Sail19 - Bioinformatics Pathway

concise overview of things learned:

  • technical area: definitely had a lot of technical issues mainly with my computer and memory space and placing of items and data
  • tools: used google for issues, used ? for help during R, used team members and STEMaway platform for help
  • soft skills: communicated with teammates on zoom meetings and on text as well as the STEmaway forum

three achievements:

  1. I figured out why I couldn’t download data onto my Rstudio with the help of Anya (had to install another windows tool)
  2. we met as a group and helped one another through some coding issues
  3. we have pretty good communication between group members

list of meetings attended including team events:

last week - attended 7/28, technical issues for 7/21, had orthodontist appt for 7/23, attended 7/24
this week - attended 7/27 & 7/28

goals for upcoming week:

  • figure out my computer memory issue
  • wrap up last weeks deliverables
  • start new deliverables
  • communicate more often with group (like zoom meetings etc)

detailed statement of tasks done:

Most of the Rstudio challenges were overcome by communicating with my group or Anya for technical and R issues. I only was able to get up to the arrayQualityMetrics (QC) part due to my computer memory (still in the works). More efficient communication with team members was another issue, and it was solved by creating our own group chat and doing zoom meetings.

Week: (8/4/2020)

Overview of Things Learned:

Technical Area: I’ve learned that there are some restraints when it comes to computer memory when using Rstudio and downloading data.

Tools: I used the group chat my group and I have created to stay updated on difficulties with R and how my groups members solved those challenges in Rstudio (even though I wasn’t able to participate in the R coding due to my computers RMA/memory threshold).

Soft Skills: Communicating with group for clarifications on charts/graphs/analyzing data and various other troubleshooting communicating.

Achievement Highlights

  1. meeting up with my team to discuss the final deliverable and interpreting the DGE analysis
  2. cherry picking the most significant downregulated and upregulated genes, mine being CNOT7. As well as researching CNOT7 genes function as well as how it is a significant target gene for doctors and what it’s role is in colorectal cancer (function: repressor gene that regulates cell reproduction/ proliferation, however, since it’s down regulated gene, this regulatory gene is lacking in colorectal patients creating an overgrowth of cells).
  3. Interpreting the volcano plot: the negative side represents downregulated genes (less expressed) while the positive side of logFC represents upregulated (more expressed). The Y-axis (or P value) just demonstrates the level of confidence in the logFC. So you want to look for genes with the most relevance, that being the upper far left and right hand corners of the plot.

Meetings attended

I was unable to attend the meetings on 8/4 due to waiting in line, online for 2 hours to register for the ACT (since I’m a senior in highschool and haven’t taken it yet). I did attend the deliverables micro-array presentation 8/4/ 2020 and presented.

Goals for the Upcoming Week

Make more room on my computer by cleaning up some memory space (with the permission of family members since it’s a shared laptop). As well as proceed to the next deliverables, and develop and understanding of what exactly each piece of R code is for. Along with being able to interpret the data especially the visuals (my favorite part!).

Tasks Done
This week I did participate in the meetings my group held separately, and did present the micro-array deliverables with my team (the heat map and the function of gene CNOT7). However, since my computer didn’t have enough memory space and R crashed a few times I could not proceed to code for the deliverables. Nevertheless, I still made sure that I understood what was being done with the R coding, interpreting the visuals, data, and known what function a significant downregulated gene (CNOT7) may have played in colorectal cancer patients.

overview of things learned:
technical area: Learning how to make more memory room on my Computer
tools: looking at Troubleshooting page to see what problems people are having
Soft skills: communicating with teammates

Achievement highlights:
Learning how to make more room on computer (RMA/memory threshold)
meeting with team to discuss functional analysis graphics and interpret them correctly.
Presenting functional analysis slides (String DB) slide

meetings attended:
8/10, I was unable to attend happy hours last week due to school registration and picking up school books. 8/14 presented functional analysis slides with group.

Goals for the upcoming week:
Research and become knowledgeable about gene ontology GSEA so I can be prepared for the presentation on Friday.

Tasks done:
Making room on computer for more memory/RMA (still in the process).
Looking up information about gene ontology GSEA.

final project/overall self-assessment concerning whole internship:
I used the internship as a way to gain insight into what it would be like to pursue bioinformatics as a career. The most difficult tasks included coding and making room for memory on my computer which took too long by the time the internship ended. Although I couldn’t participate in much of the coding I did find that going to the “troubleshooting” forum gave some insight on what problems people may come across. I enjoyed collaborating in a team. My favorite part was doing the gene function analysis of what certain genes do and what’s their role. I also enjoyed presenting an analysing the graphics that were made through using R and other platforms. I’ve gained an understanding of how R studio functions as well as GitHub and bioinformatics as a whole, and why bioinformatics is so important in the field of genetics. However, through this internship I’ve come to the understanding that I’m not tech savvy and that I prefer to do the visual and biological analysis as opposed to the actual coding. Therefore, I still need to work on my coding skills.