Search found 5106 matches

by ted
Fri Dec 15, 2017 10:35 am
Forum: Modeling networks
Topic: Executing multiple continuerun statements in run block with parameter changes
Replies: 5
Views: 22

Re: Executing multiple continuerun statements in run block with parameter changes

The most appropriate solution depends on details that have not been discussed. Do the presynaptic spike events happen at random times, or at regular intervals? Are they generated by NetStims during a run, or are the event times calculated before the simulation begins and then "played back" by VecSti...
by ted
Thu Dec 14, 2017 12:21 pm
Forum: Modeling networks
Topic: Executing multiple continuerun statements in run block with parameter changes
Replies: 5
Views: 22

Re: Executing multiple continuerun statements in run block with parameter changes

Are you trying to execute a single simulation that consists of a sequence of intervals
interval 0 from t = 0 to t0
interval 1 from t = t0 to t1
interval 2 from t = t1 to t2
etc.
with different "activated mossy fibers" in each interval?
by ted
Thu Dec 14, 2017 12:04 pm
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 14
Views: 2445

Re: na_ion mechanism not inserted in section axon

. . . In the compartment where this point process is there are density mechanisms which generate others icl currents in mA/cm2 (icl_leak, icl_pump). I expect that the icl total will be the sum of all the other currents involved : icl= icl_leak+icl_pump+syn.icl*0.000001/pi*diam*diam, but I cannot se...
by ted
Thu Dec 14, 2017 11:48 am
Forum: Getting started
Topic: Calculating Firing Frequency
Replies: 1
Views: 17

Re: Calculating Firing Frequency

proc handle() is not particularly useful. Get rid of it. Instead, use the Vector class's record method to capture the spike times to a Vector. From the recorded spike times discover the interspike intervals, and from that get spike frequency. freq = spikeTotal / (stim.dur) fails badly if firing stop...
by ted
Wed Dec 13, 2017 11:30 pm
Forum: The GUI
Topic: spike frequency vs current graph
Replies: 16
Views: 9289

Re: spike frequency vs current graph

You can discover for yourself whether your model may have a problem with initialization of ionic concentrations to steady state. First, determine whether any of the mod files used by your model is an ion accumulation mechanism (hint: any mechanism that WRITEs an intracellular or extracellular concen...
by ted
Sun Dec 10, 2017 6:39 pm
Forum: The GUI
Topic: spike frequency vs current graph
Replies: 16
Views: 9289

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: 16
Views: 9289

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: 1881

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: 17001

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: 17001

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: 7792

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: 8434

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: 10250

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: 9371

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: 7870

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)...