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Add a motor neuron network into WormSim

Past due by almost 9 years 8% complete

The following neurons project to a specific body wall muscle cell, MDL08: AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR

We want to have:

  • full multi-compartmental NeuroML2 implementations
  • best guess of ion channels implemented in NeuroML2 and attached to each neuron
  • verification/unit tests for all synapses (neurotransmitter identity, synaptic streng…

The following neurons project to a specific body wall muscle cell, MDL08: AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR

We want to have:

  • full multi-compartmental NeuroML2 implementations
  • best guess of ion channels implemented in NeuroML2 and attached to each neuron
  • verification/unit tests for all synapses (neurotransmitter identity, synaptic strengths)
  • verification/unit tests for all gap junctions (identity, conductance)
  • all neurons, channels, parameters are visible in the model completion dashboard
  • research either qualitative or quantitative electrophysiological behaviour of this circuit to use as target for optimization
  • research physiological bounds for all parameters to undergo optimization and create appropriate unit tests/SciUnit tests
  • build an optimization scaffold that is capable of integrating tests to hold network components within their physiological bounds while also meeting a target behaviour for the overall network
  • run multi-scale optimization across channels, synapses, gap junctions, current density and network activity to meet target
  • running and visualized in Geppetto, using connectivity widget and plotting activity of channels, synapses, gap junctions and cell membranes
  • designed WormSim UI additions to explore the network, including documentation and citation of paper
  • full implementation in WormSim

This follows up on openworm/OpenWorm#31 and openworm/OpenWorm#124

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