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Other Bioinformatics Monks Out There?

by BioGeek (Hermit)
on Aug 03, 2004 at 15:17 UTC ( #379692=perlquestion: print w/replies, xml ) Need Help??

BioGeek has asked for the wisdom of the Perl Monks concerning the following question:

The works of that other great monk started the field I find myself immersed in now. So I was wondering wich other Perl Monks occupy themselves with bioinformatics, and how they use Perl in it.

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Re: Other Bioinformatics Monks Out There?
by davorg (Chancellor) on Aug 03, 2004 at 15:19 UTC

    I assume that you already know about the BioPerl project.


    "The first rule of Perl club is you do not talk about Perl club."
    -- Chip Salzenberg

      I do, but haven't used it yet.

      (Congrats with the White Camel, BTW).
Re: Other Bioinformatics Monks Out There?
by kvale (Monsignor) on Aug 03, 2004 at 18:17 UTC
    Some define bioinformatics narrowly as computational genomics and proteomics. Others use bioinformatics more broadly as a term for computational biology in beneral.

    I fall into the latter category. I am a computational neurobiologist who studies how neurons in sensory systems code information using action potentials or "spikes". The analysis is purely mathematical and draws from algorithms in signal processing, nonlinear physics, and information theory.

    Perl is my first choice of language for programming in this domain. It allows me to try ideas quickly and is often fast enough for what I need. Some algorithms are CPU and/or memory intensive, in which case I'll turn to the Perl Data Language (PDL) to cut the problem down to size. PDL is the tool of choice for signal filtering, FFTs, and correlational analysis.

    I occasionally write applications in C++, but it is more to keep up my skill set than desperate need. Others in my department use Perl or Python for a similar tasks. I think Python seems to attract more numerical analysts for some reason, but PDL is nicer than the melange of numerical modules one has to deal with in Python.

    I have also worked in bioinformatics in the narrow sense. I used Perl to attack the protein folding problem using a genetic algorithm Monte Carlo technique. I am interested in doing more work in genomics and proteomics. There are a lot of fascinating problems in those domains.


      And what is your background? Are you a neurobiologist by training who happend to play a lot with programming, and found that he could put that to use in his work? Or are you a programmer by trade who realised that some of the more interesting problems - with real-life applications - are to be found in biology?
        I am a theoretical physicist who decided there is a lot of potential for quantitative techniques to be applied to neurobiological problems.

        Theoretical physics is often portrayed as one of the more difficult, deep sciences. While it is true that physicists often use esoteric mathematics, physicists pick their problems and theories to be analytically tractable, or at least analytically approximable. Biology is none of this. Biological systems are nonlinear, nonequilibrium, and nonstationary. Dealing with such systems is at the forefront of physical techniques and beyond. That is where the fun is.

        I've had a love of programming and hacking ever since I was a kid, so it is natural for me to attack these problems computationally. Perl came to the fore mostly because I can program in perl faster, with fewer bugs, than any other language I have learned before or since. In addition to PDL mentioned before, perl is used for keeping track of experimental databases, data munging, GUI design through perl /Tk, and glue that holds the whole data analysis protocol together.


Re: Other Bioinformatics Monks Out There?
by biosysadmin (Deacon) on Aug 04, 2004 at 03:42 UTC
    I'm an MS candidate in Bioinformatics working on evolutionary algorithms and their applications in cancer classification, hopefully I'll finish my thesis and move on to a PhD program.

    I use Perl on a daily basis to hack out scripts and to quickly ask questions about the datasets that I deal with. BioPerl is central to a lot of the work that I'm doing, as it makes tying a lot of Perl programs together very easy. However, every now and then I find it a bit lacking. For example, I'm currently doing a bit of work on RNA editing and trans-splicing, and I'm writing some custom objects that trans-splice and assemble sequences from trans-spliced FeatureTable definitions.

    I'm also employed as a sysadmin, and I find Perl invaluable for writing Nagios plugins, database updating scripts and testing suites for various services. Perl is just a good way to get all sorts of computer-related things done.

Re: Other Bioinformatics Monks Out There?
by bobf (Monsignor) on Aug 12, 2004 at 03:47 UTC
    I'm a wet lab researcher by training (in pharmacogenomics - a field that studies how common genetic variations affect one's ability to metabolize or respond to drugs), but I've spent the last couple of years playing with perl and developing a set of database mining programs. I haven't used bioperl much yet, but I'm hoping to get into it more in the near future.
Re: Other Bioinformatics Monks Out There?
by Itatsumaki (Friar) on Nov 10, 2004 at 23:34 UTC
    I'm doing my PhD in bioinformatics, coding primarily in Perl and R.

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