James P. McDonald Week 14
From OpenWetWare
Electronic Laboratory Notebook
- Downloaded the sample data excel file (full_schade_data) and changed the name to McDonald_Week14_ZAP1_data.xls
- Opened excel file from the Week 12 Assignment that included my transposed regulation matrix
- Copied the transposed matrix from the week 12 assignment and pasted it into the three sheets: network, network_weights, and network_thresholds
- Had to get rid of the "p" from the transcription factors in the top row (ex. changed Ace2p to ACE2)
- Deleted the ZAP1 row and column in the three sheets because I am working with the ZAP1 deleted strain
- Pasted the list of the standard names from the network sheet into the degradation_rates sheet
- Used the YEASTRACT feature to look up the systematic names of the transcription factors, then also pasted them into the degradation_rates sheet
- 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
- 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
- Pasted the systematic and standard names from the degradation_rates sheet into the production_rates sheet
- Multiplied each degradation rate by 2 and then pasted them into the production_rates sheet
- Copied and pasted the systematic and standard names into the log2_concentrations sheets, while also placing 15, 30, and 60 in the column headings
- 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
- Calculated the standard deviations for the three times points using the data from the week 9 assignment
- Copied and pasted the standard deviations for each transcription factor in the concentration_sigmas sheet
- Did not make any changes in the optimization_parameters sheet
- Changed the simulation_times sheet by inputting times from 0 to 60 in 5 minute increments
- Pasted the standard the names of the transcription factors into the network_b sheet
- Inputted all threshold values as 0.0000
- Uploaded the excel file to Lionshare and OpenWetWare
Jim's Week 14 Excel ZAP1 Input File
Class Links
- James P. McDonald
- BIOL 398 Home Page
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 11 Assignment
- Week 12 Assignment
- Week 13 Assignment
- Week 14 Assignment
Journal Entries and Assignments
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 8
- Class Journal Week 9
- Class Journal Week 11
- Class Journal Week 12
- Class Journal Week 13
- Class Journal Week 14
- James P. McDonald Week 2
- James P. McDonald Week 3
- James P. McDonald Week 4
- James P. McDonald Week 5
- James P. McDonald Week 6
- James P. McDonald Week 8
- James P. McDonald Week 9
- James P. McDonald Week 11
- James P. McDonald Week 12
- James P. McDonald Week 13
- James P. McDonald Week 14