Modelling a two-neuron network

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ergefan
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Modelling a two-neuron network

Post by ergefan » Sun Oct 17, 2010 11:19 am

Hi,

I am a beginner in NEURON modelling. I want to build an STN-GPe network (a two-cell circuit in basal ganglia) with the hoc files that describe the two cell types I have.

Should I import the hoc files into the Cell Builder in NEURON and build the network using Network Builder? I have no idea how to do it after reading the NEURON book chapter 11 and the NEURON forum.

Please help! Thanks.

Kai.

ted
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Re: Modelling a two-neuron network

Post by ted » Mon Oct 18, 2010 10:31 am

ergefan wrote:I want to build an STN-GPe network (a two-cell circuit in basal ganglia) with the hoc files that describe the two cell types I have.
Do the hoc files contain templates for two different cell classes? In other words, do you see blocks of code that start with
begintemplate Nameofcellclass
and end with
endtemplate Nameofcellclass
where Nameofcellclass will be the name of a cell class?

ergefan
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Joined: Sun Oct 17, 2010 11:04 am

Re: Modelling a two-neuron network

Post by ergefan » Mon Oct 18, 2010 10:36 am

Hi ted,

Thanks for your quick reply. I have one hoc file for each cell type (together with the mod files that describe the conductances), but they don't contain the "begin template" command. What should I do?

ted
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Re: Modelling a two-neuron network

Post by ted » Mon Oct 18, 2010 2:53 pm

The task of constructing a model network proceeds in the following steps:
1. Define the classes of cells that will be in the network. It is easiest to construct, revise, and use network models whose individual neural elements (model cells) are instances of one or more cell classes.
2. Create as many instances of each cell class as you will need in your network.
3. Set up the connections between the model cells that you created in step 2.
4. Set up whatever instrumentaton is necessary, i.e. network inputs (e.g. stimulus sources, afferent spike trains) and outputs (e.g. to record spike times, synaptic weights, time course of membrane potential or cai or whatever).

You're about to start step 1. Presumably you have models of two different cells. Are you happy with their anatomical and biophysical properties, and how they respond to injected currents and synaptic inputs, or do you need to do some testing and tuning? If the latter, it's easiest to take care of those issues now.

The next question is to what extent you should try to rely on the Network Builder and other GUI tools for (almost) everything, as opposed to writing hoc code. It is easiest to proceed if your model cells are already managed by CellBuilders; this will allow you to simply import them into NetReadyCellGUI tools, which can be used with the Network Builder to generate the cell class templates that you need. To give you the best advice on this, I should probably look at the hoc, ses, and mod files that you already have. If they are from models that are already in ModelDB, just tell me the accession numbers and which files you're using; otherwise if you zip them up and email them to
ted dot carnevale at yale dot edu
I will look at them and advise you how to proceed.

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