sbmlsim
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__author__ (in module sbmlsim)
__call__() (sbmlsim.result.datagenerator.DataGeneratorFunction method)
(sbmlsim.result.datagenerator.DataGeneratorIndexingFunction method)
__copy__() (sbmlsim.plot.Axis method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.Plot method)
__delitem__() (sbmlsim.units.UnitsInformation method)
__eq__() (sbmlsim.fit.FitParameter method)
(sbmlsim.fit.objects.FitParameter method)
__getattr__() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
__getitem__() (sbmlsim.examples.experiments.midazolam.experiments.ExperimentDict method)
(sbmlsim.experiment.experiment.ExperimentDict method)
(sbmlsim.experiment.ExperimentDict method)
(sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
(sbmlsim.units.UnitsInformation method)
__iter__() (sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.TaskNode method)
(sbmlsim.units.UnitsInformation method)
__len__() (sbmlsim.simulation.Dimension method)
(sbmlsim.simulation.range.Dimension method)
(sbmlsim.simulation.simulation.Dimension method)
(sbmlsim.units.UnitsInformation method)
__range__range_0_0_common_delta_A (in module BioModel1_repressor_activator_oscillations.sedml)
__range__range_0_0_s1_init_uM (in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
__repr__() (sbmlsim.combine.omex.Omex method)
(sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.data.DataSet method)
(sbmlsim.diff.DataSetsComparison 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.ColorType method)
(sbmlsim.plot.plotting.ColorType 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.Dimension 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)
__setitem__() (sbmlsim.units.UnitsInformation method)
__str__() (sbmlsim.combine.omex.Entry method)
(sbmlsim.combine.omex.Omex method)
(sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.TaskNode method)
(sbmlsim.data.Data method)
(sbmlsim.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.FitExperiment method)
(sbmlsim.fit.objects.FitDataInitialized method)
(sbmlsim.fit.objects.FitExperiment method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.plot.Axis method)
(sbmlsim.plot.Curve method)
(sbmlsim.plot.plotting.Axis method)
(sbmlsim.plot.plotting.Curve method)
(sbmlsim.plot.plotting.SubPlot method)
(sbmlsim.plot.SubPlot method)
(sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
(sbmlsim.units.UnitsInformation method)
__var__A (in module BioModel1_repressor_activator_oscillations.sedml)
__var__C (in module BioModel1_repressor_activator_oscillations.sedml)
__var__mRNA_A_ (in module BioModel1_repressor_activator_oscillations.sedml)
__var__mRNA_R (in module BioModel1_repressor_activator_oscillations.sedml)
__var__PrmA (in module BioModel1_repressor_activator_oscillations.sedml)
__var__PrmA_bound (in module BioModel1_repressor_activator_oscillations.sedml)
__var__PrmR (in module BioModel1_repressor_activator_oscillations.sedml)
__var__PrmR_bound (in module BioModel1_repressor_activator_oscillations.sedml)
__var__R (in module BioModel1_repressor_activator_oscillations.sedml)
__var__s0 (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
__var__s1 (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
__var__t (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
__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_sbml_str() (in module sbmlsim.test.models.test_biomodels)
_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_chunks() (sbmlsim.simulator.simulation_ray.SimulatorParallel static 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)
_engine (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
_filter_dfs() (sbmlsim.diff.DataSetsComparison class method)
_from_entries() (sbmlsim.combine.omex.Omex 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)
_omex_init() (sbmlsim.combine.omex.Omex 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_repeated_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_parse_simple_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
_parseDataDescriptions() (in module sbmlsim.test.combine.sedml.test_data)
_process_columns() (sbmlsim.diff.DataSetsComparison class method)
_redop_dims() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
_register_data() (sbmlsim.data.Data method)
_resolveXPath() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static 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)
_save_mpl_figure() (sbmlsim.fit.analysis.OptimizationAnalysis method)
_set_initial_values() (in module sbmlsim._deprecated.pk.pkpd)
_stacked (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
_time() (sbmlsim.examples.experiments.midazolam.experiments.TimecourseSim method)
(sbmlsim.simulation.timecourse.TimecourseSim method)
(sbmlsim.simulation.TimecourseSim method)
_timecourse() (sbmlsim.simulator.simulation.SimulatorWorker method)
(sbmlsim.simulator.SimulatorWorker method)
_timecourses() (sbmlsim.simulator.simulation_ray.SimulatorParallel method)
(sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial method)
_tolerance_test() (in module sbmlsim.test.test_simulator)
_units_abbreviation (sbmlsim.units.Units attribute)
_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)
actor_count (in module sbmlsim.multiprocessing.ray_example)
add_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
add_child() (sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.TaskNode method)
add_curve() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
add_data() (in module sbmlsim.plot.plotting_matplotlib)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
add_experiment_result() (sbmlsim.report.experiment_report.ReportResults method)
add_line() (in module sbmlsim.plot.plotting_altair)
(in module sbmlsim.plot.plotting_matplotlib)
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() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
algorithm_parameter_to_parameter_key() (in module sbmlsim.combine.sedml.kisao)
algorithmParameterToParameterKey() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
All_SENSITIVITY (sbmlsim.simulation.sensitivity.SensitivityType attribute)
app2sim.sedml
module
Application0 (in module app2sim.sedml)
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
Application0_0 (in module app2sim.sedml)
(in module asedmlComplex.sedml)
apply_change_to_dict() (sbmlsim.examples.experiments.midazolam.experiments.ModelSensitivity static method)
(sbmlsim.simulation.sensitivity.ModelSensitivity static method)
ARCTAN (sbmlsim.fit.options.LossFunctionType attribute)
asedml3repeat.sedml
module
asedmlComplex.sedml
module
AssignmentExperiment (class in sbmlsim.examples.experiments.initial_assignment.initial_assignment)
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)
Axis.AxisScale (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
B
BAR (sbmlsim.plot.plotting.CurveType attribute)
BARSTACKED (sbmlsim.plot.plotting.CurveType attribute)
BASE_DIR (in module sbmlsim.test.combine.sedml.test_data)
(in module sbmlsim.test.combine.sedml.test_numl)
BASE_PATH (in module sbmlsim)
(in module sbmlsim.examples.experiments.glucose)
base_path (in module sbmlsim.examples.experiments.initial_assignment.initial_assignment)
(in module sbmlsim.examples.sedml.execute_sedml)
BasePlotObject (class in sbmlsim.plot.plotting)
bcolors (class in sbmlsim.utils_logging)
Bertozzi2020 (class in sbmlsim.examples.experiments.covid.experiments)
(class in sbmlsim.examples.experiments.covid.experiments.bertozzi2020)
BGBLACK (sbmlsim.utils_logging.bcolors attribute)
BGWHITE (sbmlsim.utils_logging.bcolors attribute)
BioModel1_repressor_activator_oscillations.sedml
module
BLACK (sbmlsim.utils_logging.bcolors attribute)
BOLD (sbmlsim.utils_logging.bcolors attribute)
C
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)
check_sedml() (in module sbmlsim.combine.sedml.io)
check_uinfo() (in module sbmlsim.test.test_units)
checkSEDMLDocument() (sbmlsim.combine.sedml.tesedml.SEDMLTools class method)
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)
color_data (in module sbmlsim.test.plot.test_plotting)
ColorType (class in sbmlsim.plot)
(class in sbmlsim.plot.plotting)
column (in module sbmlsim.examples.example_scan)
combine() (sbmlsim.fit.result.OptimizationResult static method)
combineArchiveToPython() (in module sbmlsim.combine.sedml.tesedml)
connect_ray
module
conservedMoietyAnalysis (in module app2sim.sedml)
,
[1]
content (sbmlsim.model.model_resources.Source attribute)
copy_roadrunner_model() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel class method)
(sbmlsim.model.RoadrunnerSBMLModel class method)
cost (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
cost_least_square() (sbmlsim.fit.optimization.OptimizationProblem method)
cpu_count() (in module sbmlsim.simulator.simulation_ray)
create_all_zip() (in module zip_archives)
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_omex
module
create_omex_from_sedml() (in module create_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)
create_udef_examples() (in module sbmlsim.test.test_units)
create_zip_from_folder() (in module zip_archives)
createTaskTree() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
Creator (class in sbmlsim.combine.omex)
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)
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.data.Data attribute)
Data.Types (class in sbmlsim.data)
DATA_DIR (in module sbmlsim.test)
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)
dataDescriptionToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
DataFunction (class in sbmlsim.data)
dataGen_repeatedTask_0_0_A (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_C (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_mRNA_A_ (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_mRNA_R (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_PrmA (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_PrmA_bound (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_PrmR (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_PrmR_bound (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_R (in module BioModel1_repressor_activator_oscillations.sedml)
dataGen_repeatedTask_0_0_s0 (in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
dataGen_repeatedTask_0_0_s1 (in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
dataGen_task_0_0_s0 (in module app2sim.sedml)
dataGen_task_0_0_s1 (in module app2sim.sedml)
dataGen_task_0_1_s0 (in module app2sim.sedml)
dataGen_task_0_1_s1 (in module app2sim.sedml)
DataGenerator (class in sbmlsim.result.datagenerator)
DataGeneratorFunction (class in sbmlsim.result.datagenerator)
DataGeneratorIndexingFunction (class in sbmlsim.result.datagenerator)
datagenerators() (sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.initial_assignment.initial_assignment.AssignmentExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
dataGeneratorToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
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.diff)
default() (sbmlsim.serialization.ObjectJSONEncoder method)
DEFAULT_COLORS (in module sbmlsim.plot.plotting)
DemoExperiment (class in sbmlsim.examples.experiments.demo.demo)
deprecated() (in module sbmlsim.utils)
df_diff() (sbmlsim.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)
dim_max() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
dim_mean() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
dim_min() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
dim_std() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
Dimension (class in sbmlsim.simulation)
(class in sbmlsim.simulation.range)
(class in sbmlsim.simulation.simulation)
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)
dist_plot() (in module sbmlsim.plot.plotting_altair)
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)
download_jws_omex() (in module download_omex)
download_omex
module
download_omex() (in module download_omex)
dtype (sbmlsim.data.Data property)
(sbmlsim.fit.FitData property)
(sbmlsim.fit.objects.FitData property)
duration (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
E
ENDC (sbmlsim.utils_logging.bcolors attribute)
Entry (class in sbmlsim.combine.omex)
eps_plot (sbmlsim.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() (in module sbmlsim.result.datagenerator_example)
example_multiple_actors() (in module sbmlsim.examples.example_parallel)
example_parallel_timecourse() (in module sbmlsim.examples.example_parallel)
example_sampling() (in module sbmlsim.fit.sampling)
example_scan() (in module sbmlsim.result.datagenerator_example)
example_single_actor() (in module sbmlsim.examples.example_parallel)
EXAMPLES_DIR (in module create_omex)
exclude_parameters_midazolam() (in module sbmlsim.examples.experiments.midazolam.experiments)
executeCombineArchive() (in module sbmlsim.combine.sedml.tesedml)
executePython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
executeSEDML() (in module sbmlsim.combine.sedml.tesedml)
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)
ExperimentDict (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.experiment)
(class in sbmlsim.experiment.experiment)
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)
extra_args (in module app2sim.sedml)
,
[1]
,
[2]
,
[3]
(in module asedml3repeat.sedml)
,
[1]
(in module asedmlComplex.sedml)
,
[1]
(in module BioModel1_repressor_activator_oscillations.sedml)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
extract() (sbmlsim.combine.omex.Omex method)
F
FAIL (sbmlsim.utils_logging.bcolors attribute)
fig (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
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)
(sbmlsim.examples.experiments.covid.experiments.Cuadros2020 method)
(sbmlsim.examples.experiments.covid.experiments.cuadros2020.Cuadros2020 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.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.initial_assignment.initial_assignment.AssignmentExperiment 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.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
Fill (class in sbmlsim.plot.plotting)
fill (sbmlsim.plot.plotting.Marker attribute)
fit_kwargs_default (in module sbmlsim.test.fit.test_fit)
(in module sbmlsim.test.fit.test_optimization_result)
fit_kwargs_testdata (in module sbmlsim.test.fit.test_fit)
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)
fix_endpoints() (in module sbmlsim.combine.sedml.tesedml)
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.result.XResult class method)
(sbmlsim.result.xresult.XResult class method)
from_directory() (sbmlsim.combine.omex.Omex class method)
from_entries() (sbmlsim.combine.omex.Omex class 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.result.XResult static method)
(sbmlsim.result.xresult.XResult static method)
from_plots() (sbmlsim.plot.Figure static method)
(sbmlsim.plot.plotting.Figure static method)
from_sbml_doc() (sbmlsim.units.UnitsInformation static method)
from_sbml_path() (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.range)
G
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_files_by_extension() (in module sbmlsim.diff)
get_ordered_subtasks() (sbmlsim.combine.sedml.parser.SEDMLParser static method)
get_plots() (sbmlsim.plot.Figure method)
(sbmlsim.plot.plotting.Figure method)
get_quantity() (sbmlsim.data.DataSet method)
get_species_keys() (in module sbmlsim._deprecated.pk.pkpd)
get_state_path() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel method)
(sbmlsim.model.RoadrunnerSBMLModel method)
getDataGeneratorsForTask() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
getIntegratorNameForKisaoID() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
getOrderedSubtasks() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
H
HDASH (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
HEADER (sbmlsim.utils_logging.bcolors attribute)
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
indices() (sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
indices_from_dimensions() (sbmlsim.simulation.Dimension static method)
(sbmlsim.simulation.range.Dimension static method)
(sbmlsim.simulation.simulation.Dimension static method)
info() (sbmlsim.combine.sedml.task.TaskNode method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.TaskNode method)
init_amounts_changes() (in module sbmlsim._deprecated.pk.pkpd)
init_concentrations_changes() (in module sbmlsim._deprecated.pk.pkpd)
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)
INPUT_TYPE_FILE_COMBINE (in module sbmlsim.combine.sedml.io)
(sbmlsim.combine.sedml.tesedml.SEDMLTools attribute)
INPUT_TYPE_FILE_SEDML (in module sbmlsim.combine.sedml.io)
(sbmlsim.combine.sedml.tesedml.SEDMLTools attribute)
INPUT_TYPE_STR (in module sbmlsim.combine.sedml.io)
(sbmlsim.combine.sedml.tesedml.SEDMLTools attribute)
integrator_from_kisao() (in module sbmlsim.combine.sedml.kisao)
IntegratorSettingKeys (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel attribute)
(sbmlsim.model.RoadrunnerSBMLModel attribute)
interp() (in module sbmlsim.plot.plotting_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.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)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.TaskNode method)
is_path() (sbmlsim.model.model_resources.Source method)
is_supported_algorithm_for_simulation_type() (in module sbmlsim.combine.sedml.kisao)
is_task() (sbmlsim.data.Data method)
(sbmlsim.fit.FitData method)
(sbmlsim.fit.objects.FitData method)
is_timecourse() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
is_urn() (in module sbmlsim.model.model_resources)
isEmpty() (sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
isSupportedAlgorithmForSimulationType() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
J
jws_omex_dict() (in module download_omex)
K
KISAOS_ALGORITHMPARAMETERS (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_CVODE (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_GILLESPIE (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_LSODA (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_NLEQ (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_ONESTEP (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_RK4 (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_RK45 (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_STEADYSTATE (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
KISAOS_UNIFORMTIMECOURSE (in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.tesedml)
Kupferschmidt1995 (class in sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995)
kwargs_data (in module sbmlsim.plot.plotting_matplotlib)
(in module sbmlsim.plot.plotting_plotly)
kwargs_sim (in module sbmlsim.plot.plotting_matplotlib)
(in module sbmlsim.plot.plotting_plotly)
L
LATEX (sbmlsim.experiment.ExperimentReport.ReportType attribute)
(sbmlsim.report.experiment_report.ExperimentReport.ReportType attribute)
LEAST_SQUARE (sbmlsim.fit.options.OptimizationAlgorithmType attribute)
legend_fontsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
legend_loc (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.Axis.AxisScale attribute)
(sbmlsim.plot.plotting.Axis.AxisScale attribute)
linear (sbmlsim.simulation.range.UniformRangeType attribute)
lineplot() (in module sbmlsim.plot.plotting_altair)
LineType (class in sbmlsim.plot.plotting)
list_contents() (sbmlsim.combine.omex.Omex method)
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)
load_roadrunner_model() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel class method)
(sbmlsim.model.RoadrunnerSBMLModel class method)
LOADSBMLOPTIONS_RECOMPILE (in module app2sim.sedml)
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
locations_by_format() (sbmlsim.combine.omex.Omex method)
lock (in module sbmlsim.fit.runner)
log (sbmlsim.simulation.range.UniformRangeType attribute)
LOG10 (sbmlsim.plot.Axis.AxisScale attribute)
(sbmlsim.plot.plotting.Axis.AxisScale attribute)
logger (in module sbmlsim._deprecated.pk.pkpd)
(in module sbmlsim.combine.omex)
(in module sbmlsim.combine.sedml.data)
(in module sbmlsim.combine.sedml.io)
(in module sbmlsim.combine.sedml.kisao)
(in module sbmlsim.combine.sedml.numl)
(in module sbmlsim.combine.sedml.parser)
(in module sbmlsim.data)
(in module sbmlsim.diff)
(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.model_roadrunner)
(in module sbmlsim.plot.plotting)
(in module sbmlsim.plot.plotting_matplotlib)
(in module sbmlsim.plot.plotting_plotly)
(in module sbmlsim.report.experiment_report)
(in module sbmlsim.result.xresult)
(in module sbmlsim.simulation.scan)
(in module sbmlsim.simulation.sensitivity)
(in module sbmlsim.simulation.timecourse)
(in module sbmlsim.simulator.simulation)
(in module sbmlsim.simulator.simulation_ray)
(in module sbmlsim.simulator.simulation_serial)
(in module sbmlsim.units)
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)
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)
MatplotlibFigureSerializer (class in sbmlsim.plot.plotting_matplotlib)
md5_for_path() (in module sbmlsim.utils)
MIDAZOLAM_PATH (in module sbmlsim.examples.experiments.midazolam)
MidazolamSimulationExperiment (class in sbmlsim.examples.experiments.midazolam.experiments)
model (in module sbmlsim.examples.experiments.initial_assignment.initial_assignment_rr)
,
[1]
,
[2]
(in module sbmlsim.simulation.sensitivity)
MODEL_DEMO (in module sbmlsim.test)
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_GLCWB (in module sbmlsim.test)
MODEL_MIDAZOLAM (in module sbmlsim.test)
MODEL_PATH (in module sbmlsim.examples.experiments.glucose)
(in module sbmlsim.examples.experiments.midazolam)
(in module sbmlsim.examples.experiments.midazolam.experiments)
(in module sbmlsim.test)
MODEL_REPRESSILATOR (in module sbmlsim.test)
model_uid_dict() (sbmlsim.units.UnitsInformation static method)
ModelChange (class in sbmlsim.model)
(class in sbmlsim.model.model_change)
modelChangeToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
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.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.initial_assignment.initial_assignment.AssignmentExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
ModelSensitivity (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.simulation.sensitivity)
modelToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
module
app2sim.sedml
asedml3repeat.sedml
asedmlComplex.sedml
BioModel1_repressor_activator_oscillations.sedml
connect_ray
create_omex
download_omex
sbmlsim
sbmlsim._deprecated
sbmlsim._deprecated.pk
sbmlsim._deprecated.pk.pkpd
sbmlsim.combine
sbmlsim.combine.mathml
sbmlsim.combine.omex
sbmlsim.combine.sedml
sbmlsim.combine.sedml.data
sbmlsim.combine.sedml.io
sbmlsim.combine.sedml.kisao
sbmlsim.combine.sedml.numl
sbmlsim.combine.sedml.parser
sbmlsim.combine.sedml.task
sbmlsim.combine.sedml.tesedml
sbmlsim.data
sbmlsim.diff
sbmlsim.examples
sbmlsim.examples.example_model_change
sbmlsim.examples.example_parallel
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.simulate
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.initial_assignment
sbmlsim.examples.experiments.initial_assignment.initial_assignment
sbmlsim.examples.experiments.initial_assignment.initial_assignment_rr
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.sedml
sbmlsim.examples.sedml.execute_omex
sbmlsim.examples.sedml.execute_sedml
sbmlsim.experiment
sbmlsim.experiment.experiment
sbmlsim.experiment.runner
sbmlsim.fit
sbmlsim.fit.analysis
sbmlsim.fit.objects
sbmlsim.fit.optimization
sbmlsim.fit.options
sbmlsim.fit.result
sbmlsim.fit.runner
sbmlsim.fit.sampling
sbmlsim.model
sbmlsim.model.model
sbmlsim.model.model_change
sbmlsim.model.model_resources
sbmlsim.model.model_roadrunner
sbmlsim.multiprocessing
sbmlsim.multiprocessing.multiprocessing_example
sbmlsim.multiprocessing.ray_example
sbmlsim.plot
sbmlsim.plot.plotting
sbmlsim.plot.plotting_altair
sbmlsim.plot.plotting_matplotlib
sbmlsim.plot.plotting_plotly
sbmlsim.report
sbmlsim.report.experiment_report
sbmlsim.result
sbmlsim.result.datagenerator
sbmlsim.result.datagenerator_example
sbmlsim.result.xresult
sbmlsim.serialization
sbmlsim.simulation
sbmlsim.simulation.range
sbmlsim.simulation.scan
sbmlsim.simulation.sensitivity
sbmlsim.simulation.simulation
sbmlsim.simulation.timecourse
sbmlsim.simulator
sbmlsim.simulator.simulation
sbmlsim.simulator.simulation_ray
sbmlsim.simulator.simulation_serial
sbmlsim.task
sbmlsim.task.task
sbmlsim.test
sbmlsim.test.combine
sbmlsim.test.combine.sedml
sbmlsim.test.combine.sedml.test_data
sbmlsim.test.combine.sedml.test_examples
sbmlsim.test.combine.sedml.test_io
sbmlsim.test.combine.sedml.test_numl
sbmlsim.test.combine.test_omex
sbmlsim.test.data
sbmlsim.test.data.data
sbmlsim.test.data.data.data_creator
sbmlsim.test.data.diff
sbmlsim.test.data.diff.simulate_examples
sbmlsim.test.data.sed-ml
sbmlsim.test.data.sed-ml.cellml
sbmlsim.test.experiment
sbmlsim.test.experiment.test_experiment_examples
sbmlsim.test.fit
sbmlsim.test.fit.test_fit
sbmlsim.test.fit.test_fitting_example
sbmlsim.test.fit.test_objects
sbmlsim.test.fit.test_optimization_result
sbmlsim.test.fit.test_sampling
sbmlsim.test.models
sbmlsim.test.models.test_biomodels
sbmlsim.test.models.test_model
sbmlsim.test.plot
sbmlsim.test.plot.test_plotting
sbmlsim.test.plot.test_plotting_matplotlib
sbmlsim.test.processing
sbmlsim.test.processing.test_mathml
sbmlsim.test.result
sbmlsim.test.result.test_datagenerator
sbmlsim.test.result.test_results
sbmlsim.test.test_data
sbmlsim.test.test_diff
sbmlsim.test.test_model_change
sbmlsim.test.test_parallel
sbmlsim.test.test_reports
sbmlsim.test.test_scan
sbmlsim.test.test_sensitivity
sbmlsim.test.test_simulation
sbmlsim.test.test_simulator
sbmlsim.test.test_timecourse
sbmlsim.test.test_units
sbmlsim.test.test_utils
sbmlsim.units
sbmlsim.utils
sbmlsim.utils_logging
zip_archives
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
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)
NUM_PAGES (in module download_omex)
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)
OKBLUE (sbmlsim.utils_logging.bcolors attribute)
OKGREEN (sbmlsim.utils_logging.bcolors attribute)
Omex (class in sbmlsim.combine.omex)
OMEX_CSV_JWS_ADLUNG2017_FIG2G (in module sbmlsim.test.combine.sedml.test_data)
OMEX_CSV_PARAMETERS (in module sbmlsim.test.combine.sedml.test_data)
OMEX_DIR (in module create_omex)
(in module download_omex)
OMEX_PLOT_CSV (in module sbmlsim.test.combine.sedml.test_data)
OMEX_PLOT_CSV_WITH_MODEL (in module sbmlsim.test.combine.sedml.test_data)
OMEX_PLOT_NUML (in module sbmlsim.test.combine.sedml.test_data)
OMEX_PLOT_NUML_WITH_MODEL (in module sbmlsim.test.combine.sedml.test_data)
OMEX_SHOWCASE (in module sbmlsim.test.combine.test_omex)
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)
output_path (in module sbmlsim.examples.experiments.demo.demo)
(in module sbmlsim.examples.experiments.initial_assignment.initial_assignment)
(in module sbmlsim.examples.experiments.midazolam.simulate)
(sbmlsim.experiment.experiment.ExperimentResult attribute)
(sbmlsim.experiment.ExperimentResult attribute)
outputPlot2DToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
outputPlot3DToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
outputPlotSettings() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
outputReportToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
outputToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
P
panel_height (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
panel_width (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
parameter_df() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel static method)
(sbmlsim.model.RoadrunnerSBMLModel static method)
PARAMETER_SENSITIVITY (sbmlsim.simulation.sensitivity.SensitivityType attribute)
parse() (sbmlsim.combine.sedml.data.DataDescriptionParser class 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.plotting.Style static method)
parse_curve() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_dimension_description() (sbmlsim.combine.sedml.numl.NumlParser class method)
parse_figure() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_formula() (in module sbmlsim.combine.mathml)
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_simulation() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
parse_task_tree() (sbmlsim.combine.sedml.task.TaskTree static method)
parse_units() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel method)
(sbmlsim.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)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
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.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)
PlotlyFigureSerializer (class in sbmlsim.plot.plotting_plotly)
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)
POLARBAR (sbmlsim.plot.plotting.CurveType attribute)
POLARBARSTACKED (sbmlsim.plot.plotting.CurveType attribute)
POLARPOINT (sbmlsim.plot.plotting.CurveType attribute)
pop() (sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
printArchive() (in module create_omex)
printMetaDataFor() (in module create_omex)
process() (sbmlsim.result.datagenerator.DataGenerator method)
process_fits() (sbmlsim.fit.result.OptimizationResult static method)
process_trace() (in module sbmlsim.combine.sedml.tesedml)
process_traces() (sbmlsim.fit.result.OptimizationResult static method)
push() (sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
Q
Q_ (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel property)
(sbmlsim.model.RoadrunnerSBMLModel property)
(sbmlsim.simulator.simulation_serial.SimulatorSerial property)
(sbmlsim.simulator.SimulatorSerial property)
(sbmlsim.units.UnitsInformation property)
R
r (in module sbmlsim.plot.plotting_altair)
(in module sbmlsim.result.xresult)
(sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel property)
(sbmlsim.model.RoadrunnerSBMLModel property)
(sbmlsim.simulator.simulation_serial.SimulatorSerial property)
(sbmlsim.simulator.SimulatorSerial property)
Range (class in sbmlsim.simulation.range)
read_numl_document() (sbmlsim.combine.sedml.numl.NumlParser class method)
read_sedml() (in module sbmlsim.combine.sedml.io)
readSEDMLDocument() (sbmlsim.combine.sedml.tesedml.SEDMLTools class 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)
remote_function() (in module connect_ray)
remove_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
remove_model_change() (sbmlsim.simulation.Timecourse method)
(sbmlsim.simulation.timecourse.Timecourse method)
repeatedTask_0_0 (in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
repeatedTaskToPython() (sbmlsim.combine.sedml.task.Test static method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
replace_piecewise() (in module sbmlsim.combine.mathml)
report() (sbmlsim.diff.DataSetsComparison method)
(sbmlsim.fit.optimization.OptimizationProblem method)
(sbmlsim.fit.result.OptimizationResult method)
report_str() (sbmlsim.diff.DataSetsComparison method)
ReportResults (class in sbmlsim.report.experiment_report)
repressilator_omex (in module sbmlsim.examples.sedml.execute_omex)
RepressilatorExperiment (class in sbmlsim.examples.experiments.repressilator.repressilator)
repressor_activator_oscillations (in module BioModel1_repressor_activator_oscillations.sedml)
residuals() (sbmlsim.fit.optimization.OptimizationProblem method)
ResidualType (class in sbmlsim.fit.options)
resolve_model_changes() (sbmlsim.combine.sedml.parser.SEDMLParser method)
resolveModelChanges() (sbmlsim.combine.sedml.tesedml.SEDMLTools static method)
RESOURCES_DIR (in module sbmlsim)
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)
RoadrunnerSBMLModel (class in sbmlsim.model)
(class in sbmlsim.model.model_roadrunner)
rr (in module sbmlsim.multiprocessing.multiprocessing_example)
run() (in module sbmlsim.examples.experiments.initial_assignment.initial_assignment)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
(sbmlsim.fit.analysis.OptimizationAnalysis method)
run_comparisons() (in module sbmlsim.test.data.diff.simulate_examples)
run_covid_experiments() (in module sbmlsim.examples.experiments.covid.simulate)
run_demo_example() (in module sbmlsim.examples.example_units)
run_demo_experiments() (in module sbmlsim.examples.experiments.demo.demo)
run_experiments() (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_optimization() (in module sbmlsim.fit.runner)
run_repressilator_experiments() (in module sbmlsim.examples.experiments.repressilator.repressilator)
run_scan() (sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial 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_simulations() (in module sbmlsim.multiprocessing.multiprocessing_example)
(in module sbmlsim.test.data.diff.simulate_examples)
run_timecourse() (sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial method)
run_timecourse_examples() (in module sbmlsim.examples.example_timecourse)
RuntimeErrorOptimizeResult (class in sbmlsim.fit.optimization)
S
s (in module sbmlsim.examples.experiments.initial_assignment.initial_assignment_rr)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
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_paths (in module sbmlsim.test.test_units)
sbml_uids (sbmlsim.units.UnitsInformation attribute)
sbmlsim
module
sbmlsim._deprecated
module
sbmlsim._deprecated.pk
module
sbmlsim._deprecated.pk.pkpd
module
sbmlsim.combine
module
sbmlsim.combine.mathml
module
sbmlsim.combine.omex
module
sbmlsim.combine.sedml
module
sbmlsim.combine.sedml.data
module
sbmlsim.combine.sedml.io
module
sbmlsim.combine.sedml.kisao
module
sbmlsim.combine.sedml.numl
module
sbmlsim.combine.sedml.parser
module
sbmlsim.combine.sedml.task
module
sbmlsim.combine.sedml.tesedml
module
sbmlsim.data
module
sbmlsim.diff
module
sbmlsim.examples
module
sbmlsim.examples.example_model_change
module
sbmlsim.examples.example_parallel
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.simulate
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.initial_assignment
module
sbmlsim.examples.experiments.initial_assignment.initial_assignment
module
sbmlsim.examples.experiments.initial_assignment.initial_assignment_rr
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.sedml
module
sbmlsim.examples.sedml.execute_omex
module
sbmlsim.examples.sedml.execute_sedml
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.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.model_roadrunner
module
sbmlsim.multiprocessing
module
sbmlsim.multiprocessing.multiprocessing_example
module
sbmlsim.multiprocessing.ray_example
module
sbmlsim.plot
module
sbmlsim.plot.plotting
module
sbmlsim.plot.plotting_altair
module
sbmlsim.plot.plotting_matplotlib
module
sbmlsim.plot.plotting_plotly
module
sbmlsim.report
module
sbmlsim.report.experiment_report
module
sbmlsim.result
module
sbmlsim.result.datagenerator
module
sbmlsim.result.datagenerator_example
module
sbmlsim.result.xresult
module
sbmlsim.serialization
module
sbmlsim.simulation
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.simulation
module
sbmlsim.simulator.simulation_ray
module
sbmlsim.simulator.simulation_serial
module
sbmlsim.task
module
sbmlsim.task.task
module
sbmlsim.test
module
sbmlsim.test.combine
module
sbmlsim.test.combine.sedml
module
sbmlsim.test.combine.sedml.test_data
module
sbmlsim.test.combine.sedml.test_examples
module
sbmlsim.test.combine.sedml.test_io
module
sbmlsim.test.combine.sedml.test_numl
module
sbmlsim.test.combine.test_omex
module
sbmlsim.test.data
module
sbmlsim.test.data.data
module
sbmlsim.test.data.data.data_creator
module
sbmlsim.test.data.diff
module
sbmlsim.test.data.diff.simulate_examples
module
sbmlsim.test.data.sed-ml
module
sbmlsim.test.data.sed-ml.cellml
module
sbmlsim.test.experiment
module
sbmlsim.test.experiment.test_experiment_examples
module
sbmlsim.test.fit
module
sbmlsim.test.fit.test_fit
module
sbmlsim.test.fit.test_fitting_example
module
sbmlsim.test.fit.test_objects
module
sbmlsim.test.fit.test_optimization_result
module
sbmlsim.test.fit.test_sampling
module
sbmlsim.test.models
module
sbmlsim.test.models.test_biomodels
module
sbmlsim.test.models.test_model
module
sbmlsim.test.plot
module
sbmlsim.test.plot.test_plotting
module
sbmlsim.test.plot.test_plotting_matplotlib
module
sbmlsim.test.processing
module
sbmlsim.test.processing.test_mathml
module
sbmlsim.test.result
module
sbmlsim.test.result.test_datagenerator
module
sbmlsim.test.result.test_results
module
sbmlsim.test.test_data
module
sbmlsim.test.test_diff
module
sbmlsim.test.test_model_change
module
sbmlsim.test.test_parallel
module
sbmlsim.test.test_reports
module
sbmlsim.test.test_scan
module
sbmlsim.test.test_sensitivity
module
sbmlsim.test.test_simulation
module
sbmlsim.test.test_simulator
module
sbmlsim.test.test_timecourse
module
sbmlsim.test.test_units
module
sbmlsim.test.test_utils
module
sbmlsim.units
module
sbmlsim.utils
module
sbmlsim.utils_logging
module
scale (sbmlsim.plot.Axis property)
(sbmlsim.plot.plotting.Axis property)
scan_plot() (in module sbmlsim.plot.plotting_altair)
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_CSV_PARAMETERS (in module sbmlsim.test.combine.sedml.test_data)
SEDML_DIR (in module create_omex)
sedml_files (in module create_omex)
SEDML_READ_CSV (in module sbmlsim.test.combine.sedml.test_data)
SEDML_READ_NUML (in module sbmlsim.test.combine.sedml.test_data)
SEDML_READ_NUML_1D (in module sbmlsim.test.combine.sedml.test_data)
SEDML_READ_NUML_2D (in module sbmlsim.test.combine.sedml.test_data)
SEDML_READ_NUML_2DRC (in module sbmlsim.test.combine.sedml.test_data)
SEDML_READ_TSV (in module sbmlsim.test.combine.sedml.test_data)
SEDMLCodeFactory (class in sbmlsim.combine.sedml.tesedml)
SEDMLCodeFactory.Stack (class in sbmlsim.combine.sedml.tesedml)
SEDMLCodeFactory.TaskNode (class in sbmlsim.combine.sedml.tesedml)
SEDMLParser (class in sbmlsim.combine.sedml.parser)
sedmlString() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
SEDMLTools (class in sbmlsim.combine.sedml.tesedml)
sedmlToPython() (in module sbmlsim.combine.sedml.tesedml)
selectionFromVariable() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
selections (in module sbmlsim.examples.experiments.initial_assignment.initial_assignment_rr)
,
[1]
,
[2]
selections_for_task() (sbmlsim.combine.sedml.parser.SEDMLParser method)
selectionsForTask() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
sensitivity_plot() (in module sbmlsim.plot.plotting_altair)
SensitivityType (class in sbmlsim.simulation.sensitivity)
set_default_settings() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel static method)
(sbmlsim.model.RoadrunnerSBMLModel static method)
set_integrator_settings() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel static method)
(sbmlsim.model.RoadrunnerSBMLModel static method)
(sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial method)
set_model() (sbmlsim.simulator.simulation_ray.SimulatorActor method)
(sbmlsim.simulator.simulation_ray.SimulatorParallel method)
(sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial method)
set_simulator() (sbmlsim.experiment.ExperimentRunner method)
(sbmlsim.experiment.runner.ExperimentRunner method)
(sbmlsim.fit.optimization.OptimizationProblem method)
set_timecourse_selections() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel class method)
(sbmlsim.model.RoadrunnerSBMLModel class method)
(sbmlsim.simulator.simulation_ray.SimulatorActor method)
(sbmlsim.simulator.simulation_ray.SimulatorParallel method)
(sbmlsim.simulator.simulation_serial.SimulatorSerial method)
(sbmlsim.simulator.SimulatorSerial method)
set_title() (sbmlsim.plot.Figure method)
(sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Figure method)
(sbmlsim.plot.plotting.Plot method)
set_xaxis() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
set_yaxis() (sbmlsim.plot.Plot method)
(sbmlsim.plot.plotting.Plot method)
show_mpl_figures() (sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
show_versions() (in module sbmlsim)
(in module sbmlsim.utils)
sid (sbmlsim.data.Data property)
sim_info (in module sbmlsim.examples.example_parallel)
sim_scans() (sbmlsim.examples.experiments.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
simpleTaskToPython() (sbmlsim.combine.sedml.task.Test static method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
simulate() (sbmlsim.multiprocessing.ray_example.SimulatorActorPath method)
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.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.initial_assignment.initial_assignment.AssignmentExperiment 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.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
simulations_mid() (sbmlsim.examples.experiments.midazolam.experiments.kupferschmidt1995.Kupferschmidt1995 method)
SimulatorActor (class in sbmlsim.simulator.simulation_ray)
SimulatorActorPath (class in sbmlsim.multiprocessing.ray_example)
SimulatorParallel (class in sbmlsim.simulator.simulation_ray)
SimulatorSerial (class in sbmlsim.simulator)
(class in sbmlsim.simulator.simulation_serial)
SimulatorWorker (class in sbmlsim.simulator)
(class in sbmlsim.simulator.simulation)
size (sbmlsim.fit.result.OptimizationResult property)
(sbmlsim.plot.plotting.Marker attribute)
size() (sbmlsim.combine.sedml.task.Stack method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory.Stack method)
SOFT_L1 (sbmlsim.fit.options.LossFunctionType attribute)
SOLID (sbmlsim.plot.plotting.LineType attribute)
Source (class in sbmlsim.model.model_resources)
source (sbmlsim.model.model_resources.Source attribute)
SOURCE_CSV (in module sbmlsim.test.combine.sedml.test_data)
SOURCE_CSV_PARAMETERS (in module sbmlsim.test.combine.sedml.test_data)
SOURCE_NUML (in module sbmlsim.test.combine.sedml.test_numl)
SOURCE_NUML_1D (in module sbmlsim.test.combine.sedml.test_numl)
SOURCE_NUML_2D (in module sbmlsim.test.combine.sedml.test_numl)
SOURCE_NUML_2DRC (in module sbmlsim.test.combine.sedml.test_numl)
SOURCE_TSV (in module sbmlsim.test.combine.sedml.test_data)
species_df() (sbmlsim.model.model_roadrunner.RoadrunnerSBMLModel static method)
(sbmlsim.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)
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)
success (sbmlsim.fit.optimization.RuntimeErrorOptimizeResult attribute)
SUPPORTED_FORMATS (sbmlsim.combine.sedml.data.DataDescriptionParser attribute)
T
targetToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
Task (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.task)
(class in sbmlsim.task.task)
TASK (sbmlsim.data.Data.Types attribute)
task_0_0 (in module app2sim.sedml)
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
task_0_1 (in module app2sim.sedml)
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.demo.demo.DemoExperiment method)
(sbmlsim.examples.experiments.glucose.experiments.dose_response.DoseResponseExperiment method)
(sbmlsim.examples.experiments.initial_assignment.initial_assignment.AssignmentExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.MidazolamSimulationExperiment method)
(sbmlsim.examples.experiments.midazolam.experiments.SimulationExperiment method)
(sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment method)
(sbmlsim.experiment.experiment.SimulationExperiment method)
(sbmlsim.experiment.SimulationExperiment method)
taskToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
TaskTree (class in sbmlsim.combine.sedml.task)
taskTreeToPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
tefig (in module app2sim.sedml)
,
[1]
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
TEMPLATE_DIR (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory attribute)
TEMPLATE_PATH (in module sbmlsim.report.experiment_report)
terminate_trace() (in module sbmlsim.combine.sedml.tesedml)
Test (class in sbmlsim.combine.sedml.task)
test_abstractmodel_creation() (in module sbmlsim.test.models.test_model)
test_abstractmodel_creation_with_changes() (in module sbmlsim.test.models.test_model)
test_Allonen1981_Fig3A() (in module sbmlsim.test.test_data)
test_clamp1() (in module sbmlsim.test.test_model_change)
test_clamp2() (in module sbmlsim.test.test_model_change)
test_combine() (in module sbmlsim.test.fit.test_optimization_result)
test_copy_model() (in module sbmlsim.test.models.test_model)
test_covid_example() (in module sbmlsim.test.experiment.test_experiment_examples)
test_create_simulator() (in module sbmlsim.test.test_simulation)
test_create_simulator_strpath() (in module sbmlsim.test.test_simulation)
test_datagenerator_example() (in module sbmlsim.test.result.test_datagenerator)
test_dataset() (in module sbmlsim.test.test_data)
test_default_ureg() (in module sbmlsim.test.test_units)
test_demo_example() (in module sbmlsim.test.experiment.test_experiment_examples)
test_evaluate() (in module sbmlsim.test.processing.test_mathml)
test_evaluate_array() (in module sbmlsim.test.processing.test_mathml)
test_example() (in module sbmlsim.test.fit.test_fitting_example)
test_example1() (in module sbmlsim.test.test_model_change)
test_example_sampling() (in module sbmlsim.test.fit.test_sampling)
test_example_units() (in module sbmlsim.test.test_units)
test_extract() (in module sbmlsim.test.combine.test_omex)
test_Faber1978_Fig1() (in module sbmlsim.test.test_data)
test_fit_de_parallel() (in module sbmlsim.test.fit.test_fit)
test_fit_de_serial() (in module sbmlsim.test.fit.test_fit)
test_fit_lsq_parallel() (in module sbmlsim.test.fit.test_fit)
test_fit_lsq_serial() (in module sbmlsim.test.fit.test_fit)
test_fit_parameter() (in module sbmlsim.test.fit.test_objects)
test_fit_parameter_serialization() (in module sbmlsim.test.fit.test_objects)
test_fit_settings() (in module sbmlsim.test.fit.test_fit)
test_from_biomodels_url() (in module sbmlsim.test.models.test_biomodels)
,
[1]
test_from_biomodels_url_deprecated() (in module sbmlsim.test.models.test_biomodels)
test_from_biomodels_urn() (in module sbmlsim.test.models.test_biomodels)
test_glucose_example() (in module sbmlsim.test.experiment.test_experiment_examples)
test_glucose_report() (in module sbmlsim.test.test_reports)
test_list_contents() (in module sbmlsim.test.combine.test_omex)
test_load_csv() (in module sbmlsim.test.combine.sedml.test_data)
test_load_csv_parameters() (in module sbmlsim.test.combine.sedml.test_data)
test_load_numl() (in module sbmlsim.test.combine.sedml.test_numl)
test_load_numl_1D() (in module sbmlsim.test.combine.sedml.test_numl)
test_load_numl_2D() (in module sbmlsim.test.combine.sedml.test_numl)
test_load_numl_2DRC() (in module sbmlsim.test.combine.sedml.test_numl)
test_load_roadrunner_model() (in module sbmlsim.test.models.test_model)
test_load_tsv() (in module sbmlsim.test.combine.sedml.test_data)
test_locations_by_format_omex() (in module sbmlsim.test.combine.test_omex)
test_locations_by_format_omex2() (in module sbmlsim.test.combine.test_omex)
test_locations_by_format_zip() (in module sbmlsim.test.combine.test_omex)
test_locations_by_format_zip2() (in module sbmlsim.test.combine.test_omex)
test_loss_function() (in module sbmlsim.test.fit.test_fit)
test_mathml_str() (in module sbmlsim.test.processing.test_mathml)
test_midazolam_example() (in module sbmlsim.test.experiment.test_experiment_examples)
test_netcdf() (in module sbmlsim.test.result.test_results)
test_optimization_analysis() (in module sbmlsim.test.fit.test_fit)
test_parallel_multiple_actors() (in module sbmlsim.test.test_parallel)
test_parallel_single_actor() (in module sbmlsim.test.test_parallel)
test_parallel_timecourse() (in module sbmlsim.test.test_parallel)
test_parameter_df() (in module sbmlsim.test.models.test_model)
test_parse_color() (in module sbmlsim.test.plot.test_plotting)
test_parse_csv() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_csv_parameters() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_numl() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_numl_1D() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_numl_2D() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_numl_2DRC() (in module sbmlsim.test.combine.sedml.test_data)
test_parse_tsv() (in module sbmlsim.test.combine.sedml.test_data)
TEST_PATH (in module sbmlsim.test)
test_plotting() (in module sbmlsim.test.plot.test_plotting_matplotlib)
test_read_repressilator() (in module sbmlsim.test.combine.sedml.test_io)
test_repressilator_example() (in module sbmlsim.test.experiment.test_experiment_examples)
test_result() (in module sbmlsim.test.result.test_results)
test_roadrunnermodel_creation() (in module sbmlsim.test.models.test_model)
test_run_comparisons() (in module sbmlsim.test.test_diff)
test_run_simulations() (in module sbmlsim.test.test_diff)
test_scan0d() (in module sbmlsim.test.test_scan)
test_scan1d() (in module sbmlsim.test.test_scan)
test_scan1d_distribution() (in module sbmlsim.test.test_scan)
test_scan2d() (in module sbmlsim.test.test_scan)
test_sensitivity() (in module sbmlsim.test.test_sensitivity)
test_sensitivity_change() (in module sbmlsim.test.test_sensitivity)
test_sensitivity_example() (in module sbmlsim.test.test_sensitivity)
test_serialization() (in module sbmlsim.test.fit.test_optimization_result)
(in module sbmlsim.test.test_timecourse)
test_show_versions() (in module sbmlsim.test.test_utils)
test_species_df() (in module sbmlsim.test.models.test_model)
test_str() (in module sbmlsim.test.combine.test_omex)
test_timecourse() (in module sbmlsim.test.test_timecourse)
test_timecourse_combined() (in module sbmlsim.test.test_simulation)
test_timecourse_concat() (in module sbmlsim.test.test_simulation)
test_timecourse_discard() (in module sbmlsim.test.test_simulation)
test_timecourse_empty() (in module sbmlsim.test.test_simulation)
test_timecourse_simulation() (in module sbmlsim.test.test_simulation)
test_tolerances_parallel() (in module sbmlsim.test.test_simulator)
test_tolerances_parallel2() (in module sbmlsim.test.test_simulator)
test_tolerances_serial() (in module sbmlsim.test.test_simulator)
test_tolerances_serial2() (in module sbmlsim.test.test_simulator)
test_udef_to_str() (in module sbmlsim.test.test_units)
test_unit_conversion1() (in module sbmlsim.test.test_data)
test_units_from_doc() (in module sbmlsim.test.test_units)
test_units_from_sbml() (in module sbmlsim.test.test_units)
test_variables_1() (in module sbmlsim.test.processing.test_mathml)
test_variables_2() (in module sbmlsim.test.processing.test_mathml)
testInput() (in module sbmlsim.combine.sedml.tesedml)
thickness (sbmlsim.plot.plotting.Line attribute)
THIS_DIR (in module download_omex)
time_repeatedTask_0_0 (in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
time_task_0_0 (in module app2sim.sedml)
time_task_0_1 (in module app2sim.sedml)
Timecourse (class in sbmlsim.simulation)
(class in sbmlsim.simulation.timecourse)
timecourse_plot() (in module sbmlsim.plot.plotting_altair)
timeCourseSelections (in module app2sim.sedml)
,
[1]
TimecourseSim (class in sbmlsim.examples.experiments.midazolam.experiments)
(class in sbmlsim.simulation)
(class in sbmlsim.simulation.timecourse)
timeit() (in module sbmlsim.utils)
title (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
to_dataframe() (sbmlsim.result.XResult method)
(sbmlsim.result.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.Line method)
(sbmlsim.plot.plotting.Marker method)
(sbmlsim.plot.plotting.Plot 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.plotting_matplotlib.MatplotlibFigureSerializer static method)
(sbmlsim.plot.plotting_plotly.PlotlyFigureSerializer 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.result.XResult method)
(sbmlsim.result.xresult.XResult method)
to_mpl_kwargs() (sbmlsim.plot.plotting.Style method)
to_netcdf() (sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
to_simulations() (sbmlsim.simulation.scan.ScanSim method)
(sbmlsim.simulation.ScanSim method)
to_tsv() (sbmlsim.fit.result.OptimizationResult method)
(sbmlsim.result.XResult method)
(sbmlsim.result.xresult.XResult method)
tol_abs (sbmlsim.diff.DataSetsComparison attribute)
tol_rel (sbmlsim.diff.DataSetsComparison attribute)
toPython() (sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory method)
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
udef_examples (in module sbmlsim.test.test_units)
udef_to_str() (sbmlsim.units.Units class method)
UdictType (in module sbmlsim.units)
uinfo (sbmlsim.simulator.simulation_serial.SimulatorSerial property)
(sbmlsim.simulator.SimulatorSerial property)
UNDERLINE (sbmlsim.utils_logging.bcolors attribute)
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)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
UniformRangeType (class in sbmlsim.simulation.range)
unit_conversion() (sbmlsim.data.DataSet method)
Units (class in sbmlsim.units)
UnitsInformation (class in sbmlsim.units)
ureg (in module sbmlsim.simulation.scan)
(in module sbmlsim.units)
URL (in module download_omex)
(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.range.DataRange property)
(sbmlsim.simulation.range.FunctionalRange property)
(sbmlsim.simulation.range.Range property)
VDASH (sbmlsim.plot.MarkerType attribute)
(sbmlsim.plot.plotting.MarkerType attribute)
VectorRange (class in sbmlsim.simulation.range)
vectorRangeToPython() (sbmlsim.combine.sedml.task.Test static method)
(sbmlsim.combine.sedml.tesedml.SEDMLCodeFactory static method)
vrange1 (in module sbmlsim.simulation.range)
W
WARNING (sbmlsim.utils_logging.bcolors attribute)
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)
WHITE (sbmlsim.utils_logging.bcolors attribute)
work() (sbmlsim.simulator.simulation_ray.SimulatorActor method)
worker() (in module sbmlsim.fit.runner)
workingDir (in module app2sim.sedml)
(in module asedml3repeat.sedml)
(in module asedmlComplex.sedml)
(in module BioModel1_repressor_activator_oscillations.sedml)
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.result)
(class in sbmlsim.result.xresult)
xtick_labelsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Y
yaxis (sbmlsim.plot.Plot property)
(sbmlsim.plot.plotting.Plot property)
ytick_labelsize (sbmlsim.plot.Figure attribute)
(sbmlsim.plot.plotting.Figure attribute)
Z
zip_archives
module
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