www.neuron.yale.edu

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...

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.

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?

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" &qu...

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

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...

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...

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) )

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...

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 ...

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...

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...

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

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.

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...