Open Science Projects and Organizations: Difference between revisions
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* [http://brainomics.cea.fr/localizer Brainomics] - functional localizer data |
* [http://brainomics.cea.fr/localizer Brainomics] - functional localizer data |
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* [http://datasets.codeneuro.org/ CodeNeuro Datasets] |
* [http://datasets.codeneuro.org/ CodeNeuro Datasets] |
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* [http://www.brain-map.org/ Allen Institute Datasets] |
Revision as of 21:53, 21 March 2015
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...)
Discipline-specific
Please make sub-headings for your discipline as needed.
Astronomy
- Astro Hack Week - 9/28/15-10/02/15
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
- Solvers.io - yet another website to connect open source developers and scientists
- ScienceSolved - still 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
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
- 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
- Backyard Brains
- PsychoPy - a set of tools for doing stimulus presentation and capturing behavioral data
- Vision Egg - another open source stimuli presentation package
- 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
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
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
- 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
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
- 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.
Biology
Biomedical Research
Ecology
Neuroscience
- OpenfMRI
- INDI
- OASIS
- Brainomics - functional localizer data
- CodeNeuro Datasets
- Allen Institute Datasets