Search found 5213 matches

by ted
Fri Jun 22, 2018 11:05 am
Forum: NetPyNE
Topic: Setpointer when defining a synapse
Replies: 1
Views: 34

Re: Setpointer when defining a synapse

All those POINTERs are going to be a real problem in a parallelized model. Would it be better to use RxD to deal with extracellular ion accumulation?
by ted
Wed Jun 20, 2018 9:42 pm
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 5
Views: 174

Re: Parallel simulations of ephaptic connections

Is copying the value of a variable, say, vext, from source to target and viceversa, equivalent to sharing the state variable vext at a point between two processors? Am I misled if I think that this method does the former? How are the equations of the system solved when the information is passed in ...
by ted
Wed Jun 20, 2018 9:14 pm
Forum: Parallel NEURON
Topic: Stabilization Mechanism
Replies: 7
Views: 134

Re: Stabilization Mechanism

NEURON's source code comes with a directory full of example mod files along with hoc code that illustrates how to use these mechanisms in models (in the directory nrn/share/examples/nrniv/nmodl). One of the files is nadifl.mod, which has a USEION na READ ina WRITE nai statement in its NEURON block, ...
by ted
Wed Jun 20, 2018 10:35 am
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 7
Views: 144

Re: Manual Installation of NEURON Python module on Linux Mint 18

What worked for Mint18.3 Delete the NEURON and InterViews source code and whatever is installed. Then follow this recipe (copy and paste is safest). 0. Apply the latest updates to Mint. 1. Make sure the software development environment is adequate. Some or all of these may already be present on you...
by ted
Wed Jun 20, 2018 1:25 am
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 9
Views: 184

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

My rationale for using electrical stimulation for the model was that since I'm looking for the effect of fiber tract stimulation, whatever the modality, any form of stimulation would do for the model. Good rationale. A brief current pulse of sufficient amplitude applied to a single node of Ranvier ...
by ted
Tue Jun 19, 2018 3:05 pm
Forum: Parallel NEURON
Topic: Stabilization Mechanism
Replies: 7
Views: 134

Re: Stabilization Mechanism

Comments: The statement glbar_hh = 0.0000 // [S/cm^2] does nothing useful because hh doesn't have a parameter called glbar. To discover what parameters it does have, see the Programmer's Reference entry for hh, or run this toy program create soma soma insert hh soma psection() and see what that last...
by ted
Tue Jun 19, 2018 2:40 pm
Forum: Parallel NEURON
Topic: want_all_spikes recording from axon
Replies: 2
Views: 60

Re: want_all_spikes recording from axon

If your model has actually been parallelized, then as part of model setup a NetCon will have been attached to each presynaptic cell's spike trigger zone and assigned a gid (global identifier). Those gids are what want_all_spikes() uses to capture the spike times. If you want to detect spikes at one ...
by ted
Tue Jun 19, 2018 11:28 am
Forum: Parallel NEURON
Topic: Stabilization Mechanism
Replies: 7
Views: 134

Re: Stabilization Mechanism

Before we even get started, I should mention that variable names in NEURON are case sensitive. nai is not the same as Nai. ina is not the same as iNa. If you have an ion channel mechanism that WRITEs iNa, and a sodium pump that READs ina and WRITEs nai, the pump can run forever and never have any ef...
by ted
Mon Jun 18, 2018 10:38 am
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 5
Views: 174

Re: Parallel simulations of ephaptic connections

Referring back to your post from March 13 I've read about how pc.source_var and pc.target_var are used for gap junctions. . . . they copy v from source onto target, so that seems to be a one-directional coupling to me which is why two source_var - target_var pairs are used to parallelize gap junctio...
by ted
Sun Jun 17, 2018 4:41 pm
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 9
Views: 184

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

What I'm doing is making a simulation of fiber tract stimulation. I decided to work at the most basic level, with individual neurons. The hypothesis is this: stimulating the fiber tract using focused ultrasound is a viable neuromodulation modality for altering the functional plasticity between the ...
by ted
Sun Jun 17, 2018 3:36 pm
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 7
Views: 144

Re: Manual Installation of NEURON Python module on Linux Mint 18

For this particular installation, I did sudo python3 setup.py install I use NEURON and idraw from the command line, so in .bashrc I inserted PATH= $PATH:/usr/local/iv/x86_64/bin:/usr/local/nrn/x86_64/bin If you plan to launch Python and import nrn, you'll need to specify PYTHONPATH A correct stateme...
by ted
Sun Jun 17, 2018 11:24 am
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 7
Views: 144

Re: Manual Installation of NEURON Python module on Linux Mint 18

I just installed NEURON under Mint18.3 just 2 weeks ago, and setup.py ran without problems. I started with the latest development source code from Github and allowed NEURON to be installed into its default location /usr/local/nrn. Of couse that required invoking sudo for the make install steps, and ...
by ted
Fri Jun 15, 2018 9:44 pm
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 7
Views: 144

Re: Manual Installation of NEURON Python module on Linux Mint 18

I am trying to do a manual installation of the NEURON Python module
What NEURON Python module? One you picked up somewhere, or what?
by ted
Wed Jun 13, 2018 10:02 am
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 276

Re: Neuron code

Is it known that squid even have a low threshold calcium current?
by ted
Mon Jun 11, 2018 1:44 pm
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 9
Views: 184

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

I'm currently developing a detailed model of 2 (up to 5) connected neurons that need to have myelinated axons. Why do they need myelinated axons? Is some aspect of the structure or function of myelinated axons essential for the hypothesis that you plan to evaluate with your model? I will stimulate ...