MCF10A cells were seeded and transfected with two siRNAs targeting dlc1 and one control siRNA. 10 ng/ml TGFb was used to induce EMT and added 24 h after the transfection.

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)

Python, 3.12.1

amici, 0.21.2

pypesto, 0.4.1

hdf5, 1.12.1

libroadrunner, 2.5.0