MetaCell / MetaCell/NetPyNE-UI

Add option for display/editing of cell list

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#214 0 comments 0 reactions 0 assignees View on GitHub

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enhancement
Dominant language
JavaScript
Stars
23
Forks
10
PR merge metrics
No merged PRs in 30d

Description

Specifying a list of cell positions is a standard feature of NetPyNE populations, and will be crucial for loading/displaying NeuroML models, where the positions are generated in NeuroML (e.g. with pyNeuroML or NeuroMLlite) and exported to NetPyNE using "cellsList" in the popParams element, e.g. https://github.com/OpenSourceBrain/NetPyNEShowcase/blob/0fa6c7032d9b2984f169d48773e573e16b9a8505/NetPyNE/UI/HHCellNetwork.txt.json#L99.

However this is not curently supported by the UI. The cellList etc. is probably loaded in the background by netpyne core, and possibly used for generation (although possibly not, see https://github.com/MetaCell/NetPyNE-UI/issues/213), but the user can't see this. Adding this feature in the UI will make NML imported models (and an other models that use cellList) more transparent & reproducible.

Screenshot 2021-02-24 at 12 24 42

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing how NetPyNE-UI loads and edits population parameters, especially the cellsList field in popParams. Review issue #213 and the linked NetPyNEShowcase example to understand whether the list is only loaded or also used during generation. Done means users can see and edit cell positions in the UI and the values remain transparent and reproducible for imported NeuroML models.

Written by the indexing model from the issue text.

Assessment

Tech stack
javascript
Domain
frontend
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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