9.4 Bioperl Problems
Bioperl
is still a work in progress, and it has some problems.
I'd like to mention the two main problems now.First, the Bioperl documentation is incomplete. In fact, until fairly
recently, there was no document that provided a tutorial introduction
to the project. This has changed; the
bptutorial.pl document, which
you've already seen and will see more of, is an
excellent beginning, despite its occasional errors. This document
cleverly combines a tutorial with quite a few example programs that
you can run, as you'll soon see.Other documentation for Bioperl is also available, including
Internet-based tutorials, forthcoming books, example programs, and
journal articles. So, the situation has recently improved.Second, Bioperl is big (over 500 modules), written by volunteers, and
gradually evolving. The size of the project is a sign that Bioperl
addresses many interesting and useful problems, but it also means
that, for the new user of Bioperl, an overview of the available
resources is a task in itself.The majority of the Bioperl code is quite good, especially the
most-used parts of it. However, the volunteer and evolving nature of
Bioperl development means that some of the code is unfinished and not
as well integrated with other parts of the project as one would like.
Newer or less used modules may still need some shaking out by users
in real-world situations. This is where you can make an initial
contribution to the project: as you find problems, report them (more
on that later).Many of the computing world's most successful
programs are the result of the same kind of volunteer development as
Bioperl (the Perl language itself and the Apache web server are two
examples). Bioperl is well positioned to achieve a similarly central
position in the field of bioinformatics. |
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