readme.md

Gap Junctions Example

A miniapp that demonstrates how to build a network with gap junctions.

Cells

Cells have a simple ball-and-stick morphology with gap junctions attached at the end of the soma. The following mechanisms are assigned to the complete cell

• nax: gbar=0.04, sh=10
• gbar: gbar=0.0001
• kamt: gbar=0.004
• pas: e=-65 mV, g=1/12000

Soma (A=500π µm^2)

 /\\\\\\\
(  ))))))) ()=================) Dendrite (l=300 µm, r=1.5 µm)
 \///////
        * 
        GJ

Network

Cells are structured into groups ('cables') that are inter-connected by gap junctions; Groups are connected by synapses. The first cell of the first group (top left in diagram) has a current stimulus.

     c --gj-- c --gj-- c --gj-- c --gj-- c   # Cable 0
     ^                                   |
    I_s                                 syn
                                         |
     c --gj-- c --gj-- c --gj-- c --gj-- c   # Cable 1
     |
    syn
     |
     c --gj-- c --gj-- c --gj-- c --gj-- c   # Cable 2
                                         |
                                        ...

Tunable parameters

• n_cables: number of groups of cells connected by gap junctions.
• n_cells_per_cable: number of cells in a group.
• stim_duration: duration that the stimulus on the first cell is on.
• event_min_delay: minimum delay of the network.
• event_weight: weight of an event.
• sim_duration: duration of the simulation.
• print_all: print the voltages of all cells in nerwork.

An example parameter file is:

{
    "name": "small test",
    "n-cables": 3,
    "n-cells-per-cable": 5,
    "stim-duration": 30,
    "event-min-delay": 10,
    "event-weight": 0.05,
    "sim-duration": 100, 
    "print-all": false
}