Elizabeth Polidan Week14

Elizabeth Polidan

BIOL 398.03 / MATH 388

• Loyola Marymount University

• Los Angeles, CA, USA

• Email me through OpenWetWare

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Week 14 Assignment

Laboratory Notebook

1. Copied sample data file, full_schade_data.xls, to Model_Input_Polidan.xls.
2. Copied the transposed regulation matrix generated in YEASTRACT with the following changes:
   • Modified names across the top row to use same format as is used in the columns (e.g. CIN5, not Cin5p).
   • Alphabetized transcription factor names.
3. Placed modified transposed regulation matrix into three worksheets in Model_Input_Polidan.xls:
   • network
   • network_weights
   • network_thresholds
4. Created two columns of transcription factor names using list from matrix in step 2.
   • Obtained systematic names from YEASTRACT.
5. Edited the worksheet called "degradation_rates".
   • Pasted the two columns from step 4.
   • Looked up the degradation rates in a paper by Belle et al. (2006) and added them to worksheet. Used the value "0.027182242" if the degradation rate was unavailable for a transcription factor.
6. Edited worksheet called "production_rates".
   • Pasted the two columns from step 4.
   • Created equations that multiplied referenced production rates by 2.
7. Edited worksheet called "log2_concentrations".
   • Pasted the two columns from step 4.
   • Copied the values for Average Log Fold Change for times 15, 30, and 60 minutes from the file, Polidan_wildtype_data_20130402_full.xls, from Assignment 9.
8. Edited worksheet called "concentration_sigmas".
   • Pasted the two columns from step 4.
   • Calculated standard deviation of Log Fold Change for times 15, 30, and 60 minutes from the file, Polidan_wildtype_data_20130402_full.xls, from Assignment 9. Used same columns that were used in calculating the mean Log Fold Change.
   • Pasted the values into the concentration_sigmas worksheet.
9. Left the "optimization_parameters" worksheet unchanged.
10. Edited worksheet called "simulation_times". Changed times to 0, 5, 10, 15, … 60.
11. Edited worksheet called "network_b".
    • Pasted the first column from step 4 – this sheet does not have the systematic names.
    • Ensured the "threshold" value for each gene is "0.000".
12. Upload file to LionShare and sent and email to Drs. Dahlquist and Fitzpatrick with a link to the file.