emcee - seriously kick-ass MCMC… it's big in astrophysics. It has been used to study planets like our own Earth, binary stars, the Milky Way, and even astrophotographers.

In 2012 researchers at CERN discovered the Higgs Boson, the elementary particle responsible for particles having mass. One of the experiments that made this discovery, CMS, is a collaboration of more than 3,800 people from 42 different countried. cmssw is the software that powers the data-management pipeline of CMS and was built by 200 different people on GitHub.

Astropy is a community effort in the astrophysics community to develop a single core package for Astronomy in Python. Three years after the first commit more than 75 researchers have contributed over 1600 pull requests making this one of the most heavily used open source projects in astronomy.

The iPlant Collaborative are helping to solve some of the most important problems in the life sciences by building an open source platform to helps researchers access high-performance computing resources, store data and analyze their data. The iPlant Collaborative is open source and everything they do is here on GitHub.

Portland State Aerospace Society are building ultra-low-cost, open source rockets that feature some of the most sophisticated amateur rocket avionics systems available. Learn more about open source rocket science on the PSAS GitHub organization page 🚀

IPython is an environment for interactive computing that can support any programming language. IPython is can be used to analyze datasets, write books and even solve hard XKCD-inspired regex challenges.

khmer is a high-performance library built by the GED lab at Michigan State University and is used for analyzing DNA sequences.

rOpenSci build software in R to make the accessing, visualizing and sharing research data more straightforward. More than 100 different packages are available on GitHub, this particular package is an interface to the API of the open-access publisher PLOS.

PIConGPU is a fully relativistic, many GPGPU, 3D3V particle-in-cell (PIC) program, used to describe the dynamics of a plasma by computing its motion of electrons and ions.

High-performance C++ multibody dynamics/physics library for simulating articulated biomechanical and mechanical systems like vehicles, robots, and the human skeleton.

A computer algebra system written in pure Python.

Resources to get started with Software Carpentry Bootcamps.