Circuit simulation widget

[clbarnes]

Resurrected Albert's efforts from a few years ago, now as a draft PR to make it easier to find.

This implements Casey's rate models (I believe from https://www.sciencedirect.com/science/article/pii/S0092867416312429 , implemented in https://github.com/ceesem/fb_feedback_model ) in the frontend.

Example units here: https://gist.github.com/clbarnes/7b22409a41f9272c201653937df63d1b

[clbarnes]

UI thoughts:

global controls

• Units are created by adding as single skeletons (uses skeleton names) or as a group (popup asking for group name, pre-populated with e.g. comma-separated names)
  • removal done via the unit dynamics table
• total time
• advanced settings collapsed (or tabbed)
  • max iterations per timestep
  • termination criteria? hard to do right
• Checkbox for "resimulate on change"
  • performance-dependent
  • could automatically cut out at certain complexity level (e.g. n_edges * timesteps * maxit); this could be controlled in advanced settings
• Button for "normalise weights": ensure that the largest is 1 and scale appropriately
  • Could be a checkbox to do this onchange
• Button for "populate weights" to get from synapse count
  • checkbox or popup for "normalise by input fraction" (hover: "only for complete skeletons")
  • warning if weights are non-empty
• buttons for import/ export JSON
• lock all inputs during execution
• button to export traces

Tables

All tables collapsible, otherwise the controls are going to be huge. Alternatively, tables could go into content.

• Unit dynamics table

  • Checkbox for selection: act as skeleton source
  • Each added skeleton/group has a row with columns colourpicker, k, th, I_tonic, scaling, tau
    • additionally, a special top row allowing setting for all selected
  • "Remove unit" button which also clears from weight and stimulation tables
  • Allow renaming? With skeleton names as a hover
  • export as CSV

• Weight table

  • row and column added for each unit
  • each cell has a num box
  • colour cell background by relative weight?
  • export as CSV

• Stimulation table:

  • Empty by default with "add row" button for stimulation: drop-down for unit, num boxes for strength, start, stop
  • Same unit can appear multiple times for chains of stimulation
  • Allow sorting by values
  • export as CSV

[clbarnes]

Additional features

• Parameter sweeping
  • UI to run many simulations with small changes to parameters, somehow visualise them
• "Simulate circuit" button in graph widget (respecting groups etc.)

[clbarnes]

Current status

• fixed a bug which meant the plot's time series was warped
• simulation units can be uploaded from a JSON file
• results can be exported as JSON