BioPerl - Perl modules for biology
If you're new to BioPerl, you should start reading the BioPerl HOWTO's:
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.
to get documentation for the Bio::Seq object.
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.
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:
Note that only the following are supported at this time with the current API:
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.
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:
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 email@example.com, the BioPerl mailing list, where all the developers are.
Only by getting people's feedback do we know whether we are providing anything useful.
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!
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:
Please read the main bug tracking (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.
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.
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, firstname.lastname@example.org.
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.
For a more detailed history of the BioPerl project, we recommend the History of BioPerl:
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
email@example.com - General discussion
https://bioperl.org/Support.html - About the mailing lists
Please direct usage questions or support issues to the mailing list: firstname.lastname@example.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
See the individual modules for their authors.
This software is copyright (c) by many people (see the individual modules for their copyright holders).
This software is available under the same terms as the perl 5 programming language system itself.
To install BioPerl, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.