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
anddomain_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 acable_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 tosingle_cell_model.run
. Each element in the list holds the trace of one of the probes added viasingle_cell_model.probe
.
- properties#
The
cable_global_properties
of the model, including thecatalogue
.
- class arbor.trace#
Stores a trace obtained from a probe after running a model.
- variable#
Name of the variable being recorded. Currently only ‘voltage’.
- 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.