www.neuron.yale.edu

The Network Builder is designed for prototyping simple networks that have only a few cells and a few synaptic connections (where "few" means maybe half a dozen at most; more than that would exceed the patience of most mortals). Also, no more than a single instance of a particular synaptic ...

Maybe I should have been more explicit. This is what I had in mind: 1. You use your code to run a simulation in which a simple model is subjected to a simple extracellular stimulus. 2. I run a simulation using my own code that replicates your model and stimulus. 3. We compare results. The results sh...

"I guess the code works" isn't exactly a sound starting point for a modeling project. A little effort now to verify correctness could save you a lot of time in the future. I understand you're eager to get started working with complex model cells, but you really should start by verifying th...

Thank you for your interest in using NEURON in your research. For know I'm just doing basics and I write some code to reproduced the results from 10.1113/jphysiol.2012.247171 Nice paper. That's a good way to start. visualizing the v and e_extracellular recorded at soma it seems to work (at least as ...

Thanks, that's very helpful. We need to do a complete overhaul of install & config instructions.

You got the basic idea, even though in retrospect my discussion about how to deal with the forcing function was actually rather misleading. I should have written something like this: The inherent dynamics of a are goverened by the first term on the RHS of the ODE, that is, a * (1 - a). The second te...

Two questions: 1. a must not drop below 0 regardless of what b does? 2. if a == 0 and the RHS of a' = a * (1 - a) - b becomes positive, a should follow? Yes, and yes. It's a somewhat arbitrary test of enforcing boundary limits on a state variable. Using WATCH to detect when a drops below 0 keeps th...

Two questions:
1. a must not drop below 0 regardless of what b does?
2. if a == 0 and the RHS of
a' = a * (1 - a) - b
becomes positive, a should follow?

I think the problem is related to the fact that not even the original mod file does quite what one might expect. Use the GUI to add a RunControl panel, plus two graphs: one that plots obj.a vs. t (create a Voltage axis graph, Delete v, then use Plot what? to add obj.a to the plotlist), and one that ...

if I use the exact same code with a built-in mechanism like ExpSyn (in place of the custom mechamisms), the events are added at the expected times and sections Sounds like you're launching stock NEURON, rather than the nrnivmodl-created executable executable that contains the compiled mechanisms. W...

For any real neuronal morphology the soma electrically extremely compact--it is essentially isopotential for all frequencies at which the cable equation is relevant. You can run a simple test to prove this to yourself. Create a model cell in which the soma's morphology is specified using the pt3d s...

https://github.com/chlubba/PyPNS presents instructions for installation and configuration, including install & config of NEURON 7.6.7. Those instructions don't work?

Why the factor 2? Good-you're thinking for yourself. NEURON's spatial discretization uses the central difference approximation to the second spatial derivative of membrane potential. Consequently numerical integration of the discretized cable equation generates solutions at locations that correspon...

When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, it is generally a good idea to initialize the model to its steady state, and delay the onset of perturbations such as stimuli (current clamps, synaptic activations etc.) until t (h.t to all you...

You're welcome. A few things I forgot to say-- To see the effects of changing synaptic weight at the times specified in tvec require that h.tstop be set to at least 80 ms (100 would be fine). When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, i...