[SciPy-User] Optimizing odeint without a for loop

[Rob Clewley]

Barrett,

On Wed, Jun 4, 2014 at 1:06 PM, Moore, Eric (NIH/NIDDK) [F]
<eric.moore2 at nih.gov> wrote:
> This is an initial attempt to model a neural network with two differential variables per cell--voltage, and the response variable n. I can go back and add more later as needed. I have a question about this code (obviously, all constants are given):

A more "natural" way to work with your model, where you can focus on
the modeling and not worry about optimizing its implementation "under
the hood," is to use a simulator package designed for ODEs. A good
example is PyDSTool, which has minimal dependencies, is very fast for
smooth ODEs such as yours (compiles C code from your high-level model
specs automatically), and has a neural template toolbox for building
biophysical models in a modular fashion. What you've written is OK for
one-off small model scripts, but once you start building networks, or
wanting to manipulate the model parameters or structure in a more
sophisticated fashion, you'll be much better off investing in a proper
modeling tool. There are several other to choose from, depending on
your eventual needs.

-Rob