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A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

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DOI

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 πŸ’»

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 πŸ–₯️

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 βš–οΈ

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 πŸ§‘β€πŸ€β€πŸ§‘

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

πŸ”§

Akira Funahashi

πŸ”§

Alan Garny

πŸ€” πŸ”£

Aleksandar Jelenak

πŸ”§

Ali Sinan Saglam

πŸ”£

Andreas DrΓ€ger

πŸ”§

Ankita

πŸ”£

Ankur Sinha

πŸ”§

Anna Zhukova

πŸ”£

AnneGoelzer

πŸ”£

Arthur P Goldberg

πŸ€”

AurΓ©lien Naldi

πŸ”£ πŸ”§

Bilal Shaikh

πŸ’» πŸ“– πŸš‡

BioModels

πŸ”£

Brett Olivier

πŸ”§

Brian Drawert

πŸ”§

Brian simulator

πŸ”§

COPASI

πŸ”§

Center for Reproducible Biomedical Modeling

πŸ’΅ πŸ” πŸ“†

Ciaran Welsh

πŸ”§

Claudine Chaouiya

πŸ”£ πŸ”§

Dan Vasilescu

πŸ”§

Daniel Weindl

πŸ”§

David Brooks

πŸ”§

David Nickerson

πŸ€”

DeepaMahm

πŸ›

Diego

πŸ”§

Dilawar Singh

πŸ”§

Eduard Kerkhoven

πŸ”§

Eran Agmon

πŸ€”

Ermentrout

πŸ”§

Escher

πŸ”§

Fabian FrΓΆhlich

πŸ”§

Fengkai Zhang

πŸ”§

Frank Bergmann

πŸ€”

GINsim

πŸ”§

GMarupilla

πŸ’»

Helikar Lab Personal

πŸ”§

Herbert Sauro

πŸ€”

Hugh Sorby

πŸ”§

Idenfitiers.org

πŸ”£

Jan Hasenauer

πŸ”§

Jim Faeder

πŸ”§ πŸ”£

Jim Schaff

πŸ€”

Johann Rohwer

πŸ”§

John Detloff

πŸ’»

John Gennari

πŸ€” πŸ”§

John Readey

πŸ”§

John Sekar

πŸ€”

Jon Ison

πŸ”£

Jonathan Karr

πŸ’» πŸ“– 🎨

Joshua Cooper

πŸ”§

Jârn Starruß

πŸ”§

JΓΌrgen Pahle

πŸ”§

Karr whole-cell modeling lab

πŸ€”

Kyle Medley

πŸ”§ πŸ€”

LEMS

πŸ”§

LoΓ―c PaulevΓ©

πŸ”£ πŸ”§

Lucian Smith

πŸ€”

Lutz Brusch

πŸ”§

Manuel Bernal Llinares

πŸ”£

MarcDinh

πŸ”§

Matthias KΓΆnig

πŸ€”

MatΓΊΕ‘ KalaΕ‘

πŸ”£

Michael Blinov

πŸ€”

Michel Dumontier

πŸ”£

Mike Hucka

πŸ”§

Mike Wilson

πŸš‡

ModelDB

πŸ”£

Moritz E. Beber

πŸ”§

National Institute of Biomedical Imaging and Bioengineering

πŸ’΅

National Institutes of Health

πŸ’΅

National Science Foundation

πŸ’΅

NeuroML

πŸ”§

Neurosim lab

πŸ”§

OpenCOR

πŸ”§

PMR2 - the software behind the Auckland Physiome Repository

πŸ”£

Padraig Gleeson

πŸ”£ πŸ”§

Payton Thomas

πŸ”§

Pedro Mendes

πŸ”§

Pedro T. Monteiro

πŸ”§

PySCeS: The Python Simulator for Cellular Systems, provides a variety of tools for the analysis of cellular systems

πŸ”§

Raghul Kannan

πŸ”§

Rahuman Sheriff

πŸ”£

Rashika Rathi

πŸ”£

Ryan Spangler

πŸ€”

Ryann Jordan

πŸ”£

SBML Team

πŸ”§

SED-ML

πŸ”§

Sarah Keating

πŸ”§

Stefan Hoops

πŸ”§

Steve Andrews

πŸ”£ πŸ”§

StochSS

πŸ”§

SysBioINRAe

πŸ”§ πŸ”£

Systems Biology Lab, Vrije Universiteit Amsterdam

πŸ”§

Systems Biology Research Group

πŸ”£

The HDF Group

πŸ”§

The NEURON Simulator

πŸ”§

The home of CellML on Github

πŸ”§

Tommy Yu

πŸ”£

Tung Nguyen

πŸ”£

UW Sauro Lab

πŸ”§

Vega

πŸ”§

Veit SchwΓ€mmle

πŸ”£

Virtual Cell

πŸ”§ πŸ”£

Wolfram Liebermeister

πŸ”§

Yin Hoon Chew

πŸ€”

Zachary A. King

πŸ”§ πŸ”£

abulovic

πŸ”£

cjmyers

πŸ€”

dczielinski

πŸ”§

freiburgermsu

πŸ“–

jtyurkovich

πŸ”§

libsbmlsim

πŸ”§

moraru

πŸš‡ πŸ€”

obodeit

πŸ”§

openCOBRA

πŸ”§

ruleworld

πŸ”§ πŸ”£

yexilein

πŸ”§

z-haiman

πŸ”§

A key to the above emojis is available here.

Contributing to BioSimulations πŸ› οΈ

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

Funding πŸ’°

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].

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