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.idea

.idea

 
 

Test

Test

 
 

figures_paper

figures_paper

 
 

sedml_models

sedml_models

 
 

AM_BDF.pdf

AM_BDF.pdf

 
 

AM_BDF_Sucess_rate.pdf

AM_BDF_Sucess_rate.pdf

 
 

Depth1.py

Depth1.py

 
 

Depth1_KinLaw.py

Depth1_KinLaw.py

 
 

DivComb.py

DivComb.py

 
 

Input_Benchmark.py

Input_Benchmark.py

 
 

Input_Data.py

Input_Data.py

 
 

Intern_vs_Extern.py

Intern_vs_Extern.py

 
 

JWS_changeValues.py

JWS_changeValues.py

 
 

KineticLaw.py

KineticLaw.py

 
 

LinSol.pdf

LinSol.pdf

 
 

LinearRegression.py

LinearRegression.py

 
 

NonLinSol.pdf

NonLinSol.pdf

 
 

Outcome_Data.py

Outcome_Data.py

 
 

Predictor.py

Predictor.py

 
 

PredictorCV.py

PredictorCV.py

 
 

PredictorCV_2.py

PredictorCV_2.py

 
 

README.md

README.md

 
 

Sigmoid.py

Sigmoid.py

 
 

SimAllSettings.py

SimAllSettings.py

 
 

SimPriorSettings.py

SimPriorSettings.py

 
 

Simulate_multiple_BioModels.py

Simulate_multiple_BioModels.py

 
 

Simulate_single_BenchmarkModels.py

Simulate_single_BenchmarkModels.py

 
 

Simulate_single_BioModels.py

Simulate_single_BioModels.py

 
 

Substitution.py

Substitution.py

 
 

Tolerances_BoxPlot.pdf

Tolerances_BoxPlot.pdf

 
 

Tolerances_Histogram.pdf

Tolerances_Histogram.pdf

 
 

Y_testing.py

Y_testing.py

 
 

adaptModelCollection.py

adaptModelCollection.py

 
 

allError.py

allError.py

 
 

averageTime.py

averageTime.py

 
 

changeValues.py

changeValues.py

 
 

changeValues_Copasi.py

changeValues_Copasi.py

 
 

checkExperimentalData.py

checkExperimentalData.py

 
 

colourDataFrame.py

colourDataFrame.py

 
 

compareStateTrajectories_1.py

compareStateTrajectories_1.py

 
 

compareStateTrajectories_140settings_2.py

compareStateTrajectories_140settings_2.py

 
 

compareStateTrajectories_2.py

compareStateTrajectories_2.py

 
 

compareStateTrajectories_BioModels_1.py

compareStateTrajectories_BioModels_1.py

 
 

compareStateTrajectories_BioModels_2.py

compareStateTrajectories_BioModels_2.py

 
 

compareStateTrajectories_BioModels_plot.py

compareStateTrajectories_BioModels_plot.py

 
 

compareStateTrajectories_COPASI.py

compareStateTrajectories_COPASI.py

 
 

compareStateTrajectories_plot.py

compareStateTrajectories_plot.py

 
 

compareStateTrajectories_summary_Adams.pdf

compareStateTrajectories_summary_Adams.pdf

 
 

compareStateTrajectories_summary_BDF.pdf

compareStateTrajectories_summary_BDF.pdf

 
 

compareStatetrajectories_140settings_1.py

compareStatetrajectories_140settings_1.py

 
 

correctStateTrajectories.py

correctStateTrajectories.py

 
 

decomposeFormula.py

decomposeFormula.py

 
 

denominator.py

denominator.py

 
 

execute_LinearSolvers.py

execute_LinearSolvers.py

 
 

execute_NonlinearSolvers.py

execute_NonlinearSolvers.py

 
 

execute_SimAllSettings.py

execute_SimAllSettings.py

 
 

execute_SolAlg.py

execute_SolAlg.py

 
 

execute_Tolerances.py

execute_Tolerances.py

 
 

execute_WholeStudy.py

execute_WholeStudy.py

 
 

execute_changeValues.py

execute_changeValues.py

 
 

execute_loadModels.py

execute_loadModels.py

 
 

getExperimentalData.py

getExperimentalData.py

 
 

getObservables.py

getObservables.py

 
 

loadModels.py

loadModels.py

 
 

loadModels_test.py

loadModels_test.py

 
 

logging_util.py

logging_util.py

 
 

num_x_num_p.py

num_x_num_p.py

 
 

opposingBracket.py

opposingBracket.py

 
 

paper_plotAMLSODA.py

paper_plotAMLSODA.py

 
 

paper_plotAdamsBDF.py

paper_plotAdamsBDF.py

 
 

paper_plotAdamsBDF_2.py

paper_plotAdamsBDF_2.py

 
 

paper_plotAdamsBDF_3.py

paper_plotAdamsBDF_3.py

 
 

paper_plotAdamsBDF_4.py

paper_plotAdamsBDF_4.py

 
 

paper_plotBDFLSODA.py

paper_plotBDFLSODA.py

 
 

paper_plotBoxPlot.py

paper_plotBoxPlot.py

 
 

paper_plotBoxPlot_2.py

paper_plotBoxPlot_2.py

 
 

paper_plotCompareStateTrajectories.py

paper_plotCompareStateTrajectories.py

 
 

paper_plotCompareStateTrajectories_2.py

paper_plotCompareStateTrajectories_2.py

 
 

paper_plotCompareStateTrajectories_combined.py

paper_plotCompareStateTrajectories_combined.py

 
 

paper_plotCompareStateTrajectories_combined_2.py

paper_plotCompareStateTrajectories_combined_2.py

 
 

paper_plotFirstResults.py

paper_plotFirstResults.py

 
 

paper_plotFirstStudy.py

paper_plotFirstStudy.py

 
 

paper_plotFirstStudy_2.py

paper_plotFirstStudy_2.py

 
 

paper_plotFirstStudy_3.py

paper_plotFirstStudy_3.py

 
 

paper_plotHistogram.py

paper_plotHistogram.py

 
 

paper_plotLinearSolver.py

paper_plotLinearSolver.py

 
 

paper_plotLinearSolver_2.py

paper_plotLinearSolver_2.py

 
 

paper_plotNonLinSol.py

paper_plotNonLinSol.py

 
 

paper_plotNonLinSol_2.py

paper_plotNonLinSol_2.py

 
 

paper_plotNonLinSol_3.py

paper_plotNonLinSol_3.py

 
 

paper_plotNonLinSol_4.py

paper_plotNonLinSol_4.py

 
 

paper_plotScatter.py

paper_plotScatter.py

 
 

paper_plotScatter_2.py

paper_plotScatter_2.py

 
 

paper_plotScatter_3.py

paper_plotScatter_3.py

 
 

paper_plotScatter_4.py

paper_plotScatter_4.py

 
 

paper_plotTableOfAllModels.py

paper_plotTableOfAllModels.py

 
 

paper_plotTableOfAllModels_2.py

paper_plotTableOfAllModels_2.py

 
 

paper_plotTableOfAllModels_3.py

paper_plotTableOfAllModels_3.py

 
 

parameters.py

parameters.py

 
 

parameters_BioModelsDatabase.py

parameters_BioModelsDatabase.py

 
 

Repository files navigation

Assessment and Prediction of ODE Solver Performance for Biological Processes

It follows the order in which all scripts are executed.

1 Create model collection

1.1 Download all sedml and sbml models from the JWS Online Database

script_download_all_sedml_models.py

1.2 Download chosen sbml models from the BioModels Database

downloaded "by hand" --- no script available

1.3 Import all sbml models to AMICI

sbml2amici.py
sbml2amici_BioModelsDatabase.py

1.4 Check for correctly generated .so files and delete all other sbml models

no explicit script yet

1.5 Compare the state trajectories of the local simulation to the in-built simulation routine of JWS

compareStateTrajectories_1.py
compareStateTrajectories_2.py
compareStateTrajectories_plot.py

1.6 Derive the whole model collection

correctStateTrajectories.py

1.7 Plot basic properties

plot_first_results.py
stat_reac_par.py
Intern_vs_Extern.py
num_x_num_p.py

2 Solver settings study

2.1 Tolerance study

execute_Tolerances.py
plotHistogram.py
plotBoxPlot.py

2.2 Linear solver study

execute_LinearSolvers.py
plotScatter.py

2.3 Non-linear solver study

execute_NonlinearSolvers.py
(no plotting script yet)

2.4 Multistep method study

execute_SolAlg.py
plotScatter2.py
plotScatter3.py

3 Predictor model

3.1 Get the input data (by determination of the kinetic rate law) for the logistic regression

Input_Data.py

3.2 Predictor model with/without cross-validation

Predictor.py
PredictorCV.py
PredictorCV_2.py

3.3 Divide all categorical Input values into more sections

DivComb.py

3.4 Plot different results

plotAdamsBDF.py
plotAdBf.py
plotPrediction.py

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