Natalie Williams: Electronic Notebook

Protocol for MATLAB

This page will help you input and run data sets from your document into an output.

Dahlquist:GRNmap

Electronic Notebook

Fall 2014

This contains all the procedures and tasks that I completed and the trials that I ran in Fall 2014.

This contains all the procedures and tasks that I completed and the trials that I ran in Spring 2015. Most of the activities/notes for this semester focused on creating a poster for the various conferences that we attended in the Spring.

Summer 2015

This link has all the information for what occurred over the summer. A lot of it was testing the code by changing the initial weights and the threshold b values of the input sheets.

Fall 2015

November 2015

November 4, 2015

We worked on pulling out the data from the respective data sets we chose to work on --> Grace w/ Wang & myself w/ Shalem

Access was used to extract the data for the transcription factors of interest (TFoI)
Both the Access protocol and the list of TFoI can be found on Grace's page

Results
Only one TF did not have a half life associated with it: YPL248C.
Most of the TFs also had large differences between the two measured half-lives in minutes. For example, YER045C had one half-life equal to 146.871 with its second value at 12.751. Their average is 79.811 with standard deviation set at 94.837.
Many of these values, half-lives with large discrepancies between the measurements, were seen (at least for the TFoI).
I created a column where it lists TFs that had standard deviations less than 10. If those values were less than 10, the numerical value was kept; however, if the numbers were greater than 10, the value was sent to 0 for easier analysis.
The values that were sent to 0 were then counted. Out of the 202 TFoI, 136 were sent to 0.
To me, this suggests that we may not be able to use the measured half-life values from this source - just based on the raw numbers.

The data file can be seen here: Media:NW_DegRates_SpecificTFs.xlsx‎

November 11, 2015

This week Input sheets were created for the networks that we created based on the criteria of p-values.
Input sheet creation protocol can be found on Github's wiki. Some of the pages are blank, such as the degradation and production rates sheets. Some of the parameters also are blank because I did not know what values to input for them.

I may just use the values used in previous network sheets for these values (i.e. MaxIter, TolMax, etc.)

November 18, 2015

We wanted to finish creating the Input sheets before running them in MATLAB. We would try to accomplish this before our next meeting (after Thanksgiving Break)

December 2015

December 2, 2015

I finished creating my last two input sheets for the wt_added genes. We tried running our input sheets and were not

We will create a test sheet without missing values.

Fall 2016

I was abroad last spring semester, Spring 2016, so there are no notes or records of my experience in the lab at that time.

September 2016

September 14, 2016

This week's job was to understand and analyze the study of Neymotin et al (2014) to derive degradation rates from the half-life values of the genes annotated.

Personally, I received feedback on my HNRS thesis abstract that is to be submitted on Sept. 30. I made the changes and sent them to Dr. Dahlquist.

I have worked more of the R Tutorial that Dr. Dahlquist has issued to both Brandon and me. While Brandon has already coded a script to generate random matrices, our next task will be to come up with code to then generate the distribution of in-degree and out-degree via a bar graph.

September 21, 2016

Today, Wednesday 21/9/2016, I completed my task of computing the degradation rates from Neymotin et al's article. I uploaded the file to the DahlquistLab repository where it waits to be reviewed by Dr. Dahlquist.

For the completion of my task with the degradation rates, the following was done:

I downloaded the supplemental data (Table S5) from Neymotin et al
From Neymotin's data, I edited the following
- Alphabetized: Gene names were used for the alphabetization
- Isolated Half Lives: Created a separate sheet with only Systematic & Gene Names and the thalf life
  - I calculated the median half life, which will used to calculate the degradation rate of any gene with missing data
- Degradation Rates: Created an additional sheet for calcuating the degradation rate from the half lives
  - degradation rate = (ln (0.5)/ half life of specific gene)
  - For genes with missing data, the equation would be the following : (ln (0.5)/ median half life)
- I used the previous file shared with me from Dr. Dahlquist to make the comparison between this work and Harbison's list of TFs
I used Microsoft Access to pair the two data sets together using the systematic names in order to identify if there was missing data for the genes
- I created a query and chose the option to include all of Harbison's TFs but only those that matched from Neymotin's
- I also chose to include the calculated degradation rates from Neymotin's data in that query as well

I also revised my abstract and sent that to Dr. Dahlquist for review.

Documents

Summer 2015

To view the most updated powerpoint click here
To see the input sheet that was run for the fixed b trial, please click this link
To view the output file from this fixed b trial, click here
To see the input sheet that was run from the estimated b, please click this
To view the output file from the estimated b, click here
The powerpoint that reviews and analyzes the outputs can be viewed here

GRNmap Testings

This is the template for future reports: GRNmap Testing Report
GRNmap Testing Report: Strain Run Comparisons 2015-05-27
GRNmap Testing Report: Non-1 Initial Weight Guesses 2015-05-28

Natalie Williams: Electronic Notebook

Contents