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
• Year of publication: 2020
• Type: Article in Periodical
• Magazine / Source: Molecular systems biology
• Citation: KEATING, Sarah M, 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, 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 Community MEMBERS, Richard R ADAMS, NICHOLAS, ALLEN, Bastian R ANGERMANN, Marco ANTONIOTTI, Gary D BADER, Jan ČERVENÝ, Mélanie COURTOT, Chris D COX, Piero Dalle PEZZE, Emek DEMIR, William S DENNEY, Harish DHARURI, Julien DORIER, Dirk DRASDO, Ali EBRAHIM, Johannes EICHNER, Johan ELF, Lukas ENDLER, Chris T EVELO, Christoph FLAMM, Ronan MT FLEMING, Martina FRÖHLICH, Mihai GLONT, Emanuel GONÇALVES, Martin GOLEBIEWSKI, Hovakim GRABSKI, Alex GUTTERIDGE, Damon HACHMEISTER, LEONARD, HARRIS, Benjamin D HEAVNER, Ron HENKEL, William S HLAVACEK, Bin HU, Daniel R HYDUKE, Hidde de JONG, Nick JUTY, Peter D KARP, Jonathan R KARR, Douglas B KELL, Roland KELLER, Ilya KISELEV, Steffen KLAMT, Edda KLIPP, Christian KNÜPFER, Fedor KOLPAKOV, Falko KRAUSE, Martina KUTMON, Camille LAIBE, Conor LAWLESS, Lu LI, Leslie M LOEW, Rainer MACHNE, Yukiko MATSUOKA, Pedro MENDES, Huaiyu MI, Florian MITTAG, Pedro T MONTEIRO, Kedar Nath NATARAJAN, Poul MF NIELSEN, Tramy NGUYEN, Alida PALMISANO, Jean Baptiste PETTIT, Thomas PFAU, Robert D PHAIR, Tomas RADIVOYEVITCH, Johann M ROHWER, OLIVER, RUEBENACKER, Julio Saez RODRIGUEZ, Martin SCHARM, Henning SCHMIDT, Falk SCHREIBER, Michael SCHUBERT, Roman SCHULTE, Stuart C SEALFON, Kieran SMALLBONE, Sylvain SOLIMAN, Melanie I STEFAN, Devin P SULLIVAN, Koichi TAKAHASHI, Bas TEUSINK, David TOLNAY, Ibrahim VAZIRABAD, Axel von KAMP, Ulrike WITTIG, Clemens WRZODEK, Finja WRZODEK, Ioannis XENARIOS, Anna ZHUKOVA and Jeremy ZUCKER. SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři. Online. Molecular systems biology. EMBOpress, 2020, vol. 16, No 8, p. e9110. Available from: https://dx.doi.org/10.15252/msb.20199110.
• 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.