Alicia Repka-Bioinformatics Pathway-Self-Assessment

Why I joined the Bioinformatics Pathway:
I joined the June session of the BI pathway, first as an observer, but I quickly moved to a participant role as I grew more comfortable with coding and data visualization and R. As a biomedical engineering major, I was curious about the overlap between biology, biomedical engineering, and bioinformatics. Although learning the R programming language was difficult at first, I quickly found myself completely engrossed in the project, often exploring extra analyses in addition to the required deliverables. The entire process of the bioinformatics pipeline is fascinating and exciting to me. When I was asked to serve as a lead for the July session, I simply could not pass up the opportunity to inspire others about bioinformatics.

Things Learned:
Technical skills:

  • Data merging and batch correction
  • Differences between normalization methods
  • GSEA analysis
  • Transcription factor analysis
  • Survival analysis on GEPIA


  • Bioconductor packages
  • GSEA
  • MSigDB

Soft skills:

  • Leadership
  • Organizing meetings
  • Flexibility with technical problems and last-minute changes
  • Accommodating diverse technical experience within my team
  • Communication with other leads and my own team

Tasks completed:

Before the internship

  • Hosted two sessions of office hours (7/08 and 7/13) explaining the foundations for working with data sets and Bioconductor in R

During the internship

  • Hosted a webinar explaining and outlining the deliverables for week 3 of the July session
  • Organized my first team meeting as a lead for the July session
  • Lead weekly team meetings and presentations of results
  • Offered technical advice and problem solving during weekly office hours sessions
  • Completed deliverables for July week 3 (quality control)
    • Merged GSE32323 and GSE8671
    • Quality control
    • Normalization
    • Batch correction
  • Completed deliverables for July week 4 (DGE analysis)
    • Gene annotation
    • Gene filtration
    • Limma analysis
    • Data visualization: heatmaps and volcano plots
  • Hosted a webinar explaining my own code for DGE analysis
  • Completed deliverables for July week 5 (functional analysis)
    • Gene ontology analysis
    • KEGG analysis
    • Gene-concept network analysis
    • Protien-protein interaction network analysis using STRING
    • GSEA analysis
    • Transcription factor analysis
    • Survival analysis using GEPIA
  • Hosted a webinar explaining my own code for functional analysis
  • Hosted a webinar on presentation skills to prepare interns for their final presentations

Challenges faced:

One of the first challenges I faced was that during the first week, not long after we had assigned subteams, many of my team members quit the internship. I resolved this by reassigning teams, making sure to vary the levels of coding experience within each new team and also doing my best to assign members to teams in similar time zones.

Although I served as a project lead, in addition to organizing and leading team meetings, I often found myself handling most of the technical questions from my team. While I completed the deliverables each week before attending office hours to assist interns with their questions, I still had some difficulty aiding my team in troubleshooting. I have made huge progress in my understanding of the R programming language between the June and July sessions, but I still had trouble identifying ways to fix particular errors with different coding styles and often felt guilty when I was not able to provide my team with the technical advice or solutions they needed.In order to get a better understanding of these students’ problems, I completed additional research on the R packages we were using, and during office hours, I was able to redirect my team to leads that had a stronger base in the particular aspect of the code. I also helped lead webinars going over and explaining my own code to show how various packages functioned overall.

I also found it very difficult to accommodate the diverse time zones as well as school/work commitments of my team members. I addressed this by working with Sarah to find meeting times that worked for a majority of participants and recording meetings for those unable to attend. I also made myself available to answer technical questions via the STEM-Away forum and email at extended hours to help interns who were unable to attend office hours.

Further reflections:

My experience in this internship, both as a participant during the June session and as a lead during the July session, has been an incredible opportunity. I have vastly expanded my knowledge of coding, particularly in R, and I have honed my leadership skills as well. This internship has taught me to be flexible, how to work with last-minute meetings and deadlines, and how to collaborate virtually with teams all over the world. I know the skills I have gained this summer will serve me well in the future.

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