Models

Before running the code, please install eulerpi (via pip install eulerpi).

The .zip file contains 5 individual python files and a Data folder that includes all data used for inference. Three of the files are named *plot.py and can be used to reproduce the plots of our article for one respective example model. To this end, the files contain several function definitions and an executable part at the end. The *plot.py files can be executed and produce (Sub-)Figures that are saved in the ...

The folder contains the jupyter notebook for the execution of all analyses of the study. The BEST method is used in the notebook and is added in a separate python skript.

There is a class for the BEST method according to Kruschke and a class für the BEST multiple comparison.

A conda environment file with all libraries that are necessary to perform the analysis, including the package version was created. It can be easily installed via conda env create -f pymc_env.yml

The exponential decay model with all parameters, observables and conditions was specified in a yaml file.

This yaml file is converted with yaml2sbml (2020 Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schaelte and Jan Hasenauer) to a PEtab problem, which contains also the SBML model.

The SOP creates a separate SBML model for each drug and condition, as the PEtab problem contains diffrent experimental data for them.

However, the SBML models only differ in their name as for all drugs and conditions, the same exponential decay model was assumed.

The SBMLs are automatically created by yaml2sbml, when the SOP is executed. Therefore, these files are for completeness only and are not necessary to replicate the analysis.

The Folder contains:

• The MCMC and simulation results, as well as the synthetic data of the Chemical Reaction Network model (DoubleDecayIndep)
• The MCMC and simulation results, as well as the synthetic data of the Lotka-Volterra model (LotkaVolterraJoint)

Together with an executable ipynb script (Exe.ipynb) and the MCMC plotting and execution functions (MCMCFunctions.py).

This is BIOMD0000000005.

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...