Search found 5115 matches

by ted
Tue Jan 16, 2018 12:10 pm
Forum: Other questions
Topic: Vectors in MOD files
Replies: 2
Views: 233

Re: Vectors in MOD files

Note that some recent versions of NEURON may have a bug that affects recorded event times--see this thread in the Forum: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=8&t=3808 For example, I see the bug in v. 7.5 master (cb6fc3e) 2017-10-30 So be sure to test whatever you have installed to make ...
by ted
Mon Jan 15, 2018 12:25 am
Forum: Other questions
Topic: Vectors in MOD files
Replies: 2
Views: 233

Re: Vectors in MOD files

It is best to use the NetCon class's record method to capture the spike times to a Vector. Presumably your MOD file implements a point process that is actually an artificial spiking cell, which means that it generates an event every time it "spikes." If you're working in hoc and foo is an objref tha...
by ted
Sun Dec 31, 2017 12:26 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 2095

Re: neuron 7.5 crashes on cygwin 2.9.0

I'm generally in favor of using Linux rather than MSWin, but the plain truth is that half or more of the people who use NEURON are using MSWin. You might contact Marianne about the issue. I wonder if Python might provide a workaround (yes, that would require installing Python, but that's not as bad ...
by ted
Sun Dec 31, 2017 12:16 pm
Forum: NEURON + Python
Topic: Creating NetCon with null source in NEURON+Python
Replies: 10
Views: 9643

Re: Creating NetCon with null source in NEURON+Python

Nice summary, but wouldn't you like to eliminate the big transient that dominates the first 10 ms of the simulation? The model cell's resting potential is -70 mV ( == e_pas) so simply execute the statement h.v_init = -70 before calling h.run() (a good place would be right after specification of cell...
by ted
Thu Dec 28, 2017 12:48 pm
Forum: Modeling networks
Topic: Executing multiple continuerun statements in run block with parameter changes
Replies: 9
Views: 1692

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

We have reached the point where it is necessary to get into the details of what switchon() and switchoff() do. Can you provide a toy example program?
by ted
Sun Dec 24, 2017 2:13 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 2095

Re: neuron 7.5 crashes on cygwin 2.9.0

You definitely want to use a recent version of NEURON. There have been many performance improvements and bug fixes, and some new features, since the last time an installer for NEURON with cygwin was released. I need cygwin for SimTracker (by Marianne Bezaire) If cygwin is required to use SimTracker,...
by ted
Thu Dec 21, 2017 12:58 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 2095

Re: neuron 7.5 crashes on cygwin 2.9.0

You're probably the only person on the planet who is trying to run NEURON 7.5 under Cygwin. The latest NEURON installer for MSWin should produce a working installation of NEURON, and it does not need Cygwin at all. Unless you absolutely must have Cygwin for some other reason (what would that be?), s...
by ted
Mon Dec 18, 2017 12:10 am
Forum: UNIX/Linux
Topic: Neuron 7.5-2 on Manjaro Linux shows no UI elements
Replies: 2
Views: 877

Re: Neuron 7.5-2 on Manjaro Linux shows no UI elements

I installed Neuron 7.5-2 from the AUR package repositories . . . I don't see a package maintainer listed in the package information, so is this an officially maintained package? We'd be delighted if there were so many NEURON users that every Linux distribution could have its own distribution-specif...
by ted
Sun Dec 17, 2017 11:58 pm
Forum: Modeling networks
Topic: Executing multiple continuerun statements in run block with parameter changes
Replies: 9
Views: 1692

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

I have no idea what a mossyfiber.spikegen is. There are many possible traps for the unwary when it comes to simulations involving pseudorandom event sequences and sequence generators. If you're using something that I know about, such as VecStims driven by precalculated sequences, or NetStims, I can ...
by ted
Fri Dec 15, 2017 10:35 am
Forum: Modeling networks
Topic: Executing multiple continuerun statements in run block with parameter changes
Replies: 9
Views: 1692

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: 9
Views: 1692

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: 15
Views: 4370

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: 1313

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: 11312

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: 11312

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 ...