├── .flake8 ├── .gitattributes ├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── .readthedocs.yml ├── .zenodo.json ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── basico ├── .gitattributes ├── .gitignore ├── README.md ├── __init__.py ├── _version.py ├── biomodels.py ├── callbacks.py ├── compartment_array_tools.py ├── data │ ├── BIOM10-fit.cps │ ├── CircadianClock.cps │ ├── DimericMWC-stiff.cps │ ├── Genetic-2000Elo.xml │ ├── LM-test1.cps │ ├── MAPK-HF96-layout.cps │ ├── MAPKdata.txt │ ├── NF-kappaB.cps │ ├── Olsen2003_peroxidase.cps │ ├── PK_fit2.cps │ ├── YeastGlycolysis.cps │ ├── YeastGlycolysis.gps │ ├── array_1d.cps │ ├── brusselator.cps │ ├── data_2.txt │ ├── data_3.txt │ ├── linear_base.cps │ ├── mmspect3.txt │ └── turing_base.cps ├── expressions.py ├── jws_online.py ├── logging.py ├── model_info.py ├── model_io.py ├── petab │ ├── __init__.py │ ├── core.py │ └── select.py ├── processing.py ├── ssr │ ├── CopasiSSR.py │ └── __init__.py ├── task_lna.py ├── task_lyapunov.py ├── task_mca.py ├── task_optimization.py ├── task_parameterestimation.py ├── task_profile_likelihood.py ├── task_scan.py ├── task_sensitivities.py ├── task_steadystate.py └── task_timecourse.py ├── docs ├── API │ ├── basico.rst │ └── modules.rst ├── Makefile ├── _static │ ├── COPASI_Conly_176x176.png │ └── deNBI_logo.jpg ├── _templates │ └── autosummary │ │ ├── base.rst │ │ ├── class.rst │ │ └── module.rst ├── conf.py ├── index.rst ├── notebooks │ ├── Accessing_Models_from_Databases.ipynb │ ├── AllTaskSettings.ipynb │ ├── Arrays_of_Compartments.ipynb │ ├── Creating_a_simple_model.ipynb │ ├── CustomTimecourse.ipynb │ ├── Editing_Kinetics.ipynb │ ├── Elowitz_Nature2000 │ │ ├── Elowitz_Nature2000.yaml │ │ ├── experimentalCondition_Elowitz_Nature2000.tsv │ │ ├── measurementData_Elowitz_Nature2000.tsv │ │ ├── model_Elowitz_Nature2000.xml │ │ ├── observables_Elowitz_Nature2000.tsv │ │ ├── parameters_Elowitz_Nature2000.tsv │ │ └── simulatedData_Elowitz_Nature2000.tsv │ ├── FAMOS_ModelSelection.ipynb │ ├── LinearNoiseApproximation.ipynb │ ├── MCA.ipynb │ ├── Model_manipulation.ipynb │ ├── Optimization.ipynb │ ├── ParameterEstimation_Export.ipynb │ ├── Parameter_Estimation_Example.ipynb │ ├── Parameter_Scans.ipynb │ ├── Profile_likelihood.ipynb │ ├── Sensitivity_Analysis.ipynb │ ├── Setting_up_Parameter_Estimation.ipynb │ ├── Simple_simulations_and_plotting_with_basico.ipynb │ ├── Simple_simulations_with_basico.ipynb │ ├── Using_callbacks.ipynb │ ├── Working_with_Annotations.ipynb │ ├── Working_with_PEtab.ipynb │ ├── Working_with_ParameterSets.ipynb │ ├── Working_with_Plots.ipynb │ ├── Working_with_Reports.ipynb │ ├── Working_with_SBML_Ids.ipynb │ ├── Working_with_Widgets.ipynb │ ├── Working_with_ipyparallel.ipynb │ ├── index.ipynb │ ├── index_colab.ipynb │ ├── ipywidget_lorenz.gif │ └── model_selection │ │ ├── calibrated_M1_4.yaml │ │ ├── calibrated_M1_7.yaml │ │ ├── calibrated_first_iteration.yaml │ │ ├── conditions.tsv │ │ ├── measurements.tsv │ │ ├── model.xml │ │ ├── model_space.tsv │ │ ├── observables.tsv │ │ ├── parameters.tsv │ │ ├── petab_problem.yaml │ │ └── petab_select_problem.yaml ├── quickstart │ └── get-started.rst └── requirements.txt ├── examples ├── Accessing Models from Databases.py ├── Getting and setting reaction parameters,reactions and metabolites with Basico.py ├── Simple simulations and plotting with basico.py ├── Simple simulations with basico.py ├── brusselator.cps └── parallel_scan.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── 0008.tsv ├── OdeExperiment_0.txt ├── OdeExperiment_1.txt ├── OdeExperiment_2.txt ├── OdeExperiment_3.txt ├── ex_0008.tsv ├── famos.zip ├── mes_df.csv ├── model.xml ├── model_selection │ ├── calibrated │ │ ├── M1_4_0.yaml │ │ ├── M1_7_0.yaml │ │ └── calibrated_first_iteration.yaml │ ├── conditions.tsv │ ├── measurements.tsv │ ├── model.xml │ ├── model_space.tsv │ ├── 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