Search found 5990 matches

by ted
Thu Jan 20, 2022 11:44 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding delay to a graded synapse model
Replies: 6
Views: 1429

Re: Adding delay to a graded synapse model

You have to come up with a way to represent the time course of the presynaptic variable that governs transmitter release. If your presynaptic model cell is a single compartment, you can't just use a copy of its membrane potential, because that will include not only spikes but also subthreshold fluct...
by ted
Wed Jan 19, 2022 10:59 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding delay to a graded synapse model
Replies: 6
Views: 1429

Re: Adding delay to a graded synapse model

For synaptic transmission, forget FIFO--unless you can point to a paper by experimentalists that provides empirical evidence that supports the idea. Every step in synaptic transmission can be represented by one or more ODEs, or an equivalent Markov scheme (set of state transitions).
by ted
Mon Jan 10, 2022 10:52 am
Forum: Parallel NEURON
Topic: Single cell in parallel
Replies: 1
Views: 46

Re: Single cell in parallel

2500 compartments isn't particularly large. Easiest parallel simulation is via multithreaded execution, which usually doesn't require any change to your model specification code. Some NMODL mechanisms may need slight revision to make them threadsafe; there are a few mechanisms that are inherently no...
by ted
Thu Jan 06, 2022 2:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to update the weight vector of a NetCon per time step
Replies: 4
Views: 74

Re: How to update the weight vector of a NetCon per time step

is it possible to update them in the DERIVATIVE BLOCK of the synapse mod file Sure. Forget about using the NetCon's vector to store stream-specific variables other than weight[0]. Instead, make a mod file that declares as many a_plus and a_minus state variables as you need (one each for every NetCo...
by ted
Tue Jan 04, 2022 10:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to update the weight vector of a NetCon per time step
Replies: 4
Views: 74

Re: How to update the weight vector of a NetCon per time step

If the equations that govern the dynamics of a_plus and a_minus don't have an analytical solution, would a lookup table be useful?
by ted
Fri Dec 31, 2021 11:11 am
Forum: NEURON + Python
Topic: Recording multiple netcon's weight with one synapse mechanism
Replies: 3
Views: 99

Re: Recording multiple netcon's weight with one synapse mechanism

Actually, _ref_weight[1] Maybe, for your particular application. Others who read this thread should note that, in most cases, the weight (strength) of a synaptic connection is specified by the first element of the weight vector, which is weight[0]. dragon88hj is probably working with a synaptic mec...
by ted
Thu Dec 30, 2021 9:59 pm
Forum: NEURON + Python
Topic: Recording multiple netcon's weight with one synapse mechanism
Replies: 3
Views: 99

Re: Recording multiple netcon's weight with one synapse mechanism

Code: Select all

vec.record(&nc.weight[1]) // nc.weight[1]
Actually you want to record the first element of each weight vector. That element's index is 0, so the hoc statement would be

Code: Select all

vec.record(&nc.weight[0])
In Python I would try a statement of the form
vec.record(nc._ref_weight[0])
by ted
Sat Dec 04, 2021 4:57 pm
Forum: NEURON + Python
Topic: solving differential equation describing Vm
Replies: 1
Views: 153

Re: solving differential equation describing Vm

The biggest problem is omitting i_pas.

Save your time. NEURON's numerical methods are detailed in chapter 4 of The NEURON Book.
by ted
Wed Dec 01, 2021 11:34 am
Forum: General questions and discussions about computational neuroscience
Topic: Interpreting neural response
Replies: 1
Views: 164

Re: Interpreting neural response

This is a perfect opportunity to use what you know about initiation and propagation of action potentials to formulate a hypothesis that might account for your observation. Then design, perform, and interpret a computational experiment that tests this hypothesis.
by ted
Tue Nov 16, 2021 12:01 pm
Forum: NEURON + Python
Topic: hh.mod + Python + membrane potential at several points of the soma
Replies: 5
Views: 996

Re: hh.mod + Python + membrane potential at several points of the soma

If I choose the different values of "soma.L" and "soma.diam " , the results are not the same as that in the calssical HH model. Are you asking a question, or just making a statement? The model created by the python code in your post doesn't have the same anatomical structure as ...
by ted
Tue Nov 16, 2021 11:48 am
Forum: Modeling networks
Topic: How to change runtime synaptic conductance?
Replies: 5
Views: 459

Re: How to change runtime synaptic conductance?

I need to apply synaptic delay for each up state of slow oscillation cycle. For example when I start simulation the first slow oscillation cycle will also starts and I want to to change synaptic conductance after 500 ms of slow oscillation cycle for example 2nd slow oscillation cycle start at t =15...
by ted
Tue Nov 16, 2021 11:11 am
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 404

Re: elaborate visualization of neuron morphologies and synapses

What about the Shape plot class's color and color_list methods?
by ted
Sun Nov 14, 2021 1:18 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 404

Re: elaborate visualization of neuron morphologies and synapses

"Shape plots" (see the Programmer's Reference for documentation of the Shape and PlotShape classes) can be used to generate figures of parts of cells or any number of cells. These can be rendered by NEURON or by third-party Python libraries, e.g. matplotlib, plotly. To learn more, see Robe...
by ted
Fri Nov 12, 2021 5:09 pm
Forum: Modeling networks
Topic: How to model presynaptic voltage?
Replies: 7
Views: 252

Re: How to model presynaptic voltage?

Hmm, no NMODL code there, just python and xml. Or did I miss it? Was the above NMODL code machine-generated from xml?
by ted
Thu Nov 11, 2021 3:46 pm
Forum: Modeling networks
Topic: How to change runtime synaptic conductance?
Replies: 5
Views: 459

Re: How to change runtime synaptic conductance?

It's best not to change proc advance() or any other part of the standard run system to change parameters during a simulation. The safe and sure way to change parameters during a run is to use an FInitializeHandler. In the Hot tips area of the Forum look for How to change parameters during a simulati...