SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři
| 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 SHERIFF Rahuman S Malik 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 CLIFFORD SHAFFER SHAPIRO Bruce E STELLING Joerg SWAINSTON Neil TANIMURA Naoki WAGNER John SCHELLERSHEIM Martin Meier SAURO Herbert M PALSSON Bernhard BOLOURI Hamid KITANO Hiroaki FUNAHASHI Akira HERMJAKOB Henning DOYLE John C HUCKA Michael MEMBERS SBML Level Community ADAMS Richard R NICHOLAS ALLEN ANGERMANN Bastian R ANTONIOTTI Marco BADER Gary D ČERVENÝ Jan COURTOT Mélanie COX Chris D PEZZE Piero Dalle DEMIR Emek DENNEY William S DHARURI Harish DORIER Julien DRASDO Dirk EBRAHIM Ali EICHNER Johannes ELF Johan ENDLER Lukas EVELO Chris T FLAMM Christoph FLEMING Ronan MT FRÖHLICH Martina GLONT Mihai GONÇALVES Emanuel GOLEBIEWSKI Martin GRABSKI Hovakim GUTTERIDGE Alex HACHMEISTER Damon LEONARD HARRIS HEAVNER Benjamin D HENKEL Ron HLAVACEK William S HU Bin HYDUKE Daniel R JONG Hidde de JUTY Nick KARP Peter D KARR Jonathan R KELL Douglas B KELLER Roland KISELEV Ilya KLAMT Steffen KLIPP Edda KNÜPFER Christian KOLPAKOV Fedor KRAUSE Falko KUTMON Martina LAIBE Camille LAWLESS Conor LI Lu LOEW Leslie M MACHNE Rainer MATSUOKA Yukiko MENDES Pedro MI Huaiyu MITTAG Florian MONTEIRO Pedro T NATARAJAN Kedar Nath NIELSEN Poul MF NGUYEN Tramy PALMISANO Alida PETTIT Jean Baptiste PFAU Thomas PHAIR Robert D RADIVOYEVITCH Tomas ROHWER Johann M OLIVER RUEBENACKER RODRIGUEZ Julio Saez SCHARM Martin SCHMIDT Henning SCHREIBER Falk SCHUBERT Michael SCHULTE Roman SEALFON Stuart C SMALLBONE Kieran SOLIMAN Sylvain STEFAN Melanie I SULLIVAN Devin P TAKAHASHI Koichi TEUSINK Bas TOLNAY David VAZIRABAD Ibrahim KAMP Axel von WITTIG Ulrike WRZODEK Clemens WRZODEK Finja XENARIOS Ioannis ZHUKOVA Anna ZUCKER Jeremy |
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| Year of publication | 2020 |
| Type | Article in Periodical |
| Magazine / Source | Molecular systems biology |
| Citation | |
| Doi | http://dx.doi.org/10.15252/msb.20199110 |
| Keywords | computational modeling, file format, interoperability, reproducibility, systems biology |
| Description | 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. |