www.neuron.yale.edu

Hi there!

I use a model of Combe et al. 2018:

• https://doi.org/10.1523/JNEUROSCI.0449-18.2018

• https://senselab.med.yale.edu/modeldb/S ... del=244416

When I removed all tmpo2 variable usage from cell_setup.hoc:

• link to the file: https://senselab.med.yale.edu/modeldb/S ... hoc#tabs-2

• Removing this part and all other occurences of tmpo2 variable:

I discovered that in the soma after ~500 ms there are discrepancies in mV readouts:

• -15.816405568815716 - with Shape (with variable tmpo2)

• -15.828809384418346 - without Shape (without variable tmpo2)

I did all readouts through Python API, so it may also affect it.

Obviously it may be related to the rest of the code, but I think that tmpo2's Shape is quite independent from the rest of the code.

So does the usage of the Shape may affect mV readouts?

Before commenting I will need to see this for myself. The model authors describe more than one way to launch the model. Exactly what did you do?

Dear Ted,

I checked once more the code and I discovered that I use cvode(True), which means that there is a variable timestep.

My current readouts for the same model but different compartment are:
As you can see - for the constant timestep - there is almost identical value of mV. However for the variable timestep - the step differ ~0.1 ms and the readout ~0.016 mV. For this experiment I took the first mV readout which passed 50ms.

So I wonder why the usage of Shape() changes a little bit the timestep?

See my message from June 29.

Did you resolve the problem yourself, or do you still have a question?

Sorry Ted, I tried to prepare the code for you and make sure that there is no interference from the core I wrote, but then I switched to a different task, and left it for later, but I will prepare the code next week and let you know.