awesome-open-science
====================

some links to projects/tools related to "open science". add to this by
forking and pull-requesting.

in a similar vein to
[awesome-awesomeness](https://github.com/bayandin/awesome-awesomeness).

computation environments
------------------------

-   [IPython Notebook](http://ipython.org/notebook.html) (evolving into
    [Jupyter](https://jupyter.org/)): A browser-based notebook with
    support for code, rich text, mathematical expressions, inline plots
    and other rich media.
-   [Maxima](http://maxima.sourceforge.net): A computer algebra system
    developed in Lisp for (symbolic) mathematical computations.
-   [Sage Math Cloud](http://cloud.sagemath.com/): Provides Sage,
    Python, and other environments for computing on the cloud; also
    provides terminal access and git commands for cloning repositories.

peer-review
-----------

-   [Hypothes.is](https://hypothes.is/): Steps towards annotating and
    peer-reviewing the Web.

document writing
----------------

-   [Authorea](http://authorea.com/): Backed by Pandoc and Git for
    collaborative document writing.
-   [ShareLaTeX](https://www.sharelatex.com/): Online collaborative
    LaTeX editor
-   [WriteLaTeX](https://www.writelatex.com/): Online collaborative
    LaTeX editor

discovery
---------

-   [Paperscape](http://paperscape.org/)

data management
---------------

-   [Academic Torrents](http://academictorrents.com/): Publish large
    datasets as torrents.
-   [Dat-Data](http://dat-data.com/): Dat is an open source project that
    provides a streaming interface between every file format and data
    storage backend.

reproducibility
---------------

-   [Code as a Research
    Object](https://www.mozillascience.org/projects/codemeta): Assign a
    DOI to your code and make it citable.
-   [Figshare](http://figshare.com/): Platform for making research
    artefacts uploadable and citable.
-   [Reproduced papers](http://reproduced-papers.github.io/): Collection
    of links to various researchers reproducing particular papers.
-   [Zenodo](https://zenodo.org/): Platform to host versions of code
    that can be cited; can be linked to GitHub.
-   [steps towards reproducible research](http://kbroman.org/steps2rr/):
    A tutorial/best practices for making your research reproducible.

project management
------------------

-   [GitHub](https://github.com): (Naturally.)
-   [Open science framework](http://osf.io/): Collect together various
    sources (GitHub, DropBox, etc) into one spot.
-   [Trello](https://trello.com/) and
    [Libreboard](http://libreboard.com/) (open source self-hosted
    alternative): Keep track of to-do items in various lists of lists;
    keep track of figures, comments, questions, issues, etc.

organisations
-------------

-   [Center for Open Science](http://cos.io/)
-   [Mozilla Science Lab](https://www.mozillascience.org/)
-   [rOpenScience](http://ropensci.org/)

journals/preprint servers
-------------------------

-   [ArXiv](http://arxiv.org): e-Print archive
-   [ECCC](http://eccc.hpi-web.de/): The Electronic Colloquium on
    Computational Complexity - new papers in TCS.
-   [SciRate](https://scirate.com/): Front for the
    [arXiv](http://arxiv.org/), with voting and comments and accounts.

training/meetups
----------------

-   [software carpentry](http://software-carpentry.org/)

community wikis
---------------

-   [Complexity Zoo](https://complexityzoo.uwaterloo.ca/Complexity_Zoo):
    Definitions of complexity classes in theoreticaly computer science.
-   [Mozilla Science Lab Forum](https://forum.mozillascience.org/)
-   [nLab](http://ncatlab.org/nlab/): A wiki-lab for collaborative work
    on Mathematics, Physics and Philosophy — especially from the n-point
    of view: insofar as these subjects are usefully treated with tools
    and notions of category theory or higher category theory.

books
-----

-   [Opening Science. The Evolving Guide on How the Web is Changing
    Research, Collaboration and Scholarly
    Publishing](http://book.openingscience.org/): A CC-BY-NC book on the
    backgrounds of, tools, tutorials and best practices for open science

-   [Probabilistic Programming and Bayesian Methods for
    Hackers](http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/):
    an intro to Bayesian methods and probabilistic programming from a
    computation/understanding-first, mathematics-second point of view.
    Uses python with pyMC for visualizing what's going on.

operating systems
-----------------

-   [Debian Science](https://wiki.debian.org/DebianScience): Debian

    operating system has many science related packages for different
    scientific blends and tastes.

-   [Fedora Astronomy
    Spin](https://labs.fedoraproject.org/en/astronomy/): Fedora

    Fedora Astronomy brings a complete open source toolchain to both
    amateur\
    and professional astronomers.