Search found 5820 matches

by ted
Thu Jul 23, 2020 1:01 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

Is that N-I-N-I-I-I-...-I-N-I-N (i.e. 4 nodes and a bunch of internodes? Something like that: N-I-I-I-I-......-I-I-N Two nodes separated by a lot of internodes. You'll never get a propagating action potential. but you need to know diam in order to calculate gm. And you don't know diam. . . . Diamet...
by ted
Mon Jul 20, 2020 10:46 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

I meant 2 HH nodes at the beginning and the end and lots of internodes in the middle Is that N-I-N-I-I-I-...-I-N-I-N (i.e. 4 nodes and a bunch of internodes? or N-I-N-I-N-I-...-N-I-N (i.e. NNODES nodes and NNODES-1 internodes) "The slovenliness of our language allows us to think foolish though...
by ted
Mon Jul 20, 2020 5:41 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

OK, you don't need super-detailed representation of the properties of myelin. No need for extracellular. There is actually an existing literature on the effects of internode length on spike propagation. The key papers are Brill et al. Conduction velocity and spike configuration in myelinated fibres:...
by ted
Mon Jul 20, 2020 12:31 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

I said nothing at all about spatial discretization (the value to use for nseg). That's a topic for a different discussion. Nor did I address parameters. The question that triggered this essay stipulated Params : { Myelin resistance (R_m): MOhms/mm Myelin capacitance: pF/mm longitudinal resistance: M...
by ted
Mon Jul 20, 2020 12:29 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

This is written for general readership, so please excuse explicit discussion of much that you probably already know. The first and most important step in any modeling project is to develop a clear conceptual model. I will assume you want a model of an unbranched myelinated axon--a series of nodes of...
by ted
Sat Jul 18, 2020 10:21 am
Forum: Specific models
Topic: The acceptable range of channels
Replies: 1
Views: 492

Re: The acceptable range of channels

Read experimental papers. Start with the papers on which this model is based. To see a list, click on the ModelDB entry's "Citations" tab. That will also show you papers that cite this model, as well as models that this model entry cites or is cited by. Also look for this model's channels ...
by ted
Thu Jul 16, 2020 12:55 am
Forum: Suggestions and Feedback
Topic: Wrong behavior of h.parent_connection()
Replies: 1
Views: 566

Re: Wrong behavior of h.parent_connection()

h.parent_connection() is doing exactly what it should do. The example in the documentation syntax is y = h.parent_connection(sec=child) not y = h.parent_connection(child) The "sec=" part of the argument is not optional or a suggestion--it is necessary. If you leave it out, NEURON defaults ...
by ted
Mon Jul 13, 2020 10:35 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 958

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

now isst is set to the flux of sst . . . writing ssti in this block did not change the above result. Another couple of misunderstandings appear to have emerged. First, the trivial one. NMODL expects currents to be in units of absolute current (nA) or current density (mA/cm2), depending on whether t...
by ted
Mon Jul 13, 2020 2:55 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 958

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

I did not know that a current for an ion with valence 0 would affect the charge balance equation. I don't know for sure, would have to run a test to verify, but it seems reasonable. As far as I know, valence is used only by NEURON's computational engine when the ion_style settings tell NEURON to ca...
by ted
Mon Jul 13, 2020 1:10 am
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 958

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

Should I repost Not at all. They routinely monitor this part of the Forum. I was just declaring the limited scope of my own comments. I don't see a reason for inconsistencies outside of a typo I have just seen too much user-written NMODL code. One of the advantages of the rxd module is the convenie...
by ted
Sun Jul 12, 2020 2:46 pm
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 958

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

adamjhn or ramcdougal will have to answer your rxd-specific questions. I have some questions about the NMODL code: All those variable names and parameter values, but no units. You're sure there are no units inconsistencies? that no scale factors are necessary? Why USEION sst READ ssti, ssto WRITE is...
by ted
Fri Jul 10, 2020 10:58 pm
Forum: NEURON + Python
Topic: Best practice to run hundreds of simulations / remove all objects between runs
Replies: 6
Views: 816

Re: Best practice to run hundreds of simulations / remove all objects between runs

Some of the posts in those previous threads illustrate that it is always possible to write complex code that has unintended, undesirable side effects. In the past two days I used Python to work with two different implementations of simulation experiments wrapped in class definitions. One implementat...
by ted
Thu Jul 09, 2020 11:24 pm
Forum: NEURON + Python
Topic: Best practice to run hundreds of simulations / remove all objects between runs
Replies: 6
Views: 816

Re: Best practice to run hundreds of simulations / remove all objects between runs

Ah, my mistake. What worked from hoc may need modification to work from Python. For a very pertinent discussion on the forum, see this thread Running multiple simulations in one process https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=3213 Sure enough, h.delete_section() is discussed in the...
by ted
Thu Jul 09, 2020 9:56 pm
Forum: Optimization
Topic: MRF on HH voltage curve
Replies: 3
Views: 767

Re: MRF on HH voltage curve

That's all the MultiRunFItter tutorials of which I am aware. The two ModelDB entries are examples of practical application of the MRF to research problems (specifically, fitting a model to experimental results recorded from a spiking neuron). Maybe you'd be interested in BluePyOpt https://www.fronti...
by ted
Thu Jul 09, 2020 2:35 pm
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 5
Views: 737

Re: Does the usage of the Shape may affect mV readouts?

Did you resolve the problem yourself, or do you still have a question?