User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/21

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Some comments on the simulation of the AKT signaling pathway
I must also include here that I was reviewing the Cell Designer program, and it was not easy for me to understand the way this program work with the molecular networks. The problem again is not the tool, but the knowledge concerning the important subject, i.e. molecular dynamics. I need to do somthing to burst my understanding in this matter.
 * Well, today I was still working in the simulation of the AKT signaling pathway. I arrived to the conclusion that in order to really undestand what I am doing I need to learn more about genetic regulatory networks (and biochemistry in general). I think that the best thing to do is to study the Uri Alon book, and the material on Molecular Interaction Networks with nonlinear differential equations in the books:
 * Z. Szallasi: System Modeling in Cell Biology - From Concepts to Nuts and Bolts (2006). The MIT Press. Cambridge, MA, USA.
 * S. P. Ellner, J. Guckenheimer: Dynamic Models in Biology (2006). Princeton University Press, Princeton, NJ, USA.

The expositions by Anna and Kelly
Today Anna Chen (undergraduate student from University of California at Davis) and Kelly Brock (undergraduate student from Harvard University), two undergraduates working here during this summer, gave a talk to the Silver lab team about their research projects. I really liked the Kelly presentation, which concerned computer based prediction of a co-culture involving two different bacterial organisms (one of them produce the substrate for the other, which produces then molecular hydrogen, see for instance what is published in the wikipedia about this subject wikipedia). What I liked was the presentation of the project -which extensively uses computer tools involving the application of linear programming to the design of the stoichiometric matrix-. The presentation was clear, precise, and Kelly didn't use unnecessary words. The Kelly's work uses a specialized database on reactions coming from a Japan project called Kegg. As far as the Anne Chen presentation, it was also good and very interesting; it concerned the manipulation of the photosynthesis process in a given organism, as a way to encapsulate CO2, and gives the possibility to produce from it biofuel!


 * It was interesting to see that during the expositions the people can eat snack, and this act does not seem to disturb the expositor.


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