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awesome-open-science
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====================
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some links to projects/tools related to "open science". add to this by
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forking and pull-requesting.
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in a similar vein to
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[awesome-awesomeness](https://github.com/bayandin/awesome-awesomeness).
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computation environments
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------------------------
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- [IPython Notebook](http://ipython.org/notebook.html) (evolving into
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[Jupyter](https://jupyter.org/)): A browser-based notebook with
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support for code, rich text, mathematical expressions, inline plots
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and other rich media.
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- [Maxima](http://maxima.sourceforge.net): A computer algebra system
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developed in Lisp for (symbolic) mathematical computations.
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- [Sage Math Cloud](http://cloud.sagemath.com/): Provides Sage,
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Python, and other environments for computing on the cloud; also
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provides terminal access and git commands for cloning repositories.
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peer-review
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-----------
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- [Hypothes.is](https://hypothes.is/): Steps towards annotating and
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peer-reviewing the Web.
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document writing
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----------------
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- [Authorea](http://authorea.com/): Backed by Pandoc and Git for
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collaborative document writing.
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- [ShareLaTeX](https://www.sharelatex.com/): Online collaborative
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LaTeX editor
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- [WriteLaTeX](https://www.writelatex.com/): Online collaborative
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LaTeX editor
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discovery
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---------
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- [Paperscape](http://paperscape.org/)
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data management
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---------------
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- [Academic Torrents](http://academictorrents.com/): Publish large
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datasets as torrents.
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- [Dat-Data](http://dat-data.com/): Dat is an open source project that
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provides a streaming interface between every file format and data
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storage backend.
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reproducibility
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---------------
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- [Code as a Research
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Object](https://www.mozillascience.org/projects/codemeta): Assign a
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DOI to your code and make it citable.
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- [Figshare](http://figshare.com/): Platform for making research
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artefacts uploadable and citable.
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- [Reproduced papers](http://reproduced-papers.github.io/): Collection
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of links to various researchers reproducing particular papers.
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- [Zenodo](https://zenodo.org/): Platform to host versions of code
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that can be cited; can be linked to GitHub.
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- [steps towards reproducible research](http://kbroman.org/steps2rr/):
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A tutorial/best practices for making your research reproducible.
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project management
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------------------
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- [GitHub](https://github.com): (Naturally.)
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- [Open science framework](http://osf.io/): Collect together various
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sources (GitHub, DropBox, etc) into one spot.
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- [Trello](https://trello.com/) and
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[Libreboard](http://libreboard.com/) (open source self-hosted
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alternative): Keep track of to-do items in various lists of lists;
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keep track of figures, comments, questions, issues, etc.
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organisations
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-------------
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- [Center for Open Science](http://cos.io/)
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- [Mozilla Science Lab](https://www.mozillascience.org/)
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- [rOpenScience](http://ropensci.org/)
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journals/preprint servers
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-------------------------
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- [ArXiv](http://arxiv.org): e-Print archive
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- [ECCC](http://eccc.hpi-web.de/): The Electronic Colloquium on
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Computational Complexity - new papers in TCS.
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- [SciRate](https://scirate.com/): Front for the
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[arXiv](http://arxiv.org/), with voting and comments and accounts.
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training/meetups
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----------------
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- [software carpentry](http://software-carpentry.org/)
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community wikis
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---------------
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- [Complexity Zoo](https://complexityzoo.uwaterloo.ca/Complexity_Zoo):
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Definitions of complexity classes in theoreticaly computer science.
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- [Mozilla Science Lab Forum](https://forum.mozillascience.org/)
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- [nLab](http://ncatlab.org/nlab/): A wiki-lab for collaborative work
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on Mathematics, Physics and Philosophy — especially from the n-point
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of view: insofar as these subjects are usefully treated with tools
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and notions of category theory or higher category theory.
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books
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-----
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- [Opening Science. The Evolving Guide on How the Web is Changing
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Research, Collaboration and Scholarly
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Publishing](http://book.openingscience.org/): A CC-BY-NC book on the
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backgrounds of, tools, tutorials and best practices for open science
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- [Probabilistic Programming and Bayesian Methods for
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Hackers](http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/):
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an intro to Bayesian methods and probabilistic programming from a
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computation/understanding-first, mathematics-second point of view.
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Uses python with pyMC for visualizing what's going on.
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operating systems
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-----------------
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- [Debian Science](https://wiki.debian.org/DebianScience): Debian
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operating system has many science related packages for different
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scientific blends and tastes.
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- [Fedora Astronomy
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Spin](https://labs.fedoraproject.org/en/astronomy/): Fedora
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Fedora Astronomy brings a complete open source toolchain to both
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amateur\
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and professional astronomers.
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[openscience.md Github](https://github.com/silky/awesome-open-science
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)
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