Multicompartmental models (Brian 1 –> 2 conversion)

Brian 2 documentation

Support for multicompartmental models is now an integral part of Brian 2 (an early version of it was included as an experimental module in Brian 1). See the document Multicompartment models.

Brian 1 offered support for simple multi-compartmental models in the compartments module. This module allowed you to combine the equations for several compartments into a single Equations object. This is only a suitable solution for simple morphologies (e.g. “ball-and-stick” models) but has the advantage over using SpatialNeuron that you can have several of such neurons in a NeuronGroup.

If you already have a definition of a model using Brian 1’s compartments module, then you can simply print out the equations and use them directly in Brian 2. For simple models, writing the equations without that help is rather straightforward anyway:

Brian 1	Brian 2
V0 = 10*mV C = 200*pF Ra = 150*kohm R = 50*Mohm soma_eqs = (MembraneEquation(C) + IonicCurrent('I=(vm-V0)/R : amp')) dend_eqs = MembraneEquation(C) neuron_eqs = Compartments({'soma': soma_eqs, 'dend': dend_eqs}) neuron = NeuronGroup(N, neuron_eqs)	V0 = 10*mV C = 200*pF Ra = 150*kohm R = 50*Mohm neuron_eqs = ''' dvm_soma/dt = (I_soma + I_soma_dend)/C : volt I_soma = (V0 - vm_soma)/R : amp I_soma_dend = (vm_dend - vm_soma)/Ra : amp dvm_dend/dt = -I_soma_dend/C : volt''' neuron = NeuronGroup(N, neuron_eqs)