Search found 33 matches

by Yaeger
Mon Nov 18, 2013 11:54 pm
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Re: Using For Loops to Call Multiple Simulation Runs

Thank you Ted. That code ran beautifully, and, as reccomended, I am using the standard run procedure. I have a couple of questions on combining the standard run system with hoc code though. If I write dt = 0.001 in my hoc file that launches the simulation, does that instruct the run system to use th...
by Yaeger
Fri Nov 15, 2013 10:25 pm
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Re: Using For Loops to Call Multiple Simulation Runs

Ok, now I almost have something that works, but I need to close a hoc file in my code. How do I close selected hoc files? There is a load_file("file.hoc") command but I cannot find the equivalent close file command for hoc files.
by Yaeger
Fri Nov 15, 2013 5:50 pm
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Re: Using For Loops to Call Multiple Simulation Runs

Alternatively, does anyone have a better strategy for how to use a hoc file to go through mutiple simulation runs in which a parameter is changed using a loop?
by Yaeger
Thu Nov 14, 2013 12:03 am
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Re: Using For Loops to Call Multiple Simulation Runs

Now I get the error message: net_send td-t = -396 SelfEvent target=VecStim[0] 3000 flag=1 /Users/danielyaeger/Desktop/Dan_Feedback_Network/x86_64/special: line 13: 6385 Abort trap: 6 "${NRNIV}" -dll "/Users/danielyaeger/Desktop/Dan_Feedback_Network/x86_64/.libs/libnrnmech.so" "$@" nrngui exit status...
by Yaeger
Wed Nov 13, 2013 11:54 pm
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Re: Using For Loops to Call Multiple Simulation Runs

I found part of the mistake. I was missing a second } in the gocount procedure:

Code: Select all

proc gocount() { local ii
	for ii = 1,2 {
	newvec()
	interval(3000, ii, 100)
	go()
	counter()
	objref svec, vecstim
	}
}
by Yaeger
Wed Nov 13, 2013 6:00 pm
Forum: Other questions
Topic: Using For Loops to Call Multiple Simulation Runs
Replies: 8
Views: 4104

Using For Loops to Call Multiple Simulation Runs

Hi, I am trying to write a hoc file that will iterate through a user defined number of runs but I keep getting errors that Neuron says are at the end of the hoc file but which do not make much sense. The reason for iterating through the number of runs is that I am changing a list of event times on e...
by Yaeger
Fri Oct 04, 2013 1:06 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Thanks Ted! I am the only person in my lab doing computational modeling (and I am a newbie at that), so sometimes I get lost in the craziness of the parameter space. I am not so concerned about the "error" in the fit with n = 1.96, but there is another function that I am trying to fit with n = 1.75....
by Yaeger
Thu Oct 03, 2013 8:09 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Damn, I meant
G(t) = (1 - exp(-t/tau1))^n*(C1*exp(-t/tau2) + C2*exp(-t/tau3)),

e.g.

(1 - exp(-t/0.16)^1.94 * ( 0.8938*exp(-t/0.32) + 0.1062*exp(-t/9.73) )
by Yaeger
Thu Oct 03, 2013 6:33 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

How would I implement a similar synaptic mechanism, but one for which n was not an integer, i.e. G(t) = (1 - exp(-t/tau1))*(C1*exp(-t/tau2) + C2*exp(-t/tau3)) where n is not an integer. You cannot expand this into nice isolated exponential terms as when n is an integer. Synapses with conductances li...
by Yaeger
Fri Sep 06, 2013 2:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Mg block of NMDA receptors
Replies: 2
Views: 1387

Re: Mg block of NMDA receptors

Also, now that I think about it, putting the Mg2+ block equation in the INITIAL block as I have the mod file will only allow for a change in Mg2+ block at the time of the delivery of the event, so this is probably not a good place to put this. NET_RECEIVE(weight (umho), w) { A = A + weight*m*factor ...
by Yaeger
Fri Sep 06, 2013 2:04 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Mg block of NMDA receptors
Replies: 2
Views: 1387

Mg block of NMDA receptors

I am trying to implement Mg2+ block of NMDA receptors but am having a hard time figuring out where to put the equation for block. Right now I have the equation for block in the INITIAL block. m is the block equation in the code below. Otherwise the mod file for the synapse is similar to Exp2Syn exce...
by Yaeger
Wed Aug 28, 2013 7:36 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Ted, as always, thanks for all the help. I wish I could tell you that I won't need more in the future, but that surely will not be the case. I have a mod file that works for the five exponential function, which is just (1 - exp(-t/tau1)^4 * exp(-t/tau2) expanded. I plan to implement a second mod fil...
by Yaeger
Tue Aug 27, 2013 7:30 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Yes - this is the reference to which I am referring:
Bekkers, J. M. & Stevens, C. F.
Cable properties of cultured hippocampal neurons determined from sucrose-evoked miniature EPSCs.
J Neurophysiol,
1996, 75, 1250-1255
by Yaeger
Tue Aug 27, 2013 7:28 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Actually, now that I see it in this form it seems fairly straightforward to extend the Exp2Syn mod file to a "Exp5Syn" mod file. Let me see what I can do.
by Yaeger
Tue Aug 27, 2013 5:42 pm
Forum: Other questions
Topic: Implementing a Bekkers & Stevens 1996-type synapse
Replies: 13
Views: 3213

Re: Implementing a Bekkers & Stevens 1996-type synapse

Hi Ted - Thanks for the reply. I am not sure that I follow (I am mathematically challenged). From g(t) = A1 * (1 - exp(-t/tau1))^4 * (A2 * exp(-t/tau2) + A3 * exp(-t/tau3)) Neglecting the A3 term for now, I have A1 * (1 - exp(-t/tau1))^4 * A2 * exp(-t/tau2) If I multiply this out, I get, A1*A2*( exp...