Article

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

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https://scholar.colorado.edu/concern/articles/6d56zz40z
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.

Creator
Date Issued
  • 2022
Academic Affiliation
Journal Title
Journal Volume
  • 50
Ultima modifica
  • 2025-02-15
Resource Type
Dichiarazione dei diritti
License
DOI
ISSN
  • 1362-4962
Language

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