Search found 5351 matches

by ted
Mon Nov 12, 2018 12:48 pm
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 40

Re: Porting AtolTool settings to GUI-less batch simulation

Nothing in the Atol Scale tool's user interface is updated during a run, so it's not a problem. Graphs with t as the independent variable that are linked to the standard run system's plotlists will be updated during a simulation, but whether or not they pose a significant computational burden will d...
by ted
Mon Nov 12, 2018 12:14 pm
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 40

Re: Porting AtolTool settings to GUI-less batch simulation

Sounds like a cosmetic problem to me--not a beauty spot, but not exactly a wart, as long as the tool works so I don't have to manually transcribe error tolerance scale factors into hoc or Python statements. Maybe someone else can suggest a way to use the tool from Python without actually seeing its ...
by ted
Mon Nov 12, 2018 12:04 pm
Forum: Parallel NEURON
Topic: segmentation fault when recording specific time points into h.Vector
Replies: 1
Views: 8

Re: segmentation fault when recording specific time points into h.Vector

Suggest you update to the latest version of NEURON and see if that makes the problem go away. There have been many bug fixes and performance enhancements since 7.4.
by ted
Sun Nov 11, 2018 1:29 pm
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 40

Re: Porting AtolTool settings to GUI-less batch simulation

Not sure why it is necessary to do anything special. Just let your hoc code load the configured variable step control's ses file. NEURON produce the same numerical results regardless of whether it was compiled with or without InterViews, or whether it is executed on a machine that even has graphics ...
by ted
Sun Nov 11, 2018 12:32 am
Forum: General questions and discussions about computational neuroscience
Topic: Transfer impedance tool
Replies: 1
Views: 20

Re: Transfer impedance tool

NEURON calculates the transfer impedances from the model's Jacobian matrix. The Python documentation of the Impedance class goes into a bit more detail about this insofar as limitations of the calculation are concerned.
by ted
Sun Nov 11, 2018 12:28 am
Forum: General questions and discussions about computational neuroscience
Topic: Passive membrane impedance vs voltage-gated conductance
Replies: 5
Views: 60

Re: Passive membrane impedance vs voltage-gated conductance

No. You'd have to determine the gating properties and spatial variation of channel density of every kind of ion channel in the membrane of one cell. That cannot be done.
by ted
Sun Nov 11, 2018 12:21 am
Forum: General questions and discussions about computational neuroscience
Topic: Subthreshold spontaneous oscillations
Replies: 5
Views: 56

Re: Subthreshold spontaneous oscillations

Good questions. Generally what people mean by "the HH model" is one of two models proposed by Hodgkin and Huxley. One was a model of the "membrane action potential" by which they meant a spike that occurred in an isopotential patch of squid axon membrane; the other was for initiation and propagation...
by ted
Tue Nov 06, 2018 2:15 am
Forum: General questions and discussions about computational neuroscience
Topic: Passive membrane impedance vs voltage-gated conductance
Replies: 5
Views: 60

Re: Passive membrane impedance vs voltage-gated conductance

Never mind--it's true only if the ionic equilibrium potentials can be regarded as fixed. It is not true if there is a permeant species whose concentrations are determined by the transmembrane potential, e.g. chloride. at what transmembrane potential do the voltage-gated conductances start to dominat...
by ted
Tue Nov 06, 2018 2:06 am
Forum: General questions and discussions about computational neuroscience
Topic: Subthreshold spontaneous oscillations
Replies: 5
Views: 56

Re: Subthreshold spontaneous oscillations

The Hodgkin-Huxley model itself does not produce spontaneous oscillations. Don't get stuck on the HH model itself, or any other deterministic model of the processes that affect membrane potential--even though deterministic models are generally "good enough" if channel densities are high enough. Chan...
by ted
Mon Nov 05, 2018 12:24 am
Forum: General questions and discussions about computational neuroscience
Topic: Passive membrane impedance vs voltage-gated conductance
Replies: 5
Views: 60

Re: Passive membrane impedance vs voltage-gated conductance

At subthreshold levels of injected current I am guessing that the passive membrane conductance is much greater than the conductance of voltage-gated channels. Is this true? Consider the reversal potentials of the ionic species to which the membrane is permeable. The resting potential of a cell will...
by ted
Mon Nov 05, 2018 12:20 am
Forum: General questions and discussions about computational neuroscience
Topic: Subthreshold spontaneous oscillations
Replies: 5
Views: 56

Re: Subthreshold spontaneous oscillations

How are the intrinsic spontaneous subthreshold oscillations accounted for when extrinsic subthreshold stimuli are applied? If applying subthreshold stimuli to a real cell elicits subthreshold oscillations of membrane potential, then presumably the properties of that cell account for them. Or are yo...
by ted
Wed Oct 31, 2018 8:28 pm
Forum: Getting started
Topic: Program functions between Mac and Windows
Replies: 3
Views: 78

Re: Program functions between Mac and Windows

Results are supposed to be identical across operating systems, and from version to version of NEURON. That said, you didn't provide enough information to get a completely informed response to your question. What versions of NEURON are running on your Mac and MSWin machines? Lack of complete source c...
by ted
Fri Oct 26, 2018 10:37 am
Forum: Getting started
Topic: A way to implement non-linear densities in multi-nodal sections?
Replies: 1
Views: 66

Re: A way to implement non-linear densities in multi-nodal sections?

This syntax g_pas(0:1) = (0.001:.00001) works, but nobody has used it in new code for a long time for two reasons: it's rather opaque, it can only produce linear gradients along the length of any section, and there's no good way to use it to set up even a linear gradient over a set of sections. Far ...
by ted
Wed Oct 24, 2018 11:31 pm
Forum: Getting started
Topic: Frequency response function
Replies: 4
Views: 81

Re: Frequency response function

An interesting example of miscommunication. I've been thinking a lot about spiking networks lately, so I'm "stuck on spikes"--when I think of a cell's "frequency response" to an input, or the "output" that it might generate in response to an input, what comes to mind is F-I curves, and that implies ...
by ted
Wed Oct 24, 2018 9:44 pm
Forum: Getting started
Topic: Frequency response function
Replies: 4
Views: 81

Re: Frequency response function

Does it have a means for calculating the frequency response function between input (injected curren) and output (membrane potential) sites for subthreshold stimuli using a linear model? I don't think your question has an answer. What does it mean to talk about the frequency of a cell's response to ...