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https://github.com/rseng/awesome-rseng

A curated list of GitHub organizations that primarily serve open source or academic software projects.
https://github.com/rseng/awesome-rseng

List: awesome-rseng

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A curated list of GitHub organizations that primarily serve open source or academic software projects.

Awesome Lists containing this project

README 

        


  


    

  


  


  





## Awesome Research Software Engineering [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome) [![https://good-labs.github.io/greater-good-affirmation/assets/images/badge.svg](https://good-labs.github.io/greater-good-affirmation/assets/images/badge.svg)](https://good-labs.github.io/greater-good-affirmation) [![Gitter](https://badges.gitter.im/rseng/community.svg)](https://gitter.im/rseng/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)



> A curated list of GitHub organizations that primarily serve open source or academic software projects.



If you want to get involved with science and research software engineering, this is a good place to start! If you want to use the GitHub action, [see rseng/good-first-issues](https://github.com/rseng/good-first-issues).



## Contents



 - [Overview](#overview)

 - [Astrophysics](#astrophysics)

 - [Environment](#environment)

 - [Genomics](#genomics)

 - [Geoscience](#geoscience)

 - [Health and Medicine](#health-and-medicine)

   - [Epidemiology](#epidemiology)

 - [High Performance Computing](#high-performance-computing)

 - [Institutions](#institutions)

   - [Academic Groups](#academic-groups)

   - [Academic Labs](#academic-labs)

   - [National Labs](#national-labs)

 - [Materials Science](#materials-science)

   - [Neutron Scattering](#neutron-scattering)

 - [Neuroscience](#neuroscience)

 - [Probabilistic Programming](#probabilistic-programming)

 - [Psychology](#psychology)

 - [Reproducible Science](#reproducible-science)

   - [Containers](#containers)

   - [Workflows](#workflows)

 - [Training](#training)

 - [Contributing](#contributing)



## Overview



If you are interested in research software engineering, and especially looking to

help with research software, this is a small, manually curated list of GitHub

organizations that have primarily this focus. The projects are organized by domain,

and then subtopics. Please feel free to suggest a new project, or update the organization.



## Astrophysics



 - [LSST](https://github.com/lsst) the legacy survey of space and time

 - [LSST Camera Data Handling](https://github.com/lsst-camera-dh/)



## Environment



 - [The National Capital Project](https://github.com/natcap): technology for people and nature, see [the website](https://naturalcapitalproject.stanford.edu/).



## Genomics



 - [The ENCODE Data Consortium](https://github.com/encode-dcc) or "Encode DCC" serving the Encode Data Portal.



## Geoscience



 - [Pangeo](https://github.com/pangeo-data): A community effort for big data geoscience



## Health and Medicine



### Epidemiology



 - [MRC Centre for Outbreak Analysis and Modelling](https://github.com/mrc-ide/): open source software for the [MRC centre for global infectious disease analysis](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis)

 - [VIMC](https://github.com/vimc/): open source code to support the [Vaccine Impact Modelling Consortium](https://vaccineimpact.org/).

 - [Reside IC](https://github.com/reside-ic/): Research Software for the Infectious Disease Epidemiology @ Imperial College [team](https://reside-ic.github.io/about/).



## High Performance Computing



 - [CEED](https://github.com/CEED): ECP Co-Design Center for Efficient Exascale Discretizations (CEED)

 - [spack](https://github.com/spack/) a flexible package manager for multiple versions, configurations, and compilers

 - [RADIUSS](https://software.llnl.gov/radiuss/): Rapid Application Development via an Institutional Universal Software Stack



## Institutions



### Academic Groups



- [Imperial College London](https://github.com/ImperialCollegeLondon/)



### Academic Labs



 - [Nolan Lab](https://github.com/nolanlab) at Stanford University focuses on signaling in the immune system and study of oncogenic process.

 - [Poldrack Lab](https://github.com/poldracklab) at Stanford University focuses on standard

   workflows for processing structural and functional neuroimaging (MRI) data.



### National Labs



 - [SLAC](https://github.com/slaclab) National Accelerator Laboratory

 - [LINAC Coherent Light Source](https://github.com/slac-lcls/) at SLAC for experiments with High Energy Physics, Materials Science, Biologists, etc.

 - [ORNL](https://github.com/ORNL/) Oak Ridge National Laboratory

 - [OLCF](https://github.com/OLCF/) Oak Ridge Leadership Computing Facility

 - [BNL](https://github.com/BrookhavenNationalLaboratory/) Brookhaven National Laboratory

 - [BNL-SDCC](https://github.com/bnl-sdcc/) Brookhaven National Laboratory Scientific Data and Computing Center

 - [NSLS-II](https://github.com/NSLS-II) National Synchrotron Light Source II at Brookhaven National Laboratory

 - [BNL-NPP](https://github.com/BNLNPPS) Brookhaven National Laboratory Nuclear and Particle Physics Software Group

 - [LLNL](https://github.com/LLNL) Lawrence Livermore National Laboratory (and its [Software Portal](https://software.llnl.gov))



## Materials Science



### Neutron Scattering



 - [Mantid Project](https://github.com/mantidproject) Framework for analysis and visualization of neutron scattering and muon spectroscopy data

 - [neutrons](https://github.com/neutrons) Neutron Scattering Softwares, mainly for [ORNL Facilities](https://neutrons.ornl.gov/)



## Neuroscience



 - [nipreps](https://github.com/nipreps) standard workflows for processing a wide

   variety of neuroimaging (MRI) data.

 - [nipy](https://github.com/nipy) utilities for working with neuroimaging (MRI) data



## Probabilistic Programming



 - [The Turing Language](https://github.com/TuringLang) Bayesian inference with probabilistic programming using the Julia language



## Psychology



 - [The Experiment Factory](https://github.com/expfactory) tools, containers, and web based experiments



## Reproducible Science



## Containers



 - [singularityhub](https://github.com/singularityhub/) open source tools to support Singularity containers.



## Workflows



 - [Snakemake](https://github.com/snakemake/) scientific workflow manager written in Python



## Training

 

 - [CarpenPi](https://github.com/CarpenPi) Running Carpentries Training on Raspberry Pis



## Contributing



Please don't hesitate to contribute a new link. To do so, check out the [CONTRIBUTING.md](.github/CONTRIBUTING.md) for details about how to contribute.



### Add Organization to the Awesome List

The awesome list here is intended for organizations.

You can edit the README.md file here and add your link in the correct spot. If 

a category is missing, please go ahead and add it, and make sure that all

additions are in alphabetical order. Then [open a pull request](https://www.github.com/rseng/awesome-opensource-rseng/issues). 



### Add Repository



This repository also serves a "Good First Issues" portal, primarily for specific

repos that belong to the organizations listed above. If you are interested in

adding a specific repository, add it to the [repos list](.github/repos.txt).

You can add comma separated tags that you want to use as categories or topics

to identify the repository. Here is an example:



```

https://github.com/singularityhub/sregistry containers,singularity

```



## License



[![Creative Commons License](http://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg)](https://creativecommons.org/publicdomain/zero/1.0/)