User:Alondra Vega/Notebook/Research/2010/06/03

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What I did today

In the Lab

  • We did a growth experiment.
  • We also made liquid YEPD for the cultures that we will grow next week. We made about 600mL of the media.
  • We incubated at 5:35 pm.
  • We made observations for the 30°C and the 15°C plates that were made two days ago. The 15°C plates did not have any single colonies that could be observed, thus we made no observations of those plates.
  • We also made observations for previous frowth experiments and took out the plates that were grown at 15°C on 05/27/2010.

The mathematics of it

  • Dr. Fitzpatrick made a new folder that had the codes and data separated for us. This meant that we could see the original forward simulation codes.
  • The code that we were working with was the 'general_forward_sim_function' program in Matlab.
  • We recreated the Dalhquist data file that would consist of five different worksheets.
  1. parameter_values (this sheet contains the weights and the thresholds(b))
  2. the network (this is a matrix of 1's and 0's of the genes in the network)
  3. degradation_rates
  4. production_rates (These values were obtained by assuming that the system was in equilibrium. This means that we solved the equation P=2*degradation rates.)
  5. measurement_times (We want to see what this network does during these time periods.)
  • Dr. Fitzpatrick wants us to look at how sloppy our parameters are by looking at the equations given in the paper that was done for journal club.