Saturday, 17 November 2012
I have just recently discovered Ipython notebooks they are fantastics and like R sweave they are essential for Reproducible Research.
I use Perl and pdl for bioinformatics research. Being pdl a scientific tool these kind of reproducible research utilities seems a perfect match.
Some time ago in the bio(perl|python) communities they started to look to use a similar approach to sweave but I have not seen much progress on that. A cheap alternative (if your OS is called emacs ;-)) is to use org-mode babel. I like to use babel because I almost always work under ssh connection to my servers using also screen session with emacs -nw . Babel could be a substitute for sweave, but Ipython notebook is a more advanced and interactive beast. You can see this fantastic presentation from Fernando Pérez about scientific Python where he demonstrates its powers.
I don't know yet any Perl tool similar for Ipython notebooks but if it exist I would like to find and use it.
Any comments on this topic and links would be more than wellcome.