Saturday, 17 November 2012

Looking for a Perl tool like Ipython notebook.



I have just recently discovered Ipython notebooks[1] they are fantastics and like R sweave[2] 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[3]. 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 PĂ©rez about scientific Python[4] 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.

4 comments:

Matthias said...

Hi,

IPython notebook is not reserved for python,

Someone did start to wrote the ability to plug a ruby kernel some time ago.:
https://github.com/isotope11/iruby
Julia also want to transition to IPython Notebook.


So the same could (I guess) be done for perl, and if something on our side prevent from plugging perl, we'll be happy to fix it.

In the meantime you could also use %%script and %%perl magic if you want.

But we would be really happy if the notebook becomes really polyglot.
--
Matthias

Pablo Marin-Garcia said...

Thanks Matthias, that are nice news. I look forward to see Perl community contributing to the project.

By the way I discovered one month ago Julia, and if they achieve notebookintegration, I will use it more often.

V said...

You can try the Perl Data Language, PDL, which has a shell environment perldl.

Pablo Marin-Garcia said...

Thanks V, I use PDL with perldl from time to time, but what I was looking for was not the interactive part but the 'notebook' part. The point here is documenting my pipelines and write reproducible examples, like the vignettes/Sweave in R.