pgleeson / GoCModel_Basic

network of gocs with low frequency background inputs

GoCModel_Basic

Basic code to generate network of electrically coupled cerebellar Golgi cells with low frequency background inputs

Model descriptions

Channel and synapse mechanisms are in Mechanisms

Cell descriptions are in Cells/Golgi

• /solinas includes the original Solinas morphology with soma, 3 dendrites and long axon compartment (see Solinas et al, 2007 or on ModelDB ). These are also the morphologies of GoC.cell.nml and GoC_2Pools.cell.nml
• /reduced includes 10 compartment reduced models, optimised by E. Piasini (see Piasini, 2015).
• An example of full reconstructed morphology is present here

More channel density sets are stored in Parameters that when inserted into the Solinas morphology, produce autonomous firing rates of 2-9 Hz and F-I slope of 14-25 Hz/nA.

Varying channel densities

To construct new GoC files using one of the morphologies and different parameter sets, use vary_channels.py or vary_channels_2pools.py - depending on whether you want a cell of class Cell or Cell2CaPools.

Generating networks

• simulate_one_cell.py generates a network with 1 cell (from specified GoC model). For example use, see example_gen_onegoc.ipynb
• generate_simple_network.py generates network of ~40 cells, with electrical connectivity and background inputs (low frequency Poisson spiketrains). For example use, see this nb

Utils

PythonUtils has function definitions for generating connectivity (electrical or chemical)

Known Issues 👷

• Using reduced or full morphology with current channel densities causes model to fail (Vm goes to 80mV after around 500 ms -> which channel is unstable? Density adjustment for morphology?)
  • ✅ Fix: NaT reaches very small time constants at spike -> use much smaller integration dt (0.001 ms or lower)
• Constructing network with a Population that has ComponentType from class Cell2CaPools -> LEMS file fails to be generated
  • 🔹 Diagnosis: Cannot create events file using event port 'spike' - not supported for class Cell2CaPools?
• For some morphology?, synapses can only be inserted at location=0.5 along dendrite.
  • 🔹 In that case, comment line 156 and uncomment 158 that create connectionWD instances for each background input and insert them into dendrites (in generate _simple_network.py )

Requirements

• python2.7

• NeuroML and pyNeuroML python libraries

• jvm

• Neuron 7.3 or above (compile mod)