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package BioPerl;
use strict;
# At some future point, when we break the current core into more maintainable
# bits, this will have a direct VERSION number, but for now we will be using
# the root version for everything
use Bio::Root::Version;
our $VERSION = $Bio::Root::Version::VERSION;
eval $VERSION;
1;
__END__
=head1 NAME
BioPerl - Perl Modules for Biology
=head1 SYNOPSIS
If you're new to BioPerl, you should start reading the BioPerl tutorial, an
overview of the BioPerl toolkit:
L<http://www.bioperl.org/wiki/BioPerl_Tutorial>
=head2 Current Overview
Core Bioperl documentation has been split up into the following sections:
=over 3
=item * bioperl
BioPerl overview (this document)
=back
We may add more documents in the future, including:
=over 3
=item * biodatabases
How to use databases with BioPerl
=item * biodesign
A guide for authoring a BioPerl module
=item * bioscripts
Description and overview of BioPerl scripts (in the I</scripts> directory)
=back
=head2 Tutorials
=over 3
=item * BioPerl tutorial for beginners
L<http://www.bioperl.org/wiki/BioPerl_Tutorial>
=item * Institut Pasteur BioPerl tutorial (note: for older versions of BioPerl)
L<http://www.pasteur.fr/recherche/unites/sis/formation/bioperl>
=back
=head2 References for Individual Modules
For ease of maintenance and coordination amongst contributors, BioPerl
code is maintained in a modular form, as is the documentation. Refer to
the documentation for individual modules by using perldoc, i.e.
C<perldoc Bio::Seq>
to get documentation for the Bio::Seq object.
=head1 DESCRIPTION
BioPerl is the product of a community effort to produce Perl code which is
useful in biology. Examples include Sequence objects, Alignment objects and
database searching objects. These objects not only do what they are advertised
to do in the documentation, but they also interact - Alignment objects are made
from the Sequence objects, Sequence objects have access to Annotation and
SeqFeature objects and databases, Blast objects can be converted to Alignment
objects, and so on. This means that the objects provide a coordinated and
extensible framework to do computational biology.
BioPerl development focuses on Perl classes, or code that is used to create
objects representing biological entities. There are scripts provided in the
scripts/ and examples/ directories but scripts are not the main focus of the
BioPerl developers. Of course, as the objects do most of the hard work for you,
all you have to do is combine a number of objects together sensibly to make
useful scripts.
The intent of the BioPerl development effort is to make reusable tools that aid
people in creating their own sites or job-specific applications.
The BioPerl website at L<http://bioperl.org> also attempts to maintain links
and archives of standalone bio-related Perl tools that are not affiliated or
related to the core BioPerl effort. Check the site for useful code ideas and
contribute your own if possible.
=head1 DOCUMENTATION
The Bio::Perl module (not this document) is designed to flatten the learning
curve for newcomers to Perl/Bioperl. This is a good place to start if you want
some simple functionality. We have a cookbook tutorial on-line:
L<http://bioperl.org/wiki/BioPerl_Tutorial>
which has embedded documentation. Start there if learning-by-example suits you
most, or examine the BioPerl online course at:
L<http://www.pasteur.fr/recherche/unites/sis/formation/bioperl>
Make sure to check the documentation in the modules as well - there are over 900
modules in BioPerl, and counting, and there's detail in the modules'
documentation that will not appear in the general documentation.
=head1 INSTALLATION
The BioPerl modules are distributed as a tar file that expands into a standard
perl CPAN distribution. Detailed installation directions can be found in the
distribution INSTALL file. Installing on windows using ActiveState Perl is
covered in the INSTALL.WIN file. We highly suggest reading the installation
instructions on the BioPerl website:
L<http://www.bioperl.org/wiki/Installing_BioPerl>
=for TODO: Do we want to add biodesign and biodatabases back in?
The BioPerl modules can interact with local flat file and relational databases.
To learn how to set this up, look at the biodatabases.pod documentation
('perldoc biodatabases.pod' should work once BioPerl has been installed).
Some BioPerl-related distributions such as Bio::Graphics, BioPerl-db,
BioPerl-run, BioPerl-gui, corba-server, BioPerl-ext, BioPerl-pipeline,
BioPerl-microarray and corba-client packages are installed separately from
BioPerl. Please refer to their respective documentation for more information.
Note that only the following are supported at this time with the current API:
=over 3
=item BioPerl-db
=item BioPerl-network
=item BioPerl-run
=item BioPerl-pedigree
=item Bio::Graphics
=back
=head1 GETTING STARTED
A good place to start is by reading the tutorial : L<http://bioperl.org/wiki/BioPerl_Tutorial>
The distribution I<scripts/> directory has working scripts for use with BioPerl,
check the self-described I<examples/> directory as well. You are more than
welcome to contribute your script!
=for TODO Should we add bioscripts back to the distributions?
A list and brief description of all these scripts is found in bioscripts.pod.
If you have installed BioPerl in the standard way, as detailed in the INSTALL in
the distribution, these scripts should work by just running them. If you have
not installed it in a standard way you will have to change the 'use lib' to
point to your installation (see INSTALL for details).
=head1 GETTING INVOLVED
BioPerl is a completely open community of developers. We are not funded and we
don't have a mission statement. We encourage collaborative code, in particular
in Perl. You can help us in many different ways, from just a simple statement
about how you have used BioPerl to doing something interesting to contributing a
whole new object hierarchy. See L<http://bioperl.org> for more information. Here
are some ways of helping us:
=head2 Asking questions and telling us you used it
We are very interested to hear how you experienced using BioPerl. Did it install
cleanly? Did you understand the documentation? Could you get the objects to do
what you wanted them to do? If BioPerl was useless we want to know why, and if
it was great - that too. Post a message to B<bioperl-l@bioperl.org>, the BioPerl
mailing list, where all the developers are.
Only by getting people's feedback do we know whether we are providing anything
useful.
=head2 Writing a script that uses it
By writing a good script that uses BioPerl you both show that BioPerl is useful
and probably save someone elsewhere writing it. If you contribute it to the
'script central' at L<http://bioperl.org> then other people can view and use it.
Don't be nervous if you've never done this sort of work, advice is freely given
and all are welcome!
=head2 Find bugs!
We know that there are bugs in this code. If you find something which you are pretty
sure is a problem, post a bug report using our Bugzilla tracking system:
L<https://redmine.open-bio.org/projects/bioperl/>
Please read the main bug tracking (L<http://www.bioperl.org/wiki/Bugs>) for an
overview of what we expect in a bug report. Specifically, having a code and
data example where appropriate helps tremendously. We gladly accept all patches
after a quick code review.
=head2 Suggest new functionality
You can suggest areas where the objects are not ideally written and could be
done better. The best way is to find the main developer of the module (each
module was written principally by one person, except for Seq.pm). Talk to him or
her and suggest changes.
=head2 Make your own objects
If you can make a useful object we will happily include it into the core.
Probably you will want to read a lot of the documentation in L<Bio::Root::Root>
and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>.
=for TODO Add biodesign.pod back?
biodesign.pod provides documentation on the conventions and ideas
used in BioPerl, it's definitely worth a read if you would like to be a BioPerl
developer.
=head2 Writing documentation
We appreciate good documentation. It's what tells the world what's in BioPerl,
it's what instructs the user, it's what describes the rationale and inner
workings of the package. Feel free to contribute.
=head1 ACKNOWLEDGEMENTS
For a more detailed history of the BioPerl project, we recommend the History of
BioPerl:
L<http://www.bioperl.org/wiki/History_of_BioPerl>
=head1 COPYRIGHT
Copyright (c) 1996-2009 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris
Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka, and others.
All Rights Reserved. This module is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
=cut
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