MATLAB Programs for Signaling Pathway

The IL-6 ~ IL-10 signaling model  

The MATLAB model was presented in the paper " C. Moya*, Z. Huang*, P. Cheng, A. Jayaraman, and J. Hahn. Investigation of IL-6 and IL-10 Signaling in Steatosis via Mathematical Modeling. IET Systems Biology, 5, No. 1, pp. 15-26, 2011 (*equal contribution)". Please read the appendix of this paper for the detail of the ODE model and parameters. The inputs of the model are the concentrations of IL-6 and IL-10, while the outputs the model  include the concentrations of  transcription factors nuclear STAT3 dimer and C/EBPβ. 

The MATLAB program can be downloaded here. Please run the Main function to run the simulation. Please cite our paper if you use our model/program. 

The TNF-α ~ NFκB signaling model

This is the model that was presented in our paper Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn. Integrated Modeling and Experimental Approach for Determining Transcription Factor Profiles from Fluorescent Reporter Data. BMC Systems Biology 2:64 (2008).The input of the model is the concentrations of TNF-α, while the output the model  include the concentrations of  transcription factor NFκB.

The MATLAB program can be downloaded here. Please run the Main function to run the simulation. Please cite our paper if you use our model/program.

Fluorescent image analysis program

The image algorithm was presented in our paper Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn. Integrated Modeling and Experimental Approach for Determining Transcription Factor Profiles from Fluorescent Reporter Data. BMC Systems Biology 2:64 (2008). It can identifty fluorescent cell regions from fluorescent images. 

The The MATLAB program can be downloaded here (200M). Please read the readme document herebefore downloading and running the program. Please cite our paper if you use our model/program.