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