DLC1 knockdown in EMT in MCF10A cells

For modeling, the CBS model of Tian et al. (2003) was extended by DLC1. The model was calibrated using the MCF10A data after 5 days under the control and dlc1 targeted siRNA.

The Repository contains: - The CBSD model in the SBML format - A PEtab problem describing the parameter estimation problem (experimental data, observables, parameters, experimental conditions) - Script used for model calibration (Extended_CBS_Pypesto_ParEst.py) - Script used for MCMC sampling (MCMC_sampling_pypesto_workflow.py) - Jupyter notebook used for model simulation (Extended_CBS_SNAIL1_libRoadRunner_simulation.ipynb) - Jupyter notebook used for bifurcation analysis(Bifurcation_Extended_CBS_SNAIL1_PyDSTool.ipynb) - The MCMC sampling results in HDF5 - Created Visualisations - The results of the full CBSD model (with all parameters = before model reduction) - code used in Fiji for the segmentation and analysis of the IF data (get_boundaries_v9.ijm)