User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/08/11

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Perl

  • This morning I participated in a one day course on Perl. The instructor was Amir Karger (his e-mail address is the following one: akarger@cgr.harvard.edu). It was a very interesting course. In computer programming, Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall, a linguist working as a systems administrator for NASA, in 1987, as a general purpose Unix scripting language to make report processing easier. The language is mainly oriented to be used by the bioinformatics community. To be more specific: Perl is very useful to clean information recorded in huge database like the ones obtained in genomics research.
  • In the course Perl was used in the orchestra system at Harvard Medical School (I connected my Mac to the system via a X11 term: ssh -Y jm195@orchestra.med.harvard.edu, and introducing my eCommons password). It is necessary not to forget that after having the orchestra prompt the command bsub -Is -q shared_int_2h bash must be given to the system, in order to obtain Perl from the cluster.

The AKT-rictor-AKT file

Today I continue with the debugging of the Mathematica file containing my code for the simulation for the AKT-rictor-AKT. All the concerned files are compacted in Media:AKT.zip. Concernig this work I have the following doubts:

  • The simulation (if the code is okay) shows not sustained oscillatory behavior (is that right?).
  • It was not easy to compute the fixed points, since Mathematica was nor able to do that (would it be possible to do that in the cluster?).
  • I was applying Phaser also t try to compute the fixed points but it was not easy to do that (I think however that this programa may be useful in this project, in particular because with this software (here the adress: phaser; and here the guide: Media:GettingStarted.pdf) is possible to graph at the same time the behavior of the concerned system when taking into account a lot of initial conditions). If a oscillatory behavior for the AKT-rictor-AKT system is firmly established and a mathematical model is constructed (using ordinary differential equations), Phaser may be useful to characterize the parameter ranges, which is to say the vicinities of the unstable points associated to the possible limit cycles (and the corresponding robustness of the limit cycles will be then argued). Also associated to this subject I must not forget to obtain some informatuon concerning the characterization of the nonlinearity detected by David Miguez, i.e. the reinforced hysteresis.
  • I must not forget to complete the LaTeX file with the definition of all the genes and proteins involved in the AKT-rictor-AKT.
  • I was thinking at the end of the day that my LaTeX file must be more organized in order to make it more readable (in particular the equation concerning the system must be accompanied in the same page by the text indicating the meaning of all the state variables; for example x1 is [rictor] and so on).

Very important

Do not forget to study the relationships between robustness and adhesive protein relationships (optimality of recruitement and shape optimization).



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