensions to libSBML to support SBML Level 3 language packages and develop an online database of SBML Test Suite results;and finally, we will undertake development of new software resources, specifically a Java version of libSBML, and formal schemas for SBML Level 3. 1
Computation modeling is increasingly becoming a crucial aspect of biological research, and for modeling in biology to continue moving forward, researchers need to be able to create, exchange and publish models in an open format that is directly supported by most software tools. The de facto standard format for this purpose in systems biology is the Systems Biology Markup Language (SBML). Software developers and researchers who write software for modeling benefit by having certain open-source SBML software resources such as an API library (libSBML) available as starting points instead of having to program SBML support from scratch. The goals of this project are to develop, support and enhance a number of SBML software resources that have proven to be essential for the SBML-using community.
| 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
