Chapter 9. Introduction to Bioperl

Bioperl is a collection of more than 500 Perl modules for bioinformatics that have been written and maintained by an international group of volunteers. Bioperl is free (under a very unrestrictive copyright), and its home is http://bioperl.org.

One of the most difficult things about Bioperl is getting started using it. This is due to a scarcity of good documentation (which is being rectified) as well as the sheer size of the Bioperl module library. This chapter will help you get started using the Bioperl project software; it will guide you through the initial steps of getting the software, installing it, and exploring the tutorial and example material that it provides. After working through this chapter, you'll be well prepared to delve deeper into the riches of Bioperl, and, if you've also worked through the object-oriented chapters earlier in this book, you'll be in a good position to read the Bioperl code and contribute to the project yourself.

The modules in Bioperl are written in the object-oriented style. Perl programmers who do not know object-oriented programming can still use the Bioperl modules with just a bit of extra information, as outlined in Chapter 3.

The Bioperl modules cover various areas of bioinformatics, including some you've seen previously in this book. Although Bioperl includes some example programs, it is not meant to be a collection of complete user -ready programs. Rather, it's implemented as a toolkit you can dip into for help when writing your own programs. Its goal is to provide good working solutions to common bioinformatics tasks and to speed your program development.

One of the best things about Bioperl is that it's an open source project, meaning that interested developers are invited to contribute by writing code or in other ways, and the code is available to anyone interested. If you've learned enough about Perl for bioinformatics to have worked through a good portion of this book, you'll find plenty of opportunity to get involved in Bioperl if you have the time and inclination.