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Include morphology from another file #150

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pgleeson opened this issue Mar 23, 2021 · 1 comment
Open

Include morphology from another file #150

pgleeson opened this issue Mar 23, 2021 · 1 comment

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@pgleeson
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pgleeson commented Mar 23, 2021

Is your feature request related to a problem? Please describe.
Use one NML morphology in multiple active files

Describe the solution you'd like
Be able to include with one line the morphology section from another cell

Perhaps something like:

<neuroml>

  <include href="pyr_morphology.nml"/>
  <include href="pyr_biophysics.nml"/>

    <cell id="pyr_full" morphology="pyr_morphology/morph" biophysical_properties="pyr_biophysics/biophysicalProperties">

        <notes>Points to definitions in other cells</notes>

    </cell>
</neuroml>

See https://github.com/pgleeson/morphology_include/blob/main/pyr_full.cell.nml

@github-project-automation github-project-automation bot moved this to 🆕 New in NeuroML backlog Oct 2, 2023
@sanjayankur31 sanjayankur31 moved this from 🆕 New to 📋 Backlog in NeuroML backlog Oct 18, 2023
@sanjayankur31 sanjayankur31 moved this from 📋 Backlog to 🔖 Ready in NeuroML backlog May 7, 2024
@sanjayankur31 sanjayankur31 added T: enhancement Type: enhancement S: ready Status: ready C: NeuroML2 standard Component: NeuroML 2 standard S: next meeting S: needs comment labels May 7, 2024
@spanag
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spanag commented May 10, 2024

FWIW, Eden handles <morphology>s and <biophysicalProperties> outside the <cell> as attributes, as seen on:
https://gitlab.com/c7859/neurocomputing-lab/Inferior_OliveEMC/eden/-/blob/main/eden/NeuroML.cpp#L5303 and 5330 .
Because the <biophysicalProperties> can thus be used with different morphs in different cell types, they get re-interpreted for each cell type.
This behaviour was guessed by reading the schema, see https://github.com/NeuroML/NeuroML2/blob/NMLv2.1/Schemas/NeuroML2/NeuroML_v2.1.xsd#L1534 .

If we point to a LEMS path to hijack the morphologies of a different cell type, it's a bit irregular and we have to make sure no e.g dynamic properties are ever allowed to happen because they would expose the links.
How difficult would it be to spawn a child component as a subclass of an existing LEMS component, when the attribute is present? IIRC there is <Structure> support to do this, if only it wasn't optional.

sanjayankur31 added a commit to NeuroML/Documentation that referenced this issue Jun 19, 2024
@sanjayankur31 sanjayankur31 moved this from 🔖 Ready to ✅ Done in NeuroML backlog Jun 25, 2024
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