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BioSimulators: a central registry of simulation engines and services for recommending specific tools
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 too...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Oxford University Press
2022
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252793/ https://www.ncbi.nlm.nih.gov/pubmed/35524558 http://dx.doi.org/10.1093/nar/gkac331 |
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| author | Shaikh, Bilal Smith, Lucian P Vasilescu, Dan Marupilla, Gnaneswara Wilson, Michael Agmon, Eran Agnew, Henry Andrews, Steven S Anwar, Azraf Beber, Moritz E Bergmann, Frank T Brooks, David Brusch, Lutz Calzone, Laurence Choi, Kiri Cooper, Joshua Detloff, John Drawert, Brian Dumontier, Michel Ermentrout, G Bard Faeder, James R Freiburger, Andrew P Fröhlich, Fabian Funahashi, Akira Garny, Alan Gennari, John H Gleeson, Padraig Goelzer, Anne Haiman, Zachary Hasenauer, Jan Hellerstein, Joseph L Hermjakob, Henning Hoops, Stefan Ison, Jon C Jahn, Diego Jakubowski, Henry V Jordan, Ryann Kalaš, Matúš König, Matthias Liebermeister, Wolfram Sheriff, Rahuman S Malik Mandal, Synchon McDougal, Robert Medley, J Kyle Mendes, Pedro Müller, Robert Myers, Chris J Naldi, Aurelien Nguyen, Tung V N Nickerson, David P Olivier, Brett G Patoliya, Drashti Paulevé, Loïc Petzold, Linda R Priya, Ankita Rampadarath, Anand K Rohwer, Johann M Saglam, Ali S Singh, Dilawar Sinha, Ankur Snoep, Jacky Sorby, Hugh Spangler, Ryan Starruß, Jörn Thomas, Payton J van Niekerk, David Weindl, Daniel Zhang, Fengkai Zhukova, Anna Goldberg, Arthur P Schaff, James C Blinov, Michael L Sauro, Herbert M Moraru, Ion I Karr, Jonathan R |
| author_facet | Shaikh, Bilal Smith, Lucian P Vasilescu, Dan Marupilla, Gnaneswara Wilson, Michael Agmon, Eran Agnew, Henry Andrews, Steven S Anwar, Azraf Beber, Moritz E Bergmann, Frank T Brooks, David Brusch, Lutz Calzone, Laurence Choi, Kiri Cooper, Joshua Detloff, John Drawert, Brian Dumontier, Michel Ermentrout, G Bard Faeder, James R Freiburger, Andrew P Fröhlich, Fabian Funahashi, Akira Garny, Alan Gennari, John H Gleeson, Padraig Goelzer, Anne Haiman, Zachary Hasenauer, Jan Hellerstein, Joseph L Hermjakob, Henning Hoops, Stefan Ison, Jon C Jahn, Diego Jakubowski, Henry V Jordan, Ryann Kalaš, Matúš König, Matthias Liebermeister, Wolfram Sheriff, Rahuman S Malik Mandal, Synchon McDougal, Robert Medley, J Kyle Mendes, Pedro Müller, Robert Myers, Chris J Naldi, Aurelien Nguyen, Tung V N Nickerson, David P Olivier, Brett G Patoliya, Drashti Paulevé, Loïc Petzold, Linda R Priya, Ankita Rampadarath, Anand K Rohwer, Johann M Saglam, Ali S Singh, Dilawar Sinha, Ankur Snoep, Jacky Sorby, Hugh Spangler, Ryan Starruß, Jörn Thomas, Payton J van Niekerk, David Weindl, Daniel Zhang, Fengkai Zhukova, Anna Goldberg, Arthur P Schaff, James C Blinov, Michael L Sauro, Herbert M Moraru, Ion I Karr, Jonathan R |
| author_sort | Shaikh, Bilal |
| collection | PubMed |
| 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 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. |
| format | Online Article Text |
| id | pubmed-9252793 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2022 |
| publisher | Oxford University Press |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-92527932022-07-05 BioSimulators: a central registry of simulation engines and services for recommending specific tools Shaikh, Bilal Smith, Lucian P Vasilescu, Dan Marupilla, Gnaneswara Wilson, Michael Agmon, Eran Agnew, Henry Andrews, Steven S Anwar, Azraf Beber, Moritz E Bergmann, Frank T Brooks, David Brusch, Lutz Calzone, Laurence Choi, Kiri Cooper, Joshua Detloff, John Drawert, Brian Dumontier, Michel Ermentrout, G Bard Faeder, James R Freiburger, Andrew P Fröhlich, Fabian Funahashi, Akira Garny, Alan Gennari, John H Gleeson, Padraig Goelzer, Anne Haiman, Zachary Hasenauer, Jan Hellerstein, Joseph L Hermjakob, Henning Hoops, Stefan Ison, Jon C Jahn, Diego Jakubowski, Henry V Jordan, Ryann Kalaš, Matúš König, Matthias Liebermeister, Wolfram Sheriff, Rahuman S Malik Mandal, Synchon McDougal, Robert Medley, J Kyle Mendes, Pedro Müller, Robert Myers, Chris J Naldi, Aurelien Nguyen, Tung V N Nickerson, David P Olivier, Brett G Patoliya, Drashti Paulevé, Loïc Petzold, Linda R Priya, Ankita Rampadarath, Anand K Rohwer, Johann M Saglam, Ali S Singh, Dilawar Sinha, Ankur Snoep, Jacky Sorby, Hugh Spangler, Ryan Starruß, Jörn Thomas, Payton J van Niekerk, David Weindl, Daniel Zhang, Fengkai Zhukova, Anna Goldberg, Arthur P Schaff, James C Blinov, Michael L Sauro, Herbert M Moraru, Ion I Karr, Jonathan R Nucleic Acids Res Web Server Issue 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. Oxford University Press 2022-05-07 /pmc/articles/PMC9252793/ /pubmed/35524558 http://dx.doi.org/10.1093/nar/gkac331 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| spellingShingle | Web Server Issue Shaikh, Bilal Smith, Lucian P Vasilescu, Dan Marupilla, Gnaneswara Wilson, Michael Agmon, Eran Agnew, Henry Andrews, Steven S Anwar, Azraf Beber, Moritz E Bergmann, Frank T Brooks, David Brusch, Lutz Calzone, Laurence Choi, Kiri Cooper, Joshua Detloff, John Drawert, Brian Dumontier, Michel Ermentrout, G Bard Faeder, James R Freiburger, Andrew P Fröhlich, Fabian Funahashi, Akira Garny, Alan Gennari, John H Gleeson, Padraig Goelzer, Anne Haiman, Zachary Hasenauer, Jan Hellerstein, Joseph L Hermjakob, Henning Hoops, Stefan Ison, Jon C Jahn, Diego Jakubowski, Henry V Jordan, Ryann Kalaš, Matúš König, Matthias Liebermeister, Wolfram Sheriff, Rahuman S Malik Mandal, Synchon McDougal, Robert Medley, J Kyle Mendes, Pedro Müller, Robert Myers, Chris J Naldi, Aurelien Nguyen, Tung V N Nickerson, David P Olivier, Brett G Patoliya, Drashti Paulevé, Loïc Petzold, Linda R Priya, Ankita Rampadarath, Anand K Rohwer, Johann M Saglam, Ali S Singh, Dilawar Sinha, Ankur Snoep, Jacky Sorby, Hugh Spangler, Ryan Starruß, Jörn Thomas, Payton J van Niekerk, David Weindl, Daniel Zhang, Fengkai Zhukova, Anna Goldberg, Arthur P Schaff, James C Blinov, Michael L Sauro, Herbert M Moraru, Ion I Karr, Jonathan R BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title | BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title_full | BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title_fullStr | BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title_full_unstemmed | BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title_short | BioSimulators: a central registry of simulation engines and services for recommending specific tools |
| title_sort | biosimulators: a central registry of simulation engines and services for recommending specific tools |
| topic | Web Server Issue |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252793/ https://www.ncbi.nlm.nih.gov/pubmed/35524558 http://dx.doi.org/10.1093/nar/gkac331 |
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