communication on StemAway platform, Slack, and Zoom
Achievement Highlights
After reading the paper and attending meetings, I have a better understanding of the methods and data used.
Complete R and Python exercises successfully
Contacted subgroup to begin working on this week’s tasks
Meetings/ Trainings Attended
Logistic Webinar (10 June)
Technical Training (10 June)
Gene Team Meeting (11 June)
Welcome Session by Debaleena (12 June)
The Gene Team Happy Hour (12 June)
Asana Training (16 June)
Goals for Week of 15 June
complete the deliverables for next Monday
completely catch up with the webinars and trianings I have missed
Tasks Done
read/understood/analyzed research paper - it was challenging understanding some of the biological implications/ processes at first but the technical webinar (10 June) and the notes from the previous webinars helped clarify my understanding
all python and R trainings - no issues were encountered
Successfully troubleshooted teammates code and understood technical reasons behind errors.
Connected with Stem-Away people and people of interest on LinkedIn
Meetings/ Trainings Attended
Asana Training (16 June)
Python and Pandas Webinar (16 June)
Technical Training (17 June)
Gene Team Meeting (18 June)
Goals for Week of 22 June
complete the deliverables for next Monday
meet with teammates (and another team) to discuss results before next Monday
Tasks Done
completed Week 3 deliverables and met with teammates to discuss results - ran into some unavoidable issues with not having enough RAM to do gcrma normalization
signed up for Asana - some connection issues were resolved by leads
Successfully troubleshooted teammates and my code and understood technical reasons behind errors.
Obtained a better understanding of gene differential expression and analysis.
Meetings/ Trainings Attended
Gene Team Meeting (22 June)
Fireside Chat #1 (24 June)
GitHub Training (25 June)
Webinar for Bioinformatics (25 June)
Gene Team Meeting (25 June)
R Training (26 June)
Office Hours BI (26 June)
Goals for Week of 29 June
complete the deliverables for next Monday
complete the phenotype deliverables for Wednesday
meet with group 2 and 7 to prepare presentation for Thursday
Tasks Done
completed Week 4 deliverables and met with teammates to discuss results - teammates and I ran initially had different results, but we figured out our issues in our team meeting
how to extract phenotypic data from the GEO database
learned more about limma analysis from the mentors
gene ontology analysis
KEGG pathway analysis
wikiPathway analysis
Tools
R packages: GEOquery, topGO, cluserProfiler, and pathview
DAVID functional annotation tool for bioinformatics
Soft Skills
worked on presentation skills in office hours
Achievement Highlights
Completed Python Exercises # 2
Completed phenotypic data tasks
Completed Week 5 Deliverables in R (still working on DAVID analysis)
Meetings/ Trainings Attended
GT Meeting (29 June)
GitHub Webinar (1 July)
GT Meeting (2 July)
Goals for Week of 6 July
complete DAVID analysis
prepare presentation for next week
Tasks Done
phenotypic data tasks - struggled to understand recommended line of code, but figured out it was a combination of two different methods and with help from Yves post
Python 2 exercises - struggled with Problem 8, the palindromic pyramid, but figured out a solution thanks to Goral, a technical lead
presentation for Thursday - struggled with coming up with a project hypothesis due to vague instructions, but Annie, a technical lead, was able to clarify at the end of the meeting
week 5 deliverables - still running into some inconsistencies in results with my teammates, but we are planning to troubleshoot these later today
Things I Learned
This week, I didn’t really learn anything new in terms of technical skills and tools, but I became more confident in the skills that I have learned in previous weeks while preparing for the final presentation.
Soft Skills
practiced divergent thinking
learned more about presentation skills and will get to apply them in the final presentation
Achievement Highlights
Successfully implemented the pipeline learned in previous weeks to a new dataset
Prepared final presentation
Started the July session as a lead - still working out some kinks, but overall it started pretty well
resume and CV construction tips and best practices
creativity and divergent thinking
communicating virtually across different time zones
Achievement Highlights
Completed the June session with a deeper understanding of bioinformatics techniques, analysis methods, and tools used in researching genomics and transcriptomics
Debugged and helped teammates troubleshoot programming errors thus improving my own confidence in programming and teaching others.
Refined teamwork and collaboration skills especially when working across different time zones.
Final Word/ Goals for Future
I’ve really enjoyed my time as a participant in the Gene Team and getting to know everyone. Everyone I worked with was very passionate and dedicated in learning and making sure everyone understood what was going on. The leads, especially, were very helpful in troubleshooting and clarifying objectives. What I liked the most was being able to work in smaller groups and really get to know the people I was working with. I liked having smaller subgroups and then combining with another subgroup for presentations. I think getting to know a few people at a time was helpful in developing a sense of community within the larger team.
In the immediate future, I’ll be a lead for the BI pathway’s July session. This internship has definitely gotten me excited about Bioinformatics and, in the distant future, I’m thinking of pursuing the topic in higher education (grad school).