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I've been running into an issue and I'm curious what sort of work arounds may be available. My model previously had all sections with a region that was the cytosol and a region that was the endoplasmic reticulum (er). Now I'm making synaptic spines which don't always have ER, so I tried making regio...

I'm having an issue using setpointer() to connect a species concentration to a density mechanism. If I use a normal reference variable such as h._ref_t, then I don't get errors. However, if I use a line like h.setpointer(my_species.nodes(my_sec(0.5))[0]._ref_concentration, 'my_ptr', sec(0.5).mech_na...

I have been attempting to use Node.include_flux() similarly to https://senselab.med.yale.edu/ModelDB/S ... .py#tabs-2 My problem is that after setting up a simple test flux value using these lines for nd in self.ip3.nodes(sec): nd.include_flux(1000.0) the ip3 concentration value doesn't seem at all ...

I've been reading through the documentation and tutorials and I'm a bit confused on the rxd.Parameter object. I've used it to set different values between nodes for the rate in a rxd.Rate object, so I'm familiar with that usage. However, when I tried to use Parameter by multiplying a Species to set ...

I was wondering if there is some way to cause an abrupt change in concentration. My attempts at changing the concentration mid simulation by directly setting the concentration value of a node doesn't seem to have any effect. I also attempted to alter the rate of an rxd.Rate object mid simulation, bu...