Kkang117 - Bioinformatics Pathway

Certificates July 2020 Certificates Bioinformatics Workflow Self-Assessments
1

  • concise overview of things learned - break it up into technical area, tools, and soft skills:
    This was my first time using R, so I learned a lot of technical R skills and troubleshooting. From quality control to normalization to visualization, all the coding and packages that we used this past week were new and I learned a lot of the background information about these techniques while researching how to use the functions and packages. I also learned about other tools for communicating, specifically Slack, which we’ll probably be using this next week to keep in touch with each other and schedule meetings. Since the first week was quite hectic, I think I learned more soft skills in communicating with team members through different platforms, whether on zoom or through text messages, to get through roadblocks in our codes.

  • three achievement highlights:

  1. I was able to work through all the deliverables by myself and then compare with other team members
  2. Got to know the other group members better through frequent communication and scheduled meetings to discuss and get work done
  3. Successfully presented our work and results to everyone

  • list of meetings attended including social team events:
    Attended the first meeting on the 20th and went to Happy Hour last Friday.
    Also, a P.S. because I don’t know if you guys read the message I sent through the forum Monday morning about the most recent meeting, but I had a dentist appointment so I couldn’t make that one, sorry.

  • goals for the upcoming week:
    Be able to collaborate more with the group and attend office hours to get a better grasp on the concepts behind the coding.

  • detailed statement of tasks done - specifically challenges and how those challenges were overcome:
    Our team participants had trouble getting their software to work and one was added last minute so there were a couple challenges trying to get the deliverables in. We all worked on it separately and asked each other questions along the way. So, I was able to do all the deliverables and uploaded my results and plots in the google drive. I also worked on the powerpoint presentation slides. In terms of overcoming the challenges, our group messaged each other over text whenever we had trouble with our codes and we tried to meet over zoom to stay organize and discuss the results.

2

Week: July 27 (Week 4)

Overview of Things Learned:

Technical Area: Learned more about the different packages and functions of R, especially about limma. There were also many new functions on R that I learned about, such as topTable, select, and contrastMatrix.

Tools: Learned how to use GitHub to submit deliverables. Got better at navigating through the Stem-Away forum. Learned more about the annotation database.

Soft Skills: As task lead this week, I had to take more of a leadership role with the group, which included organizing times to meet on Zoom and answering questions about R.

Achievement Highlights:

  1. Learned how to use the annotation database, how to filter genes, and how to use lmFit package
  2. Was able to take concepts that we learned previously, like model matrix, heat maps, and volcano plots, and apply them to this set of deliverables.
  3. Got through the week as task lead. Was able to communicate with my group and present our results well.

Meetings attended: Team meeting, presentation, and office hours

Goals for the Upcoming Week: Our team still hasn’t been able to utilize Slack as much. So, to get the whole group to use it more to discuss our codes and results. Also, to get an early start on the next deliverables.

Tasks Done: Each participant did the coding separately and would ask each other questions along the way and compare. So, I did all the deliverables and submitted them on GitHub. In terms of specifics challenges in the coding, I had initial confusion about the select function, which I got clarification on by looking through the forum and by going to office hours. I also got feedback from fellow group members about gene filtering to make sure our codes aligned. As task leader, I organized a time and set up a Zoom to meet to discuss results, put together the presentation, and allocate slides to present. I researched one of the four most differentially expressed genes to hypothesize its function. One of the challenges was getting into contact with one of the participants. She’s been MIA for a bit and isn’t very consistent in responding to our messages. I and our group as a whole will probably try to get in contact with her to figure out where she stands in this program, and discuss with the leads what to do about the situation.

3

Week: August 3 (Week 5)

Overview of Things Learned:

Technical Area: Learned how to use enrichr() functions in R, which include enrichGO and enrichKEGG. Also learned how to create a gene concept network using the cnetplot() function.

Tools: Learned more R packages and functions to use for gene analysis. Learned about STRING database website to identify hub genes and GEPIA website for survival analysis.

Soft Skills: Had a meeting to learn and discuss about cultural competency.

Achievement Highlights:

  1. Used the enrichr packages to perform gene enrichment.
  2. Identified hub genes using STRING database and created graph for survival analysis.
  3. Started on gene set enrichment analysis and transcriptional factor analysis

Meetings attended: Team meeting

Goals for the Upcoming Week: Finish the rest of the functional analysis and begin thinking about what disease I want to research.

Tasks Done: Completed the functional enrichment analysis and survival analysis deliverables. This includes creating a gene vector of the upregulated genes with gene IDs, performing gene ontology analysis using enrichGO and creating barplots, performing KEGG analysis using enrichKEGG and creating a dotplot, using the enrichKEGG results to create a gene concept network using cnetplot(), StringDB, and using GEPIA to create a survival analysis plot. Also, downloaded the hallmark and c3 gmt files for GSEA.

4

Week: August 10-16

Overview of Things Learned:

Technical Area: Learned about GSEA analysis and transcriptional functional analysis using enrichr and how to interpret a GSEA plot. Learned how to create my own metadata csv to use for analysis.

Tools: Got more experience using the GEO database to obtain datasets for the final project.

Soft Skills: Working and managing time on my own in an individual project.

Achievement Highlights:

  1. Finished the final set of deliverables
  2. Started on the deliverables for the final project
  3. Finished the last presentation for the group project

Meetings attended: Team meeting

Goals for the Upcoming Week: Finish the deliverables for the final project and present the results well.

Tasks Done: Conducted GSEA analysis and plotted results, and transcriptional factor analysis and created cnetplot. Also started the final project by selected the disease I wanted to research further, reading the dataset into R, and conducting quality control and DGE analysis.

# self-assessment # bioinformatics # functional-analysis # final-project #