BioSimulators: a central registry of simulation engines and services for recommending specific tools | Zendy

Bilal Shaikh | Zendy; Lucian P. Smith | Zendy; Dan Vasilescu | Zendy; Gnaneswara Marupilla | Zendy; Michael Wilson | Zendy; Eran Agmon | Zendy; Henry Agnew | Zendy; Steven S. Andrews | Zendy; Azraf Anwar | Zendy; Moritz Emanuel Beber | Zendy; Frank Bergmann | Zendy; David Brooks | Zendy; Lutz Brusch | Zendy; Laurence Calzone | Zendy; Kiri Choi | Zendy; Joshua Cooper | Zendy; John Detloff | Zendy; Brian Drawert | Zendy; Michel Dumontier | Zendy; Bard Ermentrout | Zendy; James R. Faeder | Zendy; Andrew Freiburger | Zendy; Fabian Fröhlich | Zendy; Akira Funahashi | Zendy; Alan Garny | Zendy; John H. Gennari | Zendy; Padraig Gleeson | Zendy; Anne Goelzer | Zendy; Zachary B. Haiman | Zendy; Jan Hasenauer | Zendy; Joseph L. Hellerstein | Zendy; Henning Hermjakob | Zendy; Stefan Hoops | Zendy; Jon Ison | Zendy; Diego Jahn | Zendy; Henry V. Jakubowski | Zendy; Ryann Jordan | Zendy; Matúš Kalaš | Zendy; Matthias König | Zendy; Wolfram Liebermeister | Zendy; Rahuman S. MalikSheriff | Zendy; Synchon Mandal | Zendy; Robert A. McDougal | Zendy; Kyle Medley | Zendy; Pedro Mendes | Zendy; Robert Müller | Zendy; Chris J. Myers | Zendy; Aurélien Naldi | Zendy; Tung V N Nguyen | Zendy; David Nickerson | Zendy; Brett G. Olivier | Zendy; Drashti Patoliya | Zendy; Loïc Paulevé | Zendy; Linda Petzold | Zendy; Ankita Priya | Zendy; Anand Rampadarath | Zendy; Johann M. Rohwer | Zendy; Ali Sinan Saglam | Zendy; Dilawar Singh | Zendy; Ankur Sinha | Zendy; Jacky L. Snoep | Zendy; Hugh Sorby | Zendy; Ryan K. Spangler | Zendy; Jörn Starruß | Zendy; Payton J. Thomas | Zendy; David van Niekerk | Zendy; Daniel Weindl | Zendy; Fengkai Zhang | Zendy; Anna Zhukova | Zendy; Arthur P. Goldberg | Zendy; James C. Schaff | Zendy; Michael L. Blinov | Zendy; Herbert M. Sauro | Zendy; Ion I. Moraru | Zendy; Jonathan R. Karr | Zendy

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BioSimulators: a central registry of simulation engines and services for recommending specific tools

Author(s) -

Bilal Shaikh,

Lucian P. Smith,

Dan Vasilescu,

Gnaneswara Marupilla,

Michael Wilson,

Eran Agmon,

Henry Agnew,

Steven S. Andrews,

Azraf Anwar,

Moritz Emanuel Beber,

Frank Bergmann,

David Brooks,

Lutz Brusch,

Laurence Calzone,

Kiri Choi,

Joshua Cooper,

John Detloff,

Brian Drawert,

Michel Dumontier,

Bard Ermentrout,

James R. Faeder,

Andrew Freiburger,

Fabian Fröhlich,

Akira Funahashi,

Alan Garny,

John H. Gennari,

Padraig Gleeson,

Anne Goelzer,

Zachary B. Haiman,

Jan Hasenauer,

Joseph L. Hellerstein,

Henning Hermjakob,

Stefan Hoops,

Jon Ison,

Diego Jahn,

Henry V. Jakubowski,

Ryann Jordan,

Matúš Kalaš,

Matthias König,

Wolfram Liebermeister,

Rahuman S. MalikSheriff,

Synchon Mandal,

Robert A. McDougal,

Kyle Medley,

Pedro Mendes,

Robert Müller,

Chris J. Myers,

Aurélien Naldi,

Tung V N Nguyen,

David Nickerson,

Brett G. Olivier,

Drashti Patoliya,

Loïc Paulevé,

Linda Petzold,

Ankita Priya,

Anand Rampadarath,

Johann M. Rohwer,

Ali Sinan Saglam,

Dilawar Singh,

Ankur Sinha,

Jacky L. Snoep,

Hugh Sorby,

Ryan K. Spangler,

Jörn Starruß,

Payton J. Thomas,

David van Niekerk,

Daniel Weindl,

Fengkai Zhang,

Anna Zhukova,

Arthur P. Goldberg,

James C. Schaff,

Michael L. Blinov,

Herbert M. Sauro,

Ion I. Moraru,

Jonathan R. Karr

Publication year - 2022

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkac331

Subject(s) - sbml , python (programming language) , reuse , computer science , software engineering , software , interface (matter) , systems engineering , programming language , world wide web , biology , xml , operating system , engineering , ecology , markup language , bubble , maximum bubble pressure method

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.

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