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Awesome Research Software Engineering Awesome https://good-labs.github.io/greater-good-affirmation/assets/images/badge.svg Gitter

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.

Contents

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

Environment

Genomics

Geoscience

  • Pangeo: A community effort for big data geoscience

Health and Medicine

Epidemiology

High Performance Computing

  • CEED: ECP Co-Design Center for Efficient Exascale Discretizations (CEED)
  • spack a flexible package manager for multiple versions, configurations, and compilers
  • RADIUSS: Rapid Application Development via an Institutional Universal Software Stack

Institutions

Academic Groups

Academic Labs

  • Nolan Lab at Stanford University focuses on signaling in the immune system and study of oncogenic process.
  • Poldrack Lab at Stanford University focuses on standard workflows for processing structural and functional neuroimaging (MRI) data.

National Labs

  • SLAC National Accelerator Laboratory
  • LINAC Coherent Light Source at SLAC for experiments with High Energy Physics, Materials Science, Biologists, etc.
  • ORNL Oak Ridge National Laboratory
  • OLCF Oak Ridge Leadership Computing Facility
  • BNL Brookhaven National Laboratory
  • BNL-SDCC Brookhaven National Laboratory Scientific Data and Computing Center
  • NSLS-II National Synchrotron Light Source II at Brookhaven National Laboratory
  • BNL-NPP Brookhaven National Laboratory Nuclear and Particle Physics Software Group
  • LLNL Lawrence Livermore National Laboratory (and its Software Portal)

Materials Science

Neutron Scattering

Neuroscience

  • nipreps standard workflows for processing a wide variety of neuroimaging (MRI) data.
  • nipy utilities for working with neuroimaging (MRI) data

Probabilistic Programming

  • The Turing Language Bayesian inference with probabilistic programming using the Julia language

Psychology

Reproducible Science

Containers

Workflows

  • Snakemake scientific workflow manager written in Python

Training

  • 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 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.

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. 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

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

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