Use Bioperl sensibly
Inherit from existing objects
Differentiate internal from external methods
Internal methods are preceded by _ and external ones are not.
Throw exceptions
Make heavy use of the Bioperl $obj->throw syntax to throw exceptions when things look wrong. This drastically cuts down time tracking errors.
Document with Bioperl POD
Use bioperl boilerplate for method documentation.
Always test
Testing your code with the Perl test system provides for long term stability.
Your code is not written until you have written a test for it.
<<alternative statement: "Do not write your code until you have written a test for it.">>