Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

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.