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Beginning Perl For Bioinformatics

by cadfael (Friar)
on Jan 22, 2002 at 22:46 UTC ( [id://140705] : perlmeditation . print w/replies, xml ) Need Help??

O'Reilly has published a new book called Beginning Perl for Bioinformatics, by James Tisdall.

The title is accurate -- it begins with basic concepts, but it has enough useful meat that even a highly skilled programmer can feel that this is money well-spent. (not that I place myself in that category...)

The real utility of this book is the chapters on dealing with specific biological problems, and parsing such datasets as GenBank files, FASTA reports, and many others.

As such it is a cookbook of sorts, and only time will tell whether I reach for this volume as often as I reach for The Perl Cookbook.

This is the second Bioinformatics title from O'Reilly in about a year's time, indicating how quckly this field is getting attention. I will be leaving in a few days for the Bioinformatics Technology Conference, hosted by O'Reilly in Tucson AZ. The tutorial I signed up for is an all day session titled 'Parsing in Perl for Bioinformatics', led by Damian Conway. This should prove to be a rather stimulating day.

Are there any Perlmonks going? We ought to get together for something while we are out there. Send me some email at if you'd like to get together.

Ooops. Can't spell "O'Reilly". Fixed it.

"Computeri non cogitant, ergo non sunt"

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Re: Beginning Perl For Bioinformatics
by scain (Curate) on Jan 23, 2002 at 01:23 UTC
    I wanted to go to Arizona, but I can only go to one conference a year, and there are others that I should probably go to.

    As for your comment about highly skilled programmers, I suppose that may apply to non-bioinformatics-initiated programmers, but to anyone who has been doing it awhile will probably find the material covered to be a little too simple. I did find that the examples were well written, generally using strict, and using BioPerl where appropriate (that is, after it has already gone over many parsing basics that would be better handled through BioPerl--Gotta teach the new-comers how it is done).


      scain wrote: As for your comment about highly skilled programmers, I suppose that may apply to non-bioinformatics-initiated programmers, but to anyone who has been doing it awhile will probably find the material covered to be a little too simple.

      Hmmm. I seem to have initially made an over-broad statement. Your point about people who have been doing it for a while is well taken. Since my perling hasn't included much parsing, much of this seemed new ground for me. I will be very interested to see how my meager and limited efforts over the past few years can be improved by seeing how others do it.

      Just because "There's more than on way to do it!" doesn't necessarily meant that my way is just as good. If fact, I rather suspect that at the end of the parsing tutorial next Monday, I will have VERY useful things to think about.

      What are you involved in? I am the DBA for the Maize Genome Database, and the majority of my perl use is in dba tasks and cgi scripts for data presentation.

      "Computeri non cogitant, ergo non sunt"

        I suppose we are entering the private message arena, but since you asked...

        I am the lead Bioinformatisist (which is as clumsy to say as to type) for a small biotech company. When I got into Bioinformatics, much of what I did was write parsers in Perl, a task for which I was self taught (and not very well I might add.) So I learned by trial and error many of the topics covered in that book. Now that BioPerl is on the scene, many of those same things can be done much more cleanly using community maintained modules.

        Now I use Perl for lots of database connectivity, especially tying together data analysis results in a unix cluster to our database on a Windows box.


Re: Beginning Perl For Bioinformatics
by indapa (Monk) on Jan 23, 2002 at 01:39 UTC
    I wanted to go, especially since I went to college there, but scheduling conflicts prevented me from going. Let us know what you thought of the conference after you get back. And enjoy sunny Arizona.
Re: Beginning Perl For Bioinformatics
by Bukowski (Deacon) on Jun 19, 2002 at 14:13 UTC
    I went to the conference and it was great!

    My early sign up present was a copy of "Beginning Perl for Bioinformatics"

    If you're new to perl, and interested in bioinformatics, then team it up with a copy of "Learning Perl" from O'Reilly and sit down with a few coffees.

    The book really outlines the principles of data manipulation in biological questions, and takes you through many common tasks for which I'm sure, most bioinformaticians have written their own, similar programs.

    Some of the tricks are trivial, even simplistic, and I found it interesting to compare it to my own home grown routines in places. However it is not made clear (and I think this is a real let down with the book) that the majority of the manipulations are readily available and more elegantly done in Bioperl ( Whilst Bioperl gets a mention, anyone using perl in a bioinformatics environment will be using Bioperl to do these manipulations. Its a bit like rolling your own CGI scripts because you've not discovered yet.

    It has been useful, and maybe now I'm out of the 'newbie' perl phase I look down a little on some of the code, but as a new perl user, the book will give you the confidence to move forward with a clear mental toolkit for attacking future problems.

    Bukowski - aka Dan (
    "Coffee for the mind, Pizza for the body, Sushi for the soul" -Userfriendly