From: Belorion <belorion@...>
Date: 2005-04-06T06:09:52+09:00
Subject: Re: Ruby and Bioinformatics

I am a graduate student doing bioinformatics.  We use Ruby whenever
possible, and I've done almost all of my programatic work in Ruby.  In
fact, I had never even heard of Ruby until I joined this
bioinformatics group, but I've used it on a daily basis ever since.

What exactly do we use Ruby for in Bioinformatics?  We work with
genomic information (i.e. The Human Genome Project), micro-array data,
cross-species alignments, etc.  We use it for text/data processing, as
an interface to our databases (MySQL), performing data analysis, and
data transformation.  The reason we use Ruby is the fast development
time, the easy to read code, and the fact that Ruby is perfect for
data processing (i.e. parsing our data from flat files, interfacing
with the database, transforming the data, etc).  As far as I can tell,
Perl is still the defacto language of choice for most
bioinformaticists, but in large part because that's what they learned
first, it suits their needs, they have legacy code, so why try out
this Ruby thing?

I'm not sure if any of this really answers your question.  When I do a
`ps -A` or `top` and look at what most people are running on our
machines, its Perl.   But not because Ruby doesn't work just as well
if not better.  If one were to look for a bioinformatics job, knowing
Ruby might not get your foot in the door like Perl would, but I think
that is gradually starting to change.

Really it depends on where you land a job.  Just like anywhere, some
bosses are amiable to using new technology, others insist you use what
they use(d), which is likely Perl.  Some places don't care so long as
the job just gets done.

If you have any specific questions, I would be happy to at least *try*
to answer them for you.  Just drop me a line off list.

Matt

On Apr 5, 2005 3:34 PM, Phil Tomson <ptkwt@aracnet.com> wrote:
> 
> A couple of people mentioned in various threads here recently that they
> are working in Bioinformatics (with the implication that they were using
> Ruby).  I'm just wondering if anyone can comment on the use of Ruby in
> the Bioinformatics field.  Are there opportunities for Rubyists?  What
> kinds of things are you using Ruby for?
> 
> 
> Phil
> 
>