www.neuron.yale.edu

That clears up quite a bit. Just a few more queries on this: 1> Under what conditions do we get the following message on "Print Matrix Info" in LCB: Circuit equations have X inconsistencies X: number>=0 Am I correct in believing that it would come-up when we have an incomplete/invalid circ...

Remark; One could equivalently compute vi in a BEFORE BREAKPOINT block but in this case there would be no numerical difference. I was wondering about this. I tested it on two cells (nseg = 1) connected via gap junctions for a simulation duration of 0.1 ms. vi in BEFORE BREAKPOINT: oc>cella.v(0.5) -...

Just after posting the earlier query, I was about to add that interestingly when we 'Create Class' from LCB, the LinearMechanism hoc code consists of only 2x2 matrices as opposed to 3x3 when we 'Print Matrix Info' - and why the difference? - But your post already answers that. I edited my "linc...

Returning to this discussion after a long hiatus... I took your advice and decided to model R-C gap junctions using LinearMechanism. Though by now I have some grip on using LinearMechanisms, I decided to make use of the Linear Circuit Builder (LCB) to start off with and take a look at the LinearMech...

Thanks for the alpha installer... certainly much easier to get up and running! Will try out the parallel gap junction implementation with this. But since I had attempted the compile on the mercurial release, I am just a tad curious to know what I did wrong. My package versions are: Shailesh@Centurio...

Thanks Michael, that was real quick! I was eager to test it out but having some trouble in compiling the latest code from Mercurial. I believe the query would be more apt under a different head and hence have posted it here: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=5&t=3094 Would be gre...

I was trying to compile the latest development code throught Mercurial (so as to make use of http://www.neuron.yale.edu/hg/neuron/nrn/rev/294dac40175f ). I followed the instructions given here: Link 1: http://www.neuron.yale.edu/neuron/download/getdevel Link 2: http://www.neuron.yale.edu/neuron/down...

Yes I can see that would become an issue in parallel implementation of gap junctions (in presence of extracellular mechanism). Is a workaround possible in the current NEURON framework for parallel simulations? I haven't done any serious work with Parallel sims yet and so don't have much clue. I did ...

Thanks Michael! That did it. It did not occur to me to think about how the extracellular mechanism could have been interfering with the regular gap junction implementation (felt it was more likely to do with an incorrect circuit implemenation or some worrying number crunching). Glad that you were ab...

Hi, I have been trying to develop a network model involving extracellular mechanism as well as constructs using LinearMechanism. Since neither of these are intuitive (and prone to user errors), I made a small dummy model just to test my understanding of what was happening (with the LinearMechanisms ...

As far as I can tell, they just appear to be different ways of obtaining the same (or extremely) similar shape.
If results are normalized, there doesn't seem to be anything to tell them apart. Pilot simulations seem to suggest the same.

What are the peak amplitudes of functions 1 and 2? They appear to only dictate the shape, as peak amplitudes have not been explicitly stated (nor used in calculations). Reason, I suppose, being the study was more to do with regards to the time courses of junction potentials, and so amplitudes were ...

This is more of a general query hence posting here. I was having some confusion over the way the alpha function is implemented for modeling current/conductance. This is what I have seen at different places: 1>> Some books (e.g. Jack, Noble & Tsien, 1975) and papers (e.g. Purves, 1976) implement ...

Here is the scenario: > Three cells (A,B,C) coupled via gap junctions forming a chain: A ----- B ----- C > All cells have been assigned identical biophysical parameters. They are equipped with some custom active channels. > When isolated (i.e. no gap juntions), each cell has a resting potential of -...

Ok...... I think I got it this time. A more general query: I was just wondering that there are so many models on modeldb, but I have rarely come across models where: > there are two or more cells and > all these cells have extracellular fields (ecf) and > the ecfs of these cells should be linked (i....