SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah M. Keating; 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 A. 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; Richard R. Adams; Nicholas A. 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 M.T. Fleming; Martina Fröhlich; Mihai Glont; Emanuel Gonçalves; Martin Golebiewski; Hovakim Grabski; Alex Gutteridge; Damon Hachmeister; Leonard A. 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 M.F. Nielsen; Tramy Nguyen; Alida Palmisano; Jean Baptiste Pettit; Thomas Pfau; Robert D. Phair; Tomas Radivoyevitch; Johann M. Rohwer; Oliver A. 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; Jeremy Zucker

doi:10.15252/msb.20199110

SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah M. Keating, 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. SmithMaciej 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 A. 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, Richard R. Adams, Nicholas A. 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 M.T. Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A. 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 M.F. Nielsen, Tramy Nguyen, Alida Palmisano, Jean Baptiste Pettit, Thomas Pfau, Robert D. Phair, Tomas Radivoyevitch, Johann M. Rohwer, Oliver A. 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, Jeremy Zucker

Research output: Contribution to journal › Review article › peer-review

135 Scopus citations

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 (US)
Article number	e9110
Journal	Molecular Systems Biology
Volume	16
Issue number	8
DOIs	https://doi.org/10.15252/msb.20199110
State	Published - Aug 1 2020

Keywords

computational modeling
file format
interoperability
reproducibility
systems biology

ASJC Scopus subject areas

Information Systems
General Immunology and Microbiology
Applied Mathematics
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
Computational Theory and Mathematics

Access to Document

10.15252/msb.20199110

Cite this

Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie, S. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle, S., Schaff, J. C., ... Zucker, J. (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8), Article e9110. https://doi.org/10.15252/msb.20199110

Keating, SM, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, FT, Finney, A, Gillespie, CS, Helikar, T, Hoops, S, Malik-Sheriff, RS, Moodie, SL, Moraru, II, Myers, CJ, Naldi, A, Olivier, BG, Sahle, S, Schaff, JC, Smith, LP, Swat, MJ, Thieffry, D, Watanabe, L, Wilkinson, DJ, Blinov, ML, Begley, K, Faeder, JR, Gómez, HF, Hamm, TM, Inagaki, Y, Liebermeister, W, Lister, AL, Lucio, D, Mjolsness, E, Proctor, CJ, Raman, K, Rodriguez, N, Shaffer, CA, Shapiro, BE, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, HM, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, JC, Hucka, M, Adams, RR, Allen, NA, Angermann, BR, Antoniotti, M, Bader, GD, Červený, J, Courtot, M, Cox, CD, Dalle Pezze, P, Demir, E, Denney, WS, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, CT, Flamm, C, Fleming, RMT, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, LA, Heavner, BD, Henkel, R, Hlavacek, WS, Hu, B, Hyduke, DR, de Jong, H, Juty, N, Karp, PD, Karr, JR, Kell, DB, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, LM, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, PT, Natarajan, KN, Nielsen, PMF, Nguyen, T, Palmisano, A, Pettit, JB, Pfau, T, Phair, RD, Radivoyevitch, T, Rohwer, JM, Ruebenacker, OA, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, SC, Smallbone, K, Soliman, S, Stefan, MI, Sullivan, DP, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, von Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A & Zucker, J 2020, 'SBML Level 3: an extensible format for the exchange and reuse of biological models', Molecular Systems Biology, vol. 16, no. 8, e9110. https://doi.org/10.15252/msb.20199110

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title = "SBML Level 3: an extensible format for the exchange and reuse of biological models",

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.",

keywords = "computational modeling, file format, interoperability, reproducibility, systems biology",

author = "Keating, {Sarah M.} and Dagmar Waltemath and Matthias K{\"o}nig and Fengkai Zhang and Andreas Dr{\"a}ger and Claudine Chaouiya and Bergmann, {Frank T.} and Andrew Finney and Gillespie, {Colin S.} and Tom{\'a}{\v s} Helikar and Stefan Hoops and Malik-Sheriff, {Rahuman S.} and Moodie, {Stuart L.} and Moraru, {Ion I.} and Myers, {Chris J.} and Aur{\'e}lien Naldi and Olivier, {Brett G.} and Sven Sahle and Schaff, {James C.} and Smith, {Lucian P.} and Swat, {Maciej J.} and Denis Thieffry and Leandro Watanabe and Wilkinson, {Darren J.} and Blinov, {Michael L.} and Kimberly Begley and Faeder, {James R.} and G{\'o}mez, {Harold F.} and Hamm, {Thomas M.} and Yuichiro Inagaki and Wolfram Liebermeister and Lister, {Allyson L.} and Daniel Lucio and Eric Mjolsness and Proctor, {Carole J.} and Karthik Raman and Nicolas Rodriguez and Shaffer, {Clifford A.} and Shapiro, {Bruce E.} and Joerg Stelling and Neil Swainston and Naoki Tanimura and John Wagner and Martin Meier-Schellersheim and Sauro, {Herbert M.} and Bernhard Palsson and Hamid Bolouri and Hiroaki Kitano and Akira Funahashi and Henning Hermjakob and Doyle, {John C.} and Michael Hucka and Adams, {Richard R.} and Allen, {Nicholas A.} and Angermann, {Bastian R.} and Marco Antoniotti and Bader, {Gary D.} and Jan {\v C}erven{\'y} and M{\'e}lanie Courtot and Cox, {Chris D.} and {Dalle Pezze}, Piero and Emek Demir and Denney, {William S.} and Harish Dharuri and Julien Dorier and Dirk Drasdo and Ali Ebrahim and Johannes Eichner and Johan Elf and Lukas Endler and Evelo, {Chris T.} and Christoph Flamm and Fleming, {Ronan M.T.} and Martina Fr{\"o}hlich and Mihai Glont and Emanuel Gon{\c c}alves and Martin Golebiewski and Hovakim Grabski and Alex Gutteridge and Damon Hachmeister and Harris, {Leonard A.} and Heavner, {Benjamin D.} and Ron Henkel and Hlavacek, {William S.} and Bin Hu and Hyduke, {Daniel R.} and {de Jong}, Hidde and Nick Juty and Karp, {Peter D.} and Karr, {Jonathan R.} and Kell, {Douglas B.} and Roland Keller and Ilya Kiselev and Steffen Klamt and Edda Klipp and Christian Kn{\"u}pfer and Fedor Kolpakov and Falko Krause and Martina Kutmon and Camille Laibe and Conor Lawless and Lu Li and Loew, {Leslie M.} and Rainer Machne and Yukiko Matsuoka and Pedro Mendes and Huaiyu Mi and Florian Mittag and Monteiro, {Pedro T.} and Natarajan, {Kedar Nath} and Nielsen, {Poul M.F.} and Tramy Nguyen and Alida Palmisano and Pettit, {Jean Baptiste} and Thomas Pfau and Phair, {Robert D.} and Tomas Radivoyevitch and Rohwer, {Johann M.} and Ruebenacker, {Oliver A.} and Julio Saez-Rodriguez and Martin Scharm and Henning Schmidt and Falk Schreiber and Michael Schubert and Roman Schulte and Sealfon, {Stuart C.} and Kieran Smallbone and Sylvain Soliman and Stefan, {Melanie I.} and Sullivan, {Devin P.} and Koichi Takahashi and Bas Teusink and David Tolnay and Ibrahim Vazirabad and {von Kamp}, Axel and Ulrike Wittig and Clemens Wrzodek and Finja Wrzodek and Ioannis Xenarios and Anna Zhukova and Jeremy Zucker",

note = "Publisher Copyright: {\textcopyright} 2020 California Institute of Technology Published under the terms of the CC BY 4.0 license",

year = "2020",

month = aug,

day = "1",

doi = "10.15252/msb.20199110",

language = "English (US)",

volume = "16",

journal = "Molecular Systems Biology",

issn = "1744-4292",

publisher = "Nature Publishing Group",

number = "8",

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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

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

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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

SN - 1744-4292

VL - 16

JO - Molecular Systems Biology

JF - Molecular Systems Biology

IS - 8

M1 - e9110

ER -

SBML Level 3: an extensible format for the exchange and reuse of biological models

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