More comprehensive and more predictive models have the potential to advance biology, bioengineering, and medicine. Building more predictive models will likely require the collaborative efforts of many investigators. This requires teams to be able to share and reuse model components and simulations. Despite extensive efforts to develop standards such as COMBINE/OMEX, SBML, and SED-ML, it remains difficult to reuse many models and simulations. One challenge to reusing models and simulations is the diverse array of incompatible modeling formats and simulation tools.
This package provides three tools which address this challenge:
- BioSimulators is a registry of containerized simulation tools that provide consistent interfaces. BioSimulators makes it easier to find and run simulations.
- runBioSimulations is a simple web application for using the BioSimulators containers to run simulations. This tool makes it easy to run a broad range of simulations without having to install any software.
- BioSimulations is a platform for sharing and running modeling studies. BioSimulations provides a central place for investigators to exchange studies. BioSimulations uses the BioSimulators simulation tools, and builds on the functionality of runBioSimulations.
This package provides the code for the BioSimulations, runBioSimulations, and BioSimulations websites, as well as the code for the backend services for all three applications. The package is implemented in TypeScript using Angular, NestJS, MongoDB, and Mongoose.
Please use the hosted versions of BioSimulations, runBioSimulations, and BioSimulators at https://biosimulations.org, https://run.biosimulations.org, and https://biosimulators.org.
Tutorials, help and information can be found at https://docs.biosimulations.org
We welcome contributions to BioSimulations, runBioSimulations, and BioSimulations! Please see the developer guide for information about how to get started including how to install this package and how to run BioSimulations, runBioSimulations, and BioSimulators locally.
This package is released under the MIT license. This package uses a number of open-source third-party packages. Their licenses are summarized in Dependencies.
If you find this project interesting or useful, please give our repo a ⭐ and share with others that may benefit. If you use the code and tools in this repository as a part of an academic work, please cite us using the following bibtex entry.
@software{Shaikh_BioSimulations,
author = {Shaikh, Bilal and Marupilla, Gnaneswara and Wilson, Mike and Michael, Blinov L. and Moraru, Ion I. and Karr, Jonathan R.},
doi = {10.5281/zenodo.5057108},
license = {MIT},
title = {{BioSimulations}},
url = {https://github.com/biosimulations/biosimulations}
}
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York and the Center for Cell Analysis and Modeling at UConn Health as part of the Center for Reproducible Biomodeling Modeling.
Numerous individuals and groups have contributed to BioSimulations, including:
A key to the above emojis is available here.
We enthusiastically welcome contributions to BioSimulations! Please see the guide to contributing and the developer's code of conduct.
This package was developed with support from the National Institute for Bioimaging and Bioengineering (award P41EB023912).
We welcome any comments, questions, or discussion about the project. Please create a discussion or question in our discussion forum.
To privately contact the BioSimulations team, you can send us an email at [email protected].