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 [Hz].
-
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.
-
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’.
-
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.