[BioRuby] Bringing the fun back to programming! (The first BioRuby IRC conference on Dec 19th)

Francesco Strozzi francesco.strozzi at gmail.com
Mon Dec 13 13:26:34 UTC 2010

On Mon, Dec 13, 2010 at 13:29, Raoul Bonnal <bonnalraoul at ingm.it> wrote:
> Unfortunately Ruby is a terrific language which suffers from the
> association Ruby => Rails

Yes I agree, that's what I was saying when I wrote about the "just for the
web" corner. Rails is amazing and I love it, but I think now Ruby is seen
more as the language for Rails and less as a robust language that could do
almost the same things as Python, in my opinion.

> @Francesco: which are the motivation or real case studies which drive you
> to shift from Ruby to Python ?

Basically the Bio library usage. Reading through the docs and using the
different libraries, I found BioPython to be more complete and with a better
performance, in particular for parsing big files (like Blast reports,
assembly data, NGS files etc.). And the math libraries are amazing. With
matplotlib and NumPy/SciPy you could avoid using R for what I have seen. And
the documentation is vast.
Also Python syntax is quite similar to Ruby in many ways, so moving from one
to another wasn't so hard (even if mastering a language is not a matter of
few months of practice).
In the end I found myself running things in Ruby to develop web
applications(!) or for the Ruby Ensembl API, and doing everything else with
Python...that's the reason why I have written here to give my "+1", as I
completely agree with Pjotr and I'd like to learn new ways of using Ruby
(with Scala/Clojure or whatever) to do the "hard" work as well...




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