Akingsley - Bioinformatics Pathway

Things learned:
Technical area: Learned to do Gene Ontology, Kegg, and WikiPathways analysis, as well as gene enrichment with Metascape.

Tools: Metascape, String, and R packages relevant to the analysis, like topGO, org.HS.eg.db, and clusterProfiler.

Soft Skills: Learned to make a better elevator pitch and how to better format my resume.


  1. Completed the python exercises and, in doing so, greatly improved my abilities to code and, specifically, to create plots in python
  2. Completed the deliverables for week 5
  3. Worked alongside group 3 to present the deliverables for week 4

Meetings/trainings attended:
7/1 GitHub Webinar, 7/1 Group 1 and 3 Presentation Meeting, 7/2 Gene Team Meeting, 7/2 Gene Team Happy Hour, 7/6 Gene Team Meeting with Mentors, 7/7 Technical Training with Mentors, 7/8 Group 1 Meeting, 7/8 Gene Team Meeting, 7/8 New and Old Leads Meeting

Goals for upcoming week:
Work with team 7 to create a presentation about the week 5 deliverables and have a productive session of office hours.

Completed tasks:
Successfully conducted Gene Ontology, Kegg, and WikiPathways analysis created plots and csv files of the produced. I had issues with the GSEA function, which I resolved through collaborating with the rest of my group, who were having similar issues. Successfully used Metascape and STRING websites for gene and network analysis. Completed the second set of Python exercises and collaborated with group 3 to create and give a presentation on gene annotation and the week 4 deliverables.

Things learned:

Technical area: Learned to use Metascaape and String as well as to do WikiPathways, Kegg, and Gene Ontology analysis.

Tools: String, Metascape, tidyr, magrittr, org.Hs.eg.db, topGO, clusterProfiler, and pathview

Soft Skills: Presenting data and brainstorming in a group.


  1. Presented on week 5 deliverables and gene ontology analysis with group 7

  2. Attended meetings to prepare to be a new lead and held office hours.

  3. Uploaded deliverables to Github.

Meetings/trainings attended:

7/8 New and Old Leads Meeting, 7/10 Leadership Training, 7/10 Group 1 and 7 Presentation meeting, 7/13 Gene Team Meeting, 7/14 Technical Training with Mentors

Goals for upcoming week:
Start the Final project and host a successful office hours.

Completed tasks:
Submitted week 5 deliverables. I worked with my group and group 7 to create and organize the presentation on gene ontology and the deliverables. I communicated with Ali about the final deliverables, hosted office hours, presented several slides in the deliverables presentation.

Things learned:
Technical area: Reviewed and solidified the skills with R I had learned through doing the data analysis for the final deliverables and learned to use comBat handle batch effect.

Tools: Previously used R packages, the comBat function, and google groups.

Soft Skills: Brain storming and divergent thinking.


  1. Completed the data processing and plotting involved with the final deliverables
  2. Worked on the presentation of the final deliverables for Friday
  3. Scheduled meetings, created groups, and talked to my team for the July session

Meetings/trainings attended:
7/15 Gene Team Meeting, 7/16 Technical Training with Mentors, 7/16 Meeting with New Leads, 7/20 Team 2 Meeting, 7/21 Biology Webinar, 7/21 Technical Training with Mentors, 7/21 Gene Team Meeting

Goals for upcoming week:
Finish up and present my final deliverables presentation.

Completed tasks:
Downloaded, processed, and created plots for the GSE21510 dataset. Analyzed the pipeline of the paper for the final deliverables. Scheduled and helped run team 2’s first meeting, created a google group for the team, a spacetime.am to schedule further meetings, and a poll for the team’s name.

Final Self Assessment:

Things learned:
Technical area: Learned how to use R to do quality control, normalization, visualization, gene annotation and filtering, differential gene analysis, and functional analysis (including gene ontology terms, KEGG pathways and PPI networks) on microarray data. Also learned basic Python and how to analyze a bioinformatics paper and its pipeline.

• R with various bioinformatics R packages,
• Python (on Jupyter notebook)
• Asana
• Google Suite
• GitHub
• Metascape

Soft Skills:
• Working with groups
• Scheduling meetings
• Elevator pitches
• Brain storming
• Resumes
• Networking
• Presentations

Achievement highlights:

  1. Working with groups to complete all the deliverables and give presentations on them

  2. Becoming more proficient with R and learning the basics of tools like python, metascape, and STRING

  3. Overall, learning to understand and conduct a basic bioinformatics pipeline.

Future Goals:
This experience inspired me to learn even more about bioinformatics.

Final Deliverables Presentation.pdf (1.4 MB)