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Former Member
Apr 08, 2008 at 01:03 PM

Update on Bioinformatics WIKI, scripting challenges, and a general question


I am waiting for my site to go on-line at Oak Ridge National Labs (USA, Tennessee). Should be another week or so, maybe less.

When that happens, you will see a veritable explosion of scripting challenges in my wiki (Emerging Technologies->Bioinformatics.)

One general question in preparation for these challenges.

There are a number of standard bioinformatic programs that can be run interactively via the web at various sites, e.g. "BLAST" and "STRIDE".

Although these can also be run locally, this requires that you download large databases and keep them updated.

So here's my question to the scripting experts:

Are scripting languages powerful enough to submit queries to web pages and then use regex's to parse the html that is returned?

Bill Mann has used PERL to do some of the required regex parsing, but there is a lot left to do, and, his stuff only works when a perl program is invoking a bioinformatic program locally, not interactively.

If so, we all can do some beautiful stuff together , if anyone is interested ...