Sahil Patel Week 6

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Electronic Lab Notebook

Purpose

  • The purpose of this assignment is to further analyze our gene profile and create models using GRNsight and MATLAB.

Methods

Creating the GRNmap Input Workbook

production_rates sheet

  1. The sample workbook and Microsoft Access Database were provided by Dr. Dahlquist and Dr. Fitzpatrick and opened.
  2. The first sheet labeled "production_rates" contains initial guesses for the production rate parameters, P, for all genes in the network.
  3. The sheet should contain two columns titled, "id" and "production_rate".
  4. Using the database, the production rates for the genes were found and entered.

degradation_rates sheet

  1. In the Access Database, the degradation rates sheet was selected and the data for the genes required was entered into the Excel spreadsheet labeled "degradation_rates".
  2. Same protocol used as in the production rates sheet.

Expression Data Sheets for Individual Yeast Strains

  1. Each strain was given a unique name using the suffix "log2_expression" as in "wt_log2_expression"
  2. The time points considered were 15, 30, and 60 however replicates of the timepoints were also recorded.
  3. Using the expression data in the database, the information was transferred to the Excel spreadsheets for each gene of each strain at each timepoint for each replicate.

network sheet

  1. The Regulatory Matrix derived in Week 5 was copied and pasted onto this sheet.

network_weights sheet

  1. The network sheet was copied and pasted onto this sheet.

optimization_parameters sheet

  1. This sheet was copied and pasted from the sample workbook and was left untouched.

threshold_b sheet

  1. This sheet included two columns, one titled id which included the same list of genes in the same order as throughout the workbook.
  2. The second column was headed "threshold_b" and was filled with the value 0.

Dynamical Systems Modeling of your Gene Regulatory Network

  1. MATLAB was used to open the GRNmap v1.10 code and our input workbook was then analyzed.
  2. The program was run and an optimization diagnostics graphic that shows the progress of the estimation appeared.
  3. Output files were saved in the folder containing the same file destination and uploaded to BOX.

Results

  • To view the Excel workbook that was inputted into the MATLAB program, click here.
  • To view the Excel workbook after it was outputted from MATLAB, click here.
  • To view the optimization diagnostic and individual expression plots, click here.

Conclusion

  • The main goal of this assignment was to create the Input Excel Workbook using the Microsoft Access Database so that it would be ready to run in MATLAB and eventually create our visual representation using GRNsight.

Acknowledgments

  • My homework partner, Angela Abarquez, and I communicated in class and via text for clarifications regarding the assignment. She also helped me get into the Seaver Computer Lab because my LMU One Card was not encoded to open it.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Sahil Patel (talk) 06:10, 19 March 2019 (PDT)

References

  • The Sample Workbook was provided by Dr. Dahlquist and Dr. Fitzpatrick and was used to format the Input Excel Workbook.
  • The Microsoft Access Database was also provided by our instructors.
  • The Week 6 Assignment was used to formulate the methods section as well as complete the assignment.

Other Assignments

Week 1: Instructions, Class Journal and User Page

Week 2: Instructions, Class Journal and Individual Assignment

Week 3: Instructions, Class Journal and Individual Assignment

Week 4/5: Instructions, Class Journal and Individual Assignment

Week 6: Instructions, Class Journal and Individual Assignment

Week 7: Instructions, Class Journal and Individual Assignment

Week 9: Instructions, Class Journal and Individual Assignment

Week 10: Instructions, Class Journal and Individual Assignment

Week 11: Instructions, Class Journal and Individual Assignment

Week 12: Instructions, Class Journal and Individual Assignment

Week 14/15: Instructions and Individual Assignment