Networks can be regarded as graphs, where the nodes are locations on cells and the edges describe the communications between them. In Arbor, two sorts of edges are modelled: a connection abstracts the propagation of action potentials (spikes) through the network, while a gap junction is used to describe a direct electrical connection between two locations on two cells. Connections only capture the propagation delay and attenuation associated with spike connectivity: the biophysical modelling of the chemical synapses themselves is the responsibility of the target cell model.
Connection sites and gap junction sites are defined on locations on cells as part of the cell description. A recipe lets you define which sites are connected to which.
Connections implement chemical synapses between source and target cells and are characterized by having a transmission delay.
Connections in Arbor are defined in two steps:
Create labeled source and target on two separate cells as part of their cell descriptions in the recipe. Sources typically generate spikes. Targets are typically synapses with associated biophysical model descriptions. Each labeled group of sources or targets may contain multiple items on possibly multiple locations on the cell.
Declare the connection in the recipe on the target cell: from a source identified using a
global_label; a target identified using a
gidof target is the argument of the recipe method); a connection delay and a connection weight.
- action potential¶
Spikes travel over connections. In a synapse, they generate an event.
- event generator¶
Externally stimulate a synapse. Events can be delivered on a schedule. See
- gap junction¶
Gap junctions represent electrical synapses where transmission between cells is bidirectional and direct. They are modelled as a conductance between two gap junction sites on two cells.
Similarly to Connections, Gap Junctions in Arbor are defined in two steps:
Create labeled gap junction sites on two separate cells as part of their cell descriptions in the recipe. Each labeled group of gap junctions may contain multiple items on possibly multiple locations on the cell.
Declare the Gap Junction connections in the recipe on the local cell: from a peer gap junction site identified using a
global_label; to a local gap junction site identified using a
gidof the site is implicitly known); and a conductance in μS. Two of these connections are needed, on each of the peer and local cells.