Search found 5672 matches

by ted
Mon Oct 21, 2019 9:49 am
Forum: Getting started
Topic: construct a single myelinated axon
Replies: 10
Views: 752

Re: construct a single myelinated axon

I'm constructing a single myelinated axon without any nodes, just a soma connected to myelinated axon to see how the AP propagates with the change of the diameter. Then there won't be any actual "spike propagation" along your axon, even if the axolemma is full of voltage-gated channels. Why? Becaus...
by ted
Mon Oct 21, 2019 9:43 am
Forum: NEURON + Python
Topic: Problems using VClamp
Replies: 1
Views: 263

Re: Problems using VClamp

I have a cell with multiple sections where I want to inject a specific voltage in mV, coming from a cell in NEST. Since I cannot form any synapses between them, I thought about artificially stimulating the NEURON cells with the exact value that should be sent by the NEST cells. For this matter, I c...
by ted
Sun Oct 20, 2019 11:20 pm
Forum: Getting started
Topic: construct a single myelinated axon
Replies: 10
Views: 752

Re: construct a single myelinated axon

1. If I use the pas mechanism for the biophysical part of the axon, then I'm constructing a myelinated axon? No. To build a model of myelinated axon, you have to represent the electrical effects of the myelin sheath. pas is used to represent a voltage-independent membrane conductance. 2. NEURON con...
by ted
Sun Oct 20, 2019 10:38 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 1075

Re: The equilibrium between the FS and external

Perhaps you refer to Lopreore et al. 2008, PMID 18556758. I have no idea how the authors did that. Does the paper contain a mathematical description of how the rate constant varied? Too bad the source code isn't available online. Have you contacted the authors to ask them?
by ted
Fri Oct 18, 2019 2:00 pm
Forum: NEURON + Python
Topic: accessing the same instantiation of a cell template from another python script
Replies: 4
Views: 507

Re: accessing the same instantiation of a cell template from another python script

Use a GLOBAL parameter. If the values of the parameter are precalculated (known before the start of the simulation), use the Vector class's play() method to drive the GLOBAL parameter. I'll dig up an example and post it.
by ted
Wed Oct 16, 2019 11:12 am
Forum: Getting started
Topic: g_pas
Replies: 1
Views: 347

Re: g_pas

Yes
by ted
Thu Oct 10, 2019 11:14 am
Forum: NEURON + Python
Topic: Different v_init for different neurons in a network
Replies: 1
Views: 390

Re: Different v_init for different neurons in a network

No Python- or hoc-specific magic is involved. In pseudocode

Code: Select all

for each section {
  for each segment {
    set v to whatever initial value you want
  }
}
call finitialize() with no argument
Add whatever elaborations or refinements you like to do this on a cell-specific basis.
by ted
Wed Oct 09, 2019 10:29 am
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 1560

Re: 3D rotation in Cell Builder

1. From the CellBuilder export a hoc file that contains the statements that create the axon terminal. 2. Organize the "model specification" part of your code like this: code that specifies the geometry and topology of everything but the axon terminal a load_file() statement that reads the hoc file c...
by ted
Mon Oct 07, 2019 9:35 pm
Forum: Modeling networks
Topic: mixed model of artificial and conduction-based cells
Replies: 20
Views: 8572

Re: mixed model of artificial and conduction-based cells

asb wrote:Would you be happy to have a look at the model first to ensure it passes the litmus test?
If you want to suggest that a published model be included in ModelDB, then by all means, suggest it to the curator of ModelDB. That would be Tom Morse.
by ted
Mon Oct 07, 2019 11:58 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding delay to a graded synapse model
Replies: 2
Views: 393

Re: Adding delay to a graded synapse model

Forget about NetCon. A NetCon is just a threshold detector that places an event in a queue when a monitored variable crosses a threshold in a positive-going direction. Period. You're stuck with FIFO. Be prepared to explain to a reviewer what plausible physical mechanism would account for a fixed tim...
by ted
Sat Oct 05, 2019 11:49 am
Forum: Anatomically detailed models
Topic: 3D rotation in Cell Builder
Replies: 3
Views: 1560

Re: 3D rotation in Cell Builder

First question: are all of these sections supposed to belong to a single cell, or is the axon terminal stuff supposed to be presynaptic and the ball and stick postsynaptic?
by ted
Tue Oct 01, 2019 12:49 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 614

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

If your primary interest is in spike propagation along an axon, why include a soma in your model? Physiologists who study spike propagation along sciatic nerve or squid axon almost never pay any attention to the soma, and typically work on isolated axon without a soma. If your interest is in how spi...
by ted
Tue Oct 01, 2019 10:15 am
Forum: NEURON Announcements
Topic: testing
Replies: 0
Views: 82

testing

Testing creation of a new topic
by ted
Sun Sep 29, 2019 1:34 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 614

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

That's much clearer, thanks. At a minimum, you need a model axon, and something to stimulate the axon. You should also have a graph that shows membrane potential along the length of the axon for at least the following reasons: 1. To verify that the stimulus is big enough to trigger a spike but not s...
by ted
Sat Sep 28, 2019 9:48 pm
Forum: Getting started
Topic: monitor the attenuation of the peak value of the action potential with distance from the ion channel
Replies: 9
Views: 614

Re: monitor the attenuation of the peak value of the action potential with distance from the ion channel

It sounds like you're starting a modeling project and need to work closely with a collaborator on it for two reasons. First, to define exactly what you are thinking about. A big problem is that this sentence doesn't make sense: "How can I apply a stimulus at a specific ion channel (Has to be ion cha...