Single cell model

class arbor.single_cell_model

Wrapper for simplified description and execution of single cell models. Only available in the python library. Abstracts away the details of a recipe, context and domain_decomposition for simulations of single, stand-alone cable cells. The simulation can not be distributed over several machines.

single_cell_model(cable_cell)

Construct a single_cell_model from a cable_cell

run(tfinal, dt)

Run the model from time t= 0 to t= tflinal with a dt= dt.

probe(what, where, frequency)

Sample a variable on the cell:

Parameters

• what – Name of the variable to record (currently only ‘voltage’).

• where – location at which to sample the variable.

• frequency – The frequency at which to sample [kHz].

spikes()

Returns a list spike times [ms] after a call to single_cell_model.run.

traces()

Returns a list of trace after a call to single_cell_model.run. Each element in the list holds the trace of one of the probes added via single_cell_model.probe.

properties

The cable_global_properties of the model.

catalogue

The mechanism_catalogue of the model.

class arbor.trace

Stores a trace obtained from a probe after running a model.

variable

Name of the variable being recorded. Currently only ‘voltage’.

loc

location of the trace

t

Sample times [ms]

v

Sample values [units specific to sample variable]

Note

The single_cell_model is used in our tutorials. The examples illustrate how to construct a cable_cell and use it to form a single_cell_model; how to add probes; how to run the model; and how to visualize the results.