Brandon J. Klein Electronic Lab Notebook

Spring 2016

Week 1: January 15-22

Research Meeting Notes

• Early Milestones
  1. Branch Clean-Up
  2. Organize Test Files
  3. Adjust Automated L-Curve Analysis Code
  4. Address Bugs in the Code
• Assignments
  1. Set-Up OpenWetware User Page and Electronic Lab Notebook
  2. Alphabetize Genes in the Test Files
     • On the network sheets, use the following method: alphabetize column, transpose data, alphabetize new column, transpose back.
  3. Ensure that All Expression Data is Complete in the Test Files
     • Include Bell Data on expression and degradation rates.
  4. Address Missing Values in the Test Files
     • Highlight these cells in yellow and paste in averages.

Note: For assignments 3-4 I am to shadow Tessa and Kristen.

Progress

• Assignment 1: Set-Up OpenWetware User Page and Electronic Lab Notebook
  • I updated my User Page and created my Electronic Lab Notebook:
    • Brandon J. Klein OpenWetware Page
    • Brandon J. Klein Electronic Lab Notebook
• Assignments 2-4: Shadow Tessa & Kristen as they Update the Test Files
  • I met with Tessa & Kristen on Wednesday, January 20th.
    • I watched and asked questions as they made the following edits to the test files: gene names were alphabetized, expression data was completed, and missing values were addressed using the designated fix.
    • I contributed as well by introducing an Excel method that finds & highlights missing values using Conditional Formatting.
  • Method for highlighting missing values using Conditional Formatting (adapted from this forum):
    1. Select the data you would like to edit
    2. Go to Home > Conditional Formatting > New rule
    3. Click on “Format only cells that contain”
    4. Change “Cell Value” option to “Blanks”
    5. Set up formatting you want by clicking on Formatting button
       • In this case we introduce a yellow fill.
    6. Click ok.

Week 2: January 22-29

Research Meeting Notes

• Coding Updates
  • In approx. 2 weeks, the data analysis team will use the Master branch on GitHub to access GRNmap code
  • Current input-sheet format will be the same as presently used for the Beta branch
  • Goal: be able to run models by next Friday

• Assignments
  • Download the Beta branch and try to run a newly formatted input-sheet (has to be on a PC)
    • This can be used to identify errors (if any) are present prior to the upcoming update to the code
    • Process:
      1. Go to code in GitHub
      2. Go to the Beta branch
      3. Extract the code as a .zip file
      4. Open code in MatLab
      5. Open Input Sheet in MatLab
  • Read ecological modelling standards paper
  • Go to modelling standards web page and contribute based on your reading of the paper
  • Do research to gain a better understanding of how GRNmap works
  • Update work that was done on GitHub

Progress

• A newly formatted input-sheet was successfully run using the code from the Beta branch
• Read the TRACE paper on documenting model formation
• Reviewed information from several sources to further understand the project:
  1. http://www.ncbi.nlm.nih.gov/pubmed/26420504
  2. How to Format the Input File for GRNmap (beta)
  3. How to Interpret the Output File for GRNmap

Week 3: January 29-February 5

Research Meeting Notes

• Assignments
  • Help Kristen catch up with formatting her input sheets
  • Add new formatting changes
    • See GitHub to reference 3 necessary changes to input sheets
  • Generate L-curve Analyses
    • 4 Total
      1. Largest network + deletion strain
      2. Largest network - deletion strain
      3. Smallest network + deletion strain
      4. Smallest network - deletion strain
    • Graphs will have to be plotted manually in Excel
      • LSE vs. penalty with each point's alpha value labelled
    • To bypass a temporary bug, make_graphs may have to be turned off
      • Once this function has been fixed, we will be able to do mass data generation.
      • Use Beta branch for once more week.

Progress

• Meeting with Tessa on February 1, 2016.
  1. The 4 designated input sheets for L-curve analysis were properly formatted using the updated guidelines. Instances in which errors were triggered in GRNmap were resolved by searching for and correcting formatting errors in the input sheets.
  2. All 4 L-curve analyses were started and left running on the machines in Seaver 120 (with notes not to disturb these processes).
  3. Tessa and I went over the format of GRNmap research and the overall systems biology workflow of the Dahlquist Lab.
• Meeting with Tessa and Kristen on February 3, 2016.
  • 4/10 L-curve analyses were complete
  • I created a command sequence in R that can be used to output labelled graphs of the L-curves.
    • A tutorial and samples can be found here: Graphing L-Curves in R

Week 4: February 5-February 12

Research Meeting Notes

• Goal: Complete L-curve analyses to enable selection of alpha values
  • Several runs remain incomplete, but they have completed enough iterations to produce usable data
  • Data from all runs will be compiled and formatted for R
  • The above data will be used to generate a complete set of L-curves for the 4 runs from all tested families of networks

Progress

• Graphing L-curves
  • I helped members of the research team format their data for R and showed those with knowledge of R how to execute the command sequence to generate their L-curves
  • I personally graphed many of the L-curves
• I compiled a Powerpoint presentation of all L-curves generated this week: Media:LcurveAnalyses 20160205.pptx
  • This presentation was sent to Dr. Dahlquist for review.

Week 5: February 12-February 19

Research Meeting Notes

• Goals
  • Begin the Dahlquist:Microarray Data Analysis Workflow (focus: dCIN5 and WT)
    • Check normalization against Tessa's normalization data
    • Set up a meeting with Maggie to go through this workflow in parallel
    • Account for missing values during ANOVA testing if time permits
  • Create a script for generating parameter plots in R (for different alpha values) if time permits

• Progress
  • Began the Microarray Data Analysis Workflow

Important Links

• Brandon J. Klein OpenWetware Page
• Dahlquist Lab OpenWetware site