User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/12/26

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Organizing ideas
I just want to write in what follows some things that I think must be made my priorities for the next days. Well, my research interest are focused in the following subjects:

Robustness
Here I know now that the approach concerning robustness measures based on monotone system has not future -at least it is what Eduardo Sontag explain to me-. I should compulsory read the paper written by Eduardo Sontag concerning robustness measures and I must continue my discussions with Tzachi (in thsi case concerning robustness as a non conserved quantity). the philogenetic approach that we discussed the last time that we had a scientific discussion must be clarified. I need to know what happen at the end of the previous discussion, when I must left tp continue with my experimental facilities. On this subject I must match my collaboration with Alex de Luna. For the future work I need to ask pam about the idea by Sontag on the small gain theorem and the regulation of oscillatory behaviors linked to this. maybe here is where Galit could be interested. I need to contact her.

Network Theory
Considering the social niches, I must finish with the papers by Jessica Flack and I must not forget to connect all this stuff with the idea of power in science and product space in economy (I must then contact Ricardo Houssmann at JFK school of government). Social networks must offer me some insight in the role that learning play in the evolution fo the social niches and at what level -when no design is involved-.

Evolution and learning
Here I need to tackle the simulation of the Burtzev model and also develop a biologically plausible example for the Jablonka model on learning based on epigenetic cell memory. I must explore the modification of the genetic algorithm code in NetLogo, to see if it is realistic to do it. I must also not forget to send the paper of jablonka to Juan Pedraza, who works here in experimental evolution. Here seems plausible to do something in the future working with people at Silver Lab, developing memory learners -something like to add not only sensor devices, but "smart sensor devices"- using the epigenetic system existing in the cell. Fro this purpose is necessary to study the epigenetic machinary, analizing the behavior of the cell under stress and DNA damage and to re-engineering existing mechanisms. Maybe Panmela could be interested if I connect all this stuff with energy concerns. I do not know if it is possible to conceive a smart sensor. What a smart sensor is? I need to look for synthetic biology papers on this question. This is something urgent to do.

Conditioned interaction in rules-based modeling
I must consider this topic and ask Walter Fontana about it. I must focus my effort with him in future collaboration.

Biological modeling
The mathematical modeling of biological system linked to oncogenic signaling pathways must be considered the musty obvious and strategic topic to be tackled. I must red carefully the paper that Sabrina send to me and then discuss this topic with her. I must try to work with people from the Sorger lab to give continuity to this subject. I need also to include here all this question concerning individual cellular responses, using micro-fluidic technology. This is important, since I can link all this stuff with nonlinear dynamics. I think that I can continue this kind of research in Mexico.

Protein stuff
I do not know if it convenient continuing working with Pablo Ceroni in the training associated to proetin engineering. I think that I must do it, because it is an opportunity that will be not repeated again.

Strategy
To avoid my mind to be concerned by not important things, I need to establish priorities and concrete goals. I will start tomorrow by doing this. I will take the calendar and I will organize my activities in a perfect way, and I will respect my engagement.


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