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.