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Steps for data manipulation

  • The first thing I did was change the file name to one that was specific to me
  • I am using the genes that are in my Regulation Matrix
  • For the 'network' sheets, I copied and pasted in my transposed Regulation Matrix data
  • I put the genes in alphabetical order to make it easier on myself
  • Because I am working with wildtype data, I did not have to delete anything from the file
  • I used the 'degradation rates' excel file to look up the degradation rates for each of my genes
    • I also used this same sheet to find the systematic name for many of my genes
    • YEASTRACT was used for a few genes that were not in the degradation excel file
  • The degradation rates were all multiplied by two and then pasted into the production rates table
  • The data I had from the Week 9 assignment was used to find the average log fold changes for all of the genes
  • I had to create new columns to find the standard deviations in the Week 9 data because they were not included
    • Once the columns were made for standard deviations of times 15, 30, and 60, they were copied into the 'concentration sigmas' sheet
  • I changed the simulation times to go to 60 from 0 at 5 second increments in 'simulation_times'
  • In 'network_b', I put all of the genes in and made the threshold 0.000 for all of them
  • The file was then uploaded to Lionshare


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