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n1vux (1492)

n1vux
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Only started with Perl4 and Perl5 in 1995. I was doing AWK etc for 12 years before that, and resisted switching. I've been doing OO since before C++ hit bigtime, with Objective-C and SmallTalk, so I really like the (no longer new) Perl5 OO style; and the Lispish Map style is also an old friend. What do I hack with Perl? All data that passes my way; systems monitoring scripts at $DayJob, weather data at night, and I cheat on NPR word puzzles. Member: Boston.pm.org [pm.org] BLU.org [blu.org] /. LinkedIn [linkedin.com]

N1VUX is my FCC-issued ham radio callsign.

Journal of n1vux (1492)

Thursday October 27, 2005
11:13 AM

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

[ #27331 ]
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

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  • 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,
    --

    @JAPH = qw(Hacker Perl Another Just);
    print reverse @JAPH;