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

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM070923-08
Application #
8126422
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Hagan, Ann A
Project Start
2004-02-01
Project End
2013-06-30
Budget Start
2011-07-01
Budget End
2012-06-30
Support Year
8
Fiscal Year
2011
Total Cost
$745,286
Indirect Cost
Name
California Institute of Technology
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
009584210
City
Pasadena
State
CA
Country
United States
Zip Code
91125
Bergmann, Frank T; Sahle, Sven; Zimmer, Christoph (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586-8
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
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
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
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
Schreiber, Falk; Bader, Gary D; Golebiewski, Martin et al. (2015) Specifications of Standards in Systems and Synthetic Biology. J Integr Bioinform 12:258
Chelliah, Vijayalakshmi; Juty, Nick; Ajmera, Ishan et al. (2015) BioModels: ten-year anniversary. Nucleic Acids Res 43:D542-8

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