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

• Center for Open Science
• Mozilla Science Lab
• rOpenScience

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.