BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Bilal ShaikhLucian P SmithDan VasilescuGnaneswara MarupillaMichael WilsonEran AgmonHenry AgnewSteven S AndrewsAzraf AnwarMoritz Emanuel BeberFrank T BergmannDavid BrooksLutz BruschLaurence CalzoneKiri ChoiJoshua CooperJohn DetloffBrian DrawertMichel DumontierG Bard ErmentroutJames R FaederAndrew P FreiburgerFabian FröhlichAkira FunahashiAlan GarnyJohn H GennariPadraig GleesonAnne GoelzerZachary B HaimanJan HasenauerJoseph L HellersteinHenning HermjakobStefan HoopsJon C IsonDiego JahnHenry V JakubowskiRyann JordanMatúš KalašMatthias KönigWolfram LiebermeisterRahuman S Malik SheriffSynchon MandalRobert A McDougalJ Kyle MedleyPedro MendesRobert MüllerChris John MyersAurélien NaldiTung V N NguyenDavid P NickersonBrett G OlivierDrashti PatoliyaLoïc PaulevéLinda R PetzoldAnkita PriyaAnand K RampadarathJohann M RohwerAli Sinan SaglamDilawar SinghAnkur SinhaJacky L SnoepHugh SorbyRyan K SpanglerJörn StarrußPayton J ThomasDavid van NiekerkDaniel WeindlFengkai ZhangAnna ZhukovaArthur P GoldbergJames C SchaffMichael L BlinovHerbert M SauroIon I MoraruJonathan R KarrPublished in: Nucleic acids research (2022)
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 simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.