Code for simulation and model analysis

SubMIC_Carvacrol

SubMIC_Carvacrol: A predictive microbiology framework to determine the effect of Subinhibitory concentrations (working under the Minimal Inhibitory Concentration) of Carvacrol on the foodborne bacterial species Escherichia coli and Bacillus cereus. The code in the repository provides experimental data and (model-based) estimated parameters to simulate the inactivation dynamics of Escherichia coli and Bacillus cereus viable counts (log scale of CFUs/mL) under different subinhibitory concentrations of Carvarol (mg/mL) during a time-lapse of 48 hours. The code integrates the mathematical model introduced in the article (soon to come) to explain the experimental data.

The estimation of the model parameters to fit the experimental data was performed using the MATLAB optimisation toolbox AMIGO2, freely available at: https://sites.google.com/site/amigo2toolbox .

The structural identifiability analysis of the mathematical model was performed using the MATLAB toolbox STRIKE-GOLDD, freely available at: https://github.com/afvillaverde/strike-goldd .

The repository SubMIC_Carvacrol contains the following subfolders:

- Simulations:

Folder with the necessary files to run model-based simulations:

- Carvacrol_Inhibition_of_Ecoli_Bcereus-Model&Data.m: Script to run model-based simulations in the commercial computing software MATLAB.
- Carvacrol_Inhibition_of_Ecoli_Bcereus-Model&Data.R: Script to run model-based simulations in the free software for statistical computing R.

The simulation code has been kept simple so the user can introduce different parameter values and/or experimental data to simulate the model.

- Parameter_Estimation:

Folder with the necessary files to perform the estimation of model parameters using the MATLAB optimisation toolbox AMIGO2:

- Run_PE.m: Main script to run parameter estimation using AMIGO2. The user only needs to run the file Run_PE.m to perform the model calibration.

- Model_SubMIC_Carvacrol.m: Script to generate the mathematical model in AMIGO2.

- PostProcess.m: Script to plot and postprocesssing data.

- Plot_ExpData.m: Script to plot the experimental data.

- Generated_data: Folder with experimental data.

- Generated_results: Folder to save the estimation results and figures.

- Structural_Identifiability:

Folder with the necessary code to perform a multi-experiment structural identifiability analysis of the mathematical model using the MATLAB toolbox STRIKE-GOLDD.

- z_create_Model_SubMIC_Carvacrol: Script to generate the mathematical model in STRIKE-GOLDD.

- options.m: Script with STRIKE-GOLDD options setting the necessary configurations to perform the multi-experiment structural identifiability analysis of the mathematical model.

- Model_SubMIC_Carvacrol.mat: File containing the model data generated when run z_create_Model_SubMIC_Carvacrol.

To run the multi-experiment structural identifiability analysis, the user only needs to replace the default options.m file in STRIKE-GOLDD with the one provided in the repository and move the data file Model_SubMIC_Carvacrol.mat to the folder models of STRIKE-GOLDD.

Code for simulation and model analysis

v1.0.2

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SubMIC_Carvacrol

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SubMIC_Carvacrol

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Minor gramm fix