I'm trying to automate fitting certain parameters in a multicompartment neuronal model by minimizing the error between the model's somatic Vm and experimentally recorded Vm from the same protocol. I previously did this manually using the MultipleRunFitter (MRF) but find the process inefficient and error-prone as I have many variations on the model that I need to fit against several experimental traces. I've since attempted automating my fitting procedure using

*fit_praxis()*and have gotten the basic framework in place. However, I have two issues of which I'm not certain how to address thus necessitating a forum post.

1. How is the "Error Value" computed by the MRF Fitness Generator? I thought it might be least squares error between model and experimental output, so I implemented the following in my function that I pass to

*fit_praxis()*to minimize:

Code: Select all

```
// somav, somat are defined elsewhere
somav = new Vector()
somav.record(&soma[0].v(0.5))
somat = new Vector()
somat.record(&t)
run()
err = 0
for (i=0; i < somat.size(); i=i+1) {
// Need to do this since have CVode active. Iterate over somatic Vm vector of model, and
// find corresponding Vm value of experimental trace by referencing the time vector of the model.
//
// NB: expv is a 13,000 element Vector corresponding to 1.3s of recording.
err = err + (expv.x[somat.x[i]*10-1] - somav.x[i])^2
}
err = sqrt(err) // cause why not
```

*err*is vastly different than the error displayed by the MRF, by an order of magnitude (greater). Thus, I'm curious how the MRF does it.

2. More importantly, how can I set domain bounds for certain parameters in PRAXIS? In the GUI this can be done by clicking on "Parameters" in the MRF, then selecting "Domain Panel". I need this since some of the parameters are coefficients in the time constant equation for a particular ion channel, and cannot take on certain values (such as zero, or negative values). If I don't set the domain, I will eventually get integration errors in NEURON while running PRAXIS in the GUI, and thus want to avoid this situation when fully automating this procedure. I can't see anywhere in the documentation about how to handle this manually. I've seen that they are defined in the corresponding .ft1 session file in a

*ParmFitness*...

*End ParmFitness*block, but don't know what actually uses this or how to do it in an automated fashion without the MRF.

Thanks in advance for any assistance!