JSBML 1.0: providing a smorgasbord of options to encode systems biology models

JSBML, the official pure Java programming library for the SBML format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

JSBML

JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.Related Publication:</p> JSBML 1.0: providing a smorgasbord of options to encode systems biology models</p> Nicolas Rodriguez Babraham Institute, Babraham Research Campus, Cambridge, UK</p> Alex Thomas University of California, San Diego, La Jolla, CA, USA</p> Leandro Watanabe The University of Utah, Salt Lake City, UT, USA</p> Ibrahim Y. Vazirabad Marquette University, Milwaukee, WI, USA</p> Victor Kofia Princess Margaret Cancer Centre</p> Harold Gómez Boston University, Boston, MA, USA</p> Florian Mittag Center for Bioinformatics Tübingen</p> Jakob Matthes Center for Bioinformatics Tübingen</p> Jan Rudolph Center for Bioinformatics Tübingen</p> Finja Wrzodek Center for Bioinformatics Tübingen</p> Eugen Netz Center for Bioinformatics Tübingen</p> Alexander Diamantikos Center for Bioinformatics Tübingen</p> Johannes Eichner Center for Bioinformatics Tübingen</p> Roland Keller Center for Bioinformatics Tübingen</p> Clemens Wrzodek Center for Bioinformatics Tübingen</p> Sebastian Fröhlich Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany</p> Nathan E. Lewis University of California, San Diego, La Jolla, CA, USA</p> Chris J. Myers The University of Utah, Salt Lake City, UT, USA</p> Nicolas Le Novère Babraham Institute, Babraham Research Campus, Cambridge, UK</p> Bernhard Ø. Pallson University of California, San Diego, La Jolla, CA, USA</p> Michael Hucka Caltech</p> Andreas Dräger Center for Bioinformatics Tübingen</p> Bioinformatics</p> 2015-10-15</p> https://doi.org/10.1093/bioinformatics/btv341</p>en