User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/10/24

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This very important and priority is here

I will resume my previous activities and I will plan my future activities.

Meeting with Pam

Today I had a very interesting meeting with Pam. The meeting turned around the work with David. From this meeting I concluded the following things:

  1. The modeling approach followed by David at the origin, with the cartoon representing the AKT signaling pathway seems to be the right one -or at least the one that Pam want to be developed-.
  2. I need to be sure that the differential equations written by David correspond with the diagram, i.e. that the differential equations really code the cartoon.
  3. Understand the simplifications that David did in order to have a very reduced network.
  4. In order to have an insight of the modeling process I need to contact some people working in this domain. In particular. Pablo recommended to contact Peter Sorger (maybe he can say me who can help me in this question). His website is the following one: http://sysbio.med.harvard.edu/faculty/sorger/. The e-mail of Peter Sorger is the following one: peter_sorger@hms.harvard.edu.

The David's approach

I am thinking that David is working in his experimental project as if he was doing computer simulations, i.e. he is developing ideas in his mind and then he perform some experiments fixing conditions in the same way we do when working with a computer. This approach seems very appropriate to understand qualitative phenomena in biological research. For him exact protocols are not so important, because what is important is to uncover qualitative phenomena. However, once the qualitative has been uncovered it is necessary to proceed to some very careful experiments in order to calibrate mathematical models and in that way get some predictive tools.

On Networks

I installed the Network WorkBench (http://nwb.slis.indiana.edu/) for networks research in my computer and it seems that this tool is good enough for some of my purposes. I will see.