AllenInstitute / AllenInstitute/bmtk

Single-compartment Bionet cells

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Python
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Description

Hey Kael et al.! Firstly, thanks for doing an incredible amount of work on developing BMTK and the SONATA standard!

I'm trying to test-run BMTK on simple, single-compartment neurons, but after some digging into the code of both BMTK and BBP's libSONATA, it seems like this model_type (single_compartment) is either not yet or will not be implemented. Are there concrete plans to implement the single_compartment model_type, or is there an official roadmap for the future of BMTK in general? I also noticed that there may be plans to implement a model_type called point_soma, but I'm not sure if that's only meant to work with Pointnet/NEST instead of Bionet/NEURON.

I also tried using the default model_type of biophysical and then just using a different NEURON/hoc model_template, but I couldn't get this to work. I'm not sure, but from reading the code, it seems like which model_template is allowed are hardcoded, rather than being able to provide your own cell.hoc template -- am I right that the model_templates are hardcoded for each model_type?

Thanks,
Austin

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Research direction

No file or test is named. Start by reviewing BMTK and libSONATA handling of the single_compartment, point_soma, biophysical, and model_template values. Done would require a documented implementation plan or a maintainer decision about supported model types and custom NEURON/HOC templates.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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