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

Sarah M. Keating, Dagmar Waltemath, Matthias Koenig, Fengkai Zhang, Andreas Draeger, Claudine Chaouiya, Frank T. Bergmann, Andrew Finney, Colin S. Gillespie, Tomas Helikar, Stefan Hoops, Rahuman S. Malik-Sheriff, Stuart L. Moodie, Ion I. Moraru, Chris J. Myers, Aurelien Naldi, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. SmithMaciej J. Swat, Denis Thieffry, Leandro Watanabe, Darren J. Wilkinson, Michael L. Blinov, Kimberly Begley, James R. Faeder, Harold F. Gomez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L. Lister, Daniel Lucio, Eric Mjolsness, Carole J. Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A. Shaffer, Bruce E. Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier-Schellersheim, Herbert M. Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, SBML Level 3 Community members, Chris Evelo, M. Kutmon, Michael Hucka*

*Corresponding author for this work

Research output: Contribution to journal(Systematic) Review article peer-review

66 Citations (Web of Science)

Abstract

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 developedSBMLLevel 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 ofSBMLand 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 howSBMLLevel 3 provides the foundation needed to support this evolution.

Original languageEnglish
Article number9110
Number of pages21
JournalMolecular Systems Biology
Volume16
Issue number8
DOIs
Publication statusPublished - Aug 2020

Keywords

  • computational modeling
  • file format
  • interoperability
  • reproducibility
  • systems biology
  • SYSTEMS BIOLOGY
  • MARKUP LANGUAGE
  • SIMULATION
  • STANDARDS
  • SOFTWARE
  • INFORMATION
  • ENVIRONMENT
  • ANNOTATION
  • REPOSITORY
  • ONTOLOGY

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