Molecular Systems Biology (Aug 2020)
SBML Level 3: an extensible format for the exchange and reuse of biological models
- Sarah M Keating,
- Dagmar Waltemath,
- Matthias König,
- Fengkai Zhang,
- Andreas Dräger,
- Claudine Chaouiya,
- Frank T Bergmann,
- Andrew Finney,
- Colin S Gillespie,
- Tomáš Helikar,
- 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
Affiliations
- Sarah M Keating
- Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA
- Dagmar Waltemath
- Medical Informatics Institute for Community Health University Medicine Greifswald Greifswald Germany
- Matthias König
- Institute for Theoretical Biology Humboldt‐University Berlin Berlin Germany
- Fengkai Zhang
- Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MDUSA
- Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial‐Resistant Pathogens Institute for Biomedical Informatics (IBMI) University of Tübingen Tübingen Germany
- Claudine Chaouiya
- Aix‐Marseille Université CNRS Centrale Marseille Marseille France
- Frank T Bergmann
- BioQuant/COS Heidelberg University Heidelberg Germany
- Andrew Finney
- ANSYS UK Ltd Milton Park Oxfordshire UK
- Colin S Gillespie
- School of Mathematics, Statistics and Physics Newcastle University Newcastle upon Tyne UK
- Tomáš Helikar
- Department of Biochemistry University of Nebraska–LincolnLincoln NE USA
- Stefan Hoops
- Biocomplexity Institute & Initiative University of Virginia Charlottesville VA USA
- Rahuman S Malik‐Sheriff
- European Bioinformatics Institute European Molecular Biology Laboratory (EMBL‐EBI) Hinxton UK
- Stuart L Moodie
- Eight Pillars Ltd Edinburgh UK
- Ion I Moraru
- Center for Cell Analysis and Modeling UConn Health Farmington CTUSA
- Chris J Myers
- Department of Electrical and Computer Engineering University of Utah Salt Lake CityUT USA
- Aurélien Naldi
- Institut de Biologie de l'ENS (IBENS) Département de Biologie École Normale Supérieure CNRS INSERM Université PSL Paris France
- Brett G Olivier
- Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA
- Sven Sahle
- BioQuant/COS Heidelberg University Heidelberg Germany
- James C Schaff
- Applied BioMath, LLC Concord MAUSA
- Lucian P Smith
- Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA
- Maciej J Swat
- Simcyp (a Certara company) Sheffield South Yorkshire UK
- Denis Thieffry
- Institut de Biologie de l'ENS (IBENS) Département de Biologie École Normale Supérieure CNRS INSERM Université PSL Paris France
- Leandro Watanabe
- Department of Electrical and Computer Engineering University of Utah Salt Lake CityUT USA
- Darren J Wilkinson
- School of Mathematics, Statistics and Physics Newcastle University Newcastle upon Tyne UK
- Michael L Blinov
- Center for Cell Analysis and Modeling UConn Health Farmington CTUSA
- Kimberly Begley
- California Institute of Technology Pasadena CAUSA
- James R Faeder
- Department of Computational and Systems Biology University of Pittsburgh Pittsburgh PAUSA
- Harold F Gómez
- Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland
- Thomas M Hamm
- Computational Systems Biology of Infection and Antimicrobial‐Resistant Pathogens Institute for Biomedical Informatics (IBMI) University of Tübingen Tübingen Germany
- Yuichiro Inagaki
- Management & IT Consulting Division Mizuho Information & Research Institute, Inc.Tokyo Japan
- Wolfram Liebermeister
- Université Paris‐Saclay INRAE MaIAGEJouy‐en-Josas France
- Allyson L Lister
- Oxford e‐Research Centre (OeRC) Department of Engineering Science University of Oxford Oxford UK
- Daniel Lucio
- College of Sciences NC State University RaleighNC USA
- Eric Mjolsness
- Department of Computer Science University of California Irvine CAUSA
- Carole J Proctor
- Institute of Cellular Medicine Newcastle University Newcastle upon Tyne UK
- Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology (IIT) Madras Chennai India
- Nicolas Rodriguez
- The Babraham Institute Cambridge UK
- Clifford A Shaffer
- Department of Computer Science Virginia Tech Blacksburg VAUSA
- Bruce E Shapiro
- Department of Mathematics California State University Northridge CAUSA
- Joerg Stelling
- Department of Biosystems Science and Engineering SIB Swiss Institute of Bioinformatics ETH Zürich Basel Switzerland
- Neil Swainston
- Institute of Integrative Biology University of Liverpool Liverpool UK
- Naoki Tanimura
- Science Solutions Division Mizuho Information & Research Institute, Inc. Tokyo Japan
- John Wagner
- IBM Research Australia Melbourne Vic. Australia
- Martin Meier‐Schellersheim
- Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MDUSA
- Herbert M Sauro
- Department of Bioengineering University of Washington Seattle WAUSA
- Bernhard Palsson
- Department of Bioengineering University of California San Diego La Jolla CA USA
- Hamid Bolouri
- Systems Immunology Benaroya Research Institute at Virginia Mason Seattle WAUSA
- Hiroaki Kitano
- The Systems Biology Institute Tokyo Japan
- Akira Funahashi
- Department of Biosciences and Informatics Keio University Yokohama Kanagawa Japan
- Henning Hermjakob
- European Bioinformatics Institute European Molecular Biology Laboratory (EMBL‐EBI) Hinxton UK
- John C Doyle
- Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA
- Michael Hucka
- Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA
- SBML Level 3 Community members
- DOI
- https://doi.org/10.15252/msb.20199110
- Journal volume & issue
-
Vol. 16,
no. 8
pp. n/a – n/a
Abstract
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 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.
Keywords