Setup of programs I use daily

Research Software

• LyX to write articles and structured documents including citations, Check my blog post on LyX
• JabRef to manage a bibliography
• LaTeX to typeset publications, exported in PDF format
• R statistical software and the R-Studio application
• Several packages: plyr, ggplot2, FAOSTAT, testthat
• Knitr and R Markdown to produce work reports in html. Knitr and LaTeX to produce more elaborate reports in PDF
• xlsx to write data frames to Excel

OS

• Debian GNU-Linux at work
• Ubuntu and Lubuntu at home
• Until 2014 windows XP and windows 7 at work 

Office Software

• I use Firefox (renamed iceweasel on Debian) for web browsing, with the following extensions:
• Adblock to block annoying ads
• Delicious bookmarks to have mobile bookmarks across many browsers
• Mindthetime to keep track of time usage. This extension is not working any more.
• For simple image editing I use Irfanview. I crop scanned pictures or screenshots and I redimension them for web use or use in documents. Very occasionally, I use the "sharpen" function or the brightness, contrast, gamma corrections. 
• I use Microsoft word and Excel at work. I use Google documents when writing something at home.
• To work collaboratively I use media wiki with the extension Semantic Mediawiki
• Based in this review, I installed spacesniffer it helps analyse disk space usage on windows. Like Disk space analyser on GNU-Linux systems. You can use filters such as this one: "*.jpg;>100kb;>2weeks" to filter only certain type of files, sizes and dates.

Command line tools on GNU-Linux

• du to analyse disk usage. I created an alias duh for du -h.
• grep to search inside text files
• pdfgrep to search inside pdf documents
• git see programming below

Thesis writting

• Writing documents in Lyx
• Keeping track of versions with git
• Managing a bibliography with Jabref.

 Programming software

• Scite to edit code
• Git to track versions of code. See also git commands and posts tagged with git.

I want to test

• hubic remote for git annex
• Etherpad (within a company) 
• Kaban (within a company)
• Sage mathematics software 
• Panda data analysis because it brings data frame structures to python
• Montage Video sur ubuntu and Ubuntu video tools

 I stopped using

• QuickWiki Quick search of definitions
• Zotero to share search results with colleagues
• Mendeley to insert citations in Microsoft Word and to manage a bibliography (can import bibtex files form Jabref) 

Links

• On this blog, linux users describe their setup
• usethis.com another site where users such as Yihui Xie describe their setup.