SBML level 3: An extensible format for the exchange and reuse of biological models
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 forma...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal article |
| Language: | English |
| Published: |
EMBO Press
2020
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| _version_ | 1826280099627925504 |
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| author | 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 |
| author2 | SBML Level 3 Community members |
| author_facet | SBML Level 3 Community members 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 |
| author_sort | Keating, SM |
| collection | OXFORD |
| 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. |
| first_indexed | 2024-03-07T00:08:38Z |
| format | Journal article |
| id | oxford-uuid:786fefef-7e37-4253-aabc-82b5656844fd |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:08:38Z |
| publishDate | 2020 |
| publisher | EMBO Press |
| record_format | dspace |
| spelling | oxford-uuid:786fefef-7e37-4253-aabc-82b5656844fd2022-03-26T20:30:50ZSBML level 3: An extensible format for the exchange and reuse of biological modelsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:786fefef-7e37-4253-aabc-82b5656844fdEnglishSymplectic ElementsEMBO Press2020Keating, SMWaltemath, DKönig, MZhang, FDräger, AChaouiya, CBergmann, FTFinney, AGillespie, CSHelikar, THoops, SMalik-Sheriff, RSMoodie, SLMoraru, IIMyers, CJNaldi, AOlivier, BGSahle, SSchaff, JCSmith, LPSwat, MJThieffry, DWatanabe, LWilkinson, DJBlinov, MLBegley, KFaeder, JRGómez, HFHamm, TMInagaki, YLiebermeister, WLister, ALLucio, DMjolsness, EProctor, CJRaman, KRodriguez, NShaffer, CAShapiro, BEStelling, JSwainston, NTanimura, NWagner, JMeier-Schellersheim, MSauro, HMPalsson, BBolouri, HKitano, HFunahashi, AHermjakob, HDoyle, JCHucka, MSBML Level 3 Community membersSystems 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. |
| spellingShingle | 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 SBML level 3: An extensible format for the exchange and reuse of biological models |
| title | SBML level 3: An extensible format for the exchange and reuse of biological models |
| title_full | SBML level 3: An extensible format for the exchange and reuse of biological models |
| title_fullStr | SBML level 3: An extensible format for the exchange and reuse of biological models |
| title_full_unstemmed | SBML level 3: An extensible format for the exchange and reuse of biological models |
| title_short | SBML level 3: An extensible format for the exchange and reuse of biological models |
| title_sort | sbml level 3 an extensible format for the exchange and reuse of biological models |
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