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.

computation environments

IPython Notebook (evolving into Jupyter): A browser-based notebook with support for code, rich text, mathematical expressions, inline plots and other rich media.
Maxima: A computer algebra system developed in Lisp for (symbolic) mathematical computations.
Sage Math Cloud: 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: Steps towards annotating and peer-reviewing the Web.

document writing

Authorea: Backed by Pandoc and Git for collaborative document writing.
ShareLaTeX: Online collaborative LaTeX editor
WriteLaTeX: Online collaborative LaTeX editor

discovery

Paperscape

data management

Academic Torrents: Publish large datasets as torrents.
Dat-Data: 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: Assign a DOI to your code and make it citable.
Figshare: Platform for making research artefacts uploadable and citable.
Reproduced papers: Collection of links to various researchers reproducing particular papers.
Zenodo: Platform to host versions of code that can be cited; can be linked to GitHub.
steps towards reproducible research: A tutorial/best practices for making your research reproducible.

project management

GitHub: (Naturally.)
Open science framework: Collect together various sources (GitHub, DropBox, etc) into one spot.
Trello and Libreboard (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

journals/preprint servers

ArXiv: e-Print archive
ECCC: The Electronic Colloquium on Computational Complexity - new papers in TCS.
SciRate: Front for the arXiv, with voting and comments and accounts.

training/meetups

software carpentry

community wikis

Complexity Zoo: Definitions of complexity classes in theoreticaly computer science.
Mozilla Science Lab Forum
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: A CC-BY-NC book on the backgrounds of, tools, tutorials and best practices for open science
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: Debian

operating system has many science related packages for different scientific blends and tastes.
Fedora Astronomy Spin: Fedora

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