LauraTerada Individual Journal Assignment Week 14
Creating model input file
- 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.
- 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.
- Go to degradation_rate worksheet and paste list of transcription factors from network sheet into standardname column.
- Look up systemicname of genes through YEASTRACT.
- Look up degradation rates ( this file ) and include into degradation_rates sheet. If transcription factor does not appear in file, put value "0.027182242."
- 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.
- 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.
- 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.
- Leave optimization_parameters worksheet alone.
- For simulation_times worksheet, simulate in five minute increments from 0 to 60 minutes.
- For network_b worksheet, paste in standard names and threshold value for each should should be 0.000.
- Upload file to LionShare and email link to Dr. Dahlquist and Dr. Fitzpatrick.