Open Science Projects and Organizations

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Revision as of 20:52, 16 March 2015 by imported>Rmounce (Cross-discipline)
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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

Discipline-specific

Please make sub-headings for your discipline as needed.

Neuroscience

Open Source Scientific Software Projects

Cross-discipline

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

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

Linguistics

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

Discipline-specific

Please make sub-headings for your discipline as needed.

Environmental Studies

Open Science Journalism and/or Information-sharing Projects

Cross-discipline

Discipline-specific

Please make sub-headings for your discipline as needed.

Agriculture

  • CGSpace - open access materials related to agriculture in Africa

Citizen Science, Participatory Research, Crowdsourced Research

Cross-discipline

Discipline-specific

Please make sub-headings for your discipline as needed.

Astronomy

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

Ornithology

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
  • rOpenSci - an organization that makes R packages to import datasets into R
  • Dat - version control for datasets
  • DataLad - Git-based version control for datasets
  • Datadex - an implementation of a centralized repository for datasets versioned with Data/Dat
  • WISDM - the web interactive scientific data manager
  • StandardAnalytics - web interface for annotating articles and publishing research data

Discipline-specific

Biology

Biomedical Research

Ecology

Neuroscience

Please make sub-headings for your discipline as needed.