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

B. Shaikh; L.P. Smith; D. Vasilescu; G. Marupilla; M. Wilson; E. Agmon; H. Agnew; S.S. Andrews; A. Anwar; M.E. Beber; F.T. Bergmann; D. Brooks; L. Brusch; L. Calzone; K. Choi; J. Cooper; J. Detloff; B. Drawert; M. Dumontier; G.B. Ermentrout; J.R. Faeder; A.P. Freiburger; F. Frohlich; A. Funahashi; A. Garny; J.H. Gennari; P. Gleeson; A. Goelzer; Z. Haiman; J. Hasenauer; J.L. Hellerstein; H. Hermjakob; S. Hoops; J.C. Ison; D. Jahn; H.V. Jakubowski; R. Jordan; M. Kalas; M. Konig; W. Liebermeister; R.S.M. Sheriff; S. Mandal; R. McDougal; J.K. Medley; P. Mendes; R. Muller; C.J. Myers; A. Naldi; T.V.N. Nguyen; D.P. Nickerson; Jonathon R. Karr

doi:10.1093/nar/gkac331

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

B. Shaikh, L.P. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S.S. Andrews, A. Anwar, M.E. Beber, F.T. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, J. Cooper, J. Detloff, B. Drawert, M. Dumontier, G.B. ErmentroutJ.R. Faeder, A.P. Freiburger, F. Frohlich, A. Funahashi, A. Garny, J.H. Gennari, P. Gleeson, A. Goelzer, Z. Haiman, J. Hasenauer, J.L. Hellerstein, H. Hermjakob, S. Hoops, J.C. Ison, D. Jahn, H.V. Jakubowski, R. Jordan, M. Kalas, M. Konig, W. Liebermeister, R.S.M. Sheriff, S. Mandal, R. McDougal, J.K. Medley, P. Mendes, R. Muller, C.J. Myers, A. Naldi, T.V.N. Nguyen, D.P. Nickerson, Jonathon R. Karr^*

^*Corresponding author for this work

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.[GRAPHICS].

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

Keywords

FORMAT

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10.1093/nar/gkac331Licence: CC BY

Cite this

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.[GRAPHICS].",

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author = "B. Shaikh and L.P. Smith and D. Vasilescu and G. Marupilla and M. Wilson and E. Agmon and H. Agnew and S.S. Andrews and A. Anwar and M.E. Beber and F.T. Bergmann and D. Brooks and L. Brusch and L. Calzone and K. Choi and J. Cooper and J. Detloff and B. Drawert and M. Dumontier and G.B. Ermentrout and J.R. Faeder and A.P. Freiburger and F. Frohlich and A. Funahashi and A. Garny and J.H. Gennari and P. Gleeson and A. Goelzer and Z. Haiman and J. Hasenauer and J.L. Hellerstein and H. Hermjakob and S. Hoops and J.C. Ison and D. Jahn and H.V. Jakubowski and R. Jordan and M. Kalas and M. Konig and W. Liebermeister and R.S.M. Sheriff and S. Mandal and R. McDougal and J.K. Medley and P. Mendes and R. Muller and C.J. Myers and A. Naldi and T.V.N. Nguyen and D.P. Nickerson and Karr, {Jonathon R.}",

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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, Frohlich, 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, Kalas, M, Konig, M, Liebermeister, W, Sheriff, RSM, Mandal, S, McDougal, R, Medley, JK, Mendes, P, Muller, R, Myers, CJ, Naldi, A, Nguyen, TVN, Nickerson, DP & 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

TY - JOUR

T1 - BioSimulators: a central registry of simulation engines and services for recommending specific tools

AU - Shaikh, B.

AU - Smith, L.P.

AU - Vasilescu, D.

AU - Marupilla, G.

AU - Wilson, M.

AU - Agmon, E.

AU - Agnew, H.

AU - Andrews, S.S.

AU - Anwar, A.

AU - Beber, M.E.

AU - Bergmann, F.T.

AU - Brooks, D.

AU - Brusch, L.

AU - Calzone, L.

AU - Choi, K.

AU - Cooper, J.

AU - Detloff, J.

AU - Drawert, B.

AU - Dumontier, M.

AU - Ermentrout, G.B.

AU - Faeder, J.R.

AU - Freiburger, A.P.

AU - Frohlich, F.

AU - Funahashi, A.

AU - Garny, A.

AU - Gennari, J.H.

AU - Gleeson, P.

AU - Goelzer, A.

AU - Haiman, Z.

AU - Hasenauer, J.

AU - Hellerstein, J.L.

AU - Hermjakob, H.

AU - Hoops, S.

AU - Ison, J.C.

AU - Jahn, D.

AU - Jakubowski, H.V.

AU - Jordan, R.

AU - Kalas, M.

AU - Konig, M.

AU - Liebermeister, W.

AU - Sheriff, R.S.M.

AU - Mandal, S.

AU - McDougal, R.

AU - Medley, J.K.

AU - Mendes, P.

AU - Muller, R.

AU - Myers, C.J.

AU - Naldi, A.

AU - Nguyen, T.V.N.

AU - Nickerson, D.P.

AU - Karr, Jonathon 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.[GRAPHICS].

AB - 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.[GRAPHICS].

KW - FORMAT

U2 - 10.1093/nar/gkac331

DO - 10.1093/nar/gkac331

M3 - Article

C2 - 35524558

SN - 0305-1048

VL - 50

SP - W108-W114

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - W1

ER -