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

 * Mozilla Science Map of Study Groups
 * Open Science Code Sprint 2015 - March 7-8, 2015 Toronto, Canada
 * SO Data (Scientific Open Data) - March 26, 2015, Paris, France
 * Young European Associated Researchers (YEAR) Network Annual Conference - May 11-12, 2015, Helsinki, Finland
 * OpenCon - November, 2015 Somewhere in Europe (Further details soon...)
 * Open Drinks
 * New York Open Science Meetup

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

Astronomy

 * Astro Hack Week - 9/28/15-10/02/15
 * Python in Astronomy - 4/20/15-4/25/15

Neuroscience

 * Is Science Broken? If so, how can we fix it? - 17th March 2015, 4pm – 6.45pm, Department of Experimental Psychology, University College London, UK
 * Brainhack - next Hackathon: June 12-14, 2015 in Honolulu, Hawaii
 * CodeNeuro - next Hackathon: April 10, 2015 in NYC

Ecology

 * Open Data and Reproducibility Workshop: the Good Scientist in the Open Science era - April 21, 2015 in London, UK

=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
 * ScienceSolved - still yet another website to connect open source developers and scientists
 * ImageJ
 * Insight Toolkit (ITK) - scientific image analysis
 * R - a programming language for statistical analysis
 * NumPy
 * SciPy
 * Julia
 * Octave
 * Taverna - a workflow management system for assembling and running analysis pipelines (as in bioinformatics or astronomy)
 * Nextflow - pipelining software
 * Common Workflow Language - a group working to standardize data analysis workflows
 * Biostars Backend - software to run a Q&A site for scientific communities

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
 * Galaxy - workflow manager for bioinformatics
 * OMERO - a software suite for managing microscopy data

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
 * Orthanc - an open source DICOM server

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
 * emgr - empirical gramian framework for model reduction and system identification

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
 * EEGNet - a MATLAB toolbox for analyzing network connectivity in M/EEG data.
 * Backyard Brains
 * PsychoPy - a set of tools for doing stimulus presentation and capturing behavioral data
 * Vision Egg - another open source stimuli presentation package
 * PEBL - a suite of common tasks used in psychological research
 * PyXNAT - allows Python to interface with a popular neuroimaging data management tool (XNAT)
 * PyOpenWorm - Python interface to fetch C. elegans data.
 * Brain Connectivity Toolbox (BCT) - a MATLAB toolbox to perform network analyses on neuroimaging data
 * bctpy - a Python port of BCT
 * LiFE - a package to evaluate quality of white matter connectomes

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
 * ArXiv - repository of open access articles (mostly pre-release in physics, math and computer science)
 * ORCID - a digital identifier for authors of scientific publications
 * Docear - software to manage academic literature
 * PeerLibrary - a search engine for academic literature and people; a way of organizing literature
 * ImpactStory - altmetrics organization
 * Jotgit - collaborative writing software
 * Open Science Radio - podcast (mainly in german language) about the open science movement
 * open-science-de - Mailinglist in german language about open science in Switzerland, Austria, and Germany.
 * Open Journal Systems - a software project used to facilitate the creation of online journals, as well as peer review
 * OCSD - an organization examining open science practices in the Global South

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

Agriculture

 * CGSpace - open access materials related to agriculture in Africa

Neurosciences

 * Open Neuroscience - Information about open source projects for neurosciences
 * NeuralEnsemble - a website to coordinate open source neuroscience software development

=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
 * Open Humans - an organization devoted to facilitating voluntary data sharing

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

Astronomy

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

Chemistry

 * SmokyMountainScientific - tools for electrochemistry, solution handling

Genomics

 * Personal Genome Project - an effort to create a genomics dataset with willing data contributions from volunteers

Ornithology

 * Cornell Lab of Ornithology Citizen Science Projects

Oceanography

 * OpenCTD - a project to develop an open source Connectivity-Temperature-Depth sensor

Particle Physics

 * LHC@home - use unused CPU cycles to contribute to particle physics
 * Flavours of Physics: machine-learning contest - 2015-07-20 to 2015-10-12

=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
 * PyRDM - Python-based research data manager
 * Dryad
 * AcademicTorrents - data distributed via BitTorrent
 * iRODS - data management
 * rOpenSci - an organization that makes R packages to import datasets into R
 * Dat - version control for datasets
 * DataLad - Git-based version control for datasets
 * SciDB - database designed specifically for science data; includes data versioning capabilities
 * Datadex - an implementation of a centralized repository for datasets versioned with Data/Dat
 * WISDM - the web interactive scientific data manager
 * Databench - Javascript-based data analysis tool
 * StandardAnalytics - web interface for annotating articles and publishing research data
 * ContentMine - tool for extraction of facts from scientific literature using machine-based content scraping

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

Astronomy

 * Sloan Digital Sky Survey

Biology

 * Biomoby

Biomedical Research

 * Harvest
 * Synapse

Ecology

 * EcoData Retriever

Neuroscience

 * OpenfMRI
 * FCP-INDI
 * OASIS
 * NDAR
 * Brainomics - functional localizer data
 * CodeNeuro Datasets
 * Allen Institute Datasets
 * Neuroelectro
 * Study Forrest
 * Human Connectome Project

Oceanography

 * Ocean Observatories Initiative

Particle Physics

 * CERN Open Data Portal