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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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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