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====Week of February 13, 2017==== | ====Week of February 13, 2017==== | ||
Monday: I generated some random networks with Brandon's R script to be run on the model. A folder was created to hold all the input and output sheets for the random networks that are run with GRNmap. | Monday: I generated some random networks with Brandon's R script to be run on the model. A folder was created to hold all the input and output sheets for the random networks that are run with GRNmap. For further analysis, I will also look at the distribution of the in and out degrees of all the random networks compared to the network derived from the dhap4 data. | ||
*Distribution of weights (positive vs. negative) and the overall network | |||
*Are any motifs/connections conserved? | |||
*Any self or auto-regulators? | |||
*Visualization will also be seen via GRNsight | |||
==Documents== | ==Documents== | ||
Revision as of 17:12, 13 February 2017
Natalie Williams: Electronic Notebook
Protocol for MATLAB
This page will help you input and run data sets from your document into an output.
Fall 2014
This contains all the procedures and tasks that I completed and the trials that I ran in Fall 2014.
Spring 2015
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
Fall 2016
Spring 2017
January 2017
Week of January 12, 2017
Monday & Thursday: Worked on collecting sources for my thesis project. The annotated bibliography is due 20/01. I will be in Boston at that time, but I will still submit my annotated bibliography in time. We had our first lab meeting of the semester on Thursday.
Week of January 19, 2017
Monday: Worked on writing the abstract for the SCSBC at UC Irvine on Saturday, 28/01. The abstract can be found on the Dahlquist Lab repository on github.
Thursday: Not present. Interview at Harvard Medical School.
Week of January 26, 2017
Monday: Finished most of the poster that will be presented this upcoming Saturday at the conference. I wrote much of the content and analysis and Brandon worked on the formatting. Much of the analysis done was on the optimized production and threshold b value's, a motif - Hmo1 --> Msn2 --> Cin5 --> Yhp1.
Thursday: Went over poster during lab meeting. With Dahlquist's correction, I updated the poster and uploaded it to the github repositoryto be edited and reviewed by Dahlquist before printing.
February 2017
January 31, 2017 & February 2, 2017
Monday: Reran the networks derived from dgln3, dhap4, and dzap1 on bouldardii 2 for consistency so that there aren't any discrepancies from running these networks on a different computer.
Thursday:
- Compiled the optimized parameters into one file as well as the MSE values for individual genes in each of the networks. Each of the networks were visualized again on GRNsight just to ensure that the visualizations match with the output optimized weights for each network.
- Received feedback from Dr. Dahlquist on my annotated bibliography as well as additional sources to use for my thesis.
Week of February 6, 2017
Monday: Edited the 10 random output sheet's K. Grace Johnson ran last year to make them into input sheets to re-run on boulardii 2.
- I deleted all the output sheets: the sigmas, optimized_network_weights, optimized_expression, and the optimized production and threshold_b
- I copied the production and degradation rates from Brandon's dhap4 network into all the corresponding sheets in the random network input sheets
Worked on creating the working abstract for my talk during LMU's Undergraduate Research Symposium.
- The adjacency matrices from the random network files were then copied and pasted into the adjacency matrix of Brandon's file so that all parameters and information would be the same. The only difference was the network and the network weight sheets.
Thursday: I was not here due to an interview at UCSF's medical school.
Week of February 13, 2017
Monday: I generated some random networks with Brandon's R script to be run on the model. A folder was created to hold all the input and output sheets for the random networks that are run with GRNmap. For further analysis, I will also look at the distribution of the in and out degrees of all the random networks compared to the network derived from the dhap4 data.
- Distribution of weights (positive vs. negative) and the overall network
- Are any motifs/connections conserved?
- Any self or auto-regulators?
- Visualization will also be seen via GRNsight
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
Other Links
Back to User:Natalie Williams
To visit the Dahlquist Lab: click here
To see K. Grace J's Notebook: click here
