Alyssa N Gomes Week 13 Journal

• fix Week 12 assignment
  • See DNA Binding file: DNA Binding Excel
  • See PLUS expression file: Plus Expression Excel
  • See DNA Binding AND Expression file: DNA Binding and Expression Excel
  • PPT: Tessa Morris and Alyssa Gomes PPT
• open the "Input_4_gene_forward_correct_params.xlsx" file from the LionShare and use it as a template for your gene's assignment.
• copy the transposed matrix from "network" sheet of your week 12 assignment and paste it into "network" and "network_weights" of the new file
• make sure the alphabetical order is the same for the sheets
• go into the sheet "degradation_rates" and paste the list of Standard Names of your transcription factors. This will be under the Systematic Name given by YEASTRACT
• Use the Belle et al. (2006) paper to retrieve the degradation rates for your transcription factors and put into the sheet
• if a transcription factor does not appear in the file above, use the value "0.027182242" for the degradation rate.
• go into the production_rates sheet and paste the Systematic Name and StandardName columns from your other sheet into this. calculate two times the degradation rates and place into the productionRate column
• place the wild type data into the "wt" worksheet and delete the columns for times 90 and 120 (so we only see the cold shock times)
• rename the cin5 sheet to your strain, in my case, gln3. past the systematic name and standard name columns into the sheet and the gln3 data, deleting the columns for time 90 and 120
• make sure that the genes are in the same order.
• for the parameter time, replace what's in the file with 15, 30 and 60 since thats what were looking at
• for the parameter strain, replace "dcin5" with your strain you're examining, in our case "gln3"
• for the parameter deletion, leave the 0 in B16 and in C16, put the number that your strain is in on the list (gln3 is 7/24)
• for the parameter simtime, put increments of 5 from 0 to 60.
• go to the sheet "network_b" and paste the list of standard names for the transcription factors under "rows genes affected/cols genes controlling"
• put 0 to the right of each factor name.
• upload to lionshare and share with Dahlquist & Fitzpatrick