add owesome-open-science

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.

-   [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.

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

-----

-   [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.