James P. McDonald Week 14: Difference between revisions
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#Uploaded the excel file to Lionshare and OpenWetWare | #Uploaded the excel file to Lionshare and OpenWetWare | ||
[[Media:McDonald_Week14_ZAP1_data.xls|Jim's Week 14 Excel | ===Completed Input File=== | ||
[[Media:McDonald_Week14_ZAP1_data.xls|Jim's Week 14 ZAP1 Excel Input File]] | |||
===Graphs from Running Input File=== | |||
[[Media:Jimzap1graphs.pptx|Powerpoint with Graphs from running the Input File]] | |||
{{James P. McDonald}} | {{James P. McDonald}} | ||
[[Category:BIOL398-03/S13]] | [[Category:BIOL398-03/S13]] |
Revision as of 10:32, 25 April 2013
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
Completed Input File
Jim's Week 14 ZAP1 Excel Input File
Graphs from Running Input File
Powerpoint with Graphs from running the 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