User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/25

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Little b

  • Today I assisted to the Countway library to the course on Little b, which is part of the Summer Course on Systems Biology. It was very interesting. Little b is a frontend written in Lisp for Matlab, when the purpose is to write differential equations describing the dynamical behavior of biochemical networks. By the moment I am not convinced about the utility of this tool, when comparing with more international efforts like the one corresponding to Cell Designer. Little b is something like a object-oriented modeling language specialized in biochemical networks, and I think that Modelica would give better results for the purposes followed by the team of Aneil Mallavarapu, which turn around the application of computer tools to model biological systems at all levels of organization. Well, the best thing to do is to study the system and the have a more informed opinion.

Meeting with Pamela

Today I have a meeting with Pamela Silver, the boss, and the idea is to report her what I have been doing the last weeks. Essentially speaking I will explain her that I was doing the next things:

  • I am collaborating with David Miguez, developing a computer simulation for his AKT related signaling pathway, in order to have a tool to explain the bistable behavior that he is observeing experimentally. By the moment the computer simulator -existing in two versions, Mathematica and Simulink-, reproduce the behavior detected in the Euler approximation that he conceived with Matlab. The idea is now to find a toy model to describe the hysteretical behavior of the AKT signaling pathway when using the anticancer drug.
  • I am studying Robustness, and I am now focalized in the study of mutational robustness, following the book by Andreas Wagner as a reference. I am trying to understand the role of role of robustness in evolution. I contacted Yitzhak Pilpel, to discuss about the way he applies bioinformatics to understand the architecture of the regulatory networks and the role of redundancy. Moreover, i have an appointment with Walter Fontana next week in order to speak about the current research on robustness, and in particular to understand the reason behind the application of formal language tools to model biological systems.
  • I need to develop more laboratory abilities and because of that I want to be involved in a research project, like the one involving Anna Chen or Kelly.

The real meeting with Pamela

Well, as a consequence of the meeting with Pamela, I will be engaged in some experimental research working with David Miguez in the AKT signaling pathway. The idea is to analyze the dynamical behavior of a specific branch of the pathway. The purpose is to allow me learn more about biology and to be more involved in experimental activities. Pam think that the best thing to do is tackle the PDK1 protein and its role the signaling pathway. I need them to contact David and then to make something like a plan to present it to Pam. At the same she proposed me to ask David to make me to do some experiments to understand more about kinetics of regulatory networks. I profited to expose to Pamela my ideas about the conception of a monography exposing the different ways that the people follow to model the behavior of regulatory biochemical networks. She asked me to give an exposition to the people at the end of my stay here, which I think is a very good idea. I also speak with her about the idea of using results coming from the world of earthquake engineering to model the hysteretical phenomenon that David detected in his experimental activities. I must then to aske for dome help by Ruben Garrido and other people.