[bip] Bioinformatics software design

[Colin Gillespie]

Hi Nathan,

Nathan Harmston wrote:
> 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.
Out of interest, what sort of things are you doing?
> 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?
Testing stochastic models is tricky. Look at

   Evans, T.W., Gillespie, C.S. and Wilkinson, D.J. The SBML Discrete 
Stochastic Models Test Suite. Bioinformatics 2008, 24, 285-286.

to get an idea of how to test a stochastic simulator. I can email you a 
preprint separately if you wish.
>
> 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.
This depends on what you exactly you want to do.

Best wishes,

Colin

-- 
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/




-- 
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/