Kevin Matthew McKay Week 14: Difference between revisions
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*[[User:Kevin Matthew McKay|Kevin McKay]] | *[[User:Kevin Matthew McKay|Kevin McKay]] | ||
*[[BIOL398-03/S13:Week 14|Assignment]] | *[[BIOL398-03/S13:Week 14|Assignment]] | ||
*I used my transposed Regulation matrix from my week 12 assignment, copied and pasted it into "network", "network_weights", and "network_thresholds". | |||
*deleted CIN5 | |||
*made sure there were no empty rows | |||
*Next I edited degradation rates, pasted in T factors into Standard Name, and looked up systematic names and degradation rates on YEASTRACT and using the data from the Belle et al Paper, for T factors not included, used 0.027182242 | |||
*Edited production rate, pasted in systematic name and standard name, multiplied degradation rates by two for production rates. | |||
*Edited log2 concentrations, pasted names, used Average log fold change from week 9 assignment for my TFs for cold shock time points (15, 30, 60) | |||
*Concentration Sigmas: Went to statistics worksheet from week 9 assignment, calculated SD for each coldshock time point using STDEV in excel. Copied and pasted values into worksheet. | |||
*Left optimization parameters worksheet alone | |||
*In simulation times, changed top row to read from 0 to 60 by 5s. | |||
*Lastly, edited network b, pasted in standard names for my TFs, made sure threshold value was 0 for each gene. | |||
*shared excel sheets on lionshare | |||
Latest revision as of 17:04, 29 April 2013
- Kevin McKay
- Assignment
- I used my transposed Regulation matrix from my week 12 assignment, copied and pasted it into "network", "network_weights", and "network_thresholds".
- deleted CIN5
- made sure there were no empty rows
- Next I edited degradation rates, pasted in T factors into Standard Name, and looked up systematic names and degradation rates on YEASTRACT and using the data from the Belle et al Paper, for T factors not included, used 0.027182242
- Edited production rate, pasted in systematic name and standard name, multiplied degradation rates by two for production rates.
- Edited log2 concentrations, pasted names, used Average log fold change from week 9 assignment for my TFs for cold shock time points (15, 30, 60)
- Concentration Sigmas: Went to statistics worksheet from week 9 assignment, calculated SD for each coldshock time point using STDEV in excel. Copied and pasted values into worksheet.
- Left optimization parameters worksheet alone
- In simulation times, changed top row to read from 0 to 60 by 5s.
- Lastly, edited network b, pasted in standard names for my TFs, made sure threshold value was 0 for each gene.
- shared excel sheets on lionshare
