sbmlsim
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sbmlsim
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__author__ (in module sbmlsim)
__call__() (sbmlsim.combine.datagenerator.DataGeneratorFunction method)
(sbmlsim.combine.datagenerator.DataGeneratorIndexingFunction method)
__copy__() (sbmlsim.plot.Axis method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.Plot method)
(sbmlsim.plot.plotting.Style method)
__delitem__() (sbmlsim.units.UnitsInformation method)
__eq__() (sbmlsim.fit.FitParameter method)
(sbmlsim.fit.objects.FitParameter method)
__getattr__() (sbmlsim.xresult.XResult method)
__getitem__() (sbmlsim.units.UnitsInformation method)
(sbmlsim.xresult.XResult method)
__iter__() (sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.units.UnitsInformation method)
__len__() (sbmlsim.simulation.Dimension method)
(sbmlsim.simulation.range.Dimension method)
(sbmlsim.units.UnitsInformation method)
__repr__() (sbmlsim.combine.sedml.io.SEDMLReader method)
(sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.comparison.diff.DataSetsComparison method)
(sbmlsim.data.Data method)
(sbmlsim.data.DataSet method)
(sbmlsim.examples.experiments.midazolam.experiments.AbstractModel method)
(sbmlsim.examples.experiments.midazolam.experiments.Task method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.fit.FitExperiment method)
(sbmlsim.fit.FitParameter method)
(sbmlsim.fit.objects.FitExperiment method)
(sbmlsim.fit.objects.FitParameter method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.model.AbstractModel method)
(sbmlsim.model.model.AbstractModel method)
(sbmlsim.plot.Axis method)
(sbmlsim.plot.ColorType method)
(sbmlsim.plot.Curve method)
(sbmlsim.plot.Figure method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.ColorType method)
(sbmlsim.plot.plotting.Curve method)
(sbmlsim.plot.plotting.Figure method)
(sbmlsim.plot.plotting.Plot method)
(sbmlsim.plot.plotting.ShadedArea method)
(sbmlsim.plot.plotting.Style method)
(sbmlsim.simulation.algorithm.Algorithm method)
(sbmlsim.simulation.algorithm.AlgorithmParameter method)
(sbmlsim.simulation.calculation.AppliedDimension method)
(sbmlsim.simulation.calculation.Calculation method)
(sbmlsim.simulation.calculation.Parameter method)
(sbmlsim.simulation.calculation.Variable method)
(sbmlsim.simulation.Dimension method)
(sbmlsim.simulation.range.DataRange method)
(sbmlsim.simulation.range.Dimension method)
(sbmlsim.simulation.range.FunctionalRange method)
(sbmlsim.simulation.range.Range method)
(sbmlsim.simulation.range.UniformRange method)
(sbmlsim.simulation.range.VectorRange method)
(sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
(sbmlsim.simulation.simulation.Analysis method)
(sbmlsim.simulation.simulation.OneStep method)
(sbmlsim.simulation.simulation.Simulation method)
(sbmlsim.simulation.simulation.SteadyState method)
(sbmlsim.simulation.simulation.UniformTimeCourse method)
(sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
(sbmlsim.task.Task method)
(sbmlsim.task.task.Task method)
(sbmlsim.xresult.XResult method)
__setitem__() (sbmlsim.units.UnitsInformation method)
__str__() (sbmlsim.combine.sedml.io.SEDMLReader method)
(sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.comparison.diff.DataSetsComparison method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.FitExperiment method)
(sbmlsim.fit.FitMapping method)
(sbmlsim.fit.objects.FitData method)
(sbmlsim.fit.objects.FitDataInitialized method)
(sbmlsim.fit.objects.FitExperiment method)
(sbmlsim.fit.objects.FitMapping method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.plot.Axis method)
(sbmlsim.plot.Curve method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.Curve method)
(sbmlsim.plot.plotting.Plot method)
(sbmlsim.plot.plotting.ShadedArea method)
(sbmlsim.plot.plotting.SubPlot method)
(sbmlsim.plot.SubPlot method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
(sbmlsim.units.UnitsInformation method)
(sbmlsim.xresult.XResult method)
__version__ (in module sbmlsim)
_add_default_style_kwargs() (sbmlsim.plot.Curve static method)
(sbmlsim.plot.plotting.Curve static method)
_area_interpolation_points (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
_check_keys() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
_check_types() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
_constructor (sbmlsim.data.DataSeries property)
(sbmlsim.data.DataSet property)
_constructor_expanddim (sbmlsim.data.DataSeries property)
_constructor_sliced (sbmlsim.data.DataSet property)
_cost_df() (sbmlsim.fit.analysis.OptimizationAnalysis method)
_create_axis() (sbmlsim.plot.Plot static method)
(sbmlsim.plot.plotting.Plot static method)
_create_chunks() (sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR static method)
_create_experiment_class() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_create_mpl_figure() (sbmlsim.fit.analysis.OptimizationAnalysis method)
_datapoints_df() (sbmlsim.fit.analysis.OptimizationAnalysis method)
_default_ureg() (sbmlsim.units.UnitsInformation static method)
_determine_format() (sbmlsim.combine.sedml.data.DataDescriptionParser class method)
_filter_dfs() (sbmlsim.comparison.diff.DataSetsComparison class method)
_get_scale() (sbmlsim.plot.serialization_matplotlib.MatplotlibFigureSerializer class method)
_get_variables() (in module sbmlsim.combine.mathml)
_keytransform() (sbmlsim.units.UnitsInformation method)
_load_csv() (sbmlsim.combine.sedml.data.DataDescriptionParser class method)
_load_sv() (sbmlsim.combine.sedml.data.DataDescriptionParser class method)
_load_tsv() (sbmlsim.combine.sedml.data.DataDescriptionParser class method)
_metadata (sbmlsim.data.DataSeries attribute)
(sbmlsim.data.DataSet attribute)
_mpl_error_kwargs() (sbmlsim.plot.plotting.Style method)
_optimize_single() (sbmlsim.fit.optimization.OptimizationProblem method)
_parse_description() (sbmlsim.combine.sedml.numl.NumlParser class method)
_parse_dimension() (sbmlsim.combine.sedml.numl.NumlParser class method)
_parse_repeated_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_parse_simple_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_process_columns() (sbmlsim.comparison.diff.DataSetsComparison class method)
_redop_dims() (sbmlsim.xresult.XResult method)
_run_optimization_serial() (in module sbmlsim.fit.runner)
_run_tasks() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
_run_timecourses() (sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
(sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR method)
(sbmlsim.simulator.rr_simulator_serial.SimulatorSerialRR method)
(sbmlsim.simulator.SimulatorSerialRR method)
_save_mpl_figure() (sbmlsim.fit.analysis.OptimizationAnalysis method)
_selection_lookup_table() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
_set_order() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
_time() (sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
_timecourse() (sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
_units_abbreviation (sbmlsim.units.Units attribute)
_wrap_plot_in_figure() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_x_as_fit_parameters() (sbmlsim.fit.result.OptimizationResult method)
A
ABSOLUTE (sbmlsim.fit.options.ResidualType attribute)
ABSOLUTE_TO_BASELINE (sbmlsim.fit.options.ResidualType attribute)
AbstractCurve (class in sbmlsim.plot.plotting)
AbstractModel (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.model)
(class in sbmlsim.model.model)
AbstractModel.LanguageType (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.model)
(class in sbmlsim.model.model)
AbstractModel.SourceType (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.model)
(class in sbmlsim.model.model)
AbstractSim (class in sbmlsim.simulation)
(class in sbmlsim.simulation.simulation)
add_area() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
add_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
add_child() (sbmlsim.combine.sedml.task.TaskNode method)
add_curve() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
add_data() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
add_dataset() (sbmlsim.combine.sedml.report.Report method)
add_experiment_result() (sbmlsim.report.experiment_report.ReportResults method)
add_model_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
add_model_changes() (sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.simulation.AbstractSim method)
(sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
(sbmlsim.simulation.simulation.AbstractSim method)
(sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
add_plots() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
add_selections_data() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
add_subplot() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
Algorithm (class in sbmlsim.simulation.algorithm)
algorithm_parameter_to_parameter_key() (in module sbmlsim.simulation.kisaos)
AlgorithmParameter (class in sbmlsim.simulation.algorithm)
All_SENSITIVITY (sbmlsim.simulation.sensitivity.SensitivityType attribute)
AMOUNT (sbmlsim.data.Data.Symbols attribute)
Analysis (class in sbmlsim.simulation.simulation)
AppliedDimension (class in sbmlsim.simulation.calculation)
apply_change_to_dict() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
archive (in module sbmlsim.combine.validation)
ARCTAN (sbmlsim.fit.options.LossFunctionType attribute)
areas (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
astnode_to_formula() (in module sbmlsim.combine.mathml)
axes_labelsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
axes_labelweight (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
axes_titlesize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
axes_titleweight (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Axis (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
AxisScale (class in sbmlsim.plot.plotting)
B
BAR (sbmlsim.plot.plotting.CurveType attribute)
BARSTACKED (sbmlsim.plot.plotting.CurveType attribute)
BASE_PATH (in module sbmlsim)
(in module sbmlsim.examples.experiments.glucose)
BaseObject (class in sbmlsim.simulation.base)
BaseObjectSIdRequired (class in sbmlsim.simulation.base)
BasePlotObject (class in sbmlsim.plot.plotting)
benchmark_import
module
Bertozzi2020 (class in sbmlsim.examples.experiments.covid.experiments)
(class in sbmlsim.examples.experiments.covid.experiments.bertozzi2020)
biomodels_omex_base_path (in module sbmlsim.combine.examples.execute_omex)
C
Calculation (class in sbmlsim.simulation.calculation)
Carcione2020 (class in sbmlsim.examples.experiments.covid.experiments)
(class in sbmlsim.examples.experiments.covid.experiments.carcione2020)
CAUCHY (sbmlsim.fit.options.LossFunctionType attribute)
CELLML (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel.LanguageType attribute)
(sbmlsim.model.AbstractModel.LanguageType attribute)
(sbmlsim.model.model.AbstractModel.LanguageType attribute)
Change (class in sbmlsim.simulation.change)
(class in sbmlsim.task.task_new)
changes (sbmlsim.task.task_new.SubTask attribute)
check_sedml_doc() (in module sbmlsim.combine.sedml.io)
CIRCLE (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
CLAMP_SPECIES (sbmlsim.model.model_change.ModelChange attribute)
(sbmlsim.model.ModelChange attribute)
clamp_species() (sbmlsim.model.model_change.ModelChange static method)
(sbmlsim.model.ModelChange static method)
close_mpl_figures() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment class method)
(sbmlsim.experiment.experiment.SimulationExperiment class method)
(sbmlsim.experiment.SimulationExperiment class method)
color (sbmlsim.plot.plotting.Fill attribute)
(sbmlsim.plot.plotting.Line attribute)
ColorType (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
column (in module sbmlsim.examples.example_scan)
combine() (sbmlsim.fit.result.OptimizationResult static method)
COMPARTMENT (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
compartments (in module sbmlsim.examples.experiments.curve_types.model)
ComputeChange (class in sbmlsim.simulation.calculation)
(class in sbmlsim.simulation.change)
concatenate (sbmlsim.task.task_new.RepeatedTask attribute)
CONCENTRATION (sbmlsim.data.Data.Symbols attribute)
content (sbmlsim.model.model_resources.Source attribute)
copy_roadrunner_instance() (sbmlsim.model.rr_model.RoadrunnerSBMLModel class method)
cost (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
cost_least_square() (sbmlsim.fit.optimization.OptimizationProblem method)
cpu_count() (sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR static method)
create() (in module sbmlsim.examples.experiments.curve_types.model)
create_difference_dimension() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
create_mpl_figures() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
create_petab_omex() (in module sbmlsim.fit.petab_omex)
create_plots() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
create_report() (sbmlsim.experiment.ExperimentReport method)
(sbmlsim.report.experiment_report.ExperimentReport method)
create_samples() (in module sbmlsim.fit.sampling)
create_sampling_dimension() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
creators (in module sbmlsim.examples.experiments.curve_types.model)
Cuadros2020 (class in sbmlsim.examples.experiments.covid.experiments)
(class in sbmlsim.examples.experiments.covid.experiments.cuadros2020)
Curve (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
curve() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
curves (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
CurveType (class in sbmlsim.plot.plotting)
CurveTypesExperiment (class in sbmlsim.examples.experiments.curve_types.experiment)
custom_objective (in module sbmlsim.fit.pet.petab_example_01)
custom_problem (in module sbmlsim.fit.pet.petab_example_01)
D
DASH (sbmlsim.plot.plotting.LineType attribute)
DASHDOT (sbmlsim.plot.plotting.LineType attribute)
DASHDOTDOT (sbmlsim.plot.plotting.LineType attribute)
Data (class in sbmlsim.data)
data() (sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
Data.Symbols (class in sbmlsim.data)
Data.Types (class in sbmlsim.data)
data_dir (in module sbmlsim.fit.petab_omex)
data_from_datagenerator() (sbmlsim.combine.sedml.parser.SEDMLParser method)
data_generators_for_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
DATA_PATH (in module sbmlsim.examples.experiments.glucose)
DataDescriptionParser (class in sbmlsim.combine.sedml.data)
DataGenerator (class in sbmlsim.combine.datagenerator)
(class in sbmlsim.simulation.calculation)
datagenerator_example() (in module sbmlsim.examples.datagenerator_example)
datagenerator_id_from_data() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
DataGeneratorFunction (class in sbmlsim.combine.datagenerator)
DataGeneratorIndexingFunction (class in sbmlsim.combine.datagenerator)
DataProvider (class in benchmark_import)
DataRange (class in sbmlsim.simulation.range)
DataSeries (class in sbmlsim.data)
DataSet (class in sbmlsim.data)
DATASET (sbmlsim.data.Data.Types attribute)
datasets() (sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
(sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
DataSetsComparison (class in sbmlsim.comparison.diff)
default() (sbmlsim.serialization.ObjectJSONEncoder method)
DEFAULT_COLORS (in module sbmlsim.plot.plotting)
DEMO_SBML (in module sbmlsim.resources)
DemoExperiment (class in sbmlsim.examples.experiments.demo.demo)
DependentVariable (class in sbmlsim.simulation.calculation)
deprecated() (in module sbmlsim.utils)
df_diff() (sbmlsim.comparison.diff.DataSetsComparison method)
DIAMOND (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
difference_sensitivity_scan() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
DIFFERENTIAL_EVOLUTION (sbmlsim.fit.options.OptimizationAlgorithmType attribute)
Dimension (class in sbmlsim.simulation)
(class in sbmlsim.simulation.range)
dimensions() (sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.simulation.AbstractSim method)
(sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
(sbmlsim.simulation.simulation.AbstractSim method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
discard (sbmlsim.task.task_new.SubTask attribute)
distribution_sensitivity_scan() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
DistributionType (class in sbmlsim.simulation.sensitivity)
DoseResponseExperiment (class in sbmlsim.examples.experiments.glucose.experiments.dose_response)
DOT (sbmlsim.plot.plotting.LineType attribute)
dtype (sbmlsim.data.Data property)
(sbmlsim.fit.FitData property)
(sbmlsim.fit.objects.FitData property)
duration (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
E
engine (in module sbmlsim.fit.pet.petab_example_02)
eps_plot (sbmlsim.comparison.diff.DataSetsComparison attribute)
ERROR_WEIGHTING (sbmlsim.fit.options.WeightingPointsType attribute)
evaluate() (in module sbmlsim.combine.mathml)
evaluate_fit_mappings() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
example_sampling() (in module sbmlsim.fit.sampling)
example_scan() (in module sbmlsim.examples.datagenerator_example)
examples_dir (in module sbmlsim.combine.examples.execute_sedml)
exclude_parameters_midazolam() (in module sbmlsim.examples.experiments.midazolam.experiments)
execute_sedml() (in module sbmlsim.combine.sedml.runner)
exp_kwargs (in module sbmlsim.examples.experiments.midazolam.fitting_problems)
experiment (sbmlsim.experiment.experiment.ExperimentResult attribute)
(sbmlsim.experiment.ExperimentResult attribute)
(sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
ExperimentReport (class in sbmlsim.experiment)
(class in sbmlsim.report.experiment_report)
ExperimentReport.ReportType (class in sbmlsim.experiment)
(class in sbmlsim.report.experiment_report)
ExperimentResult (class in sbmlsim.experiment)
(class in sbmlsim.experiment.experiment)
ExperimentRunner (class in sbmlsim.experiment)
(class in sbmlsim.experiment.runner)
expr (in module sbmlsim.combine.mathml)
expr_from_formula() (in module sbmlsim.combine.mathml)
F
f() (in module sbmlsim.fit.pet.petab_example_01)
fig_dpi (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
fig_facecolor (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
fig_subplots_hspace (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
fig_subplots_wspace (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
fig_titlesize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
fig_titleweight (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Figure (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
figure (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
figure_mid() (sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
(sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
figure_plot_1() (sbmlsim.examples.experiments.covid.experiments.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.carcione2020.Carcione2020 method)
figures() (sbmlsim.examples.experiments.covid.experiments.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.bertozzi2020.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.carcione2020.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.Cuadros2020 method)
(sbmlsim.examples.experiments.covid.experiments.cuadros2020.Cuadros2020 method)
(sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
(sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
figures_mpl() (sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
Fill (class in sbmlsim.plot.plotting)
fill (sbmlsim.plot.plotting.Marker attribute)
fit_mappings() (sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
(sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
FitData (class in sbmlsim.fit)
(class in sbmlsim.fit.objects)
FitDataInitialized (class in sbmlsim.fit.objects)
FitExperiment (class in sbmlsim.fit)
(class in sbmlsim.fit.objects)
FitMapping (class in sbmlsim.fit)
(class in sbmlsim.fit.objects)
FitParameter (class in sbmlsim.fit)
(class in sbmlsim.fit.objects)
fitting_example() (in module sbmlsim.examples.experiments.midazolam.fitting_example)
FORMAT_CSV (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
FORMAT_NUML (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
FORMAT_TSV (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
FORMAT_URN (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
formula_to_astnode() (in module sbmlsim.combine.mathml)
from_df() (sbmlsim.data.DataSet class method)
from_dfs() (sbmlsim.xresult.XResult static method)
from_json() (in module sbmlsim.serialization)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment class method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim static method)
(sbmlsim.experiment.experiment.SimulationExperiment class method)
(sbmlsim.experiment.SimulationExperiment class method)
(sbmlsim.fit.FitParameter static method)
(sbmlsim.fit.objects.FitParameter static method)
(sbmlsim.fit.result.OptimizationResult static method)
(sbmlsim.report.experiment_report.ReportResults static method)
(sbmlsim.simulation.timecourse.TimecourseSim static method)
(sbmlsim.simulation.TimecourseSim static method)
from_mpl_kwargs() (sbmlsim.plot.plotting.Style static method)
from_netcdf() (sbmlsim.xresult.XResult static method)
from_plots() (sbmlsim.plot.Figure static method)
(sbmlsim.plot.plotting.Figure static method)
from_sbml() (sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR static method)
(sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR static method)
(sbmlsim.simulator.rr_simulator_serial.SimulatorSerialRR static method)
(sbmlsim.simulator.SimulatorSerialRR static method)
(sbmlsim.units.UnitsInformation static method)
from_sbml_doc() (sbmlsim.units.UnitsInformation static method)
from_sedml_task() (sbmlsim.combine.sedml.task.TaskTree static method)
from_source() (sbmlsim.model.model_resources.Source class method)
FUNCTION (sbmlsim.data.Data.Types attribute)
function_name() (in module sbmlsim.utils)
FunctionalRange (class in sbmlsim.simulation.calculation)
(class in sbmlsim.simulation.range)
G
get_covid19_model() (in module sbmlsim.examples.experiments.covid.omex.download_covid_models)
get_data() (sbmlsim.data.Data method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.objects.FitData method)
get_dimension() (sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
get_edata() (benchmark_import.DataProvider method)
get_files_by_extension() (in module sbmlsim.comparison.diff)
get_fixed_parameters() (benchmark_import.DataProvider method)
get_fixed_parameters_names() (benchmark_import.DataProvider method)
get_initial_states() (benchmark_import.DataProvider method)
get_integrator_setting() (sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
get_measurements() (benchmark_import.DataProvider method)
get_observableNames() (benchmark_import.DataProvider method)
get_ordered_subtasks() (sbmlsim.combine.sedml.parser.SEDMLParser static method)
(sbmlsim.combine.sedml.task.TaskTree static method)
get_plots() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
get_pscales() (benchmark_import.DataProvider method)
get_quantity() (sbmlsim.data.DataSet method)
get_state_path() (sbmlsim.model.rr_model.RoadrunnerSBMLModel method)
get_timecourse_selections() (sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
get_timepoints() (benchmark_import.DataProvider method)
get_ysigma() (benchmark_import.DataProvider method)
grad() (in module sbmlsim.fit.pet.petab_example_01)
H
HDASH (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
height (sbmlsim.plot.Figure property)
(sbmlsim.plot.plotting.Figure property)
HORIZONTALBAR (sbmlsim.plot.plotting.CurveType attribute)
HORIZONTALBARSTACKED (sbmlsim.plot.plotting.CurveType attribute)
HTML (sbmlsim.experiment.ExperimentReport.ReportType attribute)
(sbmlsim.report.experiment_report.ExperimentReport.ReportType attribute)
html_report() (sbmlsim.fit.analysis.OptimizationAnalysis method)
I
importer (in module sbmlsim.fit.pet.petab_example_02)
indices() (sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
indices_from_dimensions() (sbmlsim.simulation.Dimension static method)
(sbmlsim.simulation.range.Dimension static method)
info() (sbmlsim.combine.sedml.task.TaskNode method)
initialize() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.ExperimentRunner method)
(sbmlsim.experiment.runner.ExperimentRunner method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.optimization.OptimizationProblem method)
integrator_from_kisao() (in module sbmlsim.simulation.kisaos)
IntegratorSettingKeys (in module sbmlsim.model.rr_model)
interp() (in module sbmlsim.plot.serialization_matplotlib)
is_content() (sbmlsim.model.model_resources.Source method)
is_dataset() (sbmlsim.data.Data method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.objects.FitData method)
is_equal() (sbmlsim.comparison.diff.DataSetsComparison method)
is_function() (sbmlsim.data.Data method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.objects.FitData method)
is_http() (in module sbmlsim.model.model_resources)
is_leaf() (sbmlsim.combine.sedml.task.TaskNode method)
is_path() (sbmlsim.model.model_resources.Source method)
is_scan() (sbmlsim.xresult.XResult method)
is_supported_algorithm_for_simulation_type() (in module sbmlsim.simulation.kisaos)
is_task() (sbmlsim.data.Data method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.objects.FitData method)
is_urn() (in module sbmlsim.model.model_resources)
isEmpty() (sbmlsim.combine.sedml.task.Stack method)
K
KISAOS_ALGORITHMPARAMETERS (in module sbmlsim.simulation.kisaos)
KISAOS_CVODE (in module sbmlsim.simulation.kisaos)
KISAOS_GILLESPIE (in module sbmlsim.simulation.kisaos)
KISAOS_LSODA (in module sbmlsim.simulation.kisaos)
KISAOS_NLEQ (in module sbmlsim.simulation.kisaos)
KISAOS_ONESTEP (in module sbmlsim.simulation.kisaos)
KISAOS_RK4 (in module sbmlsim.simulation.kisaos)
KISAOS_RK45 (in module sbmlsim.simulation.kisaos)
KISAOS_STEADYSTATE (in module sbmlsim.simulation.kisaos)
KISAOS_UNIFORMTIMECOURSE (in module sbmlsim.simulation.kisaos)
Kupferschmidt1995 (class in sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995)
L
l1v4_files (in module sbmlsim.combine.examples.execute_sedml)
l1v4_l1v3_files (in module sbmlsim.combine.examples.execute_sedml)
LATEX (sbmlsim.experiment.ExperimentReport.ReportType attribute)
(sbmlsim.report.experiment_report.ExperimentReport.ReportType attribute)
lb (in module sbmlsim.fit.pet.petab_example_01)
LEAST_SQUARE (sbmlsim.fit.options.OptimizationAlgorithmType attribute)
LEFT (sbmlsim.plot.plotting.YAxisPosition attribute)
legend_fontsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
legend_loc (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
legend_position (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
LIBNUML (sbmlsim.combine.sedml.numl.NumlParser.Library attribute)
LIBSEDML (sbmlsim.combine.sedml.numl.NumlParser.Library attribute)
Line (class in sbmlsim.plot.plotting)
line_color (sbmlsim.plot.plotting.Marker attribute)
line_thickness (sbmlsim.plot.plotting.Marker attribute)
LINEAR (sbmlsim.fit.options.LossFunctionType attribute)
(sbmlsim.plot.plotting.AxisScale attribute)
linear (sbmlsim.simulation.range.UniformRangeType attribute)
LineType (class in sbmlsim.plot.plotting)
load_numl_data() (sbmlsim.combine.sedml.numl.NumlParser class method)
load_pkdb_dataframe() (in module sbmlsim.data)
load_pkdb_dataframes_by_substance() (in module sbmlsim.data)
lock (in module sbmlsim.fit.runner)
loda_model_from_source() (sbmlsim.model.rr_model.RoadrunnerSBMLModel class method)
log (sbmlsim.simulation.range.UniformRangeType attribute)
LOG10 (sbmlsim.plot.plotting.AxisScale attribute)
logger (in module sbmlsim.combine.mathml)
(in module sbmlsim.combine.sedml.data)
(in module sbmlsim.combine.sedml.io)
(in module sbmlsim.combine.sedml.numl)
(in module sbmlsim.combine.sedml.parser)
(in module sbmlsim.combine.sedml.report)
(in module sbmlsim.combine.sedml.task)
(in module sbmlsim.comparison.diff)
(in module sbmlsim.data)
(in module sbmlsim.experiment.experiment)
(in module sbmlsim.experiment.runner)
(in module sbmlsim.fit.analysis)
(in module sbmlsim.fit.objects)
(in module sbmlsim.fit.optimization)
(in module sbmlsim.fit.result)
(in module sbmlsim.fit.runner)
(in module sbmlsim.fit.sampling)
(in module sbmlsim.model.model)
(in module sbmlsim.model.model_change)
(in module sbmlsim.model.model_resources)
(in module sbmlsim.model.rr_model)
(in module sbmlsim.plot.plotting)
(in module sbmlsim.plot.serialization_matplotlib)
(in module sbmlsim.report.experiment_report)
(in module sbmlsim.simulation.algorithm)
(in module sbmlsim.simulation.kisaos)
(in module sbmlsim.simulation.scan)
(in module sbmlsim.simulation.sensitivity)
(in module sbmlsim.simulation.simulation)
(in module sbmlsim.simulation.timecourse)
(in module sbmlsim.simulator.rr_simulator_abstract)
(in module sbmlsim.simulator.rr_simulator_ray)
(in module sbmlsim.simulator.rr_simulator_serial)
(in module sbmlsim.simulator.rr_worker)
(in module sbmlsim.units)
(in module sbmlsim.utils)
(in module sbmlsim.xresult)
LOGUNIFORM (sbmlsim.fit.sampling.SamplingType attribute)
LOGUNIFORM_LHS (sbmlsim.fit.sampling.SamplingType attribute)
LossFunctionType (class in sbmlsim.fit.options)
M
Mandema1992 (class in sbmlsim.examples.experiments.midazolam.experiments.mandema1992)
MAPPING (sbmlsim.fit.options.WeightingCurvesType attribute)
MappingMetaData (class in sbmlsim.fit.objects)
MARKDOWN (sbmlsim.experiment.ExperimentReport.ReportType attribute)
(sbmlsim.report.experiment_report.ExperimentReport.ReportType attribute)
Marker (class in sbmlsim.plot.plotting)
MarkerType (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
math (sbmlsim.task.task_new.Change attribute)
MatplotlibFigureSerializer (class in sbmlsim.plot.serialization_matplotlib)
max_all_dims() (sbmlsim.xresult.XResult method)
md5_for_path() (in module sbmlsim.utils)
mean_all_dims() (sbmlsim.xresult.XResult method)
mid (in module sbmlsim.examples.experiments.curve_types.model)
MIDAZOLAM_PATH (in module sbmlsim.examples.experiments.midazolam)
MIDAZOLAM_SBML (in module sbmlsim.resources)
MidazolamSimulationExperiment (class in sbmlsim.examples.experiments.midazolam.experiments)
min_all_dims() (sbmlsim.xresult.XResult method)
model (in module sbmlsim.fit.pet.amici_example)
(in module sbmlsim.simulation.sensitivity)
(sbmlsim.task.task_new.Change attribute)
(sbmlsim.task.task_new.SubTask attribute)
(sbmlsim.task.task_new.Task attribute)
model_changes (sbmlsim.task.task_new.SubTask attribute)
model_dir (in module sbmlsim.fit.pet.amici_example)
model_from_biomodels() (in module sbmlsim.model.model_resources)
model_from_url() (in module sbmlsim.model.model_resources)
model_from_urn() (in module sbmlsim.model.model_resources)
model_manipulations (sbmlsim.task.task_new.SubTask attribute)
model_module (in module sbmlsim.fit.pet.amici_example)
model_name (in module sbmlsim.fit.pet.amici_example)
MODEL_PATH (in module sbmlsim.examples.experiments.glucose)
(in module sbmlsim.examples.experiments.midazolam)
(in module sbmlsim.examples.experiments.midazolam.experiments)
model_uid_dict() (sbmlsim.units.UnitsInformation static method)
model_units (in module sbmlsim.examples.experiments.curve_types.model)
ModelChange (class in sbmlsim.model)
(class in sbmlsim.model.model_change)
models() (sbmlsim.examples.experiments.covid.experiments.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.bertozzi2020.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.carcione2020.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.Cuadros2020 method)
(sbmlsim.examples.experiments.covid.experiments.cuadros2020.Cuadros2020 method)
(sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
ModelSensitivity (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.simulation.sensitivity)
module
benchmark_import
sbmlsim
sbmlsim.combine
sbmlsim.combine.datagenerator
sbmlsim.combine.examples
sbmlsim.combine.examples.execute_omex
sbmlsim.combine.examples.execute_sedml
sbmlsim.combine.mathml
sbmlsim.combine.sedml
sbmlsim.combine.sedml.data
sbmlsim.combine.sedml.io
sbmlsim.combine.sedml.numl
sbmlsim.combine.sedml.parser
sbmlsim.combine.sedml.report
sbmlsim.combine.sedml.runner
sbmlsim.combine.sedml.task
sbmlsim.combine.validation
sbmlsim.comparison
sbmlsim.comparison.diff
sbmlsim.data
sbmlsim.examples
sbmlsim.examples.datagenerator_example
sbmlsim.examples.example_model_change
sbmlsim.examples.example_scan
sbmlsim.examples.example_sensitivity
sbmlsim.examples.example_timecourse
sbmlsim.examples.example_units
sbmlsim.examples.experiments
sbmlsim.examples.experiments.covid
sbmlsim.examples.experiments.covid.experiments
sbmlsim.examples.experiments.covid.experiments.bertozzi2020
sbmlsim.examples.experiments.covid.experiments.carcione2020
sbmlsim.examples.experiments.covid.experiments.cuadros2020
sbmlsim.examples.experiments.covid.omex
sbmlsim.examples.experiments.covid.omex.download_covid_models
sbmlsim.examples.experiments.covid.run_omex
sbmlsim.examples.experiments.covid.simulate
sbmlsim.examples.experiments.curve_types
sbmlsim.examples.experiments.curve_types.experiment
sbmlsim.examples.experiments.curve_types.model
sbmlsim.examples.experiments.demo
sbmlsim.examples.experiments.demo.demo
sbmlsim.examples.experiments.glucose
sbmlsim.examples.experiments.glucose.experiments
sbmlsim.examples.experiments.glucose.experiments.dose_response
sbmlsim.examples.experiments.glucose.glucose
sbmlsim.examples.experiments.midazolam
sbmlsim.examples.experiments.midazolam.experiments
sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995
sbmlsim.examples.experiments.midazolam.experiments.mandema1992
sbmlsim.examples.experiments.midazolam.fitting_example
sbmlsim.examples.experiments.midazolam.fitting_problems
sbmlsim.examples.experiments.midazolam.simulate
sbmlsim.examples.experiments.repressilator
sbmlsim.examples.experiments.repressilator.repressilator
sbmlsim.examples.experiments.repressilator.repressilator_scans
sbmlsim.experiment
sbmlsim.experiment.experiment
sbmlsim.experiment.runner
sbmlsim.fit
sbmlsim.fit.analysis
sbmlsim.fit.objects
sbmlsim.fit.optimization
sbmlsim.fit.options
sbmlsim.fit.pet
sbmlsim.fit.pet.amici_example
sbmlsim.fit.pet.petab_example_01
sbmlsim.fit.pet.petab_example_02
sbmlsim.fit.petab_omex
sbmlsim.fit.result
sbmlsim.fit.runner
sbmlsim.fit.sampling
sbmlsim.model
sbmlsim.model.model
sbmlsim.model.model_change
sbmlsim.model.model_resources
sbmlsim.model.rr_model
sbmlsim.plot
sbmlsim.plot.plotting
sbmlsim.plot.serialization_matplotlib
sbmlsim.report
sbmlsim.report.experiment_report
sbmlsim.resources
sbmlsim.serialization
sbmlsim.simulation
sbmlsim.simulation.algorithm
sbmlsim.simulation.base
sbmlsim.simulation.calculation
sbmlsim.simulation.change
sbmlsim.simulation.kisaos
sbmlsim.simulation.range
sbmlsim.simulation.scan
sbmlsim.simulation.sensitivity
sbmlsim.simulation.simulation
sbmlsim.simulation.timecourse
sbmlsim.simulator
sbmlsim.simulator.rr_simulator_abstract
sbmlsim.simulator.rr_simulator_ray
sbmlsim.simulator.rr_simulator_serial
sbmlsim.simulator.rr_worker
sbmlsim.task
sbmlsim.task.task
sbmlsim.task.task_new
sbmlsim.units
sbmlsim.utils
sbmlsim.xresult
MolecularWeights (in module sbmlsim.examples.experiments.midazolam.experiments)
MPL2SEDML_LINESTYLE_MAPPING (sbmlsim.plot.plotting.Style attribute)
MPL2SEDML_MARKER_MAPPING (sbmlsim.plot.plotting.Style attribute)
Mr (sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment property)
N
name (sbmlsim.data.Data property)
NO_WEIGHTING (sbmlsim.fit.options.WeightingPointsType attribute)
NONE (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.LineType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
NORMAL_DISTRIBUTION (sbmlsim.simulation.sensitivity.DistributionType attribute)
normalize() (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.model.AbstractModel method)
(sbmlsim.model.model.AbstractModel method)
(sbmlsim.simulation.AbstractSim method)
(sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
(sbmlsim.simulation.simulation.AbstractSim method)
(sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
normalize_changes() (sbmlsim.units.UnitsInformation static method)
NORMALIZED (sbmlsim.fit.options.ResidualType attribute)
NORMALIZED_TO_BASELINE (sbmlsim.fit.options.ResidualType attribute)
notes (in module sbmlsim.examples.experiments.curve_types.model)
num_panels() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
num_subplots() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
NumlParser (class in sbmlsim.combine.sedml.numl)
NumlParser.Library (class in sbmlsim.combine.sedml.numl)
O
ObjectJSONEncoder (class in sbmlsim.serialization)
OMEX (sbmlsim.combine.sedml.io.SEDMLInputType attribute)
omex_paths (in module sbmlsim.examples.experiments.covid.omex.download_covid_models)
(in module sbmlsim.examples.experiments.covid.run_omex)
OneStep (class in sbmlsim.simulation.simulation)
op_kupferschmidt1995() (in module sbmlsim.examples.experiments.midazolam.fitting_problems)
op_mandema1992() (in module sbmlsim.examples.experiments.midazolam.fitting_problems)
op_mid1oh_iv() (in module sbmlsim.examples.experiments.midazolam.fitting_problems)
optimality (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
OptimizationAlgorithmType (class in sbmlsim.fit.options)
OptimizationAnalysis (class in sbmlsim.fit.analysis)
OptimizationProblem (class in sbmlsim.fit.optimization)
OptimizationResult (class in sbmlsim.fit.result)
optimize() (sbmlsim.fit.optimization.OptimizationProblem method)
optimizer (in module sbmlsim.fit.pet.petab_example_01)
(in module sbmlsim.fit.pet.petab_example_02)
order (sbmlsim.task.task_new.SubTask attribute)
output_path (in module sbmlsim.examples.experiments.demo.demo)
(in module sbmlsim.examples.experiments.midazolam.simulate)
(sbmlsim.experiment.experiment.ExperimentResult attribute)
(sbmlsim.experiment.ExperimentResult attribute)
P
panel_height (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
panel_width (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Parameter (class in sbmlsim.simulation.calculation)
PARAMETER (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
parameter_df() (sbmlsim.model.rr_model.RoadrunnerSBMLModel static method)
PARAMETER_SENSITIVITY (sbmlsim.simulation.sensitivity.SensitivityType attribute)
parameters (in module sbmlsim.examples.experiments.curve_types.model)
(sbmlsim.task.task_new.Change attribute)
pars (in module sbmlsim.simulation.calculation)
parse() (sbmlsim.combine.sedml.data.DataDescriptionParser class method)
parse_abstract_curve() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_algorithm_parameter() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_astnode() (in module sbmlsim.combine.mathml)
parse_axis() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_biomodels_mid() (in module sbmlsim.model.model_resources)
parse_change() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_color() (sbmlsim.plot.ColorType static method)
(sbmlsim.plot.plotting.ColorType static method)
parse_dimension_description() (sbmlsim.combine.sedml.numl.NumlParser class method)
parse_figure() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_fill() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_formula() (in module sbmlsim.combine.mathml)
parse_line() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_marker() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_mathml_str() (in module sbmlsim.combine.mathml)
parse_model() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_plot2d() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_plot3d() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_report() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_simulation() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_style() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_units() (sbmlsim.model.rr_model.RoadrunnerSBMLModel method)
parse_xpath_target() (sbmlsim.combine.sedml.parser.SEDMLParser static method)
PATH (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel.SourceType attribute)
(sbmlsim.model.AbstractModel.SourceType attribute)
(sbmlsim.model.model.AbstractModel.SourceType attribute)
path (sbmlsim.model.model_resources.Source attribute)
peek() (sbmlsim.combine.sedml.task.Stack method)
petab_yaml (in module sbmlsim.fit.pet.petab_example_02)
Plot (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
plot_correlation() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_cost_bar() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_cost_scatter() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_datapoint_scatter() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_diff() (sbmlsim.comparison.diff.DataSetsComparison method)
plot_fit() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_fit_residual() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_residual_boxplot() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_residual_scatter() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_results() (in module sbmlsim.examples.example_sensitivity)
plot_samples() (in module sbmlsim.fit.sampling)
plot_traces() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plot_waterfall() (sbmlsim.fit.analysis.OptimizationAnalysis method)
plots (sbmlsim.plot.Figure property)
(sbmlsim.plot.plotting.Figure property)
PLUS (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
POINTS (sbmlsim.fit.options.WeightingCurvesType attribute)
(sbmlsim.plot.plotting.CurveType attribute)
pop() (sbmlsim.combine.sedml.task.Stack method)
print_info() (sbmlsim.combine.sedml.parser.SEDMLParser method)
problem (in module sbmlsim.fit.pet.petab_example_02)
process() (sbmlsim.combine.datagenerator.DataGenerator method)
process_fits() (sbmlsim.fit.result.OptimizationResult static method)
process_traces() (sbmlsim.fit.result.OptimizationResult static method)
push() (sbmlsim.combine.sedml.task.Stack method)
Q
Q_ (sbmlsim.model.rr_model.RoadrunnerSBMLModel property)
(sbmlsim.units.UnitsInformation property)
query_covid19_biomodels() (in module sbmlsim.examples.experiments.covid.omex.download_covid_models)
R
r (sbmlsim.model.rr_model.RoadrunnerSBMLModel property)
Range (class in sbmlsim.simulation.range)
range (sbmlsim.task.task_new.Change attribute)
(sbmlsim.task.task_new.RepeatedTask attribute)
ranges (in module sbmlsim.simulation.range)
(sbmlsim.task.task_new.RepeatedTask attribute)
rdata (in module sbmlsim.fit.pet.amici_example)
reactions (in module sbmlsim.examples.experiments.curve_types.model)
read_numl_document() (sbmlsim.combine.sedml.numl.NumlParser class method)
read_sedml() (sbmlsim.combine.sedml.io.SEDMLReader method)
reduce() (sbmlsim.fit.FitExperiment static method)
(sbmlsim.fit.objects.FitExperiment static method)
reference_dict() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
remove_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
remove_model_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
RepeatedTask (class in sbmlsim.task.task_new)
repeatedTaskToPython() (sbmlsim.combine.sedml.task.Test static method)
replace_piecewise() (in module sbmlsim.combine.mathml)
Report (class in sbmlsim.combine.sedml.report)
report() (sbmlsim.comparison.diff.DataSetsComparison method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
report_str() (sbmlsim.comparison.diff.DataSetsComparison method)
ReportResults (class in sbmlsim.report.experiment_report)
reports() (sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
repressilator_omex (in module sbmlsim.combine.validation)
REPRESSILATOR_SBML (in module sbmlsim.resources)
RepressilatorExperiment (class in sbmlsim.examples.experiments.repressilator.repressilator)
RepressilatorScanExperiment (class in sbmlsim.examples.experiments.repressilator.repressilator_scans)
reset_model (sbmlsim.task.task_new.RepeatedTask attribute)
residuals() (sbmlsim.fit.optimization.OptimizationProblem method)
ResidualType (class in sbmlsim.fit.options)
resolve_model_changes() (sbmlsim.combine.sedml.parser.SEDMLParser method)
resolve_style() (sbmlsim.plot.plotting.Style method)
RESOURCES_DIR (in module sbmlsim)
(in module sbmlsim.resources)
result (in module sbmlsim.fit.pet.petab_example_02)
result_custom_problem (in module sbmlsim.fit.pet.petab_example_01)
RESULT_PATH (in module sbmlsim.examples.experiments.glucose)
results (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment property)
(sbmlsim.experiment.experiment.SimulationExperiment property)
(sbmlsim.experiment.SimulationExperiment property)
RIGHT (sbmlsim.plot.plotting.YAxisPosition attribute)
RoadrunnerSBMLModel (class in sbmlsim.model.rr_model)
run() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.analysis.OptimizationAnalysis method)
run_covid_examples() (in module sbmlsim.examples.experiments.covid.simulate)
run_curve_types_experiments() (in module sbmlsim.examples.experiments.curve_types.experiment)
run_demo_example() (in module sbmlsim.examples.example_units)
run_demo_experiments() (in module sbmlsim.examples.experiments.demo.demo)
run_experiments() (in module sbmlsim.experiment.runner)
(sbmlsim.experiment.ExperimentRunner method)
(sbmlsim.experiment.runner.ExperimentRunner method)
run_glucose_experiments() (in module sbmlsim.examples.experiments.glucose.glucose)
run_midazolam_experiments() (in module sbmlsim.examples.experiments.midazolam.simulate)
run_model_change_example1() (in module sbmlsim.examples.example_model_change)
run_model_clamp1() (in module sbmlsim.examples.example_model_change)
run_model_clamp2() (in module sbmlsim.examples.example_model_change)
run_omex() (in module sbmlsim.combine.examples.execute_omex)
run_optimization() (in module sbmlsim.fit.runner)
run_repressilator() (in module sbmlsim.combine.examples.execute_omex)
run_repressilator_example() (in module sbmlsim.examples.experiments.repressilator.repressilator)
run_repressilator_experiments() (in module sbmlsim.examples.experiments.repressilator.repressilator_scans)
run_scan() (sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
run_scan0d() (in module sbmlsim.examples.example_scan)
run_scan1d() (in module sbmlsim.examples.example_scan)
run_scan1d_distribution() (in module sbmlsim.examples.example_scan)
run_scan2d() (in module sbmlsim.examples.example_scan)
run_sensitivity() (in module sbmlsim.examples.example_sensitivity)
run_timecourse() (sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
run_timecourse_examples() (in module sbmlsim.examples.example_timecourse)
RuntimeErrorOptimizeResult (class in sbmlsim.fit.optimization)
S
SamplingType (class in sbmlsim.fit.sampling)
save_datasets() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
save_mpl_figures() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
save_results() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
SBML (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel.LanguageType attribute)
(sbmlsim.model.AbstractModel.LanguageType attribute)
(sbmlsim.model.model.AbstractModel.LanguageType attribute)
sbml_importer (in module sbmlsim.fit.pet.amici_example)
sbml_uids (sbmlsim.units.UnitsInformation attribute)
SBMLModelTarget (class in sbmlsim.combine.sedml.parser)
SBMLModelTargetType (class in sbmlsim.combine.sedml.parser)
sbmlsim
module
sbmlsim.combine
module
sbmlsim.combine.datagenerator
module
sbmlsim.combine.examples
module
sbmlsim.combine.examples.execute_omex
module
sbmlsim.combine.examples.execute_sedml
module
sbmlsim.combine.mathml
module
sbmlsim.combine.sedml
module
sbmlsim.combine.sedml.data
module
sbmlsim.combine.sedml.io
module
sbmlsim.combine.sedml.numl
module
sbmlsim.combine.sedml.parser
module
sbmlsim.combine.sedml.report
module
sbmlsim.combine.sedml.runner
module
sbmlsim.combine.sedml.task
module
sbmlsim.combine.validation
module
sbmlsim.comparison
module
sbmlsim.comparison.diff
module
sbmlsim.data
module
sbmlsim.examples
module
sbmlsim.examples.datagenerator_example
module
sbmlsim.examples.example_model_change
module
sbmlsim.examples.example_scan
module
sbmlsim.examples.example_sensitivity
module
sbmlsim.examples.example_timecourse
module
sbmlsim.examples.example_units
module
sbmlsim.examples.experiments
module
sbmlsim.examples.experiments.covid
module
sbmlsim.examples.experiments.covid.experiments
module
sbmlsim.examples.experiments.covid.experiments.bertozzi2020
module
sbmlsim.examples.experiments.covid.experiments.carcione2020
module
sbmlsim.examples.experiments.covid.experiments.cuadros2020
module
sbmlsim.examples.experiments.covid.omex
module
sbmlsim.examples.experiments.covid.omex.download_covid_models
module
sbmlsim.examples.experiments.covid.run_omex
module
sbmlsim.examples.experiments.covid.simulate
module
sbmlsim.examples.experiments.curve_types
module
sbmlsim.examples.experiments.curve_types.experiment
module
sbmlsim.examples.experiments.curve_types.model
module
sbmlsim.examples.experiments.demo
module
sbmlsim.examples.experiments.demo.demo
module
sbmlsim.examples.experiments.glucose
module
sbmlsim.examples.experiments.glucose.experiments
module
sbmlsim.examples.experiments.glucose.experiments.dose_response
module
sbmlsim.examples.experiments.glucose.glucose
module
sbmlsim.examples.experiments.midazolam
module
sbmlsim.examples.experiments.midazolam.experiments
module
sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995
module
sbmlsim.examples.experiments.midazolam.experiments.mandema1992
module
sbmlsim.examples.experiments.midazolam.fitting_example
module
sbmlsim.examples.experiments.midazolam.fitting_problems
module
sbmlsim.examples.experiments.midazolam.simulate
module
sbmlsim.examples.experiments.repressilator
module
sbmlsim.examples.experiments.repressilator.repressilator
module
sbmlsim.examples.experiments.repressilator.repressilator_scans
module
sbmlsim.experiment
module
sbmlsim.experiment.experiment
module
sbmlsim.experiment.runner
module
sbmlsim.fit
module
sbmlsim.fit.analysis
module
sbmlsim.fit.objects
module
sbmlsim.fit.optimization
module
sbmlsim.fit.options
module
sbmlsim.fit.pet
module
sbmlsim.fit.pet.amici_example
module
sbmlsim.fit.pet.petab_example_01
module
sbmlsim.fit.pet.petab_example_02
module
sbmlsim.fit.petab_omex
module
sbmlsim.fit.result
module
sbmlsim.fit.runner
module
sbmlsim.fit.sampling
module
sbmlsim.model
module
sbmlsim.model.model
module
sbmlsim.model.model_change
module
sbmlsim.model.model_resources
module
sbmlsim.model.rr_model
module
sbmlsim.plot
module
sbmlsim.plot.plotting
module
sbmlsim.plot.serialization_matplotlib
module
sbmlsim.report
module
sbmlsim.report.experiment_report
module
sbmlsim.resources
module
sbmlsim.serialization
module
sbmlsim.simulation
module
sbmlsim.simulation.algorithm
module
sbmlsim.simulation.base
module
sbmlsim.simulation.calculation
module
sbmlsim.simulation.change
module
sbmlsim.simulation.kisaos
module
sbmlsim.simulation.range
module
sbmlsim.simulation.scan
module
sbmlsim.simulation.sensitivity
module
sbmlsim.simulation.simulation
module
sbmlsim.simulation.timecourse
module
sbmlsim.simulator
module
sbmlsim.simulator.rr_simulator_abstract
module
sbmlsim.simulator.rr_simulator_ray
module
sbmlsim.simulator.rr_simulator_serial
module
sbmlsim.simulator.rr_worker
module
sbmlsim.task
module
sbmlsim.task.task
module
sbmlsim.task.task_new
module
sbmlsim.units
module
sbmlsim.utils
module
sbmlsim.xresult
module
sbmlsim_model_targets() (sbmlsim.combine.sedml.parser.SBMLModelTarget static method)
scale (sbmlsim.plot.Axis property)
(sbmlsim.plot.plotting.Axis property)
ScanSim (class in sbmlsim.simulation)
(class in sbmlsim.simulation.scan)
second_color (sbmlsim.plot.plotting.Fill attribute)
SEDML2MPL_LINESTYLE_MAPPING (sbmlsim.plot.plotting.Style attribute)
SEDML2MPL_MARKER_MAPPING (sbmlsim.plot.plotting.Style attribute)
SEDML_FILE (sbmlsim.combine.sedml.io.SEDMLInputType attribute)
SEDML_STRING (sbmlsim.combine.sedml.io.SEDMLInputType attribute)
sedml_symbol (sbmlsim.combine.sedml.parser.SBMLModelTarget property)
sedml_target (sbmlsim.combine.sedml.parser.SBMLModelTarget property)
SEDMLInputType (class in sbmlsim.combine.sedml.io)
SEDMLParser (class in sbmlsim.combine.sedml.parser)
SEDMLReader (class in sbmlsim.combine.sedml.io)
SEDMLSerializer (class in sbmlsim.combine.sedml.parser)
sedmltojson() (in module sbmlsim.combine.sedml.runner)
selection (sbmlsim.data.Data property)
SensitivityType (class in sbmlsim.simulation.sensitivity)
serialize_axis() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_data() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_datasets() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_figures() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_models() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_simulations() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_style() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
serialize_tasks() (sbmlsim.combine.sedml.parser.SEDMLSerializer method)
set_default_settings() (sbmlsim.model.rr_model.RoadrunnerSBMLModel static method)
set_integrator_settings() (sbmlsim.model.rr_model.RoadrunnerSBMLModel static method)
(sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
(sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR method)
(sbmlsim.simulator.rr_simulator_serial.SimulatorSerialRR method)
(sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
(sbmlsim.simulator.SimulatorSerialRR method)
set_model() (sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
(sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR method)
(sbmlsim.simulator.rr_simulator_serial.SimulatorSerialRR method)
(sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
(sbmlsim.simulator.SimulatorSerialRR method)
set_simulator() (sbmlsim.experiment.ExperimentRunner method)
(sbmlsim.experiment.runner.ExperimentRunner method)
(sbmlsim.fit.optimization.OptimizationProblem method)
set_timecourse_selections() (sbmlsim.model.rr_model.RoadrunnerSBMLModel class method)
(sbmlsim.simulator.rr_simulator_abstract.SimulatorAbstractRR method)
(sbmlsim.simulator.rr_simulator_ray.SimulatorRayRR method)
(sbmlsim.simulator.rr_simulator_serial.SimulatorSerialRR method)
(sbmlsim.simulator.rr_worker.SimulationWorkerRR method)
(sbmlsim.simulator.SimulatorSerialRR method)
set_title() (sbmlsim.plot.Figure method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Figure method)
(sbmlsim.plot.plotting.Plot method)
set_units() (sbmlsim.xresult.XResult method)
set_xaxis() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
set_yaxis() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
set_yaxis_right() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
ShadedArea (class in sbmlsim.plot.plotting)
show_mpl_figures() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
sid (sbmlsim.data.Data property)
sim_scans() (sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
simpleTaskToPython() (sbmlsim.combine.sedml.task.Test static method)
Simulation (class in sbmlsim.simulation.simulation)
simulation (sbmlsim.task.task_new.SubTask attribute)
(sbmlsim.task.task_new.Task attribute)
simulation_mid() (sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
SimulationExperiment (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.experiment)
(class in sbmlsim.experiment.experiment)
simulations() (sbmlsim.examples.experiments.covid.experiments.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.bertozzi2020.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.carcione2020.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.Cuadros2020 method)
(sbmlsim.examples.experiments.covid.experiments.cuadros2020.Cuadros2020 method)
(sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
(sbmlsim.examples.experiments.midazolam.experiments.mandema1992.Mandema1992 method)
(sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
simulations_mid() (sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
SimulationWorkerRR (class in sbmlsim.simulator.rr_worker)
SimulatorAbstractRR (class in sbmlsim.simulator.rr_simulator_abstract)
SimulatorActor (class in sbmlsim.simulator.rr_simulator_ray)
SimulatorRayRR (class in sbmlsim.simulator.rr_simulator_ray)
SimulatorSerialRR (class in sbmlsim.simulator)
(class in sbmlsim.simulator.rr_simulator_serial)
size (sbmlsim.fit.result.OptimizationResult property)
(sbmlsim.plot.plotting.Marker attribute)
size() (sbmlsim.combine.sedml.task.Stack method)
SOFT_L1 (sbmlsim.fit.options.LossFunctionType attribute)
SOLID (sbmlsim.plot.plotting.LineType attribute)
solver (in module sbmlsim.fit.pet.amici_example)
Source (class in sbmlsim.model.model_resources)
source (sbmlsim.model.model_resources.Source attribute)
species (in module sbmlsim.examples.experiments.curve_types.model)
SPECIES (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
SPECIES_AMOUNT (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
SPECIES_CONCENTRATION (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
species_df() (sbmlsim.model.rr_model.RoadrunnerSBMLModel static method)
SPECIES_SENSITIVITY (sbmlsim.simulation.sensitivity.SensitivityType attribute)
SQUARE (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
Stack (class in sbmlsim.combine.sedml.task)
STAR (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
status (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
std_all_dims() (sbmlsim.xresult.XResult method)
SteadyState (class in sbmlsim.simulation.simulation)
strip_units() (sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
Style (class in sbmlsim.plot.plotting)
SubPlot (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
SubTask (class in sbmlsim.task.task_new)
success (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
SUPPORTED_FORMATS (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
Symbol (class in sbmlsim.simulation.base)
symbol (sbmlsim.task.task_new.Change attribute)
T
Target (class in sbmlsim.simulation.base)
target (sbmlsim.task.task_new.Change attribute)
Task (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.task)
(class in sbmlsim.task.task)
(class in sbmlsim.task.task_new)
TASK (sbmlsim.data.Data.Types attribute)
TaskNode (class in sbmlsim.combine.sedml.task)
tasks() (sbmlsim.examples.experiments.covid.experiments.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.bertozzi2020.Bertozzi2020 method)
(sbmlsim.examples.experiments.covid.experiments.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.carcione2020.Carcione2020 method)
(sbmlsim.examples.experiments.covid.experiments.Cuadros2020 method)
(sbmlsim.examples.experiments.covid.experiments.cuadros2020.Cuadros2020 method)
(sbmlsim.examples.experiments.curve_types.experiment.CurveTypesExperiment method)
(sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
TaskTree (class in sbmlsim.combine.sedml.task)
TEMPLATE_PATH (in module sbmlsim.report.experiment_report)
Test (class in sbmlsim.combine.sedml.task)
thickness (sbmlsim.plot.plotting.Line attribute)
TIME (sbmlsim.combine.sedml.parser.SBMLModelTargetType attribute)
(sbmlsim.data.Data.Symbols attribute)
Timecourse (class in sbmlsim.simulation)
(class in sbmlsim.simulation.timecourse)
TimecourseSim (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.simulation)
(class in sbmlsim.simulation.timecourse)
timeit() (in module sbmlsim.utils)
timepoints (in module sbmlsim.fit.pet.amici_example)
title (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
to_dataframe() (sbmlsim.xresult.XResult method)
to_dict() (sbmlsim.data.Data method)
(sbmlsim.examples.experiments.midazolam.experiments.AbstractModel method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.Task method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.experiment.experiment.ExperimentResult method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.ExperimentResult method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.model.AbstractModel method)
(sbmlsim.model.model.AbstractModel method)
(sbmlsim.model.model_resources.Source method)
(sbmlsim.plot.Axis method)
(sbmlsim.plot.ColorType method)
(sbmlsim.plot.Curve method)
(sbmlsim.plot.Figure method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.ColorType method)
(sbmlsim.plot.plotting.Curve method)
(sbmlsim.plot.plotting.Figure method)
(sbmlsim.plot.plotting.Fill method)
(sbmlsim.plot.plotting.Line method)
(sbmlsim.plot.plotting.Marker method)
(sbmlsim.plot.plotting.Plot method)
(sbmlsim.plot.plotting.ShadedArea method)
(sbmlsim.simulation.AbstractSim method)
(sbmlsim.simulation.simulation.AbstractSim method)
(sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
(sbmlsim.task.Task method)
(sbmlsim.task.task.Task method)
to_figure() (sbmlsim.plot.serialization_matplotlib.MatplotlibFigureSerializer class method)
to_json() (in module sbmlsim.serialization)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.FitParameter method)
(sbmlsim.fit.objects.FitParameter method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.report.experiment_report.ReportResults method)
(sbmlsim.serialization.ObjectJSONEncoder method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
to_mean_dataframe() (sbmlsim.xresult.XResult method)
to_mpl_area_kwargs() (sbmlsim.plot.plotting.Style method)
to_mpl_bar_kwargs() (sbmlsim.plot.plotting.Style method)
to_mpl_curve_kwargs() (sbmlsim.plot.plotting.Style method)
to_mpl_points_kwargs() (sbmlsim.plot.plotting.Style method)
to_netcdf() (sbmlsim.xresult.XResult method)
to_simulations() (sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
to_tsv() (sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.xresult.XResult method)
tol_abs (sbmlsim.comparison.diff.DataSetsComparison attribute)
tol_rel (sbmlsim.comparison.diff.DataSetsComparison attribute)
TRIANGLEDOWN (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
TRIANGLELEFT (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
TRIANGLERIGHT (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
TRIANGLEUP (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
type (sbmlsim.plot.plotting.Line attribute)
(sbmlsim.plot.plotting.Marker attribute)
U
ub (in module sbmlsim.fit.pet.petab_example_01)
udef_to_str() (sbmlsim.units.Units class method)
UdictType (in module sbmlsim.units)
uinfo (in module sbmlsim.xresult)
UNIFORM (sbmlsim.fit.sampling.SamplingType attribute)
UNIFORM_LHS (sbmlsim.fit.sampling.SamplingType attribute)
UniformRange (class in sbmlsim.simulation.range)
uniformRangeToPython() (sbmlsim.combine.sedml.task.Test static method)
UniformRangeType (class in sbmlsim.simulation.range)
UniformTimeCourse (class in sbmlsim.simulation.simulation)
unit_conversion() (sbmlsim.data.DataSet method)
Units (class in sbmlsim.units)
units (in module sbmlsim.examples.experiments.curve_types.model)
UnitsInformation (class in sbmlsim.units)
ureg (in module sbmlsim.simulation.scan)
(in module sbmlsim.units)
URL (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel.SourceType attribute)
(sbmlsim.model.AbstractModel.SourceType attribute)
(sbmlsim.model.model.AbstractModel.SourceType attribute)
URN (sbmlsim.examples.experiments.midazolam.experiments.AbstractModel.SourceType attribute)
(sbmlsim.model.AbstractModel.SourceType attribute)
(sbmlsim.model.model.AbstractModel.SourceType attribute)
V
values (sbmlsim.simulation.base.Symbol attribute)
(sbmlsim.simulation.range.DataRange property)
(sbmlsim.simulation.range.FunctionalRange property)
(sbmlsim.simulation.range.Range property)
(sbmlsim.simulation.range.UniformRange property)
(sbmlsim.simulation.range.VectorRange property)
values() (sbmlsim.simulation.calculation.Calculation method)
Variable (class in sbmlsim.simulation.calculation)
variables (sbmlsim.task.task_new.Change attribute)
VDASH (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
VectorRange (class in sbmlsim.simulation.range)
vectorRangeToPython() (sbmlsim.combine.sedml.task.Test static method)
W
weight (sbmlsim.fit.FitMapping property)
(sbmlsim.fit.objects.FitMapping property)
WeightingCurvesType (class in sbmlsim.fit.options)
WeightingPointsType (class in sbmlsim.fit.options)
weights (sbmlsim.fit.FitExperiment property)
(sbmlsim.fit.objects.FitExperiment property)
width (sbmlsim.plot.Figure property)
(sbmlsim.plot.plotting.Figure property)
work() (sbmlsim.simulator.rr_simulator_ray.SimulatorActor method)
worker() (in module sbmlsim.fit.runner)
working_dir (in module sbmlsim.combine.examples.execute_sedml)
(in module sbmlsim.combine.validation)
X
xaxis (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
XCROSS (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
xopt (sbmlsim.fit.result.OptimizationResult property)
xopt_fit_parameters (sbmlsim.fit.result.OptimizationResult property)
XResult (class in sbmlsim.xresult)
xtick_labelsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Y
yaxis (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
yaxis_right (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
YAxisPosition (class in sbmlsim.plot.plotting)
ytick_labelsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
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