BioPerl

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Officially organized in 1995 and existing informally for several years prior, the BioPerl project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

To learn more about how the project came about see the History of BioPerl.

BioPerl is released under the Perl Artistic License. There is more information about Licensing BioPerl and using it in academic and commercial products.

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Perl Modules for Biology

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.

Get 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.

Write a Script

By writing a good script that uses Bioperl you both show that Bioperl is useful and probably save someone elsewhere writing it. Don't be nervous if you've never done this sort of work, advice is freely given and all are welcome!

Find bugs!

We know that there are bugs in there. If you find something which you are pretty sure is a problem, post a note to us via the bug tracking system.

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.

Make Your Own Objects

If you can make a useful module we will happily include it into the core. Probably you will want read Advanced BioPerl and talk to people on the Mailing list.

Write 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.

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