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Replace syn_type_id with connection_model for synapses. #23

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Replace syn_type_id with connection_model for synapses. #23

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5af93b5
Replace `syn_type_id` with `model_template` for synapses.
matz-e Apr 6, 2023
625368c
Add smallest possible recipe part.
matz-e Apr 6, 2023
be081be
Switch to unique naming.
matz-e Apr 6, 2023
b86fc2f
Tÿpõ
matz-e Apr 6, 2023
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8 changes: 6 additions & 2 deletions source/recipe.rst
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I think leaving the mandatory start of the synapse type with E or I should be OK, this will simplify the handling on the recipe code side. It can be completely removed later.

I did not add any parameter changes to the specification here, because I don't know which fields will be required for all possible models.

Original file line number Diff line number Diff line change
Expand Up @@ -267,7 +267,8 @@ To assign synapse properties, the classification field needs to be set:
.. note::

The type has to start with either ``E`` for excitatory connections or
``I`` for inhibitory connections.
``I`` for inhibitory connections. This legacy behavior may be overriden by
specifying the `connection_model` parameter for the `SynapsesClassification` section.

Two optional attributes may be set:

Expand Down Expand Up @@ -318,7 +319,7 @@ property name:
Truncated Normal distributions are limited to the central value ±σ and are
re-rolled until positive values has been obtained.

Two optional attributes can be specified, where each attribute will have to
Three optional attributes can be specified, where each attribute will have to
be given for all `SynapsesClassification` elements:

- `gsynSRSF`, the scale factor for the conductance; `SRSF`: 'synaptic receptor scaling factor'
Expand All @@ -332,6 +333,9 @@ be given for all `SynapsesClassification` elements:
where :math:`ca` denotes the simulated calcium concentration in
millimolar and :math:`y` a scalar such that at
:math:`ca = 2.0:\ u_\text{final} = u`. (Markram et al., 2015)
- `connection_model`, to specify the filename stub (without a final extension) that should
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It's a matter of personal taste, but I would more easily relate the concepts if this was named synapse_model. Please disregard if we will model connections which are not synapses

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I would prefer that we stay with the generic 'model_template' like they have specified for edges in the SONATA paper with Allen: https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md#representing-edges
In NEURON and other simulators, the generic word 'model' is used for various objects: ion channels, firing behavior, synapse, gap junction, etc

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Whatever is decided, it should match what is chosen for the column in #5. I'd prefer that we don't duplicate names in nodes and edges, simply because it makes it easier to grep for one or the other and it reduces potential confusion, but it's not a deal breaker for me.

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connection_model makes me think about the anatomical connection. synapse_model seems more appropriate to me.

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synapse_model does not work for the reason mentioned by @jamesgking - it is not only about synapses.

appear in the field with the same name in the corresponding SONATA edge file. Presence
of this attribute will suppress creating the `syn_type_id` field in the edge file.

These attributes will be copied for each synapse corresponding to its
classification. If they are not specified, no corresponding columns will
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5 changes: 3 additions & 2 deletions source/sonata_tech.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -288,10 +288,11 @@ Group column represents the HDF group where the dataset is located under /<popul
where :math:`ca` denotes the simulated calcium concentration in
millimolar and :math:`y` a scalar such that at :math:`ca = 2.0:\ u_\text{final} = u`. (Markram et al., 2015)

/0 ``syn_type_id`` uint32 Mandatory Takes the value 0 for inhibitory synapses, 100 for excitatory synapses (numerical values due to historic reasons)
/0 ``syn_type_id`` uint32 Mandatory Takes the value 0 for inhibitory synapses, 100 for excitatory synapses (numerical values due to historic reasons). Deprecated, replaced by ``connection_model``.
/0 ``connection_model` uft8 Mandatory Template or class of the model for the edge, should be an stored as an enumeration in the `@library` group.
/0 ``syn_property_rule`` uint32 Mandatory The position of the rule that leads to the synapse in the recipe
/0 ``delay`` float32 Mandatory The axonal delay (in ms, ``NaN`` for dendro-dendritic synapses).
/0/@library ``spine_morphology`` utf8 Optional Spine morphology file relative path, without the file extension.
/0 ``spine_morphology`` utf8 Optional Spine morphology file relative path, without the file extension. Should be stored as an enumeration in the `@library` group.
Example "mymorphology" or "mypath/mymorphology". Set to an empty string if synapse forms on the shaft.
/ ``edge_type_id`` int64 Mandatory Links an edge to the underlying CSV file; not used at BBP.
/ ``source_node_id`` uint64 Mandatory The id of the presynaptic neuron.
Expand Down