Toolkit for the Open Scientist

Directory

Via HackYourPhd [1]:

(excerpt only, go to original for full listing)

Data analysis

http://www.r-project.org

http://www.scipy.org

Data Visualisations

http://www.gephi.org

http://www.graphviz.org

Graph Database

http://www.neo4j.org

Class Dependency Analyzer

http://www.dependency-analyzer.org

Mind Mapping

http://www.mind42.com

Tableaux collaboratifs

http://www.socialcompare.com

Collaborative Writing

http://www.fiduswriter.org (open source; latex export support?)

http://www.editorially.com (down?)

http://www.draft.in (down?)

http://www.penflip.com (some latex support? git integration)

http://www.authorea.com (subset of latex; git integration)

http://www.writelatex.com (latex; can save to dropbox; working on git integration)

http://www.sharelatex.com (open source; latex; dropbox integration; apparently git access "coming soon" to paid version)

http://framalab.org/ (imo seems more suited to working together than for 'writing things up'; has framapad, which looks similar to etherpad)

Collaborative note-taking

http://unishared.com/about/

Other writing tools

http://www.lyx.org

http://johnmacfarlane.net/pandoc/

http://www.scribus.net

Links

https://hackpad.com/New-scientific-markup-language-utAjFcYuvvB

https://gist.github.com/mitar/9176869

Code Sharing

http://www.github.com

http://www.bitbucket.org

Data & Ressources Sharing

http://www.figshare.com

http://www.mendeley.com/ (category?)

Meta-platform

http://www.openscienceframework.org

More Information

More tools:

Open Knowledge Foundation: http://science.okfn.org/tools-for-open-science/

Open Source Software in Science : http://loci.wisc.edu/software/oss

For Bioinformatics: http://bioinformatics.unc.edu/software/opensource/

(http://hackyourphd.org/wiki/wiki/toolkit-for-open-scientist/)