[bip] Bioinformatics software design

[Nathan Harmston]

Hi,
For one of my projects I/a group of us will be developing some Systems
Biology modelling software by integrating Python, C/C++ using Ctypes and
maybe doing some R integration. And although it hasn't started I was
thinking about the design of the "API" and the methodology to be used as
well. So I thought I'd ask a few questions:

1. What would you consider to be a good "API"?
          well-documented, intuitive, best guess works, pythonic, do people
have any examples of what they consider a good API/project?

2. Testing?
          although I believe testing is very important I have not really
gone for a hardcore TDD approach before and am thinking I should do it on
this project. What frameworks do people suggest are useful, and how would
you test a function whose output was random/stochastic modelling, since it
is obviously random?

3. Would anyone like to suggest any problems they've found in developing
software for the Bioinformatics/Systems Biology user? I don't like pretty
interfaces and prefer to keep it simple and powerful and unfortunately
biologists like pretty things.

Any other comments/ideas are welcome.

Many Thanks

Nathan
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