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package BioPerl; | ||
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use strict; | ||
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# At some future point, when we break the current core into more maintainable | ||
# bits, this will have a direct VERSION number, but for now we will be using | ||
# the root version for everything | ||
use Bio::Root::Version; | ||
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our $VERSION = $Bio::Root::Version::VERSION; | ||
eval $VERSION; | ||
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1; | ||
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__END__ | ||
=head1 NAME | ||
BioPerl - Perl Modules for Biology | ||
=head1 SYNOPSIS | ||
If you're new to BioPerl, you should start reading the BioPerl HOWTO's: | ||
L<http://bioperl.org/howtos/index.html> | ||
=head2 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. | ||
C<perldoc Bio::Seq> | ||
to get documentation for the Bio::Seq object. | ||
=head1 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 L<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. | ||
=head1 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: | ||
L<http://bioperl.org/INSTALL.html> | ||
Note that only the following are supported at this time with the current API: | ||
=over 3 | ||
=item BioPerl-db | ||
=item BioPerl-network | ||
=item BioPerl-run | ||
=item BioPerl-pedigree | ||
=item Bio::Graphics | ||
=back | ||
=head1 GETTING STARTED | ||
The distribution I<scripts/> directory has working scripts for use with BioPerl, | ||
check the self-described I<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). | ||
=head1 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 L<http://bioperl.org> for more information. Here | ||
are some ways of helping us: | ||
=head2 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 B<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. | ||
=head2 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 L<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! | ||
=head2 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: | ||
L<https://github.com/bioperl/bioperl-live/issues> | ||
Please read the main bug tracking (L<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. | ||
=head2 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. | ||
=head2 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 L<Bio::Root::Root> | ||
and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>. | ||
=head2 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. | ||
=head1 ACKNOWLEDGEMENTS | ||
For a more detailed history of the BioPerl project, we recommend the History of | ||
BioPerl: | ||
L<http://bioperl.org/articles/History_of_BioPerl.html> | ||
=head1 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. | ||
=cut | ||
package BioPerl; | ||
|
||
use strict; | ||
|
||
# At some future point, when we break the current core into more maintainable | ||
# bits, this will have a direct VERSION number, but for now we will be using | ||
# the root version for everything | ||
use Bio::Root::Version; | ||
|
||
our $VERSION = $Bio::Root::Version::VERSION; | ||
eval $VERSION; | ||
|
||
1; | ||
|
||
__END__ | ||
=head1 NAME | ||
BioPerl - Perl Modules for Biology | ||
=head1 SYNOPSIS | ||
If you're new to BioPerl, you should start reading the BioPerl HOWTO's: | ||
L<http://bioperl.org/howtos/index.html> | ||
=head2 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. | ||
C<perldoc Bio::Seq> | ||
to get documentation for the Bio::Seq object. | ||
=head1 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 L<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. | ||
=head1 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: | ||
L<http://bioperl.org/INSTALL.html> | ||
Note that only the following are supported at this time with the current API: | ||
=over 3 | ||
=item BioPerl-db | ||
=item BioPerl-network | ||
=item BioPerl-run | ||
=item BioPerl-pedigree | ||
=item Bio::Graphics | ||
=back | ||
=head1 GETTING STARTED | ||
The distribution I<scripts/> directory has working scripts for use with BioPerl, | ||
check the self-described I<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). | ||
=head1 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 L<http://bioperl.org> for more information. Here | ||
are some ways of helping us: | ||
=head2 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 B<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. | ||
=head2 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 L<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! | ||
=head2 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: | ||
L<https://github.com/bioperl/bioperl-live/issues> | ||
Please read the main bug tracking (L<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. | ||
=head2 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. | ||
=head2 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 L<Bio::Root::Root> | ||
and talk to people on the BioPerl mailing list, B<bioperl-l@bioperl.org>. | ||
=head2 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. | ||
=head1 ACKNOWLEDGEMENTS | ||
For a more detailed history of the BioPerl project, we recommend the History of | ||
BioPerl: | ||
L<http://bioperl.org/articles/History_of_BioPerl.html> | ||
=head1 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. | ||
=cut |