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RFC: BioInformatics tutorial?

by rvosa (Curate)
on Sep 21, 2005 at 01:20 UTC ( #493636=perlmeditation: print w/ replies, xml ) Need Help??

Analogous to Perl & Math: A Quick Reference, I think there could be a tutorial about Perl for biologists. From time to time I can see SoPW questions pop up about DNA sequence parsing and so on, and it seems from projects like BioPerl and EnsEMBL that Perl is quite popular with biologists. I volunteer to write such a node, if I get the impression you think it's a good idea.

Comment on RFC: BioInformatics tutorial?
Re: RFC: BioInformatics tutorial?
by Tanktalus (Canon) on Sep 21, 2005 at 04:16 UTC

    Be my guest. :-) From what I gather, tutorials are written by those who feel the need to write them, not by popular acclamation and appointment/assignment to some poor sucker. I, too, have noticed a number of bio questions popping up here from time to time, and have wondered if I could ever switch careers into helping biologists use computers for their research. But then I am reminded of the smell of the biology building at my alma mater, and, well, I'll stick to my current job, I think. :-)

Re: RFC: BioInformatics tutorial?
by bwelch (Curate) on Sep 21, 2005 at 13:47 UTC
    Personally, I'd welcome a bioinformatics tutorial. I made the switch from doing general software development to research bioinformatics two years ago. With zero background in biology or genetics, there was definitely a serious learning curve.

    However, many of the problems in bioinformatics are not really that different. Once you get a handle on the terminology and types of problems involved, it's much like any other text mining, data manipulation, or analysis project.

    Two books that I found helpful:

Re: RFC: BioInformatics tutorial?
by bioMan (Beadle) on Sep 21, 2005 at 17:30 UTC

    Another Perl bioinformatics tutorial wouldn't be a bad thing if it was well written. The problem I have with the BioPerl tutorial is that it appears to have been written for computer programmers and I aint no programmer.

    I really want to understand the programming aspect of bioinformatics so I can do my job better, but my many years of existence have been spent on understanding the finer points of biology.

    Of course the biggest problem with bioinformatics is that it is a moving target, a rapidly moving target. After starting with simple text matching and text manipulations the field is evolving to use differential equations, time sequences, networks, linguistics, matrix algebra, graphs, artificial intelligence, genetic algorithms, electronic circuit theory, communication theory, ...

    If you choose to accept this mission -- good luck.

Re: RFC: BioInformatics tutorial?
by albert (Monk) on Sep 22, 2005 at 09:54 UTC
    You should keep in mind that "Bioinformatics" is a broad catchall term, which covers many different things at the intersection of biology and informatics. Very diverse questions and techniques are used in biology, which means there are a diverse set of informatic methods to accompany these.

    Therefore, you should keep in mind that a "one size fits all" tutorial may not fit all. I do think that a tutorial in Perl for biologists is a useful concept, but you should keep in mind that it can be quite a broad term. It is exactly as bwelch says. Once one gets a handle on the terminology, it is like any other analysis.

    -albert

      Taking all your replies in consideration, I think what would be most useful is a meta-tutorial, with:
      • Intro: perl for biologists, where to start.
      • Intro: biology for perlists, where to start.
      • Commonly used modules.
      • Books.
      • People, organisations, projects.
      I am collecting info on these issues, trying to boil things down to sensible proportions. I welcome all suggestions.

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