Re: Perl for science

Next time you talk to db-guy, you can point out bioperl. It is an open-source tool for bioinformatics and the source of many questions on PM. It leverages exactly Perl's strengths for processing genetic information - strings of [ATGC].

On a more abstract level, I'm curious how you are defining "science", since almost all the apps I know in science are written in either Fortran or C. If you are doing any kind of serious numerical computation, you would be hard pressed to get the kind of speed you can get out of well-optimized Fortran code, plus there's the legacy effect. I personally am trying to leverage Perl's and Fortran's strengths (they are very complementary) toward my own work, though $work is getting in the way there.

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Re^2: Perl for science by punkish (Priest) on Feb 06, 2009 at 15:19 UTC
Responding to both swampyankee and kennethk, there is little point in talking to the `db-guy` about bioperl, and for the art of computational science, we have the brilliant if needing an update wolf book. I guess an image problem is countered typically with a campaign. A consolidated campaign of the http://perlbuzz.com kind but directed to science would be a good way. By the way, I am not attempting to define or pigeon-hole science here. In my world, science is image and geographic analysis and data visualization. Perl can and does help in both, and can work in conjunction with better tools such as Processing (for visualization). Actually, come to think of it, a Perl module that interfaces with Processing would really make me smile. Thanks for the responses though. I already feel a bit better. -- when small people start casting long shadows, it is time to go to bed	[reply] [d/l]
Re^2: Perl for science by educated_foo (Vicar) on Feb 08, 2009 at 03:24 UTC
Speaking as a bio and Perl person, bioperl is usually an overengineered waste of time. As to your original question, the main factor is usually what your colleagues use. The second question is usually how easily the language interfaces with C, FORTRAN, and the shell. Biology is text-intensive, especially in its scripty parts, so Perl is a good language for it, but even with PDL, it can't compete with Octave for numerical stuff.	[reply]