Search found 86 matches

by Bill Connelly
Fri Oct 02, 2009 12:01 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Print from NMODL?
Replies: 1
Views: 1687

Print from NMODL?

The two easiest ways to figure out where you code is going wrong is to print variables, or to print an arbitrary message after certain flow control statements. But I can't figure out how to do this in from NMODL. Is there a way?
by Bill Connelly
Thu Oct 01, 2009 10:34 pm
Forum: Getting started
Topic: Making a netcon know what triggered it
Replies: 9
Views: 3198

Re: Making a netcon know what triggered it

Okay, I got it to work apart from the important bit, i.e. the sodium current doesn't shut off. I had to give net_receive an argument, or else it would compile. I suspect that is where to problem is? I don't need to set up any netcons do it? The WATCH statement is running the whole time, isn't it? TI...
by Bill Connelly
Wed Sep 30, 2009 9:28 pm
Forum: Getting started
Topic: Making a netcon know what triggered it
Replies: 9
Views: 3198

Re: Making a netcon know what triggered it

MOD code is still a bit of a dark art to me. Why does the if (v > thresh) statement need to be in the NET_RECEIVE block? Couldn't it just be in the breakpoint block? Just psuedo coding but something like if (v > thresh AND trigger == 0 ) { gnabar = 0 trigger=1 t0=t } if (trigger == 1 AND t-t0>delay)...
by Bill Connelly
Tue Sep 29, 2009 8:17 pm
Forum: Getting started
Topic: Making a netcon know what triggered it
Replies: 9
Views: 3198

Making a netcon know what triggered it

I am trying to make a cell that sets its sodium channel conductance to zero for a period of time after its action potential proc preprocess() { localobj, shutDownNetCon, nil for n=0, ncells-1 { cl.o(n).soma shutDownNetCon = new NetCon(&v(0.5), nil) shutDownNetCon.threshold = 0 shutDownNetCon.record(...
by Bill Connelly
Fri Sep 04, 2009 8:46 pm
Forum: General questions and discussions about computational neuroscience
Topic: Another Synchrony Measure
Replies: 1
Views: 7267

Another Synchrony Measure

I wasn't sure if here was the best place to ask this, or in the networks section where Bill Lytton might see it; but anyway, The Wang and Buzsaki model in gamma oscillations is pretty popular. They use a measure of synchrony that I would love to have a look at, but for the life of me, I can't figure...
by Bill Connelly
Tue Aug 18, 2009 7:11 pm
Forum: Getting started
Topic: What is the simplest way to inject a sinewave current
Replies: 1
Views: 1122

What is the simplest way to inject a sinewave current

I can think of a couple of waves to get a sine wave of current injected, but I was just wondering what the best/quickest way was? Thanks
by Bill Connelly
Tue Aug 11, 2009 6:33 pm
Forum: Other questions
Topic: Network Building
Replies: 3
Views: 2054

Re: Network Building

I'm with Ted. I made a network with 2 cells, then looked at the hoc code, and used it to make a ~200 cell model. It really is a lot simpler. This way you define template(s) for your cell types, then make a simple iterative function that links the cells up. Mine goes something like this begintemplate...
by Bill Connelly
Sun Aug 09, 2009 4:03 pm
Forum: General questions and discussions about computational neuroscience
Topic: membrane ionic current = -capacitive current
Replies: 6
Views: 17185

Re: membrane ionic current = -capacitive current

Okay. That all makes sense. Thanks a lot Ted. It's not quite as cognitively peaceful as Ohms law. But I'll just have to learn to live with it.
by Bill Connelly
Sun Aug 09, 2009 3:56 pm
Forum: General questions and discussions about computational neuroscience
Topic: Differential Attenutation of EPSPs in VC vs IC
Replies: 3
Views: 9737

Re: Differential Attenutation of EPSPs in VC vs IC

Peak amplitude of the EPSC when in voltage clamp (basal holding current to maximum deflection in current), peak amplitude of the EPSP when in current clamp (resting membrane potential to maximum deflection in membrane potential). Though I think I understand the cause of this now. The voltage clamp e...
by Bill Connelly
Sat Aug 08, 2009 8:20 pm
Forum: General questions and discussions about computational neuroscience
Topic: membrane ionic current = -capacitive current
Replies: 6
Views: 17185

Re: membrane ionic current = -capacitive current

Sorry that I'm not getting this. Everything you have said makes sense to me, but none of it seems to explain how, that if everytime charge moves in via Ii it goes out via Ic, how the membrane potential can change. But maybe this might be the explanation: Ic = C dV/dt I had always thought it was Imem...
by Bill Connelly
Fri Aug 07, 2009 8:32 pm
Forum: General questions and discussions about computational neuroscience
Topic: membrane ionic current = -capacitive current
Replies: 6
Views: 17185

Re: membrane ionic current = -capacitive current

I-ion + I-cap = 0 I-mem = I-ion + I-cap I-m = 0 No transmembrane current, no change in membrane voltage. What am I doing wrong here? I know when I plot I-ion and I-cap in neuron, (in a single compartment) they are equal and opposite. If I-ion is inward, does the apparent outward I-cap decharge/hyper...
by Bill Connelly
Fri Aug 07, 2009 5:31 am
Forum: General questions and discussions about computational neuroscience
Topic: membrane ionic current = -capacitive current
Replies: 6
Views: 17185

membrane ionic current = -capacitive current

A statement I read all the time is the "total membrane ionic current must be equal and opposite to the total membrane capacitive current" I appreciated this statement if you replace the word current with charge, i.e. any charge that goes into the cell has to EVENTUALLY come out of the cell. or other...
by Bill Connelly
Thu Aug 06, 2009 5:10 pm
Forum: General questions and discussions about computational neuroscience
Topic: Differential Attenutation of EPSPs in VC vs IC
Replies: 3
Views: 9737

Differential Attenutation of EPSPs in VC vs IC

So I was playing around with neuron last night. I had a 3x500um long cable, with passive properties vaguely like a layer V dendrite. I applied alphaSynapses over the length of the cable, and had a voltage clamp or current clamp electrode at one end. I saw your typical exponential attenuation of the ...
by Bill Connelly
Wed Aug 05, 2009 10:45 pm
Forum: Modeling networks
Topic: Variable Steps and Integration methods
Replies: 3
Views: 2177

Re: Variable Steps and Integration methods

Well I suppose that makes sense (well has much as anything which contains the phrase "the system matrix is tridiagonal" can make sense to a humble pharmacologist). But It doesn't seem to make sense that variable timestep integrators should run SLOWER.
by Bill Connelly
Wed Aug 05, 2009 6:35 pm
Forum: Modeling networks
Topic: Variable Steps and Integration methods
Replies: 3
Views: 2177

Variable Steps and Integration methods

So my gap junction, inhibitory synapse coupled network (200 cells) runs pretty slowly. I tried various variable step methods; but they all ran considerably slower. And the local step method doesn't run at all. And it's not a very noisy network; most of the time, the cells have only a subtly fluctuat...