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Where to learn about Bioinformatics?

by perrin (Chancellor)
on Dec 13, 2001 at 01:17 UTC ( #131410=perlquestion: print w/ replies, xml ) Need Help??
perrin has asked for the wisdom of the Perl Monks concerning the following question:

I'm interested in learning about bioinformatics, with an eye towards future employment opportunities. The obvious O'Reilly book on the subject, "Beginning Perl for Bioinformatics", seems like it's aimed at people who don't already know Perl. I know Perl, and would prefer not to waste time with reviews of how to use references and what not. Should I just buy this book anyway to see examples of the kind of processing involved, or does anyone have any better suggestions about where to look?

Comment on Where to learn about Bioinformatics?
Re: Where to learn about Bioinformatics?
by mortis (Pilgrim) on Dec 13, 2001 at 01:24 UTC
    Have you seen this site: bioperl.org they seem to have a good bit of info. Though there doens't seem to be much in the way of bioinformatics tutorials, the site might at least be able to point you to some references.

    There is also this site.

    hth

    Update: I just found bioinformatics.org which looks like a better place to start.

Re: Where to learn about Bioinformatics?
by dws (Chancellor) on Dec 13, 2001 at 01:34 UTC
Re: Where to learn about Bioinformatics?
by biograd (Friar) on Dec 13, 2001 at 04:55 UTC
    Developing Bioinformatics Computer Skills, again from O'Reilly, is a good source for general feel and applications. It does have some basic introductory Perl and Linux tips, but it also covers lots of interesting bioinformatics topics. It's a good, broad overview,to be used in conjunction with all the links in the above posts. I read it in short spurts over a couple weeks.

    -Jennifer

Re: Where to learn about Bioinformatics?
by princepawn (Parson) on Dec 13, 2001 at 06:12 UTC
    Why don't you go work for Lincoln Stein?

    They have had need of a scientific programmer for a long time.

    Of course, you can look forward to a 20-70% drop in pay from the typical corporate pay scale.

    But it is a lot more fun to work with AceDB, an object-oriented database thru and thru instead of all of this object-relational imitation stuff we have to put up with when using RDBMSes.

      Do you mean you'd drop in pay scale working for L. Stein in particular? Or do you mean you'd drop a pay cut working in Bioinformatics? If you meant the second one, I believe you're sorely wrong. Course, most who work in Bioinformatics are PhD's of some sort or have some second degree (i.e. Masters in CS or Biological Chemistry or other science degrees). They do get paid quite well. Although if you're just a programmer breaking into Bioinformatics... you may get a minimal... until you brush up on your science skills. Then if you're not happy working at one company - there are plenty of Pharamas(pharmacuticals) out there... as well as other companies.. (ie. Incyte, Celera, etc.). Bioinformatics seem to be the up and coming... and are definately wanted! Come to the conference to find out more!
Re: Where to learn about Bioinformatics?
by Moonie (Friar) on Dec 13, 2001 at 06:18 UTC
    You may want to look at this node - it's a review, but has links that may point you in the right direction (also, some have already been mentioned - i.e. bio.perl.org, bio.oreilly.com). You may also want to brush up on your science - Biology! Bioinformatics is a combination of both science and computer science. There are a few monks here in Bioinformatics - you may want to ask around and they will more than likely point you in the right direction. :)
    - Moon
Re: Where to learn about Bioinformatics?
by lostcause (Monk) on Dec 13, 2001 at 07:48 UTC
    Here is a Perl related bioinformatics course:
    Perl Programming Course for Bioinformatics and Internet
    And you can find many more links at:
    Bioinformatics.org have a good FAQ.
    There is a nice series of 6 or so videos online but I don't remember the link right now. I'll check to see if I have it at home and post it later.

    I have both of the O'Reilly bioinformatics books, "Beginning Perl for Bioinformatics" and "Developing Bioinformatics Computer Skills" and may even get around to written reviews one of these days. If you are already an accomplished programer/Perl programer neither will teach you much in that department but they can give you an idea of the sort of biological problems that are out there. "Developing Bioinformatics Computer Skills" gives a good rounded overview of the bioinformatics field with details about common programs. It could be worth your while checking some of the programs out to see the sort of problems people are working on and to find out what field might interest you. "Beginning Perl for Bioinformatics" has some simple but useful scripts that can form a base to your bioinformatics tool kit if you are a beginner or help you think about using Perl with some of the idiosyncrasies of the biological world. As you have more experience you may find BioPerl more your cup of tea.

    One of the standard biological books is Molecular Biology of the Cell amazon.com by Bruce Alberts, Dennis Bray (Contributor), Julian Lewis, Martin Raff, ke Roberts, James D. Watson and I highly recommend getting your hands on a copy so that you can figure out what the hell the biologist are talking about. Its clearly written and contains a wealth of basic information.

    My background is in Biochemistry although I have since moved to Analytical Chemistry (Biological mass spectrometry) and now use Perl for data munging, automating database searching, and reporting as well as many other tasks. Good luck moving into this exciting field.

Re: Where to learn about Bioinformatics?
by chdevers (Initiate) on Dec 13, 2001 at 22:23 UTC
    _Beginning Perl for Bioinformatics_ is okay, butt it's really aimed at people who know nothing about one or more of (a) Perl, (b) programming, (c) computers, or (d, distantly) biology.

    I think the author realized that at least some of these are not going to be completely alien to much of his audience, so he does a pretty good job at balancing the introduction of basic concepts on one hand and the need not to condescend to more experienced developers on the other. It's a fine line, and he mostly pulls it off well, but that doesn't change the fact that it's still an introductory Perl book, albeit one where the sample code is more relevant to this field.

    Honestly, it seems like a lot of bioinformatics (and cheminformatics) is primarily statistical analysis, so you might be able to get as much mileage by boning up on a good statistics &/or algorithms textbook, in addition to more obvious bio & chem materials.

    Obviously it would help a lot to understand the underlying biology and chemistry, but the core of what you're doing is going to revolve around finding statistically relevant patterns out of huge datasets, and while the biologists and organic chemists you end up working this will know their science well, they won't necessarily know the algorithms involved -- that's what you as a bioinformaticist (or whatever the term ends up being) bring to the effort.

    Good luck with it... :)

    --
    DO NOT LEAVE IT IS NOT REAL

Re: Where to learn about Bioinformatics?
by indapa (Monk) on Dec 13, 2001 at 23:45 UTC
    If you are already an accomplished programmer, your best bet would be to get some background in biology and statistics.

    I work at an academic genome sequencing center and most of my programming is data munging. If I didn't have a background in biology, I would still be able to implement my programs, but my job wouldn't be as interesting.

    If you are looking for good biology textbook take a look at Recombinant DNA by James Watson. Its not as behemoth as Molecular Biology of the Cell and is a classic.

Re: Where to learn about Bioinformatics?
by Anonymous Monk on Dec 14, 2001 at 02:13 UTC
    www.google.com
Start Learning the Biology
by NotJeff (Beadle) on Dec 14, 2001 at 10:02 UTC
    If you know perl, your best bet is to move on to learning the biological aspect of bioinformatics. You might try looking through the MIT Genome Center website, though it might require some background reading. A local school may offer bioinformatics classes. Since you know some perl and CS in general, the applications will become almost immediately apparent, I suspect, once the biology is in hand.
Re: Where to learn about Bioinformatics?
by Bukowski (Deacon) on Jun 20, 2002 at 13:00 UTC
    I am a 'praciticing' bioinformatician - and the best place to learn is on the job. I know that sounds trite, but you already have the coding skills - what you seem to need is a background in biology.

    You could, for instance, pick up "Developing Bioinformatics Computer Skills" an O'Reilly title, and skip the programming bits - and become familiar with the tools biologists use for data analysis.

    You would be well advised to spend some time poking around the major source of biological data online the NCBI (National Centre for Biotechnology Information) at http://www.ncbi.nlm.nih.gov/

    If you're looking for a real introduction into the bioinformatics world then its well worth looking at:
    Bioinformatics Sequence and Genome Analysis from CSHL Press. There is an associated website at http://www.bioinformaticsonline.org/

    That book will link you out to the scientific papers underlying much of bioinformatics, and pacing yourself with this book would stand you in good stead.

    How about contributing to a package at the open source site http://www.bioinformatics.org

    Keep an eye on lecture series going on at local Universities, try to attend talks on computational biology and bioinformatics.

    Read books, explore resources, get involved. Learn BioPerl (http://bio.perl.org). Get a good overview of MySQL if you don't have one yet - its frequently deployed by bioinformaticians.

    Above all enjoy - its a great field, and I wouldn't want to be anywhere else.

    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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