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<h1 id="awesome-open-science">awesome-open-science</h1>
<p>some links to projects/tools related to “open science”. add to this
by forking and pull-requesting.</p>
<p>in a similar vein to <a
href="https://github.com/bayandin/awesome-awesomeness">awesome-awesomeness</a>.</p>
<h2 id="computation-environments">computation environments</h2>
<ul>
<li><a href="http://ipython.org/notebook.html">IPython Notebook</a>
(evolving into <a href="https://jupyter.org/">Jupyter</a>): A
browser-based notebook with support for code, rich text, mathematical
expressions, inline plots and other rich media.</li>
<li><a href="http://maxima.sourceforge.net">Maxima</a>: A computer
algebra system developed in Lisp for (symbolic) mathematical
computations.</li>
<li><a href="http://cloud.sagemath.com/">Sage Math Cloud</a>: Provides
Sage, Python, and other environments for computing on the cloud; also
provides terminal access and git commands for cloning repositories.</li>
</ul>
<h2 id="peer-review">peer-review</h2>
<ul>
<li><a href="https://hypothes.is/">Hypothes.is</a>: Steps towards
annotating and peer-reviewing the Web.</li>
</ul>
<h2 id="document-writing">document writing</h2>
<ul>
<li><a href="http://authorea.com/">Authorea</a>: Backed by Pandoc and
Git for collaborative document writing.</li>
<li><a href="https://www.sharelatex.com/">ShareLaTeX</a>: Online
collaborative LaTeX editor</li>
<li><a href="https://www.writelatex.com/">WriteLaTeX</a>: Online
collaborative LaTeX editor</li>
</ul>
<h2 id="discovery">discovery</h2>
<ul>
<li><a href="http://paperscape.org/">Paperscape</a></li>
</ul>
<h2 id="data-management">data management</h2>
<ul>
<li><a href="http://academictorrents.com/">Academic Torrents</a>:
Publish large datasets as torrents.</li>
<li><a href="http://dat-data.com/">Dat-Data</a>: Dat is an open source
project that provides a streaming interface between every file format
and data storage backend.</li>
</ul>
<h2 id="reproducibility">reproducibility</h2>
<ul>
<li><a href="https://www.mozillascience.org/projects/codemeta">Code as a
Research Object</a>: Assign a DOI to your code and make it citable.</li>
<li><a href="http://figshare.com/">Figshare</a>: Platform for making
research artefacts uploadable and citable.</li>
<li><a href="http://reproduced-papers.github.io/">Reproduced papers</a>:
Collection of links to various researchers reproducing particular
papers.</li>
<li><a href="https://zenodo.org/">Zenodo</a>: Platform to host versions
of code that can be cited; can be linked to GitHub.</li>
<li><a href="http://kbroman.org/steps2rr/">steps towards reproducible
research</a>: A tutorial/best practices for making your research
reproducible.</li>
</ul>
<h2 id="project-management">project management</h2>
<ul>
<li><a href="https://github.com">GitHub</a>: (Naturally.)</li>
<li><a href="http://osf.io/">Open science framework</a>: Collect
together various sources (GitHub, DropBox, etc) into one spot.</li>
<li><a href="https://trello.com/">Trello</a> and <a
href="http://libreboard.com/">Libreboard</a> (open source self-hosted
alternative): Keep track of to-do items in various lists of lists; keep
track of figures, comments, questions, issues, etc.</li>
</ul>
<h2 id="organisations">organisations</h2>
<ul>
<li><a href="http://cos.io/">Center for Open Science</a></li>
<li><a href="https://www.mozillascience.org/">Mozilla Science
Lab</a></li>
<li><a href="http://ropensci.org/">rOpenScience</a></li>
</ul>
<h2 id="journalspreprint-servers">journals/preprint servers</h2>
<ul>
<li><a href="http://arxiv.org">ArXiv</a>: e-Print archive</li>
<li><a href="http://eccc.hpi-web.de/">ECCC</a>: The Electronic
Colloquium on Computational Complexity - new papers in TCS.</li>
<li><a href="https://scirate.com/">SciRate</a>: Front for the <a
href="http://arxiv.org/">arXiv</a>, with voting and comments and
accounts.</li>
</ul>
<h2 id="trainingmeetups">training/meetups</h2>
<ul>
<li><a href="http://software-carpentry.org/">software carpentry</a></li>
</ul>
<h2 id="community-wikis">community wikis</h2>
<ul>
<li><a
href="https://complexityzoo.uwaterloo.ca/Complexity_Zoo">Complexity
Zoo</a>: Definitions of complexity classes in theoreticaly computer
science.</li>
<li><a href="https://forum.mozillascience.org/">Mozilla Science Lab
Forum</a></li>
<li><a href="http://ncatlab.org/nlab/">nLab</a>: 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.</li>
</ul>
<h2 id="books">books</h2>
<ul>
<li><p><a href="http://book.openingscience.org/">Opening Science. The
Evolving Guide on How the Web is Changing Research, Collaboration and
Scholarly Publishing</a>: A CC-BY-NC book on the backgrounds of, tools,
tutorials and best practices for open science</p></li>
<li><p><a
href="http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/">Probabilistic
Programming and Bayesian Methods for Hackers</a>: 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.</p></li>
</ul>
<h2 id="operating-systems">operating systems</h2>
<ul>
<li><p><a href="https://wiki.debian.org/DebianScience">Debian
Science</a>: Debian</p>
<p>operating system has many science related packages for different
scientific blends and tastes.</p></li>
<li><p><a href="https://labs.fedoraproject.org/en/astronomy/">Fedora
Astronomy Spin</a>: Fedora</p>
<p>Fedora Astronomy brings a complete open source toolchain to both
amateur<br />
and professional astronomers.</p></li>
</ul>