Kristen M. Horstmann Week 14 Journal

Electronic Notebook

Assignment for 4/21/15

• Instructed in class to attempt to run GRNmodel matlab code and insert network when told, then upload any and all figures as jpg to openwetware.
• I was able to run my network and it produced 20 figures. However, it then terminated itself with the errors in the following picture (I apologize for it being upside down, no matter what I tried, I was unable to get this image flipped around... sorry!):
• Unsure if the code ran to completion as these are errors I have never seen before, and it did not run to the point we got to in class with the two figures with changing plots. Dr. Fitzpatrick said those might take a while to run through, but my program never got to that point, likely due to the errors discussed above.

Pictures of resulting graphs

• Changed long list of figures to zip file
• Media: HorstmannWeek14_Run1.zip

Notes and Errors

• After comparing Kara's and my MATLAB figures, we realized we had different numbers of data points for time point 30. We went onto our dzap1 and wt networks on the Excel and realized I had mislabeled the 1st time point 60 as a 5th data point for 30 in dzap1 and had added too many time points for 30 in wt as well. This is why our figures looked slightly different.
• This error was corrected and the corrected figures are in the following zip file
  • ZIP FILE

Assignment for 4/23/15

1. In the optimization_parameters sheet of the old input workbook [[Media:]], we set fix_b to 1, fix_P to 0, iestimate to 1, and alpha to 0.01
2. Ran GRNmodel through MATLAB and uploaded input workbook when prompted
3. Saved all graphs as jpegs
4. Created new worksheet in estimation output xlsx workbook: called estimated_weights
   • Created column of labels of the form ControllerGeneA -> TargetGeneB, replacing these generic names with the standard gene names for each regulatory pair in your network. CHANGE THAT PART
5. Extracted non-zero optimized weights from worksheet and put them in a single column next to the corresponding ControllerGeneA -> TargetGeneB CHANGE label.
6. Saved input workbook as a new file with a meaningful name as we changed fix_b to 0. Reran GRNmodel with this new input sheet.
7. Repeated above with new output
   • Media:KristenHorstmann_week14_ppt_countergraphs_fixb0.ppt
8. Created an empty excel workbook, and copied both sets of weights into worksheet
9. Created bar chart to compare the "fixed b" and "estimated b" weights
10. Repeated with the production rates
11. Copied the two bar charts into powerpoint
12. Used GRNsight to visualize the output of each run. Arrange the genes in the same order you used to display them in your Week 12 assignment for both of your model output runs. Take a screenshot of each of the results and paste it into your PowerPoint presentation. Clearly label which screenshot belongs to which run. CHANGE also might go back into week 12 and change to make alphabetical grid?

Results

• Media:Input_4_gene_forward_correct_params_KMH_take2.xlsx
• Media:Input_4_gene_forward_correct_params_KMH_take2_estimation_outputs.xlsx
• PowerPoint with all Requested Results and Figures
• Second Input from Step 5 and on

Template

Back to User: User: Kristen M. Horstmann

• BIOL398-04/S15

1. Week 1
   • BIOL398-04/S15:Week 1
   • BIOL398-04/S15:Class Journal Week 1
2. Week 2
   • BIOL398-04/S15:Week 2
   • Kristen M. Horstmann Week 2 Journal
   • BIOL398-04/S15:Class Journal Week 2
3. Week 3
   • BIOL398-04/S15:Week 3
   • Kristen M. Horstmann Week 3 Journal
   • BIOL398-04/S15:Class Journal Week 3
4. Week 4
   • BIOL398-04/S15:Week 4
   • Kristen M. Horstmann Week 4 Journal
   • BIOL398-04/S15:Class Journal Week 4
5. Week 5
   • BIOL398-04/S15:Week 5
   • Kristen M. Horstmann Week 5 Journal
   • BIOL398-04/S15:Class Journal Week 5
6. Week 6
   • BIOL398-04/S15:Week 6
   • Kristen M. Horstmann Week 6 Journal
   • BIOL398-04/S15:Class Journal Week 6
7. Week 7
   • BIOL398-04/S15:Week 7
   • Kristen M. Horstmann Week 7 Journal
   • BIOL398-04/S15:Class Journal Week 7
8. Week 8
   • BIOL398-04/S15:Week 8
   • Kristen M. Horstmann Week 8 Journal
   • BIOL398-04/S15:Class Journal Week 8
9. Week 9
   • BIOL398-04/S15:Week 9
   • Kristen M. Horstmann Week 9 Journal
   • BIOL398-04/S15:Class Journal Week 9
10. Week 10
    • BIOL398-04/S15:Week 10
    • Kristen M. Horstmann Week 10 Journal
    • BIOL398-04/S15:Class Journal Week 10
11. Week 11
    • BIOL398-04/S15:Week 11
    • Kristen M. Horstmann Week 11 Journal
    • BIOL398-04/S15:Class Journal Week 11
12. Week 12
    • BIOL398-04/S15:Week 12
    • Kristen M. Horstmann Week 12 Journal
    • BIOL398-04/S15:Class Journal Week 12
13. Week 13
    • BIOL398-04/S15:Week 13
    • Kristen M. Horstmann Week 13 Journal
    • BIOL398-04/S15:Class Journal Week 13
14. Week 14
    • BIOL398-04/S15:Week 14
    • Kristen M. Horstmann Week 14 Journal
    • BIOL398-04/S15:Class Journal Week 14
15. Week 15
    • BIOL398-04/S15:Week 15
    • Kristen M. Horstmann Week 15 Journal
    • BIOL398-04/S15:Class Journal Week 15