Computing Tools for Research

This page lists software tools that are useful for research. For obvious reasons, open source tools, relying on open standards, are emphasized:

• Document typesetting: Latex (first class typesetting and math/equation rendering, wikibook, The Not So Short Introduction to LATEX), WYSIWYG editor Kile and Lyx
• Bibliographical database: JabRef (the format is Bibtex, for Latex, and can be exported to Word and html among others)
  • The file extension is .bib. Each entry needs a unique key for which I usually use <first author last name><publication year last 2 digits><first word of title>, eg saunier11investigating (see my personal publication bibliography). Another common pitfall deals with author names: they should be <first name1> <last name1> and <first name2> <last name2> and ...
• File synchronization: syncthing, Dropbox (proprietary), rsync with ssh
• Remote desktop: clients and servers for the VNC protocole (multi-plateform), TeamViewer (proprietary)
• Virtualisation de systèmes d'exploitation: VirtualBox
• Editeurs de texte: emacs (multi-plateforme), jEdit (multi-plateforme), notepad++ (Windows), gedit (Linux)
• Version Control: Mercurial, Git, Subversion
• Programmation:
  • Python: bibliothèque scientifique scipy, visualisation avec matplotlib, shell interactif ipython, package scientifique Sage, package scientifique complet de la société Enthought (Windows)
  • R: outil standard de la communauté en statistiques, très complet (clone du langage S)
  • Octave: clone de Matlab
  • C/C++: compilateur GCC, environnements cygwin ou MinGW (Windows)
• Libraries and tools for machine learning, data mining and statistical analysis:
  • Tanagra
  • Weka
  • Gretl
• Systèmes de gestion de bases de données:
  • SQLite
  • PostgreSQL
  • MySQL
• Systèmes d'information géographique (SIG): Quantum GIS, GRASS, Spatialite
• Visualisation de données, création de graphiques: gnuplot