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

Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks; Lutz Brusch; Laurence Calzone; Kiri Choi; Joshua Cooper; John Detloff; Brian Drawert; Michel Dumontier; G. Bard Ermentrout; James R. Faeder; Andrew P. Freiburger; Fabian Fröhlich; Akira Funahashi; Alan Garny; John H. Gennari; Padraig Gleeson; Anne Goelzer; Zachary Haiman; Jan Hasenauer; Joseph L. Hellerstein; Henning Hermjakob; Stefan Hoops; Jon C. Ison; Diego Jahn; Henry V. Jakubowski; Ryann Jordan; Matúš Kalaš; Matthias König; Wolfram Liebermeister; Rahuman S.Malik Sheriff; Synchon Mandal; Robert McDougal; J. Kyle Medley; Pedro Mendes; Robert Müller; Chris J. Myers; Aurelien Naldi; Tung V.N. Nguyen; David P. Nickerson; Brett G. Olivier; Drashti Patoliya; Loïc Paulevé; Linda R. Petzold; Ankita Priya; Anand K. Rampadarath; Johann M. Rohwer; Ali S. Saglam; Dilawar Singh; Ankur Sinha; Jacky Snoep; Hugh Sorby; Ryan 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

doi:10.1093/nar/gkac331

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

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard ErmentroutJames R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Rahuman S.Malik Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurelien Naldi, Tung V.N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan 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^*

^*Corresponding author for this work

AIMMS

Research output: Contribution to Journal › Article › Academic › peer-review

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 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.

Original language	English
Pages (from-to)	W108-W114
Number of pages	7
Journal	Nucleic acids research
Volume	50
Issue number	W1
Early online date	7 May 2022
DOIs	https://doi.org/10.1093/nar/gkac331
Publication status	Published - 5 Jul 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

Funding

Funders	Funder number
National Institute of General Medical Sciences	R24GM137787

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/nar/gkac331

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Shaikh, B., Smith, L. P., Vasilescu, D., Marupilla, G., Wilson, M., Agmon, E., Agnew, H., Andrews, S. S., Anwar, A., Beber, M. E., Bergmann, F. T., Brooks, D., Brusch, L., Calzone, L., Choi, K., Cooper, J., Detloff, J., Drawert, B., Dumontier, M., ... Karr, J. R. (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic acids research, 50(W1), W108-W114. https://doi.org/10.1093/nar/gkac331

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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 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.",

author = "Bilal Shaikh and Smith, {Lucian P.} and Dan Vasilescu and Gnaneswara Marupilla and Michael Wilson and Eran Agmon and Henry Agnew and Andrews, {Steven S.} and Azraf Anwar and Beber, {Moritz E.} and Bergmann, {Frank T.} and David Brooks and Lutz Brusch and Laurence Calzone and Kiri Choi and Joshua Cooper and John Detloff and Brian Drawert and Michel Dumontier and Ermentrout, {G. Bard} and Faeder, {James R.} and Freiburger, {Andrew P.} and Fabian Fr{\"o}hlich and Akira Funahashi and Alan Garny and Gennari, {John H.} and Padraig Gleeson and Anne Goelzer and Zachary Haiman and Jan Hasenauer and Hellerstein, {Joseph L.} and Henning Hermjakob and Stefan Hoops and Ison, {Jon C.} and Diego Jahn and Jakubowski, {Henry V.} and Ryann Jordan and Mat{\'u}{\v s} Kala{\v s} and Matthias K{\"o}nig and Wolfram Liebermeister and Sheriff, {Rahuman S.Malik} and Synchon Mandal and Robert McDougal and Medley, {J. Kyle} and Pedro Mendes and Robert M{\"u}ller and Myers, {Chris J.} and Aurelien Naldi and Nguyen, {Tung V.N.} and Nickerson, {David P.} and Olivier, {Brett G.} and Drashti Patoliya and Lo{\"i}c Paulev{\'e} and Petzold, {Linda R.} and Ankita Priya and Rampadarath, {Anand K.} and Rohwer, {Johann M.} and Saglam, {Ali S.} and Dilawar Singh and Ankur Sinha and Jacky Snoep and Hugh Sorby and Ryan Spangler and J{\"o}rn Starru{\ss} and Thomas, {Payton J.} and {Van Niekerk}, David and Daniel Weindl and Fengkai Zhang and Anna Zhukova and Goldberg, {Arthur P.} and Schaff, {James C.} and Blinov, {Michael L.} and Sauro, {Herbert M.} and Moraru, {Ion I.} and Karr, {Jonathan R.}",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

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doi = "10.1093/nar/gkac331",

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Shaikh, B, Smith, LP, Vasilescu, D, Marupilla, G, Wilson, M, Agmon, E, Agnew, H, Andrews, SS, Anwar, A, Beber, ME, Bergmann, FT, Brooks, D, Brusch, L, Calzone, L, Choi, K, Cooper, J, Detloff, J, Drawert, B, Dumontier, M, Ermentrout, GB, Faeder, JR, Freiburger, AP, Fröhlich, F, Funahashi, A, Garny, A, Gennari, JH, Gleeson, P, Goelzer, A, Haiman, Z, Hasenauer, J, Hellerstein, JL, Hermjakob, H, Hoops, S, Ison, JC, Jahn, D, Jakubowski, HV, Jordan, R, Kalaš, M, König, M, Liebermeister, W, Sheriff, RSM, Mandal, S, McDougal, R, Medley, JK, Mendes, P, Müller, R, Myers, CJ, Naldi, A, Nguyen, TVN, Nickerson, DP, Olivier, BG, Patoliya, D, Paulevé, L, Petzold, LR, Priya, A, Rampadarath, AK, Rohwer, JM, Saglam, AS, Singh, D, Sinha, A, Snoep, J, Sorby, H, Spangler, R, Starruß, J, Thomas, PJ, Van Niekerk, D, Weindl, D, Zhang, F, Zhukova, A, Goldberg, AP, Schaff, JC, Blinov, ML, Sauro, HM, Moraru, II & Karr, JR 2022, 'BioSimulators: a central registry of simulation engines and services for recommending specific tools', Nucleic acids research, vol. 50, no. W1, pp. W108-W114. https://doi.org/10.1093/nar/gkac331

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AU - Shaikh, Bilal

AU - Smith, Lucian P.

AU - Vasilescu, Dan

AU - Marupilla, Gnaneswara

AU - Wilson, Michael

AU - Agmon, Eran

AU - Agnew, Henry

AU - Andrews, Steven S.

AU - Anwar, Azraf

AU - Beber, Moritz E.

AU - Bergmann, Frank T.

AU - Brooks, David

AU - Brusch, Lutz

AU - Calzone, Laurence

AU - Choi, Kiri

AU - Cooper, Joshua

AU - Detloff, John

AU - Drawert, Brian

AU - Dumontier, Michel

AU - Ermentrout, G. Bard

AU - Faeder, James R.

AU - Freiburger, Andrew P.

AU - Fröhlich, Fabian

AU - Funahashi, Akira

AU - Garny, Alan

AU - Gennari, John H.

AU - Gleeson, Padraig

AU - Goelzer, Anne

AU - Haiman, Zachary

AU - Hasenauer, Jan

AU - Hellerstein, Joseph L.

AU - Hermjakob, Henning

AU - Hoops, Stefan

AU - Ison, Jon C.

AU - Jahn, Diego

AU - Jakubowski, Henry V.

AU - Jordan, Ryann

AU - Kalaš, Matúš

AU - König, Matthias

AU - Liebermeister, Wolfram

AU - Sheriff, Rahuman S.Malik

AU - Mandal, Synchon

AU - McDougal, Robert

AU - Medley, J. Kyle

AU - Mendes, Pedro

AU - Müller, Robert

AU - Myers, Chris J.

AU - Naldi, Aurelien

AU - Nguyen, Tung V.N.

AU - Nickerson, David P.

AU - Olivier, Brett G.

AU - Patoliya, Drashti

AU - Paulevé, Loïc

AU - Petzold, Linda R.

AU - Priya, Ankita

AU - Rampadarath, Anand K.

AU - Rohwer, Johann M.

AU - Saglam, Ali S.

AU - Singh, Dilawar

AU - Sinha, Ankur

AU - Snoep, Jacky

AU - Sorby, Hugh

AU - Spangler, Ryan

AU - Starruß, Jörn

AU - Thomas, Payton J.

AU - Van Niekerk, David

AU - Weindl, Daniel

AU - Zhang, Fengkai

AU - Zhukova, Anna

AU - Goldberg, Arthur P.

AU - Schaff, James C.

AU - Blinov, Michael L.

AU - Sauro, Herbert M.

AU - Moraru, Ion I.

AU - Karr, Jonathan R.

PY - 2022/7/5

Y1 - 2022/7/5

N2 - 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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BioSimulators: a central registry of simulation engines and services for recommending specific tools

Abstract

Bibliographical note

Funding

UN SDGs

Access to Document

Persistent URL (handle)

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