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

Authors

Sarah M. Keating, California Institute of TechnologyFollow
Dagmar Waltemath, University Medicine Greifswald, GermanyFollow
Tomáš Helikar, University of Nebraska-LincolnFollow
Michael Hucka, California Institute of TechnologyFollow
50 additional co-authors, various

ORCID IDs

Sarah M Keating https://orcid.org/0000-0002-3356-3542

Dagmar Waltemath https://orcid.org/0000-0002-5886-5563

Tomas Helikar https://orcid.org/0000-0003-3653-1906

Michael Hucka https://orcid.org/0000-0001-9105-5960

Date of this Version

2020

Citation

Molecular Systems Biology 16: e9110 (2020)

DOI 10.15252/msb.20199110

Comments

Copyright 2020 California Institute of Technology. Published under the terms of the CC BY 4.0 license

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 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 constraintbased 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.

Additional authors include: Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Stefan Hoops, Rahuman S Malik-Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, 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, John C Doyle, Michael Hucka, & SBML Level 3 Community members