lib/BioPerl.pm

   1 package BioPerl;
   2
   3 use utf8;
   4 use strict;
   5 use warnings;
   6
   7 # ABSTRACT: Perl modules for biology
   8 # AUTHOR: See the individual modules for their authors.
   9 # OWNER: many people (see the individual modules for their copyright holders)
  10 # LICENSE: Perl_5
  11
  12 =head1 SYNOPSIS
  13
  14 If you're new to BioPerl, you should start reading the BioPerl HOWTO's:
  15
  16 L<http://bioperl.org/howtos/index.html>
  17
  18 =head2 References for Individual Modules
  19
  20 For ease of maintenance and coordination amongst contributors, BioPerl
  21 code is maintained in a modular form, as is the documentation.  Refer to
  22 the documentation for individual modules by using perldoc, i.e.
  23
  24 C<perldoc Bio::Seq>
  25
  26 to get documentation for the Bio::Seq object.
  27
  28 =head1 DESCRIPTION
  29
  30 BioPerl is the product of a community effort to produce Perl code which is
  31 useful in biology. Examples include Sequence objects, Alignment objects and
  32 database searching objects. These objects not only do what they are advertised
  33 to do in the documentation, but they also interact - Alignment objects are made
  34 from the Sequence objects, Sequence objects have access to Annotation and
  35 SeqFeature objects and databases, Blast objects can be converted to Alignment
  36 objects, and so on. This means that the objects provide a coordinated and
  37 extensible framework to do computational biology.
  38
  39 BioPerl development focuses on Perl classes, or code that is used to create
  40 objects representing biological entities. There are scripts provided in the
  41 scripts/ and examples/ directories but scripts are not the main focus of the
  42 BioPerl developers. Of course, as the objects do most of the hard work for you,
  43 all you have to do is combine a number of objects together sensibly to make
  44 useful scripts.
  45
  46 The intent of the BioPerl development effort is to make reusable tools that aid
  47 people in creating their own sites or job-specific applications.
  48
  49 The BioPerl website at L<http://bioperl.org> also attempts to maintain links
  50 and archives of standalone bio-related Perl tools that are not affiliated or
  51 related to the core BioPerl effort. Check the site for useful code ideas and
  52 contribute your own if possible.
  53
  54 =head1 INSTALLATION
  55
  56 The BioPerl modules are distributed as a tar file that expands into a standard
  57 perl CPAN distribution. Detailed installation directions can be found in the
  58 distribution INSTALL file. Installing on windows using ActiveState Perl is
  59 covered in the INSTALL.WIN file.  We highly suggest reading the installation
  60 instructions on the BioPerl website:
  61
  62 L<http://bioperl.org/INSTALL.html>
  63
  64 Note that only the following are supported at this time with the current API:
  65
  66 =over 3
  67
  68 =item BioPerl-db
  69
  70 =item BioPerl-network
  71
  72 =item BioPerl-run
  73
  74 =item BioPerl-pedigree
  75
  76 =item Bio::Graphics
  77
  78 =back
  79
  80 =head1 GETTING STARTED
  81
  82 The distribution I<scripts/> directory has working scripts for use with BioPerl,
  83 check the self-described I<examples/> directory as well. You are more than
  84 welcome to contribute your script!
  85
  86 If you have installed BioPerl in the standard way, as detailed in the INSTALL in
  87 the distribution, these scripts should work by just running them.
  88
  89 =head1 GETTING INVOLVED
  90
  91 BioPerl is a completely open community of developers. We are not funded and we
  92 don't have a mission statement. We encourage collaborative code, in particular
  93 in Perl. You can help us in many different ways, from just a simple statement
  94 about how you have used BioPerl to doing something interesting to contributing a
  95 whole new object hierarchy. See L<http://bioperl.org> for more information. Here
  96 are some ways of helping us:
  97
  98 =head2 Asking questions and telling us you used it
  99
 100 We are very interested to hear how you experienced using BioPerl. Did it install
 101 cleanly? Did you understand the documentation? Could you get the objects to do
 102 what you wanted them to do? If BioPerl was useless we want to know why, and if
 103 it was great - that too. Post a message to B<bioperl-l@bioperl.org>, the BioPerl
 104 mailing list, where all the developers are.
 105
 106 Only by getting people's feedback do we know whether we are providing anything
 107 useful.
 108
 109 =head2 Writing a script that uses it
 110
 111 By writing a good script that uses BioPerl you both show that BioPerl is useful
 112 and probably save someone elsewhere writing it. If you contribute it to the
 113 'script central' at L<http://bioperl.org> then other people can view and use it.
 114 Don't be nervous if you've never done this sort of work, advice is freely given
 115 and all are welcome!
 116
 117 =head2 Find bugs!
 118
 119 We know that there are bugs in this code. If you find something which you are pretty
 120 sure is a problem, post a bug report using our Bugzilla tracking system:
 121
 122 L<https://github.com/bioperl/bioperl-live/issues>
 123
 124 Please read the main bug tracking (L<http://www.bioperl.org/articles/Bugs.html>) for an
 125 overview of what we expect in a bug report. Specifically, having a code and
 126 data example where appropriate helps tremendously.  We gladly accept all patches
 127 after a quick code review.
 128
 129 =head2 Suggest new functionality
 130
 131 You can suggest areas where the objects are not ideally written and could be
 132 done better. The best way is to find the main developer of the module (each
 133 module was written principally by one person, except for Seq.pm). Talk to him or
 134 her and suggest changes.
 135
 136 =head2 Make your own objects
 137
 138 If you can make a useful object we will happily include it into the core.
 139 Probably you will want to read a lot of the documentation in L<Bio::Root::Root>
 140 and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>.
 141
 142 =head2 Writing documentation
 143
 144 We appreciate good documentation. It's what tells the world what's in BioPerl,
 145 it's what instructs the user, it's what describes the rationale and inner
 146 workings of the package. Feel free to contribute.
 147
 148 =head1 ACKNOWLEDGEMENTS
 149
 150 For a more detailed history of the BioPerl project, we recommend the History of
 151 BioPerl:
 152
 153 L<http://bioperl.org/articles/History_of_BioPerl.html>
 154
 155 =cut
 156
 157
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