MSymond1 Week 15

Progress Report

Milestone 3 continued

• I was able to obtain the data from the yeastmine website by scrolling down and selecting the table with “all verified uncharacterized dubious ORFs”, the data table included all of the columns that Dr. Dahlquist suggested I include in the table
• The production and degradation tables could be saved as txt files which could then be opened in excel directly
• The metadata table was created with assistance from my professor in which she helped us gather the necessary materials for it

Milestone 4

• The database creation went mostly well with a few issues along the way such as
• Importing the tables from excel led to some problems of all values being either 0 or 1 on production rates or degradation rates tables, so we started to export the tables from excel as a txt file and then open them in access at txt files
• In the relationships window, we connected the systematic name column for each of the tables to ensure they would all be connected since that column was the primary key in each of the data tables

Milesone 5

• The quality assurance team was able to verify that the database was correct and had all necessary fields

Milestone 6

• We were informed by the data analysts that they selected profile 41 to analyze, this profile included 23 genes initially
• At first we were stuck and were not sure how to obtain the necessary data for the GRNmap, but Dr. Dahlquist pointed out that we can use the database that we created to run queries and find the necessary fields for each of the 23 genes
• I was informed that Andrew had completed the first three queries for the first three tables on the GRNmap excel sheet
• I followed the sample GRNmap excel sheet as a template for the queries. and I was running into problems running the query with the network table
• We imported profile 41 genes into access as another table to run queries with
• I noticed the problem was that profile 41 only included standard names of the genes rather than the systematic names, which was not the primary key for most of the database, and the network table did not include the standard names so I could not link those two tables together using it
• My solution was to link the gene table to the profile table using their standard names. However, I noticed that the gene table did not include the standard names for the genes, so I imported another gene table from yeastmine that does include the standard names. Then I was able to link the profile 41 table to the gene table using the standard names and then I was able to run a query using the query design and I was able to answer question 4.
• I also noticed that the first three questions were incorrect since they did not include all of the genes, I'm not sure how that happened with Andrew's queries, but I went ahead and ran them again and fixed that issue
• Dr. Dahlquist also noticed that Andrew's queries included the data from the control expression group rather than the CHP treated expression group, so I fixed that too
• I followed the rest of the directions for the rest of the questions for milestone 6 and ran into no problems
• I was able to give the GRNmap excel file to Dr. Dahlquist for her to run it

Presentation

Progress

• We were able to complete the presentation to the best of our abilities following the directions listed in the project deliverables page
• The biggest issues we ran into was structuring the presentation in a way that made sense since we all had a great understanding of our own part of the project but we did not know everyone else's as well, so we had to learn a little bit about everyone's part of the project in order to create a cohesive presentation that made sense
• We also did our best to take into account our feedback from the last presentation and tried to make our titles more descriptive and also make our bullet points more useful

slides presentation

Team Journal Assignment

1. This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
2. Each team member should reflect on the team's progress:
   1. The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
   2. The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
   3. To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

Acknowledgements

I utilized all of my group members and my professor in the past two weeks to assist in completing this project. Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Msymond1 (talk) 19:03, 2 May 2024 (PDT)

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