User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/10/21

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The ATK project

Today I had a very interesting speech with David. Well, the interest turned around two important points: the first one concerns his future work at the lab. david will leave the lab at the middle of the next year. he is then obligated to finish with his research as soon as possible and I think that there will be no continuation of this project in the lab. David asked me to try to find a way to described the hysteretical behavior observed in the AKT signaling pathway when applying the Zstk drug, maybe modifying the simulink -simulating the model that he obtained from the cartoon describing the modified version of the signaling pathway-. The idea is to include a time delay to allow the creation of a pool of one the involved proteins. I will check this issue. A possible alternative concerns the creation of a a new model obtained from a extremely modified version of the network, focusing the development in the negative feedback loop involved with the action of the drug. I think that this approach could be better for the purpose of the final stage of the project, which essentially consist in the submission of the results to an important journal.

Networks

I went today to the course on networks and this time the class was very interesting, since the subject concerned the dynamics of networks. When being in the class I was thinking about the possibility to find a number to measure the level of design, I think that such a number must only take into account the structure of the network, without the consideration of the underlying process being carried out by the network. I will work in this question these days, just to try to have a proposal of the number as far as possible. Cesar Hidalgo, the instructor of the course gave us an information concerning an online software that can be used to describe information at some different level with an emphasis in network-like structures. The address to find this software is the following one: http://services.alphaworks.ibm.com/manyeyes/home.

Noise and robustness

Tzachi Pilpel sent me some links to have access to his recent papers. I am studying the one concerning noise:

  1. A. Bar-Even, J. Paulsson, N. Maheshri, M. Carmi, E. O'Shea, Y. Pilpel, N. Barkai (2006): Noise in protein expression scales with natural protein abundance. Nature genetics, DOI:10.1038/ng1807. The paper is here: Media:pilpel2006.pdf.

The idea is to discuss about robustness as a by-product of fight against noise. I think that I must read the paper and to propose later a possible experiment -as fast as possible, because I will have not to much time in the nera future-. I need also to speak about this question with Alex in Mexico.


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