SBML Level 3: an extensible format for the exchange and reuse of biological models. Issue 8 (26th August 2020)

• Record Type: Journal Article
• Authors: Keating, Sarah M; Waltemath, Dagmar; König, Matthias; Zhang, Fengkai; Dräger, Andreas; Chaouiya, Claudine; Bergmann, Frank T; Finney, Andrew; Gillespie, Colin S; Helikar, Tomáš; Hoops, Stefan; Malik‐Sheriff, Rahuman S; Moodie, Stuart L; Moraru, Ion I; Myers, Chris J; Naldi, Aurélien; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Swat, Maciej J; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J; Blinov, Michael L; Begley, Kimberly; Faeder, James R; Gómez, Harold F; Hamm, Thomas M; Inagaki, Yuichiro; Liebermeister, Wolfram; Lister, Allyson L; Lucio, Daniel; Mjolsness, Eric; Proctor, Carole J; Raman, Karthik; Rodriguez, Nicolas; Shaffer, Clifford A; Shapiro, Bruce E; Stelling, Joerg; Swainston, Neil; Tanimura, Naoki; Wagner, John; Meier‐Schellersheim, Martin; Sauro, Herbert M; Palsson, Bernhard; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning; Doyle, John C; Hucka, Michael;
• Other Names: Adams Richard R investigator.; Allen Nicholas A investigator.; Angermann Bastian R investigator.; Antoniotti Marco investigator.; Bader Gary D investigator.; Červený Jan investigator.; Courtot Mélanie investigator.; Cox Chris D investigator.; Dalle Pezze Piero investigator.; Demir Emek investigator.; Denney William S investigator.; Dharuri Harish investigator.; Dorier Julien investigator.; Drasdo Dirk investigator.; Ebrahim Ali investigator.; Eichner Johannes investigator.; Elf Johan investigator.; Endler Lukas investigator.; Evelo Chris T investigator.; Flamm Christoph investigator.; Fleming Ronan MT investigator.; Fröhlich Martina investigator.; Glont Mihai investigator.; Gonçalves Emanuel investigator.; Golebiewski Martin investigator.; Grabski Hovakim investigator.; Gutteridge Alex investigator.; Hachmeister Damon investigator.; Harris Leonard A investigator.; Heavner Benjamin D investigator.; Henkel Ron investigator.; Hlavacek William S investigator.; Hu Bin investigator.; Hyduke Daniel R investigator.; de Jong Hidde investigator.; Juty Nick investigator.; Karp Peter D investigator.; Karr Jonathan R investigator.; Kell Douglas B investigator.; Keller Roland investigator.; Kiselev Ilya investigator.; Klamt Steffen investigator.; Klipp Edda investigator.; Knüpfer Christian investigator.; Kolpakov Fedor investigator.; Krause Falko investigator.; Kutmon Martina investigator.; Laibe Camille investigator.; Lawless Conor investigator.; Li Lu investigator.; Loew Leslie M investigator.; Machne Rainer investigator.; Matsuoka Yukiko investigator.; Mendes Pedro investigator.; Mi Huaiyu investigator.; Mittag Florian investigator.; Monteiro Pedro T investigator.; Natarajan Kedar Nath investigator.; Nielsen Poul MF investigator.; Nguyen Tramy investigator.; Palmisano Alida investigator.; Pettit Jean‐Baptiste investigator.; Pfau Thomas investigator.; Phair Robert D investigator.; Radivoyevitch Tomas investigator.; Rohwer Johann M investigator.; Ruebenacker Oliver A investigator.; Saez‐Rodriguez Julio investigator.; Scharm Martin investigator.; Schmidt Henning investigator.; Schreiber Falk investigator.; Schubert Michael investigator.; Schulte Roman investigator.; Sealfon Stuart C investigator.; Smallbone Kieran investigator.; Soliman Sylvain investigator.; Stefan Melanie I investigator.; Sullivan Devin P investigator.; Takahashi Koichi investigator.; Teusink Bas investigator.; Tolnay David investigator.; Vazirabad Ibrahim investigator.; von Kamp Axel investigator.; Wittig Ulrike investigator.; Wrzodek Clemens investigator.; Wrzodek Finja investigator.; Xenarios Ioannis investigator.; Zhukova Anna investigator.; Zucker Jeremy investigator.;
• Is Part Of: Molecular systems biology. Volume 16:Issue 8(2020)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2020-08-26
• Subjects: computational modeling -- file format -- interoperability -- reproducibility -- systems biology; Molecular biology -- Periodicals; Systems biology -- Periodicals; 572.8
• DOI: 10.15252/msb.20199110
• Languages: English
• ISSNs: 1744-4292

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. Abstract : Over the past two decades, scientists from different fields have been developing SBML, a standard format for encoding computational models in biology and medicine. This article summarizes recent progress and gives perspectives on emerging challenges.