NAME
BioPerl - Perl Modules for Biology
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
Current Overview
Core Bioperl documentation has been split up into the following sections:
bioperl
BioPerl overview (this document)
We may add more documents in the future, including:
biodatabases
How to use databases with BioPerl
biodesign
A guide for authoring a BioPerl module
bioscripts
Description and overview of BioPerl scripts (in the /scripts directory)
Tutorials
BioPerl tutorial for beginners
Institut Pasteur BioPerl tutorial (note: for older versions of BioPerl)
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl
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.
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.
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://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:
GETTING STARTED
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).
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://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.
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://www.bioperl.org/wiki/History_of_BioPerl
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.