Natalie Williams Spring Electronic Notebook 2015

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Spring GRNmap 2015

January 2015

I met the other people that are working on this project - Juan, Trixie, and Grace. For this month, we discussed where the project was heading and what parts of the code need to be changed. During these meetings, Profs. Dahlquist and Fitzpatrick gave overviews of the research project and all the computational functions that the model requires.

February 2015

February 6, 2015

I reran the protocol for microarray data that I received from Dr. Dahlquist. The protocol can be found here.

  • First, I created files on my desktop to host the Ontario and GCAT data
    • Each folder contained the following:
      1. The script for either Ontario or GCAT
      2. The target files for those scripts --> Ontario_Targets and GCAT_Targets
      3. The .gpr files from the microarrays were also located in the individual files
  • I downloaded and unzipped the files that were listed under the protocol
Note that Ontario was saved under Ontario and GCAT with GCAT
  • The R used was the 32-bit
The directory had to be changed to the folder where the files that would be corrected were extracted to
  • The Ontario script was run first and then followed by GCAT
  • There will be two different outputs from running GCAT. We want the Final_Normalized_Data

My file was then sent to Grace J., who then began to compare the results that we got.

February 12/13, 2015

I spent this day searching literature for data sets of transcription rates with Grace J. We wrote an abstract to submit to the Undergraduate Research Symposium to present what was done last semester. The abstract was submitted the following Friday.

February 19/20, 2015

Spring Break

February 26/27, 2015

We worked on the poster for our presentation at the 7th Annual Undergraduate Research Symposium. We compiled the data that we were going to use and present on our poster. For the random networks, we gathered the LSE's to compare to the lierature-derived. We chose Random Networks 1 and 4 due to them having the lowest and the highest LSE output.

March 2015

March 5/6, 2015

We added more information to our poster.

March 12/13, 2015

We continued to edit our poster for the 7th Annual Research Symposium. We edited the results section and changed the layout of the poster. We also edited the abstract that we submitted for the symposium to enter ourselves in the WCBSURC (West Coast Biological Sciences Undergraduate Research Conference). We found out the next day that we were accepted to present on April 25, 2015.

For Friday, we continued to look for production and degradation rates in the literature.

March 19/20, 2015

For this week, we finalized our poster for presenting at LMU's symposium. The Results section as well as some of the background information were edited. Images, graphs, and the layout of the poster were formatted to be clearer and easier to follow. The graph titles as well as the scales were altered so that each graph had the same axises. Furthermore, some of the section headings were edited to summarize the main finding for each result. We printed out our posters to put them up on Friday morning.

On Friday, we continued to look for the various degradation and production rates of mRNA.

March 26/27, 2015

I was not in the lab this week. From Thursday to Sunday, I attended NSBE's (National Society for Black Engineers) National Convention in Anaheim.

April 2015

In April, not much was done on mine and Grace J.'s part. For this month, we both completed the homework assignments for my upper division biomathematics course BIOL398-04/S15. For the following weeks in April, we worked on Assignments from Week 11 - Week 14. We no longer met on Fridays for this month due to a lack of having assignments.

April 9, 2015

Last week was Easter break. This week we met up to discuss our progress with the mRNA production and degradation rates. Grace J. and I combined our findings from the literature into one document and sent it to our mentors and professors - Drs. Dahlquist and Fitzpatrick.

April 16, 2015

We discussed the results that Grace J. got from completing the Assignment due that week. My feedback is seen on my electronic notebook from that course.

April 23, 2015

We talked about the conference that we would be attending WCBSURC Saturday. Again, we discussed Grace's results from completing that week's assignments.

April 24, 2015
The conference went well. A few groups of students came by and visited our poster, wanting to know about our research. A few professors stopped by to ask questions about our methods, results, as well as future ideas and goals for the project.

April 30, 2015

We discussed the plan for summer research.

  • Journal Clubs
    • 12-2; Lunch time meeting
  • Weekly meetings where we discuss what occurred during the week
  • First week training process of going through all the data
  • Focusing on sigmoidal model to get results for publications

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