Pycotools
master
PyCoTools
Getting started
Build a model with antimony
Create an antmiony string from an existing model
Simulate a time course
Visualise a time course
Tutorials
Running Time-Courses
Create a model
Deterministic Time Course
Visualization
Plot in Phase Space
Save to file
Alternative Solvers
Stochastic MM
Run a Time Course Using Direct Method
Plot stochastic time course
Insert Parameters
Build a demonistration model
Insert Parameters from Python Dictionary
Insert Parameters from Pandas DataFrame
Insert Parameters from Parameter Estimation Output
Insert Parameters using the
model.Model().insert_parameters
method
Change parameters using
model.Model().set
Parameter Scan
Two Way Parameter Scan
Repeat Scan Items
Parameter Estimation Tutorial
Build a Model
Collect some experimental data
The Config Object
Running multiple parameter estimations
A shortcut for configuring the
ParameterEstimation.Config
object
Examples
Simple Parameter Estimation
Parameter estimation with multiple models
API documentation
The model module
pycotools3.model.Model
pycotools3.model.ImportSBML
pycotools3.model.InsertParameters
pycotools3.model.BuildAntimony
pycotools3.model.Build
The tasks module
pycotools3.tasks.TimeCourse
pycotools3.tasks.ParameterEstimation.Config
pycotools3.tasks.ParameterEstimation
pycotools3.tasks.ParameterEstimation.Context
pycotools3.tasks.Sensitivities
pycotools3.tasks.Scan
pycotools3.tasks.Reports
The viz module
pycotools3.viz.Parse
pycotools3.viz.PlotTimeCourse
pycotools3.viz.Boxplots
Pycotools
Docs
»
Index
Edit on GitHub
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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V
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__init__() (pycotools3.model.Build method)
(pycotools3.model.BuildAntimony method)
(pycotools3.model.ImportSBML method)
(pycotools3.model.InsertParameters method)
(pycotools3.model.Model method)
(pycotools3.tasks.ParameterEstimation method)
(pycotools3.tasks.Reports method)
(pycotools3.tasks.Scan method)
(pycotools3.tasks.Sensitivities method)
(pycotools3.tasks.TimeCourse method)
(pycotools3.viz.Boxplots method)
(pycotools3.viz.Parse method)
(pycotools3.viz.PlotTimeCourse method)
A
active_parameter_set (pycotools3.model.Model attribute)
adaptive_tau_leap() (pycotools3.tasks.TimeCourse method)
add() (pycotools3.model.Model method)
add_compartment() (pycotools3.model.Model method)
add_component() (pycotools3.model.Model method)
add_experiments() (pycotools3.tasks.ParameterEstimation.Context method)
add_function() (pycotools3.model.Model method)
add_global_quantity() (pycotools3.model.Model method)
add_list_of_variables_element() (pycotools3.tasks.Sensitivities method)
add_local_parameter() (pycotools3.model.Model method)
add_metabolite() (pycotools3.model.Model method)
add_models() (pycotools3.tasks.ParameterEstimation.Context method)
add_reaction() (pycotools3.model.Model method)
add_setting() (pycotools3.tasks.ParameterEstimation.Context method)
add_settings() (pycotools3.tasks.ParameterEstimation.Context method)
add_state() (pycotools3.model.Model method)
add_validation_experiments() (pycotools3.tasks.ParameterEstimation.Context method)
add_working_directory() (pycotools3.tasks.ParameterEstimation.Context method)
all_variable_names (pycotools3.model.Model attribute)
area_unit (pycotools3.model.Model attribute)
avagadro (pycotools3.model.Model attribute)
B
Boxplots (class in pycotools3.viz)
Build (class in pycotools3.model)
BuildAntimony (class in pycotools3.model)
C
clear_all_reports() (pycotools3.tasks.Reports method)
compartments (pycotools3.model.Model attribute)
configure() (pycotools3.tasks.ParameterEstimation.Config method)
constants (pycotools3.model.Model attribute)
constraint_items (pycotools3.tasks.ParameterEstimation.Config attribute)
convert() (pycotools3.model.ImportSBML method)
convert_molar_to_particles() (pycotools3.model.Model static method)
convert_particles_to_molar() (pycotools3.model.Model static method)
copasi_file (pycotools3.model.Model attribute)
copasi_filename() (pycotools3.model.ImportSBML method)
create_directory() (pycotools3.viz.Boxplots method)
create_new_report() (pycotools3.tasks.Sensitivities method)
create_problem() (pycotools3.tasks.Sensitivities method)
create_scan() (pycotools3.tasks.Scan method)
create_sensitivity_task() (pycotools3.tasks.Sensitivities method)
create_task() (pycotools3.tasks.TimeCourse method)
D
define_report() (pycotools3.tasks.Scan method)
deterministic() (pycotools3.tasks.TimeCourse method)
direct() (pycotools3.tasks.TimeCourse method)
divide_data() (pycotools3.viz.Boxplots method)
do_checks() (pycotools3.tasks.ParameterEstimation method)
E
execute() (pycotools3.tasks.Scan method)
experiment_filenames (pycotools3.tasks.ParameterEstimation.Config attribute)
experiment_names (pycotools3.tasks.ParameterEstimation.Config attribute)
experiments (pycotools3.tasks.ParameterEstimation.Config attribute)
F
fit_dir (pycotools3.tasks.ParameterEstimation attribute)
fit_item_order (pycotools3.model.Model attribute)
fit_items (pycotools3.tasks.ParameterEstimation.Config attribute)
from_chaser_estimations() (pycotools3.viz.Parse method)
from_folder() (pycotools3.viz.Parse method)
from_json() (pycotools3.tasks.ParameterEstimation.Config method)
from_multi_parameter_estimation() (pycotools3.viz.Parse static method)
from_parameter_estimation (pycotools3.viz.Parse attribute)
from_profile_likelihood() (pycotools3.viz.Parse method)
from_timecourse() (pycotools3.viz.Parse method)
from_yaml() (pycotools3.tasks.ParameterEstimation.Config method)
functions (pycotools3.model.Model attribute)
G
get() (pycotools3.model.Model method)
get_model_objects_from_strings() (pycotools3.tasks.ParameterEstimation method)
get_report_key() (pycotools3.tasks.Scan method)
(pycotools3.tasks.Sensitivities method)
(pycotools3.tasks.TimeCourse method)
get_single_object_references() (pycotools3.tasks.Sensitivities method)
get_variable_names() (pycotools3.model.Model method)
gibson_bruck() (pycotools3.tasks.TimeCourse method)
global_quantities (pycotools3.model.Model attribute)
(pycotools3.tasks.ParameterEstimation attribute)
H
hybrid_lsoda() (pycotools3.tasks.TimeCourse method)
hybrid_rk45() (pycotools3.tasks.TimeCourse method)
hybrid_runge_kutta() (pycotools3.tasks.TimeCourse method)
I
ImportSBML (class in pycotools3.model)
insert() (pycotools3.model.InsertParameters method)
insert_compartments() (pycotools3.model.InsertParameters method)
insert_global_quantities() (pycotools3.model.InsertParameters method)
insert_locals() (pycotools3.model.InsertParameters method)
insert_metabolites() (pycotools3.model.InsertParameters method)
insert_parameters() (pycotools3.model.Model method)
InsertParameters (class in pycotools3.model)
K
key (pycotools3.model.Model attribute)
L
length_unit (pycotools3.model.Model attribute)
load() (pycotools3.model.BuildAntimony method)
load_model() (pycotools3.model.ImportSBML method)
local_parameters (pycotools3.model.Model attribute)
(pycotools3.tasks.ParameterEstimation attribute)
M
metabolites (pycotools3.model.Model attribute)
(pycotools3.tasks.ParameterEstimation attribute)
Model (class in pycotools3.model)
model_objects (pycotools3.tasks.ParameterEstimation.Config attribute)
models (pycotools3.tasks.ParameterEstimation attribute)
models_dir (pycotools3.tasks.ParameterEstimation attribute)
multi_parameter_estimation() (pycotools3.tasks.Reports method)
N
name (pycotools3.model.Model attribute)
number_of_reactions (pycotools3.model.Model attribute)
O
open() (pycotools3.model.Model method)
P
parameter_descriptions (pycotools3.model.Model attribute)
parameter_estimation() (pycotools3.tasks.Reports method)
parameter_sets (pycotools3.model.Model attribute)
ParameterEstimation (class in pycotools3.tasks)
ParameterEstimation.Config (class in pycotools3.tasks)
ParameterEstimation.Context (class in pycotools3.tasks)
parameters (pycotools3.model.InsertParameters attribute)
(pycotools3.model.Model attribute)
Parse (class in pycotools3.viz)
parse() (pycotools3.viz.Parse method)
parse_scan() (pycotools3.viz.Parse method)
plot() (pycotools3.viz.Boxplots method)
(pycotools3.viz.PlotTimeCourse method)
PlotTimeCourse (class in pycotools3.viz)
problem_dir (pycotools3.tasks.ParameterEstimation attribute)
process_data() (pycotools3.tasks.Sensitivities method)
profile_likelihood() (pycotools3.tasks.Reports method)
Q
quantity_unit (pycotools3.model.Model attribute)
R
reactions (pycotools3.model.Model attribute)
reference (pycotools3.model.Model attribute)
refresh() (pycotools3.model.Model method)
remove() (pycotools3.model.Model method)
remove_compartment() (pycotools3.model.Model method)
remove_function() (pycotools3.model.Model method)
remove_global_quantity() (pycotools3.model.Model method)
remove_metabolite() (pycotools3.model.Model method)
remove_reaction() (pycotools3.model.Model method)
remove_report() (pycotools3.tasks.Reports method)
remove_scans() (pycotools3.tasks.Scan method)
remove_state() (pycotools3.model.Model method)
replace_sensitivities_task() (pycotools3.tasks.Sensitivities method)
Reports (class in pycotools3.tasks)
reset_cache() (pycotools3.model.Model method)
results_directory (pycotools3.tasks.ParameterEstimation attribute)
root (pycotools3.model.Model attribute)
run() (pycotools3.tasks.ParameterEstimation method)
(pycotools3.tasks.Reports method)
run_task() (pycotools3.tasks.Sensitivities method)
S
save() (pycotools3.model.Model method)
Scan (class in pycotools3.tasks)
scan() (pycotools3.model.Model method)
(pycotools3.tasks.Reports method)
Sensitivities (class in pycotools3.tasks)
sensitivity() (pycotools3.tasks.Reports method)
sensitivity_task_key() (pycotools3.tasks.Sensitivities method)
set() (pycotools3.model.Model method)
(pycotools3.tasks.ParameterEstimation.Context method)
set_cause() (pycotools3.tasks.Sensitivities method)
set_default_fit_items_dct() (pycotools3.tasks.ParameterEstimation.Config method)
set_default_fit_items_str() (pycotools3.tasks.ParameterEstimation.Config method)
set_effect() (pycotools3.tasks.Sensitivities method)
set_method() (pycotools3.tasks.Sensitivities method)
set_report() (pycotools3.tasks.Sensitivities method)
(pycotools3.tasks.TimeCourse method)
set_scan_options() (pycotools3.tasks.Scan method)
set_secondary_cause() (pycotools3.tasks.Sensitivities method)
set_subtask() (pycotools3.tasks.Sensitivities method)
set_timecourse() (pycotools3.tasks.TimeCourse method)
simulate() (pycotools3.tasks.TimeCourse method)
states (pycotools3.model.Model attribute)
T
tau_leap() (pycotools3.tasks.TimeCourse method)
time_unit (pycotools3.model.Model attribute)
TimeCourse (class in pycotools3.tasks)
timecourse() (pycotools3.tasks.Reports method)
to_antimony() (pycotools3.model.Model method)
to_dict() (pycotools3.model.InsertParameters method)
to_json() (pycotools3.tasks.ParameterEstimation.Config method)
to_sbml() (pycotools3.model.Model method)
to_yaml() (pycotools3.tasks.ParameterEstimation.Config method)
V
validation_filenames (pycotools3.tasks.ParameterEstimation.Config attribute)
validation_names (pycotools3.tasks.ParameterEstimation.Config attribute)
validations (pycotools3.tasks.ParameterEstimation.Config attribute)
volume_unit (pycotools3.model.Model attribute)
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