Re: [pydstool-users] simulation with many auxiliary equations

[gyro f. <gyr...@gm...>]

On 5/24/2012 7:33 AM, Ludo Visser wrote:
> Hi,
> 
> I'm not completely sure what the problem is that you're running into.
> 
> If the complexity of the conversion equations is an issue, then you can use either the symbolic manipulation tools provided by PyDSTool (although I have no experience with that) or SymPy (I have a lot of experience with that, and SymPy plays really quite nice with PyDSTool) to take semi-automate the generation of the ODEs. Since all equations are specified as string expression, some clever string manipulation can get you a long way.
> 
> For the rest, the problem you describe seems an ordinary first order system, so a single Generator instance, like used in the harmonic oscillation example, should work.
> 
> Regards,
> Ludo Visser
> 

Thank you for the reply, Ludo.

The problem is one of ignorance. I am accustomed to ODE integrators
like scipy.odeint or MATLAB's ode45, where one writes a function
that returns the numerical rhs of the ODE system at a given time
point and the ODE solver takes this function as an argument.

Although I am a decent Python programmer, the object oriented
structure of the PyDSTool framework and the idea of specifying
equations and parameters using strings and dictionaries is foreign
to me.

For instance, there is an example in the Elementary Tutorial for a
calcium channel model that looks something like this:
-----
DSargs = dst.args(name='Calcium channel model')
DSargs.pars = { 'vl': -60, 'vca': 120, 'i': 0, ...
DSargs.fnspecs  = {'minf': (['v'], '0.5 * ...
DSargs.varspecs = {'v': '( i + gl * (vl - v) - gca * minf(v) *
(v-vca) )/c','w': 'v-w' }
DSargs.ics = {'v': 0, 'w': 0 }
----

When I compare this to my model, it is unclear where my conversion
equations should go and what syntax I should use.

If you, or others, could show me a brief example, that would be
greatly appreciated.

Thank you.

Best regards,
gyro