BioPerl.pm

   1 package BioPerl;
   2
   3 use strict;
   4
   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;
   9
  10 our $VERSION = $Bio::Root::Version::VERSION;
  11 eval $VERSION;
  12
  13 1;
  14
  15 __END__
  16
  17 =head1 NAME
  18
  19 BioPerl - Perl Modules for Biology
  20
  21 =head1 SYNOPSIS
  22
  23 If you're new to BioPerl, you should start reading the BioPerl HOWTO's:
  24
  25 L<http://www.bioperl.org/wiki/HOWTOs>
  26
  27 =head2 References for Individual Modules
  28
  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.
  32
  33 C<perldoc Bio::Seq>
  34
  35 to get documentation for the Bio::Seq object.
  36
  37 =head1 DESCRIPTION
  38
  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.
  47
  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.
  54
  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.
  57
  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.
  62
  63 =head1 INSTALLATION
  64
  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:
  70
  71 L<http://www.bioperl.org/wiki/Installing_BioPerl>
  72
  73 Note that only the following are supported at this time with the current API:
  74
  75 =over 3
  76
  77 =item BioPerl-db
  78
  79 =item BioPerl-network
  80
  81 =item BioPerl-run
  82
  83 =item BioPerl-pedigree
  84
  85 =item Bio::Graphics
  86
  87 =back
  88
  89 =head1 GETTING STARTED
  90
  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!
  94
  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).
  99
 100 =head1 GETTING INVOLVED
 101
 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:
 108
 109 =head2 Asking questions and telling us you used it
 110
 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.
 116
 117 Only by getting people's feedback do we know whether we are providing anything
 118 useful.
 119
 120 =head2 Writing a script that uses it
 121
 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!
 127
 128 =head2 Find bugs!
 129
 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:
 132
 133 L<https://github.com/bioperl/bioperl-live/issues>
 134
 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.
 139
 140 =head2 Suggest new functionality
 141
 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.
 146
 147 =head2 Make your own objects
 148
 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>.
 152
 153 =head2 Writing documentation
 154
 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.
 158
 159 =head1 ACKNOWLEDGEMENTS
 160
 161 For a more detailed history of the BioPerl project, we recommend the History of
 162 BioPerl:
 163
 164 L<http://www.bioperl.org/wiki/History_of_BioPerl>
 165
 166 =head1 COPYRIGHT
 167
 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.
 172
 173 =cut