User:Alondra Vega/Notebook/Research/2010/06/01

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What was done today

In the Lab

  • We prepared overnights for growth experiments and to prepare some glycerols.
  • We also prepared cultures for 9 strains to streak at 15°C and 30°C.
  • Dr. Dahlquist did the re-streaking for these cultures
  • We also saw Dr. Dahlquist perform the protocol to purify RNA.
  • Finally, we took pictures and made observations of previous growth experiments at 5 o'clock.

The Mathematics of it

  • We went to the computer lab and started to work on the test_data_file.xls. This file contains a simple network of four genes along with their designated parameter values, degradation rates, production rates and measurement times. We worked on the GOOD_matlab_folder with the codes that Dr, Fitzpatrick had already written. We used the general_forward_sim_driver_test.m in matlab.
  • Parameter values consists of weights and thresholds. The weights show how wide the transition is and the threshold shows where the turning point is.
  • Dr. Fitzpatrick helped us observe the changes that would occur when the network or paramae4ters were changed. The highest number of parameter values that we had was 32 and that was when all genes were affecting each other. The smallest value of parameter values that we tried was when we had 8 parameter values. That was a cyclic cycle. (gene2 affects gene1, gene 3 affects gene2, etc.)
Note: The oscillations that were observed in some of the graphs may be caused by the default setting of the software, Matlab.