All the Perl that's Practical to Extract and Report

Major win for Open Source Science -- and BioPerl too?

n1vux on 2005-10-27T16:13:40

Duplicating a SubmitStory for the record ...

BBC reporting "Gene map points to personal drugs"

"Experts say the study should simplify genetic research Scientists have completed a map of the most common differences in the human genome, which could lead to personalised treatments for diseases."

This is a major ($100M) OpenSource science project -- their CopyLeft License on the data requires foreswearing patenting results of research using the HapMap. Article

Bio::PopGen::IO::hapmap.pm is a part of BioPerl SDK. I'm not sure if only the data is accessed via BioPerl, or if the HapMap was built with BioPerl too. But the whole HapMap website runs on cgi-perl.

Back story -- from 2003 launch of HapMap: 1; 2

Heavy Lifting work done with C

TeeJay on 2005-10-28T10:23:55

Once of my friends works at the Sanger Institute at Cambridge and I asked if they used perl.. his response was :

"Perl code? No, it'd still be running ...
Well tuned C.
Almost all the output probably gets parsed by perl though and the web site
is definitely done in perl - they can't do anything else. "

The hapmap part of the project in the States may have used more bio-perl, and I guess most of the data munging is also handled by perl - it is used a fair amoun by the scientists at the place where my mate works, as well as some of the pretty hard math.