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Dear developers I have written the following mod file describing a GABA synapse with DSI (depolarization-induced suppression of inhibition) according to the equations of page 544 in Zachriou et al 2014 https://pubmed.ncbi.nlm.nih.gov/25123173/. I am in the process of correcting/debugging/compiling t...

thanks, Ted in the link you sent there is only one mod file and the calcium dynamics seem to be implemented within that one mod file. Is there any example where a mod file reads a variable from another mod file? For example, I want my GABA current equations (GABA.mod) to take into consideration AG s...

thank you Ted is it in principle possible to have a network where some of my mechanisms are given as mod files while others are written in python? One problem I encountered doing this is with the definition of my integration step. h.dt=0.5 (for my hoc code) but I also have derivatives to integrate i...

Dear NEURON/Python community

Why is it that the synapse mechanisms or ion channels are traditionally written in NMODL (mod files) when the majority of the code is in python, and can I write those mechanisms as python classes? Any template examples where this is done?

thank you,
Alexandra

thank you Ted Suppose the MyPyr class contains GABA synapses already (as part of the class definitions). I would like to record from those existing GABA synapses (somatic area). Naive question: Is foo = h.GABAa(dend3(0.5)) attaching a new GABA synapse on my MyPyr, aside from the ones attached alread...

thank you Ted I am working on this now. I had a question for you. My GABAa mod file has this nonspecific "i" current which is defined at the BREAKPOINT as "i = g*(v - Erev)". Why can I not record this "i" current using the pointer ...._ref_i? NEURON { POINT_PROCESS GABA...

Dear NEURON/Python community I have a population model and I want to record somatic synaptic currents and somatic voltage from a given excitatory cell. I have my GABAa mod file and GABA synapses are inserted in my excitatory cell model. Using the code below I can successfully record the somatic volt...

in addition to my previous question, I would like to recreate the visualization methods used by netpynne GUI. In the tutorials, they only refer to matplotlib examples however, I would like to use the tool on the graphical interface ideally. Any directions on how to find and install that visualizatio...

thanks. What about 3D markers? The example you sent, very useful, appears to work on 2D dendrites. How do I adjust this for 3D?

thank you this is useful for layer color-coding. I would still like to be able to color-code the different synapses (inhibitory-excitatory) or even from different presynaptic populations. I see that netpynne graphics do that on different examples. I am looking into those examples to see what graphic...

thank you Ted I am looking for a way to annotate 3D points with layer information, or a method for displaying layers as well as indicating different synapse types by e.g. different colors. I haven't been able to find a method that does that using matplotlib according to the Shape plot documentation....

hello I am looking for visualization tools of neural morphology to elaborately visualize the synapses on dendrites. I have noticed that NetPynne provides some pretty detailed visualizations of the cells and I was wondering what tools are used for that and/or whether NEURON provides any tools for ela...

thank you! As a follow-up, I am using a script of yours Ted, to interpolate over the swc points in a hoc file. The "def interplocs" below expects two arguments, I realize the sec refers to the section and locs to the pt3 points. How do I call this definition from a separate python script t...

Hello I have a file called pyrcellfile.hoc, which contains a hoc template that defines a cell class called PYR. I want to use a Python script to load and instantiate my hoc file. My python script, myscript.py, looks like his: from neuron import h h.load_file("pyrcellfile.hoc") newpyr = h.P...

thanks for this most didactic response. My apologies for what may seem like excessive pedantry, but in writing these entries I realize that they will also be read by others who may not have the same background or local resources as the person who asked the question in the first place. I recently bo...