James P. McDonald Week 14

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Electronic Laboratory Notebook

  1. Downloaded the sample data excel file (full_schade_data) and changed the name to McDonald_Week14_ZAP1_data.xls
  2. Opened excel file from the Week 12 Assignment that included my transposed regulation matrix
  3. Copied the transposed matrix from the week 12 assignment and pasted it into the three sheets: network, network_weights, and network_thresholds
  4. Had to get rid of the "p" from the transcription factors in the top row (ex. changed Ace2p to ACE2)
  5. Deleted the ZAP1 row and column in the three sheets because I am working with the ZAP1 deleted strain
  6. Pasted the list of the standard names from the network sheet into the degradation_rates sheet
  7. Used the YEASTRACT feature to look up the systematic names of the transcription factors, then also pasted them into the degradation_rates sheet
  8. Used the file from Belle et al. (2006) to look up the degradation rates of all my transcription factors and pasted them into the sheet
  9. Three transcription factor degradation rates were not available in the file so I placed 0.027182242 in the sheet for those three and highlighted them in yellow
  10. Pasted the systematic and standard names from the degradation_rates sheet into the production_rates sheet
  11. Multiplied each degradation rate by 2 and then pasted them into the production_rates sheet
  12. Copied and pasted the systematic and standard names into the log2_concentrations sheets, while also placing 15, 30, and 60 in the column headings
  13. Used the excel file from the week 9 assignment to look up the average log fold changes of the transcription factors and then pasted them into the log2_concentrations sheet
  14. Calculated the standard deviations for the three times points using the data from the week 9 assignment
  15. Copied and pasted the standard deviations for each transcription factor in the concentration_sigmas sheet
  16. Did not make any changes in the optimization_parameters sheet
  17. Changed the simulation_times sheet by inputting times from 0 to 60 in 5 minute increments
  18. Pasted the standard the names of the transcription factors into the network_b sheet
  19. Inputted all threshold values as 0.0000
  20. Uploaded the excel file to Lionshare and OpenWetWare

Jim's Week 14 Excel ZAP1 Input File

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