Awesome

Awesome Research Software Engineering

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
• Astrophysics
• Environment
• Genomics
• Geoscience
• Health and Medicine
  • Epidemiology
• High Performance Computing
• Institutions
  • Academic Groups
  • Academic Labs
  • National Labs
• Materials Science
  • Neutron Scattering
• Neuroscience
• Probabilistic Programming
• Psychology
• Reproducible Science
  • Containers
  • Workflows
• Training
• 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 the legacy survey of space and time
• LSST Camera Data Handling

Environment

• The National Capital Project: technology for people and nature, see the website.

Genomics

• The ENCODE Data Consortium or "Encode DCC" serving the Encode Data Portal.

Geoscience

• Pangeo: A community effort for big data geoscience

Health and Medicine

Epidemiology

• MRC Centre for Outbreak Analysis and Modelling: open source software for the MRC centre for global infectious disease analysis
• VIMC: open source code to support the Vaccine Impact Modelling Consortium.
• Reside IC: Research Software for the Infectious Disease Epidemiology @ Imperial College team.

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

• Imperial College London

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

• Mantid Project Framework for analysis and visualization of neutron scattering and muon spectroscopy data
• neutrons Neutron Scattering Softwares, mainly for ORNL Facilities

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

• The Experiment Factory tools, containers, and web based experiments

Reproducible Science

Containers

• singularityhub open source tools to support Singularity 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