I and my group use the Rational documentation process and follow their templates. Look here
for an idea of what they do. Bookwise check out the Addison Wesley Object Technology Series
with Booch, Jacobsen and Runbaugh as the series editors. A good book to start with is 'The Rational Unified Process An Introduction, Second Edition' - this is required reading within my group. 'Managing Software Requirements' by Leffingwell and Widrig of the same series is a good practical book on requirements gathering and documentation, IMO.I suspect if you look around the web for a bit you'll see templates to use somehwere.
yet another biologist hacking perl....