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DLC1 knockdown in EMT in MCF10A cells
Mar 21, 2025 - Mathematical modeling and simulation of cellular systems
Höpfl, Sebastian; Radde, Nicole, 2025, "DLC1 knockdown in EMT in MCF10A cells", https://doi.org/10.18419/DARUS-4240, DaRUS, V1
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...
all_parameters_estimated.zip
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
ZIP Archive - 28.3 MB - MD5: 76a0ba8b915781461f0ec37570945ea6
Model calibration and MCMC results of the not reduced CBSD model
Bifurcation_analysis.zip
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
ZIP Archive - 13.8 MB - MD5: 80a109261dea1a57bc7bc1236f4fe887
Skripts to perform the Bifurcation analysis using PyDSTools
CBSD_global_parameter_variation_RACIPE.py
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
Python Source Code - 17.3 KB - MD5: 6f7f286f961b2490fc107539b2baec56
Script for the modified RACIPE analysis of the CBSD model
CBSD_libRoadRunner_simulation.ipynb
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
Jupyter Notebook - 6.4 MB - MD5: d59fd8cdae24a08a96ddfc3e3bc3469d
Jupyter notebook for deterministic and stochastic CBSD simulation
CBSD_MCMC_chain.hdf5
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
Hierarchical Data Format - 122.1 MB - MD5: 452f4f6ede41fc70fcdc0184d9c3ebfc
Complete posterior samples from MCMC sampling in HDF5
CBSD_PEtab.zip
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
ZIP Archive - 6.5 KB - MD5: 263e316228d02aa4da0c4476ba2c06d6
PEtab files for the CBSD model including the CBSD SBML model. Can be used to reproduce the parameter estimation, simulation and sampling.
CBSD_Pypesto_Parameters.hdf5
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
Hierarchical Data Format - 118.4 KB - MD5: 7a5b0997d318069f5aeb7ced5d66cd10
Model calibration results in HFD5 format
CBSD_Pypesto_Parameters_optimization_dictionary.json
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
JSON - 931 B - MD5: b79c3cfb6b6ab7ceda22fd319c5337db
Dictionary containing the optimized parameter values
CBSD_single_reactions_SSA.xml
Mar 21, 2025 - DLC1 knockdown in EMT in MCF10A cells
XML - 34.5 KB - MD5: ee6c89ff248f53a6cbb07eabfef12fa7
SBML CBSD model for stochastic simulations - models all subreactions individually
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