Oss projects by domain

We'd like to improve our outreach to non-CS majors in the sciences by finding open source projects in their disciplines. We plan to use this information both in our publicity and when we're looking for projects to help students contribute to. To that extent, we're asking both for short testimonials (for publicity) as well as insight on how accessible these projects are to newcomers.

= Instructions =

Please add information and testimonials wherever you see fit. If a discipline is missing, please add it. You can add the same project to multiple disciplines.

Please format disciplines in the following way:


 * Name of Discipline
 * Projects
 * OSS project that is used within this discipline. Make sure to leave a URL to the project website and if possible a brief description of the software.
 * Comments & Testimonials:
 * This project is poorly documented.
 * This project has a really active, friendly maintainer.
 * "This is a testimonial about the project. It's great, I use it all the time in my research!  I am totally okay with OpenHatch using my testimonial in outreach emails and similar materials."  (Optional attribution - name, position, url of person leaving the testimonial.)
 * Another project
 * Comments & Testimonials:
 * Comment
 * Testimonial
 * A project previously mentioned in another discipline: please see 'name of other discipline'
 * Resources
 * Links to places to find more info about projects in this discipline.

= Domains/Departments =


 * Aeronautics and astronautics
 * Projects
 * SunPy, a solar physics library actively maintained by NASA GSFC.
 * Comments & Testimonials:
 * MakerPlane, a project for building personal planes (article)
 * Comments & Testimonials:
 * Resources:
 * Portland State (open source) Aerospace Society: http://psas.pdx.edu/
 * NASA Open Source list at code.nasa.gov


 * Atmospheric sciences
 * Projects
 * CMAQ - EPA's development project: a suite of programs for conducting air quality model simulations
 * Comments & Testimonials:
 * GEMPAK - soon to be replaced with AWIPS II - a weather forecasting, display and analysis package, lead developer: National Weather Service
 * Comments & Testimonials:
 * OpenMadrigal - a database for accessing/archiving geospace data (does geospace == atmospheric science?)
 * Comments & Testimonials:
 * Resources
 * MIT's Haystack has some open projects
 * OpenRadar has radio-related oss projects
 * UCAR list


 * Astronomy
 * Projects
 * Java Mission-planning and Analysis for Remote Sensing (JMARS)
 * Comments & Testimonials:
 * Resources:
 * Wikipedia Article


 * Biochemistry
 * Projects
 * BioPython - a set of tools for biological computation written in Python
 * Comments & Testimonials:
 * BioPerl
 * Comments & Testimonials:
 * OpenBabel - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
 * Comments & Testimonials:
 * ImageJ
 * Comments & Testimonials:
 * R - a programming language for statistical analysis
 * Comments & Testimonials:
 * Resources


 * Biology
 * Projects
 * BioPython (see Biochemistry)
 * BioPerl (see Biochemistry)
 * ImageJ (see Biochemistry)
 * R (see Biochemistry)
 * Resources


 * Biomedical Engineering
 * Projects
 * BioSig - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 * Comments & Testimonials:
 * OpenSim - tool for modeling and simulation of movement
 * Comments & Testimonials:
 * Resources


 * Chemistry
 * Projects
 * OpenBabel (see Biochemistry)
 * Resources:
 * Wikipedia article


 * Economics
 * Projects
 * R (see Biochemistry)
 * Resources:


 * Geosciences
 * Projects
 * GeoForge
 * Comments & Testimonials:
 * Resources:
 * Wikipedia article


 * Linguistics
 * Projects
 * Python Natural Language Toolkit
 * Comments & Testimonials:
 * Joshua Machine Translation Toolkit
 * Comments & Testimonials:
 * Kura, a multi-user open source linguistic database
 * Comments & Testimonials:
 * Apertium open source machine translation
 * Comments & Testimonials:
 * Praat open source tool used to annotate speech / phonetics
 * Comments & Testimonials:
 * TextBlob Natural Language Processing tool
 * Comments & Testimonials:
 * DISSECT Distributional Semantics toolkit
 * Comments & Testimonials:


 * Resources:
 * LINGUIST email discussion list and software index
 * List of open source statistical NLP tools
 * Sourceforge.net list of language-related software


 * Materials science
 * Projects
 * ESPRESSO - a software package for performing and analyzing simulations of “coarse-grained” models as used in soft-matter research
 * Comments & Testimonials:
 * Resources
 * 2008 discussion of open source in materials science


 * Mathematics
 * Projects
 * Sage Math - a popular software system combining many projects into a common Python-based interface
 * Comments & Testimonials:
 * GAP - a system for computational discrete algebra
 * Comments & Testimonials:
 * CoCoA - a system for computations in commutative algebra
 * Comments & Testimonials:
 * Resources
 * Wikipedia article
 * Another Wiki article
 * a list from MathOverflow


 * Neuroscience
 * Projects
 * NeuroDebian - a turnkey Linux distribution with major open source neuroimaging packages included
 * Comments & Testimonials:
 * Neurosynth - an online platform to perform meta-analyses on neuroimaging studies
 * Comments & Testimonials:
 * AFNI - software for performing neuroimaging analyses maintained by the NIH
 * Comments & Testimonials:
 * SPM - software for doing statistical parametric mapping analysis
 * Comments & Testimonials:
 * ANTs - software to put individual fMRI scans in a common space that can be compared across subjects
 * Comments & Testimonials:
 * Nipype - a common Python interface to a variety of neuroimaging packages
 * Comments & Testimonials:
 * Nibabel - a Python package to load in neuroimaging data files
 * Comments & Testimonials:
 * C-PAC - a Python package to configure resting state fMRI analyses
 * Comments & Testimonials:
 * Octave - an open source version of Matlab; many Matlabpbased neuroimaging packages could work with Octave with some extra development
 * Comments & Testimonials:
 * Backyard Brains
 * Comments & Testimonials:
 * PsychoPy - a set of tools for doing stimulus presentation and capturing behavioral data
 * Comments & Testimonials:
 * Very friendly, active maintainers but difficult setup process, especially for Windows.
 * PyXNAT - allows Python to interface with a popular neuroimaging data management tool
 * Comments & Testimonials:
 * PyOpenWorm - Python interface to fetch C. elegans data.
 * Comments & Testimonials:
 * R (see Biochemistry)
 * BioSig (see Biomedical Engineering)
 * Resources:
 * List of tools
 * another list of tools


 * Nuclear Engineering
 * Projects
 * LAMMPS - a molecular dynamics library that can be used to model parallel atomic/subatomic processes at large scale, lead by Sandia National Laboratories
 * Comments & Testimonials:
 * OpenGeiger - an open source, open hardware Geiger Counter
 * Comments & Testimonials:
 * Resources
 * Article on OSS responses to Fukushima


 * Physics
 * Projects
 * R (see Biochemistry)
 * Octave (see Neuroscience)
 * Sage Math (see Physics)
 * Resources:
 * Wikipedia Article


 * Political science
 * Projects
 * Coding Analysis Toolkit (CAT) - a suite of tools for analysis of text datasets
 * Comments & Testimonials:
 * | Civic Commons - a website for sharing government tools
 * Comments & Testimonials:
 * Seems to be abandoned by its maintainers.
 * R (see Biochemistry)
 * Resources
 * A number of | these government/civic projects might be applicable, though there are some proprietary projects mixed in. The site itself is an open source project, though an abandoned one.


 * Psychology
 * Projects
 * BioSig (see Biomedical Engineering)
 * PsychoPy (see Neuroscience)
 * R (see Biochemistry)
 * Resources:
 * List of tools


 * Statistics
 * Projects
 * NumPy
 * Comments & Testimonials:
 * SciPy
 * Comments & Testimonials:
 * R (see Biochemistry)
 * Resources:
 * Wikipedia article