Thursday, February 18, 2010

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


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

 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) 


1 comment:

Paul said...

One issue with KnitR and Markdown is that Markdown doesn't have automatic figure captions. I could use brew and pander to produce pandoc markdown. But as said here, if I realy need a complex system, I'd rather switch to LaTeX.