BioSimulations 🧬

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.

Getting started ▶️

Users 💻

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

Developers 🖥️

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.

License ⚖️

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.

Show your support 🤝

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}
}

Contributors 🧑‍🤝‍🧑

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:

AMICI 🔧	Akira Funahashi 🔧	Alan Garny 🤔 🔣	Aleksandar Jelenak 🔧	Ali Sinan Saglam 🔣	Andreas Dräger 🔧	Ankita 🔣
Ankur Sinha 🔧	Anna Zhukova 🔣	AnneGoelzer 🔣	Arthur P Goldberg 🤔	Aurélien Naldi 🔣 🔧	Bilal Shaikh 💻 📖 🚇	BioModels 🔣
Brett Olivier 🔧	Brian Drawert 🔧	Brian simulator 🔧	COPASI 🔧	Center for Reproducible Biomedical Modeling 💵 🔍 📆	Ciaran Welsh 🔧	Claudine Chaouiya 🔣 🔧
Dan Vasilescu 🔧	Daniel Weindl 🔧	David Brooks 🔧	David Nickerson 🤔	DeepaMahm 🐛	Diego 🔧	Dilawar Singh 🔧
Eduard Kerkhoven 🔧	Eran Agmon 🤔	Ermentrout 🔧	Escher 🔧	Fabian Fröhlich 🔧	Fengkai Zhang 🔧	Frank Bergmann 🤔
GINsim 🔧	GMarupilla 💻	Helikar Lab Personal 🔧	Herbert Sauro 🤔	Hugh Sorby 🔧	Idenfitiers.org 🔣	Jan Hasenauer 🔧
Jim Faeder 🔧 🔣	Jim Schaff 🤔	Johann Rohwer 🔧	John Detloff 💻	John Gennari 🤔 🔧	John Readey 🔧	John Sekar 🤔
Jon Ison 🔣	Jonathan Karr 💻 📖 🎨	Joshua Cooper 🔧	Jörn Starruß 🔧	Jürgen Pahle 🔧	Karr whole-cell modeling lab 🤔	Kyle Medley 🔧 🤔
LEMS 🔧	Loïc Paulevé 🔣 🔧	Lucian Smith 🤔	Lutz Brusch 🔧	Manuel Bernal Llinares 🔣	MarcDinh 🔧	Matthias König 🤔
Matúš Kalaš 🔣	Michael Blinov 🤔	Michel Dumontier 🔣	Mike Hucka 🔧	Mike Wilson 🚇	ModelDB 🔣	Moritz E. Beber 🔧
National Institute of Biomedical Imaging and Bioengineering 💵	National Institutes of Health 💵	National Science Foundation 💵	NeuroML 🔧	Neurosim lab 🔧	OpenCOR 🔧	PMR2 - the software behind the Auckland Physiome Repository 🔣
Padraig Gleeson 🔣 🔧	Payton Thomas 🔧	Pedro Mendes 🔧	Pedro T. Monteiro 🔧	PySCeS: The Python Simulator for Cellular Systems, provides a variety of tools for the analysis of cellular systems 🔧	Raghul Kannan 🔧	Rahuman Sheriff 🔣
Rashika Rathi 🔣	Ryan Spangler 🤔	Ryann Jordan 🔣	SBML Team 🔧	SED-ML 🔧	Sarah Keating 🔧	Stefan Hoops 🔧
Steve Andrews 🔣 🔧	StochSS 🔧	SysBioINRAe 🔧 🔣	Systems Biology Lab, Vrije Universiteit Amsterdam 🔧	Systems Biology Research Group 🔣	The HDF Group 🔧	The NEURON Simulator 🔧
The home of CellML on Github 🔧	Tommy Yu 🔣	Tung Nguyen 🔣	UW Sauro Lab 🔧	Vega 🔧	Veit Schwämmle 🔣	Virtual Cell 🔧 🔣
Wolfram Liebermeister 🔧	Yin Hoon Chew 🤔	Zachary A. King 🔧 🔣	abulovic 🔣	cjmyers 🤔	dczielinski 🔧	freiburgermsu 📖
jtyurkovich 🔧	libsbmlsim 🔧	moraru 🚇 🤔	obodeit 🔧	openCOBRA 🔧	ruleworld 🔧 🔣	yexilein 🔧
z-haiman 🔧

A key to the above emojis is available here.

Contributing to BioSimulations 🛠️

We enthusiastically welcome contributions to BioSimulations! Please see the guide to contributing and the developer's code of conduct.

Funding 💰

This package was developed with support from the National Institute for Bioimaging and Bioengineering (award P41EB023912).

Questions and comments ❓

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].