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Update sonata_tech.rst #5

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2 changes: 1 addition & 1 deletion source/sonata_tech.rst
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Expand Up @@ -72,7 +72,7 @@ Group column represents the HDF group where the dataset is located under /<popul
/0 ``mtype`` utf8 Mandatory Defines the morphological type of the node.
/0 ``me_combo`` utf8 Optional Deprecated Replaced by dynamics_params.
Foreign key to me combo tsv file.
/0 ``synapse_class`` utf8 Mandatory Defines the synapse type of the node; whether the neuron is inhibitory or excitatory. "EXC" or "INH".
/0 ``synapse_class`` utf8 Mandatory Defines the synapse type of the node; whether the neuron is inhibitory or excitatory. "EXC" or "INH".(or "MOD" - Define a third class of synapse (other than excitatory and inhibitory class) which is neuromodulatory.)
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@matz-e matz-e Sep 2, 2022 •
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/0 ``synapse_class`` utf8 Mandatory Defines the synapse type of the node; whether the neuron is inhibitory or excitatory. "EXC" or "INH".(or "MOD" - Define a third class of synapse (other than excitatory and inhibitory class) which is neuromodulatory.)
/0 ``synapse_class`` utf8 Mandatory Defines the synapse type of the node; whether the neuron is inhibitory, excitatory, or neuromodulatory. "EXC", "INH", or "MOD".

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I think "MOD" is too general. Would suggest "Cholinergic." It will prevent confusion down the line once additional neuromodulatory types are added.

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@vignan21 can you update accordingly ?
@MWolfR @romani79 no other comment ?

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@vignan21 vignan21 Sep 13, 2022 •
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I think the changes made by @matz-e seem reasonable. @dkeller9 - we are trying to define a third class of neuron types which are neuromodulatory. So under "MOD", all types of neuromodulatory neurons will fall. What do you think?

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@vignan21 I like your suggest. The synapse class remains MOD, but then we can have different synapse class for each neuromodulator. We can start with M1 for Acetylcholine. I think this is enough for now. We can always append new type/neuromodulator depending on our needs. Listing "all" the neuromodulators and their combinations may be too much. Let's start simple.

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@romani79 romani79 Mar 9, 2023 •
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what is the impact of the first, concretely?

My first reaction is that this seems redundant if we assume that for a given synapses the presynaptic terminal releases the neurotransmitter compatible with the postsynaptic receptors. This is a fair assumption and we avoid useless complications.
I would ask the other scientists if I am missing obvious exceptions for which we should specify presynaptic neurotransmitters.

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I think it depends a bit for which simulator aspects we are gonna use this. If e.g. this relates to which MOD files to load etc., it might not be redundant information. Let's say we have a presynaptic GABA release mechanism, but it gets picked up by GABA-A and GABA-B receptors, in that case it might be useful to separate neurotransmitter (or release mechanism?) from receptor. Of course, we're talking about the future, I'm not sure we have a use case right now.

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Apparently, I created a bit of mess here. The topic is about node file, while I was discussion more in terms of edge file. During the meeting, we commented that the column on Exc/Inh in the node file may be redundant if we have the postsynapse receptor information in the edge file.

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@romani79 romani79 Mar 9, 2023 •
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@wvangeit the redundancy is at the level of neurotransmitter release, but both receptor and model files are essential information as you pointed out. The proposal we had in the meeting is to store the information on receptor in the edge file, and the information on which mod file to use outside the edge file (e.g. recipe, Neurodamus).

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The proposal we had in the meeting is to store the information on receptor in the edge file, and the information on which mod file to use outside the edge file (e.g. recipe, Neurodamus).

I don't think I like this proposal. The format is a "circuit model definition", so which mod file to load should be defined in the circuit as we do with morphologies, or with the e-model to load. That is the information that is needed to the simulator.

/0 ``region`` utf8 Optional Attribute assigning a brain region to the associated cell.
/0/dynamics_params ``threshold_current`` float32 Mandatory The minimal amplitude (in nA) of a step current clamp injection that triggers an action potential.
/0/dynamics_params ``holding_current`` float32 Mandatory The current clamp amplitude (in nA) necessary to hold the cell at a predefined holding voltage (typically around -85 mV for BBP).
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