Search found 5820 matches

by ted
Sat Aug 22, 2020 12:03 pm
Forum: Modeling networks
Topic: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism
Replies: 4
Views: 744

Re: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism

Great, you are off to a good start! My first suggestion is that you approach the problem in the same way that an experimentalist would explore the properties of a real neuron. If you already have some wet lab experience, some this may be obvious to you in retrospect. An experimentalist would have th...
by ted
Mon Aug 17, 2020 11:14 am
Forum: MSWin
Topic: DLL LOAD FAILED importing python packages from anaconda into neuron
Replies: 1
Views: 590

Re: DLL LOAD FAILED importing python packages from anaconda into neuron

Suggest you uninstall whatever version of NEURON is currently on your PC and get 7.8.1 which is now available from www.neuron.yale.edu and is likely to include a fix for the problem you encountered.
by ted
Wed Aug 12, 2020 10:43 am
Forum: MSWin
Topic: DLL load failed in Windows10
Replies: 4
Views: 646

Re: DLL load failed in Windows10

Instead of

import neuron
import hoc

try this:
from neuron import h

What happens?
by ted
Tue Aug 11, 2020 1:35 pm
Forum: NEURON + Python
Topic: Multiple stimulation of POINT_PROCESS per run
Replies: 3
Views: 517

Re: Multiple stimulation of POINT_PROCESS per run

modeldb.yale.edu/140828's NMDA_Mg_T.mod should be revised so that it is driven by events, instead of using a POINTER to a variable controlled by some other mod file (release_BMK.mod in this case). The changes required are minimal and I will be glad to implement them so you can get on with your proje...
by ted
Mon Aug 03, 2020 11:32 pm
Forum: NEURON + Python
Topic: Ephaptic coupling of Axons
Replies: 1
Views: 380

Re: Ephaptic coupling of Axons

A good place to start looking for answers to your question: ModelDB.
by ted
Mon Aug 03, 2020 10:23 am
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 747

Re: initialization of calcium concentration in a segment with attached point process

And what happened in your case is that after you called the ion_style function with the cinit slot = 0, adding the synapse that READ cai, promoted it (for that segment only) back to 1. . . . Which suggests that the use of ion_style is surrounded by caveats, because a later change (e.g. adding of a ...
by ted
Fri Jul 31, 2020 3:03 pm
Forum: General questions and discussions about computational neuroscience
Topic: What does SWC stand for?
Replies: 5
Views: 14218

Re: What does SWC stand for?

The most authoritative answers to such questions might be obtainable from the authors of one or both of these papers, at least a few of whom are probably still alive.
by ted
Wed Jul 29, 2020 10:04 am
Forum: Other questions
Topic: trouble with e_extracellular and play
Replies: 3
Views: 591

Re: trouble with e_extracellular and play

When using an unfamiliar feature, work through a series of toy exercises before addressing the task that is giving you difficulty. 1. Use Vector.play to drive the value of a scalar. 2. Create a single section model with nseg==1 and use Vector.play to drive the segment's v. 3. Insert extracellular in...
by ted
Wed Jul 29, 2020 9:36 am
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 747

Re: initialization of calcium concentration in a segment with attached point process

One other change I'd make to L5PC-db.py: get rid of this part of the cell class definition for secname in self.sections: if secname == "axon": continue h.ion_style("ca_ion",3,2,1,1,0,sec=self.sections[secname]) self.sections[secname].cao = 1.2 for seg in self.sections[secname]: s...
by ted
Tue Jul 28, 2020 11:32 pm
Forum: Other questions
Topic: initialization of calcium concentration in a segment with attached point process
Replies: 5
Views: 747

Re: initialization of calcium concentration in a segment with attached point process

I see what you mean. Python statements in the L5neuron class's definition explicitly assign values to cai (1.0e-3 mM) and cao (1.2 mM) in each segment that has a mechanism with a USEION ca statement. And when you create a new L5neuron instance, those are the calcium concentrations in those segments....
by ted
Tue Jul 28, 2020 3:42 pm
Forum: Other questions
Topic: SWC file refinements
Replies: 1
Views: 304

Re: SWC file refinements

Adding new 3D points that lie on the straight line between existing points and have diameters midway between those of the existing points will have no effect on L, diam, or surface area of any section and will not affect simulation results.
by ted
Tue Jul 28, 2020 12:17 am
Forum: NEURON + Python
Topic: Modelling a chain of HH cell with myelinated axon
Replies: 16
Views: 1487

Re: Modelling a chain of HH cell with myelinated axon

Before addressing fac or l2a(), note that NEURON has a concept called "currently accessed section" that allows one to write code that refers to parameters and variables that belong to a particular section without having to specifically name a particular section in the same line. forall is ...
by ted
Sun Jul 26, 2020 3:17 pm
Forum: Modeling networks
Topic: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism
Replies: 4
Views: 744

Re: Synaptic input model for dopaminergic neuron to examine pacemaking mechanism

How can I specify the interspike interval/firing frequency while using a NetCon object to connect two neurons? Make the presynaptic neuron fire with the desired ISI or frequency. NetStim generates artificial presynaptic stimuli No, it generates "100% organic" events that NetCons can deliv...
by ted
Fri Jul 24, 2020 6:41 pm
Forum: NEURON + Python
Topic: Modelling a chain of HH cell with myelinated axon
Replies: 16
Views: 1487

Re: Modelling a chain of HH cell with myelinated axon

With regard to your class BallAndStick . . . Nice clean code, great start. Just a couple of things to resolve, and you'll be ready to extend your program so that a parameter can be used to specify how many nodes and internodes the axon has. If you're going to define an axon class, the name of the cl...
by ted
Fri Jul 24, 2020 3:55 pm
Forum: NEURON + Python
Topic: Is it possible to track "value explosions" and out of range errors
Replies: 2
Views: 409

Re: Is it possible to track "value explosions" and out of range errors

Interesting problem. How big does the network itself have to be (total # cells, total # synapses)? At what point (time) in the simulation does it occur? The first thing to do is to see if there are any peculiarities about the NMODL code itself that might cause problems, and the quickest way to do th...