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Getting into Bioinformatics

by adamk (Chaplain)
on Jul 21, 2002 at 04:44 UTC ( #183772=perlquestion: print w/ replies, xml ) Need Help??
adamk has asked for the wisdom of the Perl Monks concerning the following question:

So I'm moving to Europe from Oz, and I'm looking through the Job ads. There seems to be a reasonable number of Perl Bio-informatics job in Europe.

These seem to be broken into two types. The first are the "Masters or PhD level Microbiology, with Perl" type jobs ( which I have no aspirations for ), and then there are "the other guy" type jobs. Solid Perl, with some knowledge of Microbiology of Genetics Concepts. Writing wrappers and interfaces and optomizations etc etc for the "real" Bioinformatitions.

It sounds great, and I would love to have a shot at it. I know some of the basics, but I'd love to push my level of knowledge out the point I could grab one of these "the other guy" jobs. Has anyone gone down this path before? Is there a "Microbiology, Genetics and Bioinformatics for Perl Programmers" type book anywhere? Where the hell should I start, cause I've got no ideas on this one.

I'm happy my Perl is strong enough to handle just about anything, but the Microbiology needs some improvement.

Comment on Getting into Bioinformatics
Re: Getting into Bioinformatics
by perrin (Chancellor) on Jul 21, 2002 at 04:58 UTC
    I asked about this here and got a lot of good responses back.
Re: Getting into Bioinformatics
by elusion (Curate) on Jul 21, 2002 at 14:06 UTC
    Another book, Genomic Perl, is due out soon (hmm... under a different name?). It looks like it introduces both biology and perl as is needed to solve the problems presented. I would think it'd be your best bet for finding a book that's not designed just for biologists.

    elusion : http://matt.diephouse.com

Re: Getting into Bioinformatics
by DigitalKitty (Parson) on Jul 22, 2002 at 03:00 UTC
    Hi AdamK.

    Since the field of bioinformatics is evolving so quickly, I am anticipating quite a few books to appear within 9 - 12 months ( my $estimate ). Assuming you have had ( or are currently enrolled in ) a molecular biology class ( or at least an in-depth general bio course for majors - ideally ), I would recommend:

    Beginning Perl for Bioinformatics
    James D. Tisdall
    List Price: $39.95
    ISBN: 0596000804


    Or...if you would like a more in-depth text:

    Developing Bioinformatics Computer Skills
    Cynthia Gibas, Per Jambeck
    List Price: $34.95
    ISBN: 1565926641


    Both books use perl && *nix for examples and discuss the nuances of parsing databases, the FASTA format, etc. on genomic structures. For a beginning bioinformatics student, I would highly recommend the first title.

    Hope this was helpful,
    -Katie.
Re: Getting into Bioinformatics
by Bukowski (Deacon) on Nov 17, 2002 at 12:05 UTC
    As a working bioinformatician, I had to make the same leap - except that I had the PhD (genetics)- but no Perl experience!

    You can read my comments in the other threads that have been pointed to - but have you considered doing a part time MSc in Bioinformatics? A lot of Uni's are now offering these (in the UK at least) Birkbeck, Manchester, Leeds and I know Imperial College are starting one too.

    There are 2 groups of people mainly moving into Bioinformatics - biologists who are sick of the bench with a technical edge and CS graduates who have stumbled into the field. Both of course are welcome, and tbe interface in the middle of these two groups is where it gets really interesting.

    I don't think you should be scared for applying for these jobs. We've just hired a CS postgrad and a CS grad for a bioinformatics group with no previous experience of biology (but a willingness to learn).

    Maybe you should also check out bioinformatics.org for ideas about what people are doing, FAQs etc.

    Invest in a couple of genetics textbooks - and if you have any questions /msg me ;)

    Bukowski - aka Dan (dcs@black.hole-in-the.net)
    "Coffee for the mind, Pizza for the body, Sushi for the soul"
    -Userfriendly

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