User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/06

The Notebook of JCMG

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Summer Course on Systems Biology Today I assisted to the third session of the Summer Course on Systems Biology at Harvard Medical School. The instructor of the session was Jennifer Waters, Phd. I only assited to the lecture part of the session, which concerned essentially the description of the confocal microscopy technique. I must request later to Nikon Image Center at HMS for training in some microscopy matters. During the course I was thinking in the possibility to develop a chaotic motion system to improve the quality of light obtention of the spinning disk confocal technique. In fact I must focus my training in the way this system work (as far as the laser scanning of the pinhole array concerns). Matlab and Mathematica Installation Today I installed Matlab and Mathematica in my laptop. It was an easy procedure, because I followed the instruction given in the installation procedure at Information Technology Department at HMS. I must review some of the available toolboxes, in particular I must see what is possible to do with the Bioinformatics, the Genetic Algorithms, and the Virtual Reality toolboxes. I must also see what concerns the parallelization of matlab algorithms. David Miguez's files David Miguez gave me some files in order to analyze the behavior of the mathematical model that he is developing to describe the observed dynamics of the AKT system. The diagram of the network concerning the ATK drug: The file with the matlab code of the mathematical model which describes the ATK system: Media:bistability_9.m The zip file which contains all the files concerned by the ATK network (I must not forget to update this file when necessary!): Media:ATK.zip. I also recovered the PDF file of a paper by Madalena Chaves, which concerns some connections between input-state-stable systems and bistability in biochemical pathways. The file is here: Media:chaves-et-al-IEEE-TAC_preprint-1.pdf.