User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/11/03

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Working from the scratch

I decided to work in the modeling task concerning the modified AKT signaling following a raw data approach. I asked to David to give the original data that he obtained from the experiments that he performed. He send me a message with the requested data, which are given in the next figure:

Raw data.png

Then, I decided to follow three different approaches:

  1. Design a neural network just to match the data.
  2. Model the modified AKT signaling pathway using the SimBiology toolbox of MatLab.
  3. Directly obtain a model using the nonlinear differential equations formalism.

I think that a perceptron based network will be good for the first purpose. I suppose that a network can be configured in order to have two different inputs (the Zstk drug concentration and the mTOR raptor inhibitor). The idea is to have a black-box model which display the two different given behaviors (with or without mTOR raptor inhibitor). For the second approach the advantage would be to have a model easily available for anybody working with the Matlab framework.

Meeting with Pilpel

Tomorrow I will read again the Pilpel papers. I asked him to have a meeting next Wednesday.