cell_cycle_petab is a repository that stores several cell cycle model versions and their corresponding PEtab problems. The data in the measurement tables stems from snapshot measurements by Stallaert et al. (2021) in RPE1 cells. Pseudo-time courses were reconstructed with reCAT. Visualisations of these time courses can be found in the cell_cycle_time_course repository. The model generation process is documented in the cell_cycle_model repository. For further details, please refer to Paul Lang's dissertation.
Models are of different degree of complexity.
- v2.1.4: basic cell cycle model in SBML format.
- v3.0.0: same as v2.1.4 in BNGL.
- v3.0.1: added refinements to reaction rules of v3.0.0.
- v3.1.0: added DNA damage checkpoint (SKP2 and TP53 and CDKN1A).
- v3.2.0: added CDKN1B.
- v4.0.0: added compartments.
This repository contains a /versions/ directory with subdirectories for the versions mentioned above and Excel documents containing the raw output of the saCeSS optimiser. The /versions/v* directories contain YAML files specifying the PEtab problem for the latest optimisation run. Often, preliminary runs had do be performed to refine the optimisation procedure (e.g. updating bounds). Files in /versions/v* that are not mentioned in the YAML file were typically used for preliminary runs.
The /versions/v*results_/ directories often contain a sacess_to_petab.py script, which extracts an optimisation result from Excel (saCeSS raw output) and plugs them as nominalValues into a parameters_v*_optimized.tsv file. plot_time_cours.py scripts simulate the results and produce an optimisation.tsv file. Sometimes (manual) modifications such as removing noise parameters from the parameter and observable tables were necessary to run the simulation. plot_sacess_*_manu.py scripts use the optimisation.tsv file to plot figures in manuscript quality.
Figures for the manuscript Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells that show fits of PEtab problems to RPE1 cells can be plotted with the following scrips:
Barebones SBML files with parameters optimized to fit the time courses of RPE1 cells can be found for the following model versions:
If you use this repository in your research, please cite this paper:
@article{lang_reusable_2024,
title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in {RPE}-1 cells},
doi = {10.1371/journal.pcbi.1011151},
journal = {PLOS Computational Biology},
author = {Lang, Paul F. and Penas, David R. and Banga, Julio R. and Weindl, Daniel and Novak, Bela},
year = {2024},
}