[Bioperl-l] Resources for Perl newbies

Mark A. Jensen maj at fortinbras.us
Mon Mar 16 08:56:27 EDT 2009

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:

- here you can find excellent links, plus directions for signing up
 a newsgroup devoted to questions at all levels

Extremely sane, erudite, helpful, and patient responses can be had at


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

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: 
These are just Perl programs; nothing scary about them.
Another repos directory of interest is "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-

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