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Summary

BioPerl - Perl Modules for Biology

Package variables

Included modules

Synopsis

If you're new to BioPerl, you should start reading the BioPerl tutorial, an
overview of the BioPerl toolkit:
http://www.bioperl.org/wiki/BioPerl_Tutorial Core Bioperl documentation has been split up into the following sections:
   BioPerl overview (this document)
We may add more documents in the future, including:
   How to use databases with BioPerl
   A guide for authoring a BioPerl module
   Description and overview of BioPerl scripts (in the /scripts directory)
http://www.bioperl.org/wiki/BioPerl_Tutorial
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl
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.
perldoc Bio::Seq
to get documentation for the Bio::Seq object.

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 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.

Methods description

None available.

Methods code

No methods available.

General 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:
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:
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.

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:
http://www.bioperl.org/wiki/Installing_BioPerl
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:

A good place to start is by reading the tutorial : http://bioperl.org/wiki/BioPerl_Tutorial
The distribution scripts/ directory has working scripts for use with BioPerl,
check the self-described examples/ directory as well. You are more than
welcome to contribute your script!
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).

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 http://bioperl.org for more information. Here
are some ways of helping us:

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 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.

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 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!

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:
https://redmine.open-bio.org/projects/bioperl/
Please read the main bug tracking (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.

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.

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 Bio::Root::Root
and talk to people on the BioPerl mailing list, bioperl-l@bioperl.org.

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.

For a more detailed history of the BioPerl project, we recommend the History of
BioPerl:
http://www.bioperl.org/wiki/History_of_BioPerl

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.