GENESIS: Documentation

Related Documentation:

Physical Processes and Model Variables

The Model of a Connection

Connections are made between event-generators and event-receivers. The Neurospaces / GENESIS 3 model-container defines a template for event-receiving entities. Projections then run algorithms that instantiate these entities and attach them pre-synaptically to event-generators and post-synaptically to continuous-time state variables. The template attributes of ’delay and ’weight’ are inherited by the template instantiations created by the projection algorithms.

Computing Connections

For most network models connections are algorithmically calculated, for example based on the distance between neurons and the synaptic contact points in the dendrite. That is why the model-container contains special algorithms to compute the connections between neurons.

Storing Connections

The connections in a network model can be stored in two different ways:

• Connections can be enumerated in the NDF file. For example:

  CONNECTION_GROUP NMDA       CONNECTION n1         PARAMETERS           PARAMETER ( PRE = Fiber[0]/spikegen ),           PARAMETER ( POST = Granule[0]/Granule_soma/mf_NMDA/synapse ),           PARAMETER ( WEIGHT = 1.0 ),           PARAMETER ( DELAY = 0.0 ),         END PARAMETERS       END CONNECTION       CONNECTION n2         PARAMETERS           PARAMETER ( PRE = Fiber[1]/spikegen ),           PARAMETER ( POST = Granule[0]/Granule_soma/mf_NMDA/synapse ),           PARAMETER ( WEIGHT = 1.0 ),           PARAMETER ( DELAY = 0.0 ),         END PARAMETERS       END CONNECTION     END CONNECTION_GROUP

• Because connections in a large network model easily outnumber the other components of a model, the model-container can store them in a memory efficient way. Most algorithms that compute the connections in a network will store them in memory in a compact manner. Some algorithms may compute the connections on the fly when they are needed. This includes algorithms that compress the connection matrix.

Summary