[Nolug] Genome Sequencing uses: Perl

Since someone on this list asked how much Perl was actually used in
bioinformatics, I thought I'd share this. I'm in a discussion with
someone at the Genome Sequencing Lab at WUSTL and he told me the
following:

    Yes, Perl is the language of choice. Other languages (C, Java)
    are used very infrequently and their use are driven either by the
    needs of the program (C) or the knowledge of the developer (Java).
    Shell scripting is also used for small stuff.

Plus, in case you don't think they have large projects:

    While we are a research facility, we are also a ``genome
    sequencing factory''. So our task as computer and software people
    is doubly hard: keep things up 7 days a week while constantly
    adapting to a changing environment. We get funded because we are
    efficient, both in time and cost. So we are always trying to
    improve our lab processes. This means software must be changed a
    lot as the lab changes. Also, the entire lab is not yet
    ``automated'' (driven by our on-line transaction processing (OLTP)
    database), so there is always a lot of work to be done to
    integrate new parts of the lab into the database; requiring new
    software and modifications of old software ...

Also, the other day I was looking for information on Perl and genome
sequencing and came across the following:

    http://www.columbia.edu/cu/biology/courses/w3037/

    Biology W3037 :: Whole Genome Bioinformatics

    ...

    A practical introduction to the Perl programming language and a
    computer lab are part of the course.

A number of other similar pages can be found.

In the name of fairness, I should note that there are a number of
Open Source contributions to bioinformatics and these are in a number
of languages. Check out bioperl.org, biojava.org, biopython.org, and
bioruby.org, among others.

Mark.

-- 
If you want to know who is funding terrorists, look in the vanity
mirror as you turn the key of your SUV.
    -- http://philip.greenspun.com/politics/israel/
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