Speaking as a bio and Perl person, bioperl is usually an overengineered waste of time. As to your original question, the main factor is usually what your colleagues use. The second question is usually how easily the language interfaces with C, FORTRAN, and the shell. Biology is text-intensive, especially in its scripty parts, so Perl is a good language for it, but even with PDL, it can't compete with Octave for numerical stuff.