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)
  • Latex is used a lot with the emergence and ease of use of https://www.overleaf.com (there are some 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 ...
  • zotero is another good tool, with a quick web-based tool to create your bibliography that can be exported to common formats https://zbib.org/
• File synchronization: syncthing, Dropbox (proprietary), rsync with ssh
• Remote desktop: clients and servers for the VNC protocol (multi-plateform), TeamViewer (proprietary)
  • see Linux_Resources for more info to connect to a linux server
• Operating system virtualization: VirtualBox
• Text editors: emacs (multi-plateforme), atom, sublimetext, jEdit (multi-plateforme), notepad++ (Windows), gedit (Linux)
• Programming resources, including databases
• Data science resources, including spatial data
• Research Software Engineering with Python https://third-bit.com/py-rse/