sbmlsim.examples.experiments.midazolam.experiments

Submodules

• sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995
• sbmlsim.examples.experiments.midazolam.experiments.mandema1992

Package Contents

Classes

SimulationExperiment	Generic simulation experiment.
ExperimentDict	Dictionary for experiments.
AbstractModel	Abstract base class to store a model in sbmlsim.
TimecourseSim	Timecourse simulation consisting of multiple concatenated timecourses.
ModelSensitivity	Helpers for calculating model sensitivity.
Task	Tasks combine models with simulations.
MidazolamSimulationExperiment	Base class for all GlucoseSimulationExperiments.

Functions

exclude_parameters_midazolam(pid)

Filter for excluding parameter ids in sensitivity.

Attributes

MODEL_PATH
MolecularWeights

class sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)

Generic simulation experiment.

Consists of models, datasets, simulations, tasks, results, processing, figures

Parameters

• sid (str) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• ureg (sbmlsim.units.UnitRegistry) –

initialize(self)

Initialize SimulationExperiment.

Initialization must be separated from object construction due to the parallel execution of the problem later on. Certain objects cannot be serialized and must be initialized. :return:

Return type

None

__str__(self)

Get string representation.

Return type

str

models(self)

Define model definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.model.AbstractModel]

datasets(self)

Define dataset definitions (experimental data).

The child classes fill out the information.

Return type

Dict[str, sbmlsim.data.DataSet]

tasks(self)

Define task definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.task.Task]

simulations(self)

Define simulation definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.simulation.AbstractSim]

fit_mappings(self)

Define fit mappings.

Mapping reference data on observables. Used for the optimization of parameters. The child classes fill out the information.

Return type

Dict[str, sbmlsim.fit.FitMapping]

datagenerators(self)

Define DataGenerators including functions.

All data which is accessed in a simulation result must be defined in a data generator. The data generators are important for defining the selections of a simulation experiment.

Return type

None

add_selections(self, selections, task_ids=None, reset=False)

Add selections to given tasks.

Selections are necessary to access data from simulations. Here these selections are added to the tasks. If no tasks are given, the selections are added to all tasks.

Parameters

• reset (bool) – drop and reset all selections.

• selections (Iterable[str]) –

• task_ids (Iterable[str]) –

property results(self)

Access simulation results.

Results are mapped on tasks based on the task_ids. E.g. to get the results for the task with id ‘task_glciv’ use ```

simexp.results[“task_glciv”] self.results[“task_glciv”]

```

Return type

Dict[str, sbmlsim.result.XResult]

figures(self)

Figure definition.

Selections accessed in figures and analyses must be registered beforehand via datagenerators.

Most figures do not require access to concrete data, but only abstract data concepts.

Return type

Dict[str, sbmlsim.plot.Figure]

_check_keys(self)

Check keys in information dictionaries.

_check_types(self)

Check for correctness of types.

run(self, simulator, output_path=None, show_figures=True, save_results=False, figure_formats=None, reduced_selections=True)

Execute given experiment and store results.

Parameters

• output_path (pathlib.Path) –

• show_figures (bool) –

• save_results (bool) –

• figure_formats (List[str]) –

• reduced_selections (bool) –

Return type

ExperimentResult

_run_tasks(self, simulator, reduced_selections=True)

Run simulations and scans.

This should not be called directly, but the results of the simulations should be requested by the results property. This allows to hash executed simulations.

Parameters

reduced_selections (bool) –

evaluate_fit_mappings(self)

Evaluate fit mappings.

to_json(self, path=None, indent=2)

Convert experiment to JSON for exchange.

Parameters

path – path for file, if None JSON str is returned

Returns

to_dict(self)

Convert to dictionary.

This is the basis for the JSON serialization.

classmethod from_json(cls, json_info)

Load experiment from json path or str.

Parameters

json_info (Union[pathlib.Path, str]) –

Return type

SimulationExperiment

save_datasets(self, results_path)

Save datasets.

Parameters

results_path (pathlib.Path) –

Return type

None

save_results(self, results_path)

Save results (mean timecourse).

Parameters

results_path (pathlib.Path) –

Returns

Return type

None

create_mpl_figures(self)

Create matplotlib figures.

Return type

Dict[str, Union[sbmlsim.plot.plotting_matplotlib.FigureMPL, sbmlsim.plot.Figure]]

show_mpl_figures(self, mpl_figures)

Show matplotlib figures.

Parameters

mpl_figures (Dict[str, sbmlsim.plot.plotting_matplotlib.FigureMPL]) –

Return type

None

save_mpl_figures(self, results_path, mpl_figures, figure_formats=None)

Save matplotlib figures.

Parameters

• results_path (pathlib.Path) –

• mpl_figures (Dict[str, sbmlsim.plot.plotting_matplotlib.FigureMPL]) –

• figure_formats (List[str]) –

Return type

Dict[str, List[pathlib.Path]]

classmethod close_mpl_figures(cls, mpl_figures)

Close matplotlib figures.

Parameters

mpl_figures (Dict[str, sbmlsim.plot.plotting_matplotlib.FigureMPL]) –

class sbmlsim.examples.experiments.midazolam.experiments.ExperimentDict

Bases: dict

Dictionary for experiments.

__getitem__(self, k)

Get item k.

class sbmlsim.examples.experiments.midazolam.experiments.AbstractModel(source, sid=None, name=None, language=None, language_type=LanguageType.SBML, base_path=None, changes=None, selections=None)

Bases: object

Abstract base class to store a model in sbmlsim.

Depending on the model language different subclasses are implemented.

Parameters

• source (Union[str, pathlib.Path]) –

• sid (Optional[str]) –

• name (Optional[str]) –

• language (Optional[str]) –

• language_type (LanguageType) –

• base_path (Optional[pathlib.Path]) –

• changes (Dict) –

• selections (List[str]) –

class LanguageType

Bases: enum.Enum

Language types.

SBML = 1

CELLML = 2

class SourceType

Bases: enum.Enum

Source types.

PATH = 1

URN = 2

URL = 3

__repr__(self)

Get string representation.

Return type

str

normalize(self, uinfo)

Normalize values to model units for all changes.

Parameters

uinfo (sbmlsim.units.UnitsInformation) –

to_dict(self)

Convert to dictionary.

class sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim(timecourses, selections=None, reset=True, time_offset=0.0)

Bases: sbmlsim.simulation.AbstractSim

Timecourse simulation consisting of multiple concatenated timecourses.

In case of a single timecourse, only the single timecourse is executed.

Parameters

• timecourses (Union[Timecourse, List[Timecourse]]) –

• selections (Optional[List[str]]) –

• reset (bool) –

• time_offset (float) –

__repr__(self)

Get representation.

Return type

str

_time(self)

Calculate the time vector complete simulation.

Return type

numpy.ndarray

dimensions(self)

Get dimensions.

Return type

List[sbmlsim.simulation.Dimension]

add_model_changes(self, model_changes)

Add model changes to given simulation.

Parameters

model_changes (Dict) –

Return type

None

normalize(self, uinfo)

Normalize timecourse simulation.

Parameters

uinfo (sbmlsim.units.UnitsInformation) –

Return type

None

strip_units(self)

Strip units from simulation.

Return type

None

to_dict(self)

Convert to dictionary.

Return type

Dict[str, Any]

to_json(self, path=None)

Convert definition to JSON.

Parameters

path (pathlib.Path) –

Return type

str

static from_json(json_info)

Load from JSON.

Parameters

json_info (Union[str, pathlib.Path]) –

Return type

TimecourseSim

__str__(self)

Get string representation.

Return type

str

class sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity

Bases: object

Helpers for calculating model sensitivity.

static difference_sensitivity_scan(model, simulation, difference=0.1, stype=SensitivityType.PARAMETER_SENSITIVITY, exclude_filter=None, exclude_zero=True, zero_eps=1e-08)

Create a parameter sensitivity scan for given TimecourseSimulation.

Parameters

• model (sbmlsim.model.RoadrunnerSBMLModel) – model for execution (needed to select parameters)

• simulation (sbmlsim.simulation.TimecourseSim) – timecourse simulation to scan

• difference (float) – change in parameters, i.e. every parameter (which is not excluded) is changed to ‘(1.0 - difference) * value’ and ‘(1.0 + difference) * value’

• stype (SensitivityType) – which sensitivity (parameters or species)

• exclude_filter – filter function which defines which parameters should be excluded from scan

• exclude_zero (bool) – parameters with a value of abs(value)<zero_eps are excluded from scan

• zero_eps (float) – epsilon for zero values

Returns

Return type

sbmlsim.simulation.ScanSim

static distribution_sensitivity_scan(model, simulation, cv=0.1, size=10, distribution=DistributionType.NORMAL_DISTRIBUTION, stype=SensitivityType.PARAMETER_SENSITIVITY, exclude_filter=None, exclude_zero=True, zero_eps=1e-08)

Get sensitivity scan based on distributions for values.

Parameters

• model (sbmlsim.model.RoadrunnerSBMLModel) –

• simulation (sbmlsim.simulation.TimecourseSim) –

• cv (float) –

• size (int) –

• distribution (DistributionType) –

• stype (SensitivityType) –

• exclude_zero (bool) –

• zero_eps (float) –

Return type

sbmlsim.simulation.ScanSim

static create_sampling_dimension(model, changes=None, cv=0.1, size=10, distribution=DistributionType.NORMAL_DISTRIBUTION, stype=SensitivityType.PARAMETER_SENSITIVITY, exclude_filter=None, exclude_zero=True, zero_eps=1e-08)

Create list of dimensions for sampling parameter values.

Only parameters relevant for “GU_”, “LI_” and “KI_” models are sampled.

cv: coeffient of variation (sigma/mean) -> sigma = cv*mean

Parameters

• model (sbmlsim.model.RoadrunnerSBMLModel) –

• changes (Dict) –

• cv (float) –

• size (int) –

• distribution (DistributionType) –

• stype (SensitivityType) –

• exclude_zero (bool) –

• zero_eps (float) –

Return type

sbmlsim.simulation.Dimension

static create_difference_dimension(model, changes=None, difference=0.1, stype=SensitivityType.PARAMETER_SENSITIVITY, exclude_filter=None, exclude_zero=True, zero_eps=1e-08)

Create list of dimensions for sampling parameter values.

Only parameters relevant for “GU_”, “LI_” and “KI_” models are sampled.

cv: coeffient of variation (sigma/mean) -> sigma = cv*mean

Parameters

• model (sbmlsim.model.RoadrunnerSBMLModel) –

• changes (Dict) –

• difference (float) –

• stype (SensitivityType) –

• exclude_zero (bool) –

• zero_eps (float) –

Return type

sbmlsim.simulation.Dimension

static reference_dict(model, changes=None, stype=SensitivityType.PARAMETER_SENSITIVITY, exclude_filter=None, exclude_zero=True, zero_eps=1e-08)

Get key:value dict for sensitivity analysis.

Values are based on the reference state of the model with the applied changes. Values in current model state are used.

Parameters

• model (sbmlsim.model.RoadrunnerSBMLModel) –

• exclude_filter – filter function to exclude parameters, excludes parameter id if the filter function is True

• exclude_zero (bool) – exclude parameters which are zero

• changes (Dict) –

• stype (SensitivityType) –

• zero_eps (float) –

Returns

Return type

Dict

static apply_change_to_dict(ref_dict, change=0.1)

Apply relative change to reference dictionary.

Parameters

• ref_dict – {key: value} dictionary to change

• change (float) – relative change to apply.

Returns

class sbmlsim.examples.experiments.midazolam.experiments.Task(model, simulation)

Tasks combine models with simulations.

This allows to execute the same simulation with different model variants.

Parameters

• model (str) –

• simulation (str) –

__repr__(self)

Get representation.

Return type

str

to_dict(self)

Convert to dictionary.

Return type

Dict[str, str]

sbmlsim.examples.experiments.midazolam.experiments.MODEL_PATH

sbmlsim.examples.experiments.midazolam.experiments.MolecularWeights

sbmlsim.examples.experiments.midazolam.experiments.exclude_parameters_midazolam(pid)

Filter for excluding parameter ids in sensitivity.

Parameters

pid (str) –

Return type

bool

class sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)

Bases: sbmlsim.experiment.SimulationExperiment

Base class for all GlucoseSimulationExperiments.

Parameters

• sid (str) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• ureg (sbmlsim.units.UnitRegistry) –

models(self)

Define model definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.model.AbstractModel]

tasks(self)

Define task definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.task.Task]

simulations(self, simulations=None)

Define simulation definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.simulation.TimecourseSim]

property Mr(self)