biostudies-literatureKeating SMCancer Research UKNIBIB NIH HHSNIDDK NIH HHSNIAID NIH HHSAlan Turing InstituteBiotechnology and Biological Sciences Research CouncilNIGMS NIH HHSe9110https://www.ebi.ac.uk/biostudies/studies/S-EPMC8411907biostudies-literatureUnknown16(8)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.Molecular systems biologySBML Level 3: an extensible format for the exchange and reuse of biological models.PMC841190726815R01 GM095485TU/ASG/R-SPEH-115U24 EB028887R01 GM080219R01 GM111510BB/N019482/1U19 AI117873BB/M017702/1R01 GM057089R01 GM070923R01 GM075742P41 EB023912P41 GM103313P41 GM103712R35 GM119771R01 DK046943R01 GM123032P41 GM103504R35 GM119770Rohwer JMZhang FLucio DTolnay DKarr JRGlont MGomez HFMachne RNaldi AKarp PDKell DBMonteiro PTElf JKutmon MWrzodek FWatanabe LEbrahim AChaouiya CSchreiber FKeller RKonig MSmith LPAngermann BRDenney WSHu BHarris LADrasdo DPfau TSahle SCox CDGrabski HMalik-Sheriff RSMendes PFunahashi ASauro HMHenkel RTeusink BPalsson BPalmisano ADemir EWaltemath DMyers CJLister ALEndler LAntoniotti MKlamt SDrager AKeating SMGutteridge ACourtot MInagaki YPettit JBFaeder JRRaman KLoew LMWrzodek CStefan MIKitano HSealfon SCSullivan DPZucker JMoodie SLRuebenacker OAHelikar TXenarios IHyduke DRSaez-Rodriguez JPhair RDMoraru IISchmidt HMjolsness ETanimura NNatarajan KNBergmann FTSmallbone KSchubert MKlipp EStelling JShaffer CADorier JVazirabad IProctor CJBolouri HScharm MBegley KHermjakob HMittag FSwainston NKnupfer CWagner JHachmeister DLi LFrohlich Mvon Kamp AJuty NEvelo CTFlamm CLiebermeister WZhukova AWilkinson DJWittig UMi HRodriguez NLawless CMeier-Schellersheim MHlavacek WSGolebiewski MOlivier BGFinney ADharuri HSchaff JCLaibe CBlinov MLHucka MGoncalves EKrause FBader GDTakahashi KDalle Pezze PThieffry DSwat MJHoops SNguyen THeavner BDSchulte RAdams RRde Jong HRadivoyevitch TNielsen PMDoyle JCShapiro BEGillespie CSCerveny JAllen NAMatsuoka YEichner JHamm TMKolpakov FKiselev ISoliman SFleming RMSBML Level 3 Community membersfalseSBML 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 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.2020-01-01T00:00:00Z2020 Aug2024-11-14T20:49:44.963Z2022-02-11T10:57:51.47ZS-EPMC84119073284508510.15252/msb.20199110