Open Science Projects and Organizations

Please feel free to add organizations and projects to this list. If an org or project can be listed under multiple headings, please pick one heading for the main entry, and add a link to that entry under the other headings.

Required fields for an entry are name and link to website (or other long-lasting web presence). Optional but encouraged fields include: short description, social media links, contact info, related tags.

=Open Science Conferences, Meetups, and other Community Events=

Cross-discipline

 * Open Science Code Sprint 2015 - March 7-8, 2015

Discipline-specific
Please make sub-headings for your discipline as needed.

Neuroscience

 * Brainhack - next Hackathon: June 12-14, 2015 in Honolulu, Hawaii
 * CodeNeuro - next Hackathon: April 10, 2015 in NYC

=Open Source Scientific Software Projects=

Cross-discipline

 * Interdisciplinary Programming - a website to connect software developers and scientists (possibly inactive)
 * Alpha Research Base - another website to connect open source developers and scientists
 * Solvers.io - yet another website to connect open source developers and scientists
 * ImageJ
 * R - a programming language for statistical analysis
 * NumPy
 * SciPy
 * Julia
 * Octave

Discipline-specific
Please make sub-headings for your discipline as needed.

Aeronautics and astronautics

 * SunPy, a solar physics library actively maintained by NASA GSFC.
 * MakerPlane, a project for building personal planes (article)

Atmospheric sciences

 * CMAQ - EPA's development project: a suite of programs for conducting air quality model simulations
 * GEMPAK - soon to be replaced with AWIPS II - a weather forecasting, display and analysis package, lead developer: National Weather Service
 * OpenMadrigal - a database for accessing/archiving geospace data (does geospace == atmospheric science?)

Astronomy

 * Java Mission-planning and Analysis for Remote Sensing (JMARS)

Biochemistry

 * BioPython - a set of tools for biological computation written in Python
 * BioPerl
 * OpenBabel - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas

Biology

 * Synbiota - synthetic biology development platform

Biomedical Engineering

 * BioSig - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 * OpenSim - tool for modeling and simulation of movement

Geography

 * Roadright - a tool for modeling road maintenance

Geosciences

 * GeoForge

Linguistics

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

Materials Science

 * ESPRESSO - a software package for performing and analyzing simulations of “coarse-grained” models as used in soft-matter research

Mathematics

 * Sage Math - a popular software system combining many projects into a common Python-based interface
 * GAP - a system for computational discrete algebra
 * CoCoA - a system for computations in commutative algebra

Neuroscience

 * NeuroDebian - a turnkey Linux distribution with major open source neuroimaging packages included
 * Neurosynth - an online platform to perform meta-analyses on neuroimaging studies
 * Neurostars - a Q&A site in the style of StackOverflow but for neuroinformatics
 * AFNI - software for performing neuroimaging analyses maintained by the NIH
 * SPM - software for doing statistical parametric mapping analysis
 * ANTs - software to put individual fMRI scans in a common space that can be compared across subjects
 * Freesurfer - software used to perform cortical surface analyses
 * SUMA - software for performing cortical surface analyses maintained by the AFNI team
 * EEGLAB - a Matlab toolbox for EEG analysis
 * Brainstorm - a Matlab toolbox for MEG/EEG analysis, specifically focusing on localizing brain activity
 * MNE - software for MEG/EEG analysis (developed in conjunction with Brainstorm)
 * Nipype - a common Python interface to a variety of neuroimaging packages
 * Nibabel - a Python package to load in neuroimaging data files
 * C-PAC - a Nipype-based package to configure resting state fMRI analyses
 * Backyard Brains
 * PsychoPy - a set of tools for doing stimulus presentation and capturing behavioral data
 * PyXNAT - allows Python to interface with a popular neuroimaging data management tool (XNAT)
 * PyOpenWorm - Python interface to fetch C. elegans data.

Nuclear Engineering

 * LAMMPS - a molecular dynamics library that can be used to model parallel atomic/subatomic processes at large scale, lead by Sandia National Laboratories
 * OpenGeiger - an open source, open hardware Geiger Counter

=Open Science Projects with an Educational or Instructional Focus=

Cross-discipline

 * Software Carpentry
 * Data Carpentry
 * Software Sustainability Institute - works on educating researchers about good practices in software development/community organizing
 * Open Science Training Initiative
 * CodersCrowd - intended to teach code review skills

Discipline-specific
Please make sub-headings for your discipline as needed.

Environmental Studies

 * Public Lab

=Open Science Journalism and/or Information-sharing Projects=

Cross-discipline

 * Mozilla Science
 * Open Knowledge Foundation
 * The Open Access Button - searches for publicly available versions of paywalled articles
 * Open Article Gauge - determines the license of an academic article

Discipline-specific
Please make sub-headings for your discipline as needed.

=Citizen Science, Participatory Research, Crowdsourced Research=

Cross-discipline

 * Zooniverse
 * SciStarter
 * CitizenScience.org - database of projects from the Cornell Lab of Ornithology
 * PyBossa - framework to create a new crowdsourced project
 * Crowdcrafting - a crowdsourcing website that uses Pybossa for its projects
 * Citizen Cyberscience Centre

Discipline-specific
Please make sub-headings for your discipline as needed.

Astronomy

 * SETI@home - use unused CPU cycles to look for extraterrestrial life

Ornithology

 * Cornell Lab of Ornithology Citizen Science Projects

=Open Scientific Data Sources & Resources=

Cross-discipline

 * Dataverse
 * Open Science Framework
 * SciTran - a scientific data management system geared toward facilitating reproducible research; originated in neuroscience community but meant to be generalizable to other fields
 * Dryad
 * AcademicTorrents - data distributed via BitTorrent
 * iRODS - data management
 * Dat - version control for datasets
 * DataLad - Git-based version control for datasets
 * WISDM - the web interactive scientific data manager

Biology

 * Biomoby

Biomedical Research

 * Harvest
 * Synapse

Ecology

 * EcoData Retriever

Neuroscience

 * OpenfMRI
 * INDI
 * OASIS
 * Brainomics - functional localizer data

Please make sub-headings for your discipline as needed.