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Re: Beginning Perl For Bioinformatics

by scain (Curate)
on Jan 23, 2002 at 01:23 UTC ( #140738=note: print w/replies, xml ) Need Help??


in reply to Beginning Perl For Bioinformatics

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).

Scott

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Re: Re: Beginning Perl For Bioinformatics
by cadfael (Friar) on Jan 23, 2002 at 19:37 UTC
    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.

      Scott

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