Brandon J. Klein Electronic Lab Notebook: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(added progress from week 5 and notes for week 6) |
(created heading for Fall 2016) |
||
Line 1: | Line 1: | ||
==Fall 2016== | |||
===Week 1: August 29--September 5=== | |||
===Week 2: September 5--September 12=== | |||
===Week 3: September 12--September 19=== | |||
===Week 4: September 19--September 26=== | |||
==Spring 2016== | ==Spring 2016== | ||
===Week 1: January 15-22=== | ===Week 1: January 15--22=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
*Early Milestones | *Early Milestones | ||
Line 35: | Line 46: | ||
**#Click ok. | **#Click ok. | ||
===Week 2: January 22-29=== | ===Week 2: January 22--29=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
*Coding Updates | *Coding Updates | ||
Line 64: | Line 75: | ||
*#[https://github.com/kdahlquist/GRNmap/wiki/How-to-format-the-input-file-for-GRNmap-(beta)#production_rates_sheet How to Interpret the Output File for GRNmap] | *#[https://github.com/kdahlquist/GRNmap/wiki/How-to-format-the-input-file-for-GRNmap-(beta)#production_rates_sheet How to Interpret the Output File for GRNmap] | ||
===Week 3: January 29-February 5=== | ===Week 3: January 29--February 5=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
*Assignments | *Assignments | ||
Line 92: | Line 103: | ||
***A tutorial and samples can be found here: [[Graphing L-Curves in R]] | ***A tutorial and samples can be found here: [[Graphing L-Curves in R]] | ||
===Week 4: February 5-February 12=== | ===Week 4: February 5--February 12=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
*Goal: Complete L-curve analyses to enable selection of alpha values | *Goal: Complete L-curve analyses to enable selection of alpha values | ||
Line 106: | Line 117: | ||
**This presentation was sent to [[User:Kam D. Dahlquist | Dr. Dahlquist]] for review. | **This presentation was sent to [[User:Kam D. Dahlquist | Dr. Dahlquist]] for review. | ||
===Week 5: February 12-February 19=== | ===Week 5: February 12--February 19=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
*Goals | *Goals | ||
Line 128: | Line 139: | ||
**An updated description can be found here: [[Graphing L-Curves in R]] | **An updated description can be found here: [[Graphing L-Curves in R]] | ||
===Week 6: February 19-February 26=== | ===Week 6: February 19--February 26=== | ||
'''Research Meeting Notes''' | '''Research Meeting Notes''' | ||
Next Meeting: Friday February 26 (2:30-3:30) | Next Meeting: Friday February 26 (2:30-3:30) | ||
Line 141: | Line 152: | ||
*Wrote a script to convert adjacency matrices to edge lists using the package ''igraph'' | *Wrote a script to convert adjacency matrices to edge lists using the package ''igraph'' | ||
**[[Converting Adjacency Matrices to Edge Lists in R]] | **[[Converting Adjacency Matrices to Edge Lists in R]] | ||
Revision as of 18:15, 21 September 2016
Fall 2016
Week 1: August 29--September 5
Week 2: September 5--September 12
Week 3: September 12--September 19
Week 4: September 19--September 26
Spring 2016
Week 1: January 15--22
Research Meeting Notes
- Early Milestones
- Branch Clean-Up
- Organize Test Files
- Adjust Automated L-Curve Analysis Code
- Address Bugs in the Code
- Assignments
- Set-Up OpenWetware User Page and Electronic Lab Notebook
- Alphabetize Genes in the Test Files
- On the network sheets, use the following method: alphabetize column, transpose data, alphabetize new column, transpose back.
- Ensure that All Expression Data is Complete in the Test Files
- Include Bell Data on expression and degradation rates.
- 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:
- 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):
- Select the data you would like to edit
- Go to Home > Conditional Formatting > New rule
- Click on “Format only cells that contain”
- Change “Cell Value” option to “Blanks”
- Set up formatting you want by clicking on Formatting button
- In this case we introduce a yellow fill.
- Click ok.
- I met with Tessa & Kristen on Wednesday, January 20th.
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:
- Go to code in GitHub
- Go to the Beta branch
- Extract the code as a .zip file
- Open code in MatLab
- 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
- Download the Beta branch and try to run a newly formatted input-sheet (has to be on a PC)
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:
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
- Largest network + deletion strain
- Largest network - deletion strain
- Smallest network + deletion strain
- 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.
- 4 Total
Progress
- Meeting with Tessa on February 1, 2016.
- 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.
- All 4 L-curve analyses were started and left running on the machines in Seaver 120 (with notes not to disturb these processes).
- 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
- Begin the Dahlquist:Microarray Data Analysis Workflow (focus: dCIN5 and WT)
Progress
- Began the Microarray Data Analysis Workflow
- Thursday, February 11- Began the Dahlquist:Microarray Data Analysis Workflow with Dr. Dahlquist
- Completed the normalization
- The results of this normalization were cross-checked using Tessa's normalization from SURP 2015
- Wednesday, February 17- Walked Maggie through the normalization and continued the Dahlquist:Microarray Data Analysis Workflow
- Completed the within-strain ANOVA for wt & dCIN5
- Sanity check results: Media:Wt-dCIN5 StatsResults BK20160217.pptx
- Completed the within-strain ANOVA for wt & dCIN5
- Updated the R command sequence used to generate L-curves
- This sequence was scripted to automatically generate L-curves
- The script is interactive, prompting users to input the pathway to the data and provide a name for the graph
- An updated description can be found here: Graphing L-Curves in R
Week 6: February 19--February 26
Research Meeting Notes Next Meeting: Friday February 26 (2:30-3:30)
- Goals:
- Continue the Dahlquist:Microarray Data Analysis Workflow with Maggie and cross-check results
- Write a script in R to convert adjacency matrices to edge lists
- If time permits...
- Account for missing values during ANOVA testing
- Create a script for generating parameter plots in R
Progress
- Wrote a script to convert adjacency matrices to edge lists using the package igraph