Quantitative modeling of P-TEFb mediated CTD phosphorylation identifies local cooperativity

Quantitative modeling of P-TEFb mediated CTD phosphorylation identifies local cooperativity OverviewThis folder contains the code accompanying the manuscript, Quantitative modeling of P-TEFb mediated CTD phosphorylation identifies local cooperativity Contents **analytical_implementations/**: Analytical implementations for the uniform distributive and fully processive models, along with a `run_optimization.py` script for parameter estimation. **data/**: Mass spectrometry time-course data used in this study, obtained from [Czudnochowski et al. (2012)](https://doi.org/10.1038/ncomms1846). A list of phosphorylation patterns and their corresponding PySB species IDs. **figures/**: Output figures generated by the scripts in `plotting_scripts`. **optimization_profiling_scripts/**: Scripts for running optimization, profiling, and MCMC sampling. **optimization_results/**: Parameter estimation and profiling results for all models. **parameter_estimates_table/**: Table containing parameter estimates for all models. **petab_models/**: PEtab model definitions for all models used in this study. **plotting_scripts/**: Scripts used to generate all figures for the main manuscript and supplementary information. Each model folder contains its own `README.md` with additional details. TutorialThe `run_optimization.py` and `run_profiling.py` scripts located in the `optimization_profiling_scripts` or `analytical_implementations` folders can be used to rerun optimization, parameter profiling, and MCMC sampling.To reproduce a figure from the main manuscript or supplementary information, execute the corresponding script from the `plotting_scripts` folder. ContactIf you have nay questions, please feel free to contact any of the corresponding authors: Domagoj Doresic (domagoj.doresic@uni-bonn.de) Aaron Callenbach (aaron.callenbach@uni-bonn.de) Jan Hasenauer (jan.hasenauer@uni-bonn.de)