Search found 5101 matches

by ted
Sun Dec 10, 2017 6:39 pm
Forum: The GUI
Topic: spike frequency vs current graph
Replies: 14
Views: 8589

Re: spike frequency vs current graph

finitialize(v_init) initializes all voltage-dependent gating variables to their steady state values at v = v_init. It also executes whatever initialization code exists in ion transport and accumulation mechanisms. But it does nothing--and it can't do anything--that ensures ionic concentrations have ...
by ted
Thu Dec 07, 2017 8:58 pm
Forum: The GUI
Topic: spike frequency vs current graph
Replies: 14
Views: 8589

Re: spike frequency vs current graph

Before discussing determining the f-I relationship, let's talk about your model. Does it matter to you whether the model cell is initialized to a steady resting state? If yes, how do you know that proc init() { finitialize(v_init) soma.cai = cai_init } initializes the model cell to steady state? Bes...
by ted
Tue Dec 05, 2017 11:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using Ca2+ currents in point and distributed processes
Replies: 6
Views: 1337

Re: Using Ca2+ currents in point and distributed processes

I have a chloride leak current expressed in mA/cm2 and an accumulation mechanisms. An accumulation mechanism for what? Chloride? I had a gabaa synapse point process which writes a ligand-gated chloride current in nA. I would like to counterbalance with the cl pump Just guessing here--your accumulat...
by ted
Tue Dec 05, 2017 12:26 am
Forum: Adding new mechanisms and functions to NEURON
Topic: "My mechanisms don't load!"
Replies: 18
Views: 15871

Re: "My mechanisms don't load!"

You figured it out. Drag and drop one mod file onto mknrndll, and you get a library that contains one compiled mechanism. Drag and drop another mod file, and you overwrite what you previously had with a library that contains a different compiled mechanism. Drag and drop the whole folder of mod files...
by ted
Mon Dec 04, 2017 10:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: "My mechanisms don't load!"
Replies: 18
Views: 15871

Re: "My mechanisms don't load!"

1. Does this "I drag the mod files to mknrndll." mean that you dragged the folder that contained the mod files onto mknrndll? 2. Is the x86_64 folder in the same folder that contains your mod files and your hoc file? 3. Use a plain text editor to create a text file called hello.hoc that contains the...
by ted
Fri Dec 01, 2017 11:43 am
Forum: Getting started
Topic: Dynamic clamp?
Replies: 9
Views: 7184

Re: Dynamic clamp?

I want to use the SEClamp as a conductance clamp. So I should play my time dependent conductance g(t) into SEClamp.rs, right? But then I did not know how to set the reversal potential of the, as synapse abused, SEClamp. Set the SEClamp's dur1 to 1e9, and set its amp1 to the value you want for the r...
by ted
Wed Nov 29, 2017 10:27 am
Forum: Parallel NEURON
Topic: summation of matrix on different computer nodes
Replies: 2
Views: 7644

Re: summation of matrix on different computer nodes

Do you want to add up all the elements of the matrices? That doesn't seem like a useful thing to do--it would produce a single number on each host. Or do you just want to write the time course of each cell's membrane potential, in each compartment, to one or more files? That doesn't seem very practi...
by ted
Mon Nov 27, 2017 12:02 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Which libnrnmech.so file to load on linux/mac
Replies: 3
Views: 9683

Re: Which libnrnmech.so file to load on linux/mac

The problem is that, as the interface can start NEURON simulations in parallel, there are several folders each containing the hoc files for each run (e.g. several current steps for calculating an F-I relationship). Hence I would have to copy that x86_64 folder (or what ever it is called on that sys...
by ted
Mon Nov 27, 2017 11:26 am
Forum: Other questions
Topic: computing impedances...
Replies: 15
Views: 8702

Re: computing impedances...

is it possible to change the initial conditions at which the impedance tools performs its measurement? Eg initialise at a given voltage and then calculate? Absolutely. First I should point out that any model should always be properly initialized before the Impedance tools (or the Impedance class's ...
by ted
Thu Nov 23, 2017 4:50 pm
Forum: NetPyNE
Topic: How to set initial voltage of simulation
Replies: 6
Views: 7426

Re: How to set initial voltage of simulation

A common theme is emerging in these posts: many things that are easy to do with plain vanilla NEURON are either no longer available or require specialized syntax if one uses NetPyNE. For example, in the case of a model specified with hoc (or Python), assigning a value to v_init (h.v_init for Python)...
by ted
Fri Nov 17, 2017 2:34 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Which libnrnmech.so file to load on linux/mac
Replies: 3
Views: 9683

Re: Which libnrnmech.so file to load on linux/mac

Why bother with that level of detail? Just put the necessary mod files in the same directory as the main program (the hoc or Python file that starts everything), let prospective users compile them in that location, and let NEURON automatically find and load the binaries for itself when it starts up....
by ted
Tue Nov 14, 2017 9:50 am
Forum: Other questions
Topic: Values for Gas and Faraday constants
Replies: 4
Views: 9820

Re: Values for Gas and Faraday constants

The values of all empirically derived constants have changed over time. These variations are much smaller than the errors inherent in most if not all of the experimental measurements that are used as the basis for mechanistic computational modeling. The chief practical consequence is limited but sti...
by ted
Tue Nov 14, 2017 9:32 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 23364

Re: pump kinetic scheme

I won't have the opportunity to look into this until after I return from the SFN meeting later this week or early next week.
by ted
Tue Nov 14, 2017 9:30 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Inconsistent behavior on modeling p2y2 Receptor
Replies: 3
Views: 11491

Re: Inconsistent behavior on modeling p2y2 Receptor

I'll have to get back to you about this after the end of the SFN meeting.
by ted
Fri Nov 10, 2017 9:56 pm
Forum: Modeling networks
Topic: Error using nc.record
Replies: 5
Views: 14234

Re: Error using nc.record

You could use Vector play to drive the parameter in question, especially if you want to make a lot of changes or implement continuous variation of a parameter. If you're only doing a few parameter changes that occur at just a handful of times, you could use events--see Using events to implement para...