LauraTerada Individual Journal Assignment Week 14

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Creating model input file

  1. Download sample file data input file from last week, change file to my name and include my data from transposed Regulation Matrix from Week 12 Assignment.
  2. Copy transposed matrix and paste into network, network_weights and network_thresholds worksheet.
    • Change transcription factors so they are the same (no "p").
    • Delete strain in row and column if working with a deletion strain.
  3. Go to degradation_rate worksheet and paste list of transcription factors from network sheet into standardname column.
    • Look up systemicname of genes through YEASTRACT.
  4. Look up degradation rates ( this file ) and include into degradation_rates sheet. If transcription factor does not appear in file, put value "0.027182242."
  5. For production_rate sheet, paste systemicname and standardname from degradation_rate sheet into production_rate sheet.
    • Calculate degradation rate times two and input into productionrate column.
  6. For log2_concentrations sheet, paste systemicname and standardname.
    • Column headings should be 15, 30 and 60. Look up average log fold change from previous spreadsheet and include here.
  7. For concentration_sigmas sheet, use week 9 assignment spreadsheet, go to statistics worksheet, and calculate standard deviation for each of the cold shock timepoints using STDEV function in Excel.
  8. Leave optimization_parameters worksheet alone.
  9. For simulation_times worksheet, simulate in five minute increments from 0 to 60 minutes.
  10. For network_b worksheet, paste in standard names and threshold value for each should should be 0.000.
  11. Upload file to LionShare and email link to Dr. Dahlquist and Dr. Fitzpatrick.