Provided by: libbio-perl-perl_1.7.8-1_all 
NAME
BioPerl - Perl modules for biology
VERSION
version 1.7.8
SYNOPSIS
If you're new to BioPerl, you should start reading the BioPerl HOWTO's:
<http://bioperl.org/howtos/index.html>
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.
"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.
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:
<http://bioperl.org/INSTALL.html>
Note that only the following are supported at this time with the current API:
BioPerl-db
BioPerl-network
BioPerl-run
BioPerl-pedigree
Bio::Graphics
GETTING STARTED
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.
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 <http://bioperl.org> for more information. Here are some
ways of helping us:
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 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.
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 <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!
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:
<https://github.com/bioperl/bioperl-live/issues>
Please read the main bug tracking (<http://www.bioperl.org/articles/Bugs.html>) 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.
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.
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 Bio::Root::Root and talk to people on the BioPerl mailing list,
bioperl-l@bioperl.org.
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.
ACKNOWLEDGEMENTS
For a more detailed history of the BioPerl project, we recommend the History of BioPerl:
<http://bioperl.org/articles/History_of_BioPerl.html>
FEEDBACK
Mailing lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
https://bioperl.org/Support.html - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to
the module maintainer directly. Many experienced and reponsive experts will be able look at the problem
and quickly address it. Please include a thorough description of the problem with code and data examples
if at all possible.
Reporting bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution.
Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR
See the individual modules for their authors.
COPYRIGHT
This software is copyright (c) by many people (see the individual modules for their copyright holders).
This software is available under the same terms as the perl 5 programming language system itself.