BioSimulators: a central registry of simulation engines and services for recommending specific tools
Research output: Contribution to journal › Research article › Contributed › peer-review
Contributors
- Washington University St. Louis
- University of Connecticut
- Stanford University
- LibreTexts
- New York University
- Unseen Bio ApS
- University Hospital Heidelberg
- The University of Auckland
- Institut Curie
- North Carolina State University
- Independent University, Bangladesh
- Maastricht University
- University of Pittsburgh
- Victoria University
- Keio University
- Queen Mary University of London
- Université Paris-Saclay
- University of California at San Francisco
- University of Bonn
- Virginia State University
- Université de Bordeaux
- College of Saint Benedict and Saint John's University
- University of Bergen
- Humboldt University of Berlin
- Yale University
- Autodesk Inc
- University of Colorado Boulder
- INRIA Saclay Centre
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.
Details
Original language | English |
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Article number | W1 |
Pages (from-to) | 108-114 |
Number of pages | 7 |
Journal | Nucleic acids research |
Volume | 50 |
Issue number | W1 |
Publication status | Published - 5 Jul 2022 |
Peer-reviewed | Yes |
External IDs
Scopus | 85134730260 |
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dblp | journals/nar/ShaikhSVMWAAAAB22 |
ORCID | /0000-0003-3649-2433/work/141544957 |
ORCID | /0000-0003-0137-5106/work/142244259 |
ORCID | /0000-0001-6774-5507/work/142252986 |
Keywords
Keywords
- Morpheus