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Cited by 285

The DOI matches its Crossref record; 128 of the 128 references it cites were found in a registry or an index.

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

Open access
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, SBML Level 3 Community members, 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 MT, 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 MF, 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·2020·Molecular Systems Biology
DOI 10.15252/msb.20199110
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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.

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Authors
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., Smith, L. P., Swat, M. J., Thieffry, D., Watanabe, L., Wilkinson, D. J., Blinov, M. L., Begley, K., Faeder, J. R., Gómez, H. F., Hamm, T. M., Inagaki, Y., Liebermeister, W., Lister, A. L., Lucio, D., Mjolsness, E., Proctor, C. J., Raman, K., Rodriguez, N., Shaffer, C. A., Shapiro, B. E., Stelling, J., Swainston, N., Tanimura, N., Wagner, J., Meier‐Schellersheim, M., Sauro, H. M., Palsson, B., Bolouri, H., Kitano, H., Funahashi, A., Hermjakob, H., Doyle, J. C., Hucka, M., members, S. L. 3. C., Adams, R. R., Allen, N. A., Angermann, B. R., Antoniotti, M., Bader, G. D., Červený, J., Courtot, M., Cox, C. D., Dalle Pezze, P., Demir, E., Denney, W. S., Dharuri, H., Dorier, J., Drasdo, D., Ebrahim, A., Eichner, J., Elf, J., Endler, L., Evelo, C. T., Flamm, C., Fleming, R. M., Fröhlich, M., Glont, M., Gonçalves, E., Golebiewski, M., Grabski, H., Gutteridge, A., Hachmeister, D., Harris, L. A., Heavner, B. D., Henkel, R., Hlavacek, W. S., Hu, B., Hyduke, D. R., de Jong, H., Juty, N., Karp, P. D., Karr, J. R., Kell, D. B., Keller, R., Kiselev, I., Klamt, S., Klipp, E., Knüpfer, C., Kolpakov, F., Krause, F., Kutmon, M., Laibe, C., Lawless, C., Li, L., Loew, L. M., Machne, R., Matsuoka, Y., Mendes, P., Mi, H., Mittag, F., Monteiro, P. T., Natarajan, K. N., Nielsen, P. M., Nguyen, T., Palmisano, A., Pettit, J., Pfau, T., Phair, R. D., Radivoyevitch, T., Rohwer, J. M., Ruebenacker, O. A., Saez‐Rodriguez, J., Scharm, M., Schmidt, H., Schreiber, F., Schubert, M., Schulte, R., Sealfon, S. C., Smallbone, K., Soliman, S., Stefan, M. I., Sullivan, D. P., Takahashi, K., Teusink, B., Tolnay, D., Vazirabad, I., von Kamp, A., Wittig, U., Wrzodek, C., Wrzodek, F., Xenarios, I., Zhukova, A., & Zucker, J.
Venue
Molecular Systems Biology
Publisher
Springer Science and Business Media LLC
Published
2020-08
Volume
16
Issue
8
Pages
e9110-e9110
ISSN
1744-4292 (ISSN-L)
DOI
10.15252/msb.20199110
OpenAlex
W3080133182
Cited by
285
References
128
FWCI
12.59
Type
journal article
Language
en
Open access
gold

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CoChat. (2026). Citation check: SBML Level 3: an extensible format for the exchange and reuse of biological models. https://app.cochat.ai/papers/10.15252/msb.20199110
The paper
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. https://doi.org/10.15252/msb.20199110

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.