User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/20

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The Simulink code for the AKT signaling pathway

  • Today I was working some hours with the Simulink code of the AKT signaling pathway. I was looking from some ways to the simulation of the signaling pathway more interactive (in order to analyze the behavior of the network when changing some parameters). One possibility is to execute the simulation with programmed blocks associated to some particular important variables or constants (perturbations included). For example, I included at the output of the integrator corresponding to [rictor] a SUM BLOCK which allows me to add to the this particular state a fixed constant value (during some seconds, at a precise time). Another possibility is to develop a graphic User Interface in matlab and call from it the Simulink code. By the moment I hace not an answer about what is the better choice to make.

The Mathematica version

I included in the Mathematica simulator of the AKT signaling pathway a line to ask to the user for some values (in this case X8, i.e. PP2A, and X), i.e. PTEN). I was considering the possibility to build a Graphic User Interface. I suppose that the best thing to do is to develop the Mathematica version and the Simulink version at the same time.

The LaTeX version file sent to David Miguez

I send to David Miguez the PDF file corresponding to the LaTeX file. My purpose is to ask him for some information concerning the constant, and variables, that will be useful to interact with when simulating the AKT signaling pathway.

Cell Designer

It maybe convenient for me to also develop the model of the AKT signaling pathway in Cell Designer. I will check it.