Interconnectivity

Networks can be regarded as a sort of graph, where the nodes are 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 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 (more on cells here). A recipe lets you define which sites are connected to which.

Connections

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:

  1. Create Source and Target on two cells: a source defined on one cell, and a target defined on another.

  2. Declare the connection in the recipe: with a source and target identified using cell_member, a connection delay and a connection weight.

Gap junctions

Gap junctions represent electrical synapses where transmission between cells is bidirectional and direct. They are modeled as a conductance between two gap junction sites on two cells.

Similarly to Connections, Gap Junctions in Arbor are defined in two steps:

  1. A gap junction site is created on each of the two cells. These locations need to be declared on the cell.

  2. Gap Junction instantiation in the recipe: The gap junction sites are indexed using cell_member because a single cell may have more than one gap junction site. A gap junction is instantiated by providing two gap junction sites’ and a conductance in μS.

    Note

    Only cable cells support gap junctions as of now.