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

Electronic notebook of changes made

  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