Paul Magnano: Week 14 Individual Journal

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BIOL398-03/S13:Week 14 Paul Magnano BIOL398-03/S13 User: Paul Magnano

Class Journals

Assignments/Individul Journals

  1. Download sample file data input file change file to my name and input my data from Week 12 Assignment.
  2. Copy matrix and paste into network, network_weights and network_thresholds worksheet.
  3. Go to degradation_rate worksheet and paste list of transcription factors
    • Look up systematicname of genes through YEASTRACT.
  4. Look up degradation rates and 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 X two and put into production rate column.
  6. For log2_concentrations sheet, paste systematicname and standard name.
    • Column headings should be 15, 30 and 60. Put in average log fold change from week 9 spreadsheet.
  7. For concentration_sigmas sheet, cal standard deviation for 15, 30 , and 60 timepoints
  8. Leave optimization_parameters worksheet alone.
  9. For simulation_times worksheet, simulate in five minute increments from 0 to 60 minutes.
  10. Paste in standard names for next worksheet.
  11. Upload to LionShare
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