Kevin Matthew McKay Week 14

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(assignment)
Current revision (19:04, 29 April 2013) (view source)
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[[Category:BIOL398-03/S13]]
[[Category:BIOL398-03/S13]]
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[[User:Kevin Matthew McKay|Kevin McKay]]
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*[[User:Kevin Matthew McKay|Kevin McKay]]
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[[BIOL398-03/S13:Week 14|Assignment]]
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*[[BIOL398-03/S13:Week 14|Assignment]]
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*I used my transposed Regulation matrix from my week 12 assignment, copied and pasted it into "network", "network_weights", and "network_thresholds".
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*deleted CIN5
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*made sure there were no empty rows
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*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
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*Edited production rate, pasted in systematic name and standard name, multiplied degradation rates by two for production rates.
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*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)
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*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.
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*Left optimization parameters worksheet alone
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*In simulation times, changed top row to read from 0 to 60 by 5s.
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*Lastly, edited network b, pasted in standard names for my TFs, made sure threshold value was 0 for each gene.
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*shared excel sheets on lionshare

Current revision

  • 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
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