User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/26

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More on Little b

I assisted today to the second part of the course on little b and my opinions are the following ones:

  1. Little b has been conceived as a modeling tool for systems biology purposes. This specialized object-oriented language seems to be good, however I think it is still not mature to really be the 'right choice' for biologist. The little b envioronment is not as friendly as the environment of modeling languages like the ones developed for Modelica. It must be pointed out that litle b has not the the possibility to include delay differential equations in the modeling process -if necessary the resulting matlab program can be modified-.
  2. Even if the system is not completely functional, it is a nice tool to automatize the production of matlab code for the simulation of biochemical systems. This is a real advantage, in particular for people who does not want to write their simulation code in matlab.
  3. It is true that little b is open source, but in order to use it is necessary to have a matlab licence, and this is a bad thing.
  4. I think that little b must has its own ODE and its graphic environment to avoid the dependence on matlab. An interface with Scilab would be appreciated.
  5. What really interested me was Lisp (this a online Media:onlisp.pdf) as a tool for biology issues. I must then obtain more information on Lisp and to install a Mac OS x version in my computer (this is a list of Lisp free implementations, including Mac OS X : listaLisp).

On modeling of biology systems

I must study the open version of Modelica (openmodelica) as tools for systems biology purposes.

Some ideas about possible MSc and PhD thesis on systems Biology Modeling

These are some ideas concerning training of students:

  1. A MSc comparing little b with openmodelica would be interesting at Cinvestav (little be would be the right choice in order to maintain collaboration with the Harvard group).
  2. A possible PhD thesis applying little b: modeling calcium channels (to support what Refugio is doing).

The project at HMS

I can include little b in my own research project. So, I can develop computer modeling code and also simulation code with the following tools:

  1. Mathematica.
  2. Matlab+Simulink.
  3. Little b (I can profit to learn Lisp and biochemistry at the same time).
  4. OpenModelica.
  5. Cell Designer.

( that is the right thing to do!!).

The Experimental Project

I discussed with David MIguez about the experimental activities. He proposed to tackle the role of the mTOR protein. The idea is furst to find information concerning the activity of mTOR and rictor in the AKT sugnaling pathway. The idea is to try to detect the changes in the equilibrium between mTOR and rictor. The proposed methodology is the following one:

  1. To make a bibliography study, just to know if someone had studied the mTOR activity with fluorescence techniques.
  2. If such previous work existed made a little report.
  3. If the study does not exist to proposed an experimental protocol.