{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Shaikh B"],"funding":["National Institutes of Health","NIBIB","NIGMS NIH HHS","NIH HHS"],"pubmed_abstract":["Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulat"],"journal":["Nucleic acids research"],"pagination":["gkac331"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9252793"],"repository":["biostudies-literature"],"pubmed_title":["BioSimulators: a central registry of simulation engines and services for recommending specific tools."],"pmcid":["PMC9252793"],"funding_grant_id":["R24GM137787","R35GM119771","P41EB023912","R35 GM119771"],"pubmed_authors":["Medley JK","Rohwer JM","Zhang F","Cooper J","Sinha A","Hellerstein JL","Karr JR","Muller R","Petzold LR","Starruß J","Spangler R","Kalas M","Moraru II","Wilson M","Beber ME","Nguyen TVN","Brooks D","Vasilescu D","Bergmann FT","Naldi A","Marupilla G","Shaikh B","Ermentrout GB","Goldberg AP","Goelzer A","Nickerson DP","Andrews SS","Hermjakob H","Ison JC","Smith LP","Konig M","van Niekerk D","Sorby H","Agnew H","Frohlich F","Anwar A","Sheriff RSM","Thomas PJ","Mendes P","Rampadarath AK","Liebermeister W","Zhukova A","Funahashi A","Garny A","Sauro HM","Agmon E","Choi K","Olivier BG","Priya A","Saglam AS","Gleeson P","Myers CJ","Gennari JH","Detloff J","Schaff JC","Haiman Z","Jahn D","Snoep J","Blinov ML","Mandal S","Jordan R","Freiburger AP","Calzone L","Drawert B","Hasenauer J","Brusch L","McDougal R","Faeder JR","Jakubowski HV","Hoops S","Dumontier M","Pauleve L","Singh D","Weindl D","Patoliya D"],"additional_accession":[]},"is_claimable":false,"name":"BioSimulators: a central registry of simulation engines and services for recommending specific tools.","description":"Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulat","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 May","modification":"2025-04-05T13:34:05.783Z","creation":"2022-07-20T01:47:08.368Z"},"accession":"S-EPMC9252793","cross_references":{"pubmed":["35524558"],"doi":["10.1093/nar/gkac331"]}}