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.
| Original language | English |
|---|---|
| Article number | e9110 |
| Journal | Molecular systems biology |
| Volume | 16 |
| Issue number | 8 |
| DOIs | |
| Publication status | Published - 2020 Aug 1 |
Keywords
- computational modeling
- file format
- interoperability
- reproducibility
- systems biology
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Immunology and Microbiology(all)
- Agricultural and Biological Sciences(all)
- Applied Mathematics
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SBML Level 3 : an extensible format for the exchange and reuse of biological models. / 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; Adams, Richard R.; Allen, Nicholas A.; Angermann, Bastian R.; Antoniotti, Marco; Bader, Gary D.; Červený, Jan; Courtot, Mélanie; Cox, Chris D.; Dalle Pezze, Piero; 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 M.T.; Fröhlich, Martina; Glont, Mihai; Gonçalves, Emanuel; Golebiewski, Martin; Grabski, Hovakim; Gutteridge, Alex; Hachmeister, Damon; Harris, Leonard A.; Heavner, Benjamin D.; Henkel, Ron; Hlavacek, William S.; Hu, Bin; Hyduke, Daniel R.; de Jong, Hidde; 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 M.F.; Nguyen, Tramy; Palmisano, Alida; Pettit, Jean Baptiste; Pfau, Thomas; Phair, Robert D.; Radivoyevitch, Tomas; Rohwer, Johann M.; Ruebenacker, Oliver A.; Saez-Rodriguez, Julio; 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; von Kamp, Axel; Wittig, Ulrike; Wrzodek, Clemens; Wrzodek, Finja; Xenarios, Ioannis; Zhukova, Anna; Zucker, Jeremy.
In: Molecular systems biology, Vol. 16, No. 8, e9110, 01.08.2020.Research output: Contribution to journal › Review article › peer-review
}
TY - JOUR
T1 - SBML Level 3
T2 - an extensible format for the exchange and reuse of biological models
AU - Keating, Sarah M.
AU - Waltemath, Dagmar
AU - König, Matthias
AU - Zhang, Fengkai
AU - Dräger, Andreas
AU - Chaouiya, Claudine
AU - Bergmann, Frank T.
AU - Finney, Andrew
AU - Gillespie, Colin S.
AU - Helikar, Tomáš
AU - Hoops, Stefan
AU - Malik-Sheriff, Rahuman S.
AU - Moodie, Stuart L.
AU - Moraru, Ion I.
AU - Myers, Chris J.
AU - Naldi, Aurélien
AU - Olivier, Brett G.
AU - Sahle, Sven
AU - Schaff, James C.
AU - Smith, Lucian P.
AU - Swat, Maciej J.
AU - Thieffry, Denis
AU - Watanabe, Leandro
AU - Wilkinson, Darren J.
AU - Blinov, Michael L.
AU - Begley, Kimberly
AU - Faeder, James R.
AU - Gómez, Harold F.
AU - Hamm, Thomas M.
AU - Inagaki, Yuichiro
AU - Liebermeister, Wolfram
AU - Lister, Allyson L.
AU - Lucio, Daniel
AU - Mjolsness, Eric
AU - Proctor, Carole J.
AU - Raman, Karthik
AU - Rodriguez, Nicolas
AU - Shaffer, Clifford A.
AU - Shapiro, Bruce E.
AU - Stelling, Joerg
AU - Swainston, Neil
AU - Tanimura, Naoki
AU - Wagner, John
AU - Meier-Schellersheim, Martin
AU - Sauro, Herbert M.
AU - Palsson, Bernhard
AU - Bolouri, Hamid
AU - Kitano, Hiroaki
AU - Funahashi, Akira
AU - Hermjakob, Henning
AU - Doyle, John C.
AU - Hucka, Michael
AU - Adams, Richard R.
AU - Allen, Nicholas A.
AU - Angermann, Bastian R.
AU - Antoniotti, Marco
AU - Bader, Gary D.
AU - Červený, Jan
AU - Courtot, Mélanie
AU - Cox, Chris D.
AU - Dalle Pezze, Piero
AU - Demir, Emek
AU - Denney, William S.
AU - Dharuri, Harish
AU - Dorier, Julien
AU - Drasdo, Dirk
AU - Ebrahim, Ali
AU - Eichner, Johannes
AU - Elf, Johan
AU - Endler, Lukas
AU - Evelo, Chris T.
AU - Flamm, Christoph
AU - Fleming, Ronan M.T.
AU - Fröhlich, Martina
AU - Glont, Mihai
AU - Gonçalves, Emanuel
AU - Golebiewski, Martin
AU - Grabski, Hovakim
AU - Gutteridge, Alex
AU - Hachmeister, Damon
AU - Harris, Leonard A.
AU - Heavner, Benjamin D.
AU - Henkel, Ron
AU - Hlavacek, William S.
AU - Hu, Bin
AU - Hyduke, Daniel R.
AU - de Jong, Hidde
AU - Juty, Nick
AU - Karp, Peter D.
AU - Karr, Jonathan R.
AU - Kell, Douglas B.
AU - Keller, Roland
AU - Kiselev, Ilya
AU - Klamt, Steffen
AU - Klipp, Edda
AU - Knüpfer, Christian
AU - Kolpakov, Fedor
AU - Krause, Falko
AU - Kutmon, Martina
AU - Laibe, Camille
AU - Lawless, Conor
AU - Li, Lu
AU - Loew, Leslie M.
AU - Machne, Rainer
AU - Matsuoka, Yukiko
AU - Mendes, Pedro
AU - Mi, Huaiyu
AU - Mittag, Florian
AU - Monteiro, Pedro T.
AU - Natarajan, Kedar Nath
AU - Nielsen, Poul M.F.
AU - Nguyen, Tramy
AU - Palmisano, Alida
AU - Pettit, Jean Baptiste
AU - Pfau, Thomas
AU - Phair, Robert D.
AU - Radivoyevitch, Tomas
AU - Rohwer, Johann M.
AU - Ruebenacker, Oliver A.
AU - Saez-Rodriguez, Julio
AU - Scharm, Martin
AU - Schmidt, Henning
AU - Schreiber, Falk
AU - Schubert, Michael
AU - Schulte, Roman
AU - Sealfon, Stuart C.
AU - Smallbone, Kieran
AU - Soliman, Sylvain
AU - Stefan, Melanie I.
AU - Sullivan, Devin P.
AU - Takahashi, Koichi
AU - Teusink, Bas
AU - Tolnay, David
AU - Vazirabad, Ibrahim
AU - von Kamp, Axel
AU - Wittig, Ulrike
AU - Wrzodek, Clemens
AU - Wrzodek, Finja
AU - Xenarios, Ioannis
AU - Zhukova, Anna
AU - Zucker, Jeremy
N1 - Funding Information: B.A.'s work on SBML Level 3 was supported by the National Institutes of Health (NIH, US) and he is currently employed by AstraZeneca. Funding Information: G.B. was supported by National Resource for Network Biology (NRNB, US), award 5P41‐GM103504. Funding Information: M.L.B. was supported by grant P41‐GM103313 and R01‐GM095485 from the NIH (US) to the University of Connecticut School of Medicine. Funding Information: J.Č. was supported by the Czech Research Infrastructure Infrastructure for Systems Biology C4SYS, project LM2015055; GA ČR, grant 18‐24397S; and the MEYS of the Czech Republic under OP RDE grant CZ.02.1.01/0.0/0.0/16_026/0008413 “Strategic Partnership for Environmental Technologies and Energy Production”. Funding Information: D.D. was supported by grant iLite (Innovations for LIver and Tissue Engineering) from Agence nationale de la recherche (ANR, France) to INRIA, Paris, France; by grant LiSyM (Liver Systems Medicine) from Bundesministerium für Bildung und Forschung (BMBF, Germany) to IfADo, Dortmund, Germany; by grant VLN (Virtual Liver Network) from Bundesministerium für Bildung und Forschung (BMBF, Germany) to IfADo, Dortmund, Germany; by grant Physicancer from Institut national de la santé et de la recherche médicale (INSERM, France) to INRIA, Paris, France; and by grant NOTOX (Predicting long‐term toxic effects using computer models based on systems characterisations of organotypic cultures) from EU 7 Framework Programme to INRIA, Paris, France. th Funding Information: C.E. was supported by CHARME, COST, Action CA15110 MoU (PI: Chris Evelo) to Maastricht University. Funding Information: R.F. was supported by the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant DE‐SC0010429. Funding Information: A.G. was supported by the Japanese Society for the Promotion of Science. Funding Information: M.G. was supported by funding to HITS from the German Federal Ministry of Education and Research (BMBF) as part of the Liver Systems Medicine Network LiSyM (FKZ 031L0056) and through the MulticellML project (FKZ 01ZX1707B), as well as from the European Union Horizon2020 framework programme of the European Commission under Grant Agreement 825843 and from the Klaus Tschira Foundation (KTS). Funding Information: M.G.G. was supported by European Molecular Biology Laboratory (EMBL) core funding. Funding Information: W.S.H. was supported by grant R01‐GM111510 from the National Institute of General Medical Sciences (NIGMS, US) of the NIH. Funding Information: D.K. was supported by Novo Nordisk Foundation grant NNF10CC1016517. Funding Information: E.K. was supported by Deutsche Forschungsgemeinschaft (DFG, GRK1772, GRK 2290 and TRR175) and by People Programme (Marie Skłodowska‐Curie Actions H2020‐MSCA‐ITN‐2015‐675585). Funding Information: F.K. was supported by the Russian Foundation for Basic Research, 17‐00‐00296, Institute of Computational Technologies of SB RAS, Novosibirsk, 630090, Russian Federation (PI: Fedor Kolpakov). Funding Information: J.K. was supported by grants R35‐GM119771 and P41‐EB023912 from the NIH (US) to the Icahn School of Medicine. Funding Information: P.K. was supported by NIH grant GM075742 from the NIH (US) to SRI International. Funding Information: S.K. was supported by grant 031L104B (de.NBI partner project “ModSim”) by the German Federal Ministry of Education and Research to MPI Magdeburg. Funding Information: L.M.L. was supported by grant P41‐GM103313 from the NIH (US) to the University of Connecticut School of Medicine. Funding Information: P.M. was supported by grant GM080219 from the NIH (US). Funding Information: P.T.M was supported by grant PTDC/EEI‐CTP/2914/2014 from Fundação para a Ciência e a Tecnologia (FCT) to INESC‐ID. Funding Information: S.C.S. was supported by grant U19‐AI117873 from the NIH (US).
PY - 2020/8/1
Y1 - 2020/8/1
N2 - 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.
AB - 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.
KW - computational modeling
KW - file format
KW - interoperability
KW - reproducibility
KW - systems biology
UR - http://www.scopus.com/inward/record.url?scp=85089933733&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85089933733&partnerID=8YFLogxK
U2 - 10.15252/msb.20199110
DO - 10.15252/msb.20199110
M3 - Review article
C2 - 32845085
AN - SCOPUS:85089933733
VL - 16
JO - Molecular Systems Biology
JF - Molecular Systems Biology
SN - 1744-4292
IS - 8
M1 - e9110
ER -