Search found 6021 matches

by ted
Fri Jun 24, 2022 12:16 pm
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 5
Views: 70

Re: Extracellular Stim using python and/or xtra.mod

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...
by ted
Thu Jun 23, 2022 12:42 pm
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 5
Views: 70

Re: Extracellular Stim using python and/or xtra.mod

"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...
by ted
Fri Jun 10, 2022 11:42 am
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 5
Views: 70

Re: Extracellular Stim using python and/or xtra.mod

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 ...
by ted
Tue Jun 07, 2022 2:28 pm
Forum: OS X
Topic: Bad xdarwin link in troubleshooting tip
Replies: 1
Views: 75

Re: Bad xdarwin link in troubleshooting tip

Thanks, that's very helpful. We need to do a complete overhaul of install & config instructions.
by ted
Tue Jun 07, 2022 2:24 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Does POINTER make NET_RECEIVE slower?
Replies: 9
Views: 242

Re: Does POINTER make NET_RECEIVE slower?

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...
by ted
Mon Jun 06, 2022 4:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Does POINTER make NET_RECEIVE slower?
Replies: 9
Views: 242

Re: Does POINTER make NET_RECEIVE slower?

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...
by ted
Mon May 30, 2022 1:32 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Does POINTER make NET_RECEIVE slower?
Replies: 9
Views: 242

Re: Does POINTER make NET_RECEIVE slower?

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?
by ted
Thu May 26, 2022 1:42 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Does POINTER make NET_RECEIVE slower?
Replies: 9
Views: 242

Re: Does POINTER make NET_RECEIVE slower?

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 ...
by ted
Tue May 24, 2022 12:14 pm
Forum: NEURON + Python
Topic: Mechanisms ignored when attempting to initialize events
Replies: 2
Views: 218

Re: Mechanisms ignored when attempting to initialize events

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...
by ted
Thu May 19, 2022 9:47 am
Forum: General questions and discussions about computational neuroscience
Topic: Numerical Integration in Computational Neuroscience
Replies: 3
Views: 201

Re: Numerical Integration in Computational Neuroscience

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...
by ted
Thu May 19, 2022 9:36 am
Forum: MSWin
Topic: NEURON 7.6.7 - Permission denied. Python not available.
Replies: 21
Views: 513

Re: NEURON 7.6.7 - Permission denied. Python not available.

https://github.com/chlubba/PyPNS presents instructions for installation and configuration, including install & config of NEURON 7.6.7. Those instructions don't work?
by ted
Wed May 18, 2022 11:29 am
Forum: General questions and discussions about computational neuroscience
Topic: Numerical Integration in Computational Neuroscience
Replies: 3
Views: 201

Re: Numerical Integration in Computational Neuroscience

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...
by ted
Thu May 12, 2022 1:54 pm
Forum: Hot tips
Topic: Defer perturbations until after the start of a simulation
Replies: 0
Views: 115

Defer perturbations until after the start of a simulation

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...
by ted
Thu May 12, 2022 1:51 pm
Forum: Modeling networks
Topic: Vector play issue
Replies: 3
Views: 244

Re: Vector play issue

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...
by ted
Tue May 10, 2022 4:09 pm
Forum: Modeling networks
Topic: Vector play issue
Replies: 3
Views: 244

Re: Vector play issue

Interesting problem. You're very close to getting it right. No need to disclose your model cell; it's easy enough to make an isolated soma and use that for interactive software development. from neuron import h, gui # the built-in GUI is very convenient for development and debugging soma = h.Section...