Correct 'directory' section
[bioperl-live.git] / BioPerl.pm
blob586da4c2b198b59e204f07f985cc22ce02bdabbe
1 package BioPerl;
3 use strict;
5 # At some future point, when we break the current core into more maintainable
6 # bits, this will have a direct VERSION number, but for now we will be using
7 # the root version for everything
8 use Bio::Root::Version;
10 our $VERSION = $Bio::Root::Version::VERSION;
11 eval $VERSION;
15 __END__
17 =head1 NAME
19 BioPerl - Perl Modules for Biology
21 =head1 SYNOPSIS
23 If you're new to BioPerl, you should start reading the BioPerl HOWTO's:
25 L<http://www.bioperl.org/wiki/HOWTOs>
27 =head2 References for Individual Modules
29 For ease of maintenance and coordination amongst contributors, BioPerl
30 code is maintained in a modular form, as is the documentation. Refer to
31 the documentation for individual modules by using perldoc, i.e.
33 C<perldoc Bio::Seq>
35 to get documentation for the Bio::Seq object.
37 =head1 DESCRIPTION
39 BioPerl is the product of a community effort to produce Perl code which is
40 useful in biology. Examples include Sequence objects, Alignment objects and
41 database searching objects. These objects not only do what they are advertised
42 to do in the documentation, but they also interact - Alignment objects are made
43 from the Sequence objects, Sequence objects have access to Annotation and
44 SeqFeature objects and databases, Blast objects can be converted to Alignment
45 objects, and so on. This means that the objects provide a coordinated and
46 extensible framework to do computational biology.
48 BioPerl development focuses on Perl classes, or code that is used to create
49 objects representing biological entities. There are scripts provided in the
50 scripts/ and examples/ directories but scripts are not the main focus of the
51 BioPerl developers. Of course, as the objects do most of the hard work for you,
52 all you have to do is combine a number of objects together sensibly to make
53 useful scripts.
55 The intent of the BioPerl development effort is to make reusable tools that aid
56 people in creating their own sites or job-specific applications.
58 The BioPerl website at L<http://bioperl.org> also attempts to maintain links
59 and archives of standalone bio-related Perl tools that are not affiliated or
60 related to the core BioPerl effort. Check the site for useful code ideas and
61 contribute your own if possible.
63 =head1 INSTALLATION
65 The BioPerl modules are distributed as a tar file that expands into a standard
66 perl CPAN distribution. Detailed installation directions can be found in the
67 distribution INSTALL file. Installing on windows using ActiveState Perl is
68 covered in the INSTALL.WIN file. We highly suggest reading the installation
69 instructions on the BioPerl website:
71 L<http://www.bioperl.org/wiki/Installing_BioPerl>
73 Note that only the following are supported at this time with the current API:
75 =over 3
77 =item BioPerl-db
79 =item BioPerl-network
81 =item BioPerl-run
83 =item BioPerl-pedigree
85 =item Bio::Graphics
87 =back
89 =head1 GETTING STARTED
91 The distribution I<scripts/> directory has working scripts for use with BioPerl,
92 check the self-described I<examples/> directory as well. You are more than
93 welcome to contribute your script!
95 If you have installed BioPerl in the standard way, as detailed in the INSTALL in
96 the distribution, these scripts should work by just running them. If you have
97 not installed it in a standard way you will have to change the 'use lib' to
98 point to your installation (see INSTALL for details).
100 =head1 GETTING INVOLVED
102 BioPerl is a completely open community of developers. We are not funded and we
103 don't have a mission statement. We encourage collaborative code, in particular
104 in Perl. You can help us in many different ways, from just a simple statement
105 about how you have used BioPerl to doing something interesting to contributing a
106 whole new object hierarchy. See L<http://bioperl.org> for more information. Here
107 are some ways of helping us:
109 =head2 Asking questions and telling us you used it
111 We are very interested to hear how you experienced using BioPerl. Did it install
112 cleanly? Did you understand the documentation? Could you get the objects to do
113 what you wanted them to do? If BioPerl was useless we want to know why, and if
114 it was great - that too. Post a message to B<bioperl-l@bioperl.org>, the BioPerl
115 mailing list, where all the developers are.
117 Only by getting people's feedback do we know whether we are providing anything
118 useful.
120 =head2 Writing a script that uses it
122 By writing a good script that uses BioPerl you both show that BioPerl is useful
123 and probably save someone elsewhere writing it. If you contribute it to the
124 'script central' at L<http://bioperl.org> then other people can view and use it.
125 Don't be nervous if you've never done this sort of work, advice is freely given
126 and all are welcome!
128 =head2 Find bugs!
130 We know that there are bugs in this code. If you find something which you are pretty
131 sure is a problem, post a bug report using our Bugzilla tracking system:
133 L<https://github.com/bioperl/bioperl-live/issues>
135 Please read the main bug tracking (L<http://www.bioperl.org/wiki/Bugs>) for an
136 overview of what we expect in a bug report. Specifically, having a code and
137 data example where appropriate helps tremendously. We gladly accept all patches
138 after a quick code review.
140 =head2 Suggest new functionality
142 You can suggest areas where the objects are not ideally written and could be
143 done better. The best way is to find the main developer of the module (each
144 module was written principally by one person, except for Seq.pm). Talk to him or
145 her and suggest changes.
147 =head2 Make your own objects
149 If you can make a useful object we will happily include it into the core.
150 Probably you will want to read a lot of the documentation in L<Bio::Root::Root>
151 and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>.
153 =head2 Writing documentation
155 We appreciate good documentation. It's what tells the world what's in BioPerl,
156 it's what instructs the user, it's what describes the rationale and inner
157 workings of the package. Feel free to contribute.
159 =head1 ACKNOWLEDGEMENTS
161 For a more detailed history of the BioPerl project, we recommend the History of
162 BioPerl:
164 L<http://www.bioperl.org/wiki/History_of_BioPerl>
166 =head1 COPYRIGHT
168 Copyright (c) 1996-2009 Georg Fuellen, Richard Resnick, Steven E. Brenner, Chris
169 Dagdigian, Steve Chervitz, Ewan Birney, James Gilbert, Elia Stupka, and others.
170 All Rights Reserved. This module is free software; you can redistribute it
171 and/or modify it under the same terms as Perl itself.
173 =cut