simulate¶

Simulation of CellML models with libopencor.

libopencor is part of the simulate extra; it is imported when a simulation runs, so the rest of the package works without it. See LIBOPENCOR_INSTALL.

SimulationError ¶

Bases: RuntimeError

libopencor reported issues for the file, the document or the run.

run_timecourse ¶

run_timecourse(
    cellml_path,
    start=0.0,
    end=100.0,
    steps=100,
    relative_tolerance=None,
    absolute_tolerance=None,
    maximum_number_of_steps=MAXIMUM_NUMBER_OF_STEPS,
)

Run a uniform timecourse of a CellML model.

Parameters:

Name	Type	Description	Default
`cellml_path`	`Path`	path of the CellML file.	required
`start`	`float`	start time of the output.	`0.0`
`end`	`float`	end time of the output.	`100.0`
`steps`	`int`	number of steps, the output has `steps + 1` rows.	`100`
`relative_tolerance`	`float \| None`	relative tolerance of the ODE solver, the libopencor default when `None`.	`None`
`absolute_tolerance`	`float \| None`	absolute tolerance of the ODE solver, the libopencor default when `None`.	`None`
`maximum_number_of_steps`	`int`	number of internal steps the ODE solver may take between two time points of the output.	`MAXIMUM_NUMBER_OF_STEPS`

Returns:

Type	Description
`DataFrame`	The timecourse with the variable of integration in the first column
`dict[str, str]`	followed by the states, the algebraic variables, the constants and
`tuple[DataFrame, dict[str, str]]`	the computed constants, and the units of every column. A model
`tuple[DataFrame, dict[str, str]]`	without a variable of integration (an algebraic model, which
`tuple[DataFrame, dict[str, str]]`	libopencor solves as a steady state) has the same values at every
`tuple[DataFrame, dict[str, str]]`	time point, in a first column `time` of the requested time points.

Raises:

Type	Description
`ImportError`	if libopencor is not installed.
`SimulationError`	if libopencor reports issues, e.g., for a model which is not valid or not fully constrained, or two result columns get the same name.

plot_timecourse ¶

plot_timecourse(df, units, show=True)

Plot every column of a timecourse against the first column.

Parameters:

Name	Type	Description	Default
`df`	`DataFrame`	timecourse from `run_timecourse`.	required
`units`	`dict[str, str]`	units of the columns from `run_timecourse`.	required
`show`	`bool`	call `matplotlib.pyplot.show`.	`True`

Returns:

Type	Description
`Figure`	The figure.