[Bioperl-l] Resources for Perl newbies

Mark A. Jensen maj at fortinbras.us
Mon Mar 16 10:46:16 EDT 2009

Hey All-

Have collated this thread in a refactor of

cheers- MAJ

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Monday, March 16, 2009 10:27 AM
Subject: Re: [Bioperl-l] Resources for Perl newbies

> Don't forget the very useful (shout out to Dave M!) Deobfuscator:
> http://www.bioperl.org/wiki/Deobfuscator
> chris
> On Mar 16, 2009, at 7:56 AM, Mark A. Jensen wrote:
>> Hi All-
>> I thought that I would run down a couple of nice resources
>> full of friendly patient folk for biologists new to Perl. While
>> many of us are happy to chime in on Perl-specific questions,
>> this list is mainly for questions that relate directly to
>> BioPerl modules, or difficulties/ideas for applying those
>> modules to specific tasks. Since BioPerl is written at a
>> high level in sometimes terse code, the new perler jumping
>> in is apt to stumble. No problem--just have a look at some
>> of the following:
>> http://learn.perl.org/faq/beginners.html
>> - here you can find excellent links, plus directions for signing up
>>   to
>> http://www.nntp.perl.org/group/perl.beginners/,
>> a newsgroup devoted to questions at all levels
>> Extremely sane, erudite, helpful, and patient responses can be had at
>> http://www.perlmonks.org/
>> where there are perl resources for all user levels. When I
>> google an error message, and see a perlmonks link, that's
>> the one I click first (unless Hilmar appears in the links, of
>> course).
>> I've found that the best way to learn any language and
>> make it stay learned is to work through a smarter/more
>> experienced person's code. There are plenty of opportunities
>> for that in the BioPerl distributions. Wondering about that
>> error? Read the error message, which contains the line number
>> in the module that threw it, then open that module and dig in!
>> Another great resource for seeing how the developers expect
>> their modules to work are the regression tests, found in the
>> ../t directories of the BioPerl distribution directory (find it
>> at the Subversion repository:
>> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/t.)
>> These are just Perl programs; nothing scary about them.
>> Another repos directory of interest is "examples":
>> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/examples
>> where many many examples of BioPerl module use reside.
>> And don't forget the many introductory resources on the
>> BioPerl wiki (http://www.bioperl.org/wiki), including the
>> HOWTOs (http://www.bioperl.org/wiki/HOWTO) and
>> the Scrapbook (http://www.bioperl.org/wiki/Category:Scrapbook).
>> There are many short and simple code snippets in these places.
>> Happy Coding-
>> Mark
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