Jonas Küttner

This project contains the scripts that were used for simulations and plots presented in my Bachelor thesis. The model is based on the a growth model which which was published in Altenburg et al., 2018, NPJ systems biology and applications.

The Antimony models used in this project are in the /antimony_models folder

• mechanicalSizeControl.txt: the adjusted model from Altenburg et al.
• size_regulation.txt: the core model of the project which is plugged into the growth model from Altenburg et al.
• sbf_whi5_module.txt: model containing only the interactions of Sbf, Whi5 and Cln12. Is used to calculate steady states to initialize the continuation curve in bifurcation analysis.
• size_regulation_nodil.txt model which was used for the simulation in which the Whi5 concentration was kept constant.

The model was tested under different initial conditions. Therefore different parameter scans were used. They are all based on the simulation of the ODE-system over a time span. The corresponding scripts are stored under /simulations/param_scans. Three different scans were performed:

• volume_scan: The model is initialized with different initial volumes and the simulation results are stored for each initial volume.
• param_scan The model is initialized with different growth rates. The function can be used to vary any parameter but was only used to scan for growth rates. The growth rate can not be directly set. It results from the properties of the growth model. Varying growth creates are produced by changing the k_nutrient parameter of the growth model.
• p_vdiv_scan This scan is a combination of two parameter scans. The model is initialized with m growth rates and n initial volumes. For every combination the transition state is evaluated. The model produces m x n simulation results. Originally they were stored in a nested list which contained m x n array with the trajectories. Since I only use the transition states for further analysis I provide dataframes which contains the transition states associated with each growth rates and initial volume.

The simulation results of the p_vdiv_scans are pandas data frames and stored under /simulation_data/transformed_kg_vdiv_scans. The simulation results of volume_scan and param_scan are nested lists stored under /simulation_data/param_scans.

Every script is associated with a plotting function which plots the simulation results. The scripts which were used to create the specific plots presented in my thesis, are stored under /plots

The model was compared to experimental data published in Garmendia-Torres et al., eLife, 2018. The record can be downloaded under https://charvin.igbmc.science/yeastcycledynamics. To download and integrate the record into this project, run /dataset_analysis/data_g_torres.py.

The steady states of the Sbf, Whi5 and Cln12 subsystem were analysed using the PyDSTools continuation curve analysis. The script containing the reduced model and the simulation can be found under /simulations/bifurcation_data.

The simulation results I used for the plots in the Thesis are named according to the parameter changes made to the standard configuration contained in the antimony txt file. A more detailed description is provided in the excel sheet simulation_datasets_desc.xslx.