Search found 6305 matches
- Tue Nov 14, 2023 3:50 pm
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 90390
Re: Conditional termination of simulation
Good try. There is no need to write any NMODL code--everything can be done with hoc or Python or a combination of the two. Here's an example that assumes the existence of a section called soma with 100 um2 surface area and hh membrane properties. Omitted is the "from neuron import h, gui" ...
- Tue Nov 14, 2023 11:36 am
- Forum: Other questions
- Topic: Applying Sinusoidal Voltage to Membrane
- Replies: 6
- Views: 53021
Re: Applying Sinusoidal Voltage to Membrane
First you need to decide exactly what you are trying to do. This "apply a sinusoidal voltage to vary the membrane potential over time" means you want to force membrane potential to follow a specific time course. That is best done with a voltage clamp--specifically, an instance of NEURON's ...
- Fri Nov 10, 2023 12:48 pm
- Forum: Modeling networks
- Topic: neuronal response to magnetically induced electric fields
- Replies: 4
- Views: 36063
Re: neuronal response to magnetically induced electric fields
So changes to nrnivmodl since NEURON 7.8 have interfered with NEMO. Where did you find NEMO and what is the paper that presents this tool? I wonder if its developers would be interested in making it work under the latest version of NEURON, if that doesn't require too much of their effort.
- Sun Nov 05, 2023 1:18 am
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 90390
Re: Conditional termination of simulation
Use events. Specifically, 1. use an FInitializeHandler to set the spike count to 0 at the start of the simulation 2. usethe NetCon class's record() method to call a function every time the cell spikes. This function should do the following: increase the spike count by 1 if spike count == 1 tnow = t ...
- Sun Nov 05, 2023 1:00 am
- Forum: Modeling networks
- Topic: neuronal response to magnetically induced electric fields
- Replies: 4
- Views: 36063
Re: neuronal response to magnetically induced electric fields
if there is some function implemented in NEURON to simulate the characteristics of magnetically induced electric fields That is not included with NEURON. However, there are a lot of smart NEURON users who are interested in related problems, so maybe one or more of them has already implemented their...
- Fri Oct 27, 2023 9:48 am
- Forum: NEURON + Python
- Topic: Dealing with objects defined in functions
- Replies: 1
- Views: 14202
Re: Dealing with objects defined in functions
Here's an implementation that does almost everything via procedures, and contains some (not so) latent hints. Imports and definitions first from neuron import h, gui ### Model and simulation parameters # KISS when developing/debugging # this means small nets, short run times, few spikes # make symbo...
- Mon Oct 23, 2023 11:44 am
- Forum: NEURON + Python
- Topic: CoreNeuron verbose output
- Replies: 3
- Views: 14134
Re: CoreNeuron verbose output
Actually, h.verbose could be an interesting feature.
Just out of curiosity: what performance boost are you getting?
Just out of curiosity: what performance boost are you getting?
- Sat Oct 21, 2023 10:56 pm
- Forum: NEURON + Python
- Topic: CoreNeuron verbose output
- Replies: 3
- Views: 14134
Re: CoreNeuron verbose output
Try inserting
coreneuron.verbose = 0
after
coreneuron.enable = True
You might glean some other useful stuff from
https://github.com/neuronsimulator/nrn/ ... _direct.py
coreneuron.verbose = 0
after
coreneuron.enable = True
You might glean some other useful stuff from
https://github.com/neuronsimulator/nrn/ ... _direct.py
- Mon Oct 16, 2023 12:51 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 68550
Re: Extracellular stimulation and recording
Please do.I am assuming I should proceed with that first part of your reply?
- Mon Oct 16, 2023 12:36 pm
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 15557
Re: Accessing tpre and tpost from STDP mod file
I forgot to mention that the NetCon that monitors the postsynaptic potential should have the same threshold as is specified in the NMODL's WATCH statement. For STDPE2, that would be the value of the RANGE variable thresh. For a synaptic mechanism S that can handle multiple input streams, the cleanes...
- Mon Oct 16, 2023 12:13 pm
- Forum: NEURON + Python
- Topic: h.parallelContext in a model being simulated on a cluster
- Replies: 3
- Views: 13517
Re: h.parallelContext in a model being simulated on a cluster
Interesting problem. Just in case you ran into a NEURON bug: what version of NEURON is running on your Mac, and what version is the cluster using?
- Fri Oct 13, 2023 1:17 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 68550
Re: Extracellular stimulation and recording
Yow, instead of quoting your message and replying to it, in a hurry I made the mistake of editing your message. At least I captured your questions so we can continue the discussion.
- Wed Oct 11, 2023 4:20 pm
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 15557
Re: Accessing tpre and tpost from STDP mod file
The easy way to discover tpost is to attach a NetCon to the segment that has the instance of the STDPE2 class, and use that NetCon's record() method to capture local postsynaptic "spike times" to a Vector. What's not so clear to me is how you are capturing the tpre values. Are you recordin...
- Fri Oct 06, 2023 1:01 pm
- Forum: MSWin
- Topic: New installation of NEURON + Python
- Replies: 4
- Views: 40280
Re: New installation of NEURON + Python
I've noticed the installer from https://www.neuron.yale.edu/neuron/download is version 8.2.0, and it kept giving one of my students a "no module named hoc" error. They eventually used the installer found on nrn.readthedocs.io and it is version 8.2.3 and this works fine. Just thought I sho...
- Wed Oct 04, 2023 11:44 am
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 15557
Re: Accessing tpre and tpost from STDP mod file
The first step is for you to disclose the code of the mod file that you are actually using (either include it in your next post, or better yet provide a URL to where you found it). Statements like
"the STDP mod file created by so and so"
mean almost nothing because text files are fungible.
"the STDP mod file created by so and so"
mean almost nothing because text files are fungible.