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

Research output: Contribution to journalResearch articleContributedpeer-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
  • Korea Institute for Advanced Study
  • 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
  • European Molecular Biology Laboratory
  • 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 languageEnglish
Article numberW1
Pages (from-to)108-114
Number of pages7
JournalNucleic acids research
Volume50
Issue numberW1
Publication statusPublished - 5 Jul 2022
Peer-reviewedYes

External IDs

Scopus 85134730260
dblp journals/nar/ShaikhSVMWAAAAB22

Keywords

Keywords

  • Morpheus

Library keywords