The basic idea is to talk a bit about the way scientists in the life sciences, more specifically in the field of Biological Sciences, can profit from the use of open source software.

What this means for my work

Starting from the design of this web site…

• Specifically, Emacs was used as the main text editor, in particular, Emacs org mode.
• I often also use the very powerful and flexible TextMate editor (unfortunately available only for Mac OSX).
• The org mode files can be converted into Markdown files (which is the format required by Jekyll). Jekyll is the engine behind the generation of these web pages.
• Jekyll runs under the Ruby language environment.

…to managing bibliography…

• Bibliographical research and bibliography collections are handled using Zotero.

…all the way to data management and analysis…

• All of the modelling, data handling, analysis and statistics are done using R.

…modelling, graphical simulation…

• Simulations and graphical modelling are done using Processing.

…and not forgetting image manipulation and vectorialized drawing…

• In which case the open source packages GIMP and Inkscape are just great!
• Also ImageJ (Fiji) is a very powerful package for image processing and analysis, specifically designed for microscopy imaging applications.

The open sourcerer’s toolkit:

Acknowledgements also to: