SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah Keating(California Institute of Technology), Dagmar Waltemath(Universitätsmedizin Greifswald), Matthias König(Humboldt-Universität zu Berlin), Fengkai Zhang(National Institutes of Health), Andreas Dräger(German Center for Infection Research), Claudine Chaouiya(Centre National de la Recherche Scientifique), Frank Bergmann(Heidelberg University), Andrew Finney(Ansys (United Kingdom)), Colin S. Gillespie(Newcastle University), Tomáš Helikar(University of Nebraska–Lincoln), Stefan Hoops(Biocom), Rahuman S. Malik‐Sheriff(European Bioinformatics Institute), Stuart Moodie, Ion I. Moraru(UConn Health), Chris J. Myers(University of Utah), Aurélien Naldi(Centre National de la Recherche Scientifique), Brett G. Olivier(California Institute of Technology), Sven Sahle(Heidelberg University), James C. Schaff(Applied BioMath (United States)), Lucian P. Smith(California Institute of Technology), Maciej J. Swat(Simcyp (United Kingdom)), Denis Thieffry(Centre National de la Recherche Scientifique), Leandro Watanabe(University of Utah), Darren J. Wilkinson(Turing Institute), Michael L. Blinov(UConn Health), Kimberly Begley(California Institute of Technology), James R. Faeder(University of Pittsburgh), Harold Gómez(ETH Zurich), Thomas M. Hamm(University of Tübingen), Yuichiro Inagaki(BH Consulting (Ireland)), Wolfram Liebermeister(Université Paris-Saclay), Allyson Lister(University of Oxford), Daniel Lucio(North Carolina State University), Eric Mjolsness(University of California, Irvine), Carole J. Proctor(Newcastle University), Karthik Raman(Indian Institute of Technology Madras), Nicolás Rodríguez(Babraham Institute), Clifford A. Shaffer(Virginia Tech), Bruce E. Shapiro(California State University, Northridge), Joerg Stelling(SIB Swiss Institute of Bioinformatics), Neil Swainston(University of Liverpool), Naoki Tanimura(SC Solutions (United States)), John Wagner(IBM Research - Australia), Martin Meier‐Schellersheim(National Institutes of Health), Herbert M. Sauro(University of Washington), Bernhard Ø. Palsson(University of California San Diego), Hamid Bolouri(Virginia Mason Medical Center), Hiroaki Kitano(Okinawa Institute of Science and Technology Graduate University), Akira Funahashi(Keio University), Henning Hermjakob(European Bioinformatics Institute), John C. Doyle(California Institute of Technology), Michael Hucka(California Institute of Technology), SBML Level 3 Community members, Richard R. Adams, Nicholas Allen(National Institutes of Health), Bastian R. Angermann(University of Milano-Bicocca), Marco Antoniotti(University of Toronto), Gary D. Bader(Masaryk University), Jan Červený(Terry Fox Research Institute), Mélanie Courtot(University of Tennessee at Knoxville), Chris D. Cox(Babraham Institute), Piero Dalle Pezze(Oregon Health & Science University), Emek Demir(New England Biolabs (United Kingdom)), William S. Denney(Illumina (United States)), Harish Dharuri, Julien Dorier, Dirk Drasdo(University of California San Diego), Ali Ebrahim(Shanghai Center For Bioinformation Technology), Johannes Eichner(Uppsala University), Johan Elf, Lukas Endler(Maastricht University), Chris T. Evelo(University of Klagenfurt), Christoph Flamm(Medical University of Vienna), Ronan M. T. Fleming(German Cancer Research Center), Martina Fröhlich(European Bioinformatics Institute), Mihai Glont(European Bioinformatics Institute), Emanuel Gonçalves(Heidelberg Institute for Theoretical Studies), Martin Golebiewski(Russian-Armenian University), Hovakim Grabski(GlaxoSmithKline (United Kingdom)), Alex Gutteridge(Microsoft (Germany)), Damon Hachmeister(Vanderbilt University), Leonard A. Harris(University of Washington), Ben Heavner(University of Rostock), Ron Henkel(Los Alamos National Laboratory), William S. Hlavacek, Bin Hu, Daniel R. Hyduke, Hidde de Jong(European Bioinformatics Institute), Nick Juty(SRI International), Peter D. Karp(Icahn School of Medicine at Mount Sinai), Jonathan R Karr(Universitätsklinikum Tübingen), Douglas B. Kell(Universitätsklinikum Tübingen), Roland Keller(Institute of Information and Computational Technologies), Ilya Kiselev(Max Planck Institute for Dynamics of Complex Technical Systems), Steffen Klamt(Max Planck Institute for Molecular Genetics), Edda Klipp(Friedrich Schiller University Jena), Christian Knüpfer(Institute of Information and Computational Technologies), Fedor Kolpakov(Humboldt-Universität zu Berlin), Falko Krause(Maastricht University), Martina Kutmon(European Bioinformatics Institute), Camille Laibe(University of Newcastle Australia), Conor Lawless(École Polytechnique), Lu Li, Leslie M. Loew(Heinrich Heine University Düsseldorf), Rainer Machné(Systems Biology Institute), Yukiko Matsuoka(Rede de Química e Tecnologia), Pedro Mendes(University of Southern California), Huaiyu Mi(University of Tübingen), Florian Mittag(Instituto Gulbenkian de Ciência), Pedro T. Monteiro(University of Southern Denmark), Kedar Nath Natarajan(University of Auckland), Poul MF Nielsen(University of Utah), Tramy Nguyen(Virginia Tech), Alida Palmisano(European Bioinformatics Institute), Jean‐Baptiste Pettit(University of Luxembourg), Thomas Pfau, Robert D. Phair(Cleveland Clinic), Tomas Radivoyevitch(Stellenbosch University), Johann M. Rohwer(Broad Institute), Oliver Ruebenacker(Heidelberg University), Julio Sáez-Rodríguez(University of Rostock), Martin Scharm(University of Rostock), Henning Schmidt(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Falk Schreiber(Laboratoire de Biologie du Développement de Villefranche-sur-Mer), Michaël Schubert(University of Tübingen), Roman Schulte(Icahn School of Medicine at Mount Sinai), Stuart C. Sealfon(University of Manchester), Kieran Smallbone, Sylvain Soliman(California Institute of Technology), Melanie I. Stefan(Tamedia (Switzerland)), Devin P. Sullivan(Shinshu University), Koichi Takahashi(University of Amsterdam), Bas Teusink(California Institute of Technology), David Tolnay(Versiti Blood Center of Wisconsin), Ibrahim Vazirabad(Max Planck Institute for Dynamics of Complex Technical Systems), Axel von Kamp(Heidelberg Institute for Theoretical Studies), Ulrike Wittig(Universitätsklinikum Tübingen), Clemens Wrzodek(Universitätsklinikum Tübingen), Finja Wrzodek, Ioannis Xénarios, Anna Zhukova(Pacific Northwest National Laboratory), Jeremy Zucker
Cited by 306Open Access
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.
Related Papers
No related papers found
Powered by citation graph analysis