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Developing Bioinformatics Computer Skills

by deprecated (Priest)
on Sep 18, 2001 at 22:25 UTC ( #113165=bookreview: print w/replies, xml ) Need Help??
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Item Description: Comprehensive, Comprehendible, Concise, Computer oriented introduction to Bioinformatics and Genetic Sequence Analysis

Review Synopsis:

I've been hacking at this book for a little while now, and I am pretty impressed with it. The firs thing that struck me about it was just how available the meat of the book was.

I never studied much math (at least not this kind of math, I was going to be an automotive engineer) or biology in College. Yet, when reading this book, I grokked almost all the concepts, and was able to surmise from context just what tha authors were getting at when I did not.

You might be surprised that with a title like Developing Bioinformatics Computer Skills that a decent size portion of the book is actually dedicated to perl. There is some coverage of Python and Csh scripting as well. In general, however, this book is not intended to be read as a "perl book" like, say, The Camel would be. Nay, it is intended for people wanting to move into bioinformatics who need to begin to learn things like perl and unix.

That having been said, this book even provides an excellent (if terse) introduction to Unix, the shell, and even perl. Seems to me, just about any Scientist could pick this book up and begin hacking perl, or begin to think about bioinformatics from a practical or applied point of view. Certainly one could begin to understand the relevant terminology after reading this book.

Being an OReilly book, I naturally approached it with a higher expectation than I do with, say, Que or Sams. However, I was pleasantly surprised. The authors appear to be Linux (redhat) Zealots, and as such, the tone of the book is friendly yet comprehensive, jovial yet casually serious. You understand what I mean if you've read many of the other ORA books.

I have made recent posts discussing my flirting with Bioinformatics and going back to school. If that thread struck a chord with anyone, I'd really suggest dropping the $25 on it. It's a good 1-2 day read and you'll probably even learn something. :-)

Brother dep.

  • Comment on Developing Bioinformatics Computer Skills
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Re: Developing Bioinformatics Computer Skills
by Hanamaki (Chaplain) on Sep 18, 2001 at 23:48 UTC
      Perl and Bioinformatics go well .. hand in hand. There are many modules and tools dedicated to Bioinformatics written in Perl. Here's a good site if you're interested in checking it out -

      - Moon
      They also host a bioinformatics mailing list; see here for more info.


        For those coming late to this discussion, I would like to point out that the O'Reilly list is no longer active. I suggest people look at the lists instead

        Bukowski - aka Dan (
        "Coffee for the mind, Pizza for the body, Sushi for the soul" -Userfriendly
Re: Developing Bioinformatics Computer Skills
by thraxil (Prior) on Sep 19, 2001 at 19:41 UTC

    i've read this one too. my observations:

    the intended audience is definitely not programmers who are looking to get into bioinformatics (although they'll still find it a good read). it's biologists who are looking to learn more computer skills to help them with bioinformatics. it does a good job at that. most perlmonks would probably find the technical stuff (in particular the section on perl) very introductory.

    similarly, the biology/genetics sections are fairly brisk; they seem to be intended to review the material just enough that the biologists can understand the context of the CS material without getting too bored.

    it also skips over some of the more advanced topics with only a brief mention (eg, hidden markov models and support vector machines) but i can hardly blame an introductory book for that.

    that said, it is an excellent introduction for people with more bio background than CS and not a bad reference for anyone else. the unix tutorial is one of the best that i've seen in any book and does a very good job of explaining streams and conveying the power of the unix philosophy.

    plus, the book mentions my former bioinformatics prof, bill grundy (err, now "william stafford noble", i guess), one of the authors of Meta-MEME. :)

    anders pearson

Re: Developing Bioinformatics Computer Skills
by Bukowski (Deacon) on Jun 19, 2002 at 14:03 UTC
    As a practicing bioinformatician, I picked this book up thinking that it would be useful for handing out to people in the office to deflect some of the more obvious questions.

    I would like to say though that this book is a primer, and its a primer for the BIOLOGIST. It is a comprehensive list of popular bioinformatics resources, and how to use them -but it will not teach you to write perl. It will take you through a unix primer though - useful for people with not such a great computing background.

    If you are a CS person with a hankering to get into bioinformatics, well you will find the biology primers useful, they are clear and concise. But you will not need the database/coding aspects of it.

    It's a good read, it is useful, but it is a primer - and it will not get you to the meat of subjects such as HMM's (Hidden Markov Models) and algorithm development.

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

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