Combining different model sources for my own model.
Posted: Tue Oct 11, 2016 2:24 pm
Wow,
I've tried to scan through this forum to find answers, most of the questions are very specific.
I'm kind of a new to NEURON environment, so sorry if my question is too abstract.
I'm trying to make my own model but I use parts from other models from ModelDB.
So I imported Topology from ModelDB Accession number : 140828, using Cell Builder Management Top Level import function (rc19.hoc file).
I took the mod files for the conductances and Ca "diffusion" from there as well : cad.mod CaT.mod, h.mod, kca.mod, kir.mod, km.mod,
and cal.mod, ka.mod, kdr.mod, naf.mod, nap.mod, skahp.mod from ModelDB Accession: 168858; also nadifi.mod from ModelDB Accession: 136715.
The files are compiled and start from dll.
Now, I'm trying to run it and as a first thing I just tried to run a IClamp of 0.3 nA, what it does is, just, jump by certain voltage on the voltage graph and stays there.
I'm sure, I'm doing something wrong, so the global question is - how to do it right.
More specific, I do want to use 140828 topology, I do want to use the conductances mentioned, since there is differential distribution of conductances across cellular compartments, I need to specify each dendrite separately. Which I'm sure can be done faster by using subsets, but when you import the topology, there is no control over it in subsets, and the compartments show up only in geometry.
Which makes me wonder if defining the conductances gonna work at all, or can I actually define byophisical mechanisms to imported topology that will work. If yes, so it's just an elaborate process of tweaking the model, if not - how can I make a realistic model not from scratch, but by using other's available parts.
Also the used Neuron version is 7.4.
Sorry again for such an abstract inquiry, I do understand that it might not be simply answered. But any help is appreciated.
Thank you.
I've tried to scan through this forum to find answers, most of the questions are very specific.
I'm kind of a new to NEURON environment, so sorry if my question is too abstract.
I'm trying to make my own model but I use parts from other models from ModelDB.
So I imported Topology from ModelDB Accession number : 140828, using Cell Builder Management Top Level import function (rc19.hoc file).
I took the mod files for the conductances and Ca "diffusion" from there as well : cad.mod CaT.mod, h.mod, kca.mod, kir.mod, km.mod,
and cal.mod, ka.mod, kdr.mod, naf.mod, nap.mod, skahp.mod from ModelDB Accession: 168858; also nadifi.mod from ModelDB Accession: 136715.
The files are compiled and start from dll.
Now, I'm trying to run it and as a first thing I just tried to run a IClamp of 0.3 nA, what it does is, just, jump by certain voltage on the voltage graph and stays there.
I'm sure, I'm doing something wrong, so the global question is - how to do it right.
More specific, I do want to use 140828 topology, I do want to use the conductances mentioned, since there is differential distribution of conductances across cellular compartments, I need to specify each dendrite separately. Which I'm sure can be done faster by using subsets, but when you import the topology, there is no control over it in subsets, and the compartments show up only in geometry.
Which makes me wonder if defining the conductances gonna work at all, or can I actually define byophisical mechanisms to imported topology that will work. If yes, so it's just an elaborate process of tweaking the model, if not - how can I make a realistic model not from scratch, but by using other's available parts.
Also the used Neuron version is 7.4.
Sorry again for such an abstract inquiry, I do understand that it might not be simply answered. But any help is appreciated.
Thank you.