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not to feed any flame wars here: there's also http://www.biopython.org/ and http://www.bioruby.org/ ;)
But I'm just trying to make a point here for the position of these kind of languages in sciences.

It's not 'hard numbers', but then, a lot of people have already pointed out that hard numbers may not REALLY be what you want. (After all, since when is "Everybody's doin' it" a persuasive argument for a good scientist?)

On the other hand, I see there are still lots of applications listed at the Scientific Applications on Linux site and the NCBI Toolbox of Bioinformatics code compiles and runs just fine on my linux box, and BioPerl, BioJava, and BioPython all run just fine on Linux (there are even a couple of fledgling BioPHP projects out just getting started out there, which will obviously also work.

Disclaimer - both of the semi-active "BioPHP" type projects that I know of - Here and here - were started independently by individual amateurs...and one of them is me. Both projects are still in the early stages (Genephp has more code available at the moment) and have different development approaches, but are slowly working on trying to combine development towards a 'formal' set of "BioPHP" modules. Blatant plug - if you are interested in helping with friendly advice or actual development or testing, please join the mailing list which both projects use)

Nice cut-and-paste job.

And related stuff that may interest you...
* BioPython
* BioCORBA
* BioXML
* BioJava
* BioRuby
* BioExchange Software tools (other tools for working with bio*, interesting.)

I switched language when I left uni for the real world (IDL is nice but bloody expensive) and settled for python.
Actually, more like python+numeric+c

I usually experiment in pure python+numeric first and then optimise the parts that need in c. I really love how easy it is to interface c and python (especially compared to IDL). No problems passing numeric arrays to and from python, etc, etc...

Don't forget to check biopython which is always a good place to start. Dunno if there's anything for processing microarrays, though.

Check this out:

Bioperl
Biopython
Biojava
BioXML
BioCORBA

I couldn't find anything for ruby (either linked from bioperl, as those were, or on their own app list) but you can bet it's coming. I'd personally love to see it. But there's plenty of options for bioinformatics other than perl, although perl's excellent text handling makes it a very suitable choice.

"I may not have morals, but I have standards."

Anyone tried to do non trivial changes to his old Perl programms?

My Perl programs were those that were the hardest to get understood after I had stopped working with them for some weeks. It is usually easier to rewrite them.

Nonetheless I valued the good performance of Perl programs and was thus sceptical to other kids on the scripting language block, like Python.

Months later, I must say that the much saner syntax of Python, the formidable documentation and the large library have changed my scripting preference from Perl to Python. Like Perl, Python has been ported to a lot of platforms.

Ruby is a language I have not looked into yet. Its strong Japanese supporter base, has led to a lot of FreeBSD ports. So I might have a look soon.

BTW, there are bioperl, biopython, bioruby and biojava efforts - anyone spotted a bioc or bioc++ one? And some dork registered www.biofortran.org.

There are a lot of open source bioinformatics projects. These are typically spawned by university or other public research projects. You mention Python and Perl, so try bioperl or biopyhon for a start.

The one thing I didn't like about the biotech industry was how their research and information distribution was tied closely to their purse strings.

You will have a lot of open source (where the majority of development money will come from public research funds) and a lot of commercial applications.

It is unlikely that a large bunch of hackers will revolutionize this field. This is because you need a lot of domain specific knowledge and because a lot of work that needs to be done is too tedious or uncool to attract open source people from outside the bioinformatics field.

Something like the Gimp could be done, because nearly everyone needs such a tool - but who needs for example a multiple sequence alignment editor besides biologists?

Did you see some open source satelite control software or hydrodynamic simulation from outside their engineers communities?

my particular bias is life science it will show with the following URLS: bioperl.org, biojava.org, biopython.org. Find projects like these in whatever dicipline you are interested and you will find lots of science-capable programmers either actively contributing or participating in discussion. Don't spam the mailing lists with job listings of course - be a bit more subtle and find out things like what school programs are producing these folks, what conferences & events they attend etc. etc.