Disha - Bioinformatics Pathway

Self-assessment 1 (06/16):

Concise Overview of Things Learned

  • Technical Area: Microarrays, Different types of RNA, R for data analysis
  • Tools: RStudio, GEO Database, Stem-Away forums, Google Drive
  • Soft Skills: I am learning how to collaborate in a virtual environment

Three Achievement Highlights

  • This is my first exposure to Bioinformatics. I am beginning to understand the different data processing and analysis steps and how they fit together.
  • I am beginning to get better at R with the help of the assigned exercises as well as by exploring related ones.
  • I got the right answer to Erin’s trivia question (lol)

List of Meetings/ Training Attended Including Social Team Events

  • Team introduction meetings (Alex and Erin)
  • Technical webinars
  • R training (two)
  • Asana training

Goals For The Upcoming Week

I am still a little bit behind because a lot of this is new to me. However, I will try to catch up by the end of next week and get to know my team. Thank you @egunduz and @yvesgaetan for all the guidance.

Here is an animation that I found helpful in understanding how micro RNAs silence/regulate genes:

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Self Assessment 2 (06/23/20)

Concise Overview of Things Learned

  • Technical Area: New R packages (for example: affy), how to read the affy QC Report, plot RLE and NUSE histograms, and PCA Plot.
  • Tools: More RStudio experience, Asana, csv files
  • Soft Skills: Scheduling meetings with teammates, participation in team building (happy hour), working in a team of new people

Three Achievement Highlights

  • I have become more comfortable with new R packages and how to apply them for different tasks.
  • I managed to understand the six-page affy QC report by looking through the bioconductor documentation and through some additional internet searching.
  • My team managed to finish the deliverable on time despite losing a team member.

List of Meetings/ Training Attended Including Social Team Events

  • Team meetings
  • Technical webinars
  • Happy Hour (Family Feud)

Tasks Completed
I completed all steps of the Week 3 assignment using the Bioconductor package documentation to help solve issues. I initially struggled with plotting the histograms but found that the issue was pretty simple and was able to fix it. I also had to rewrite some code since RStudio crashed, but that wasn’t too much of an issue.

Goals For The Upcoming Week

I want to go over the deliverable solutions provided by Yves (thank you for the fast grading!), so I can be ready for the next deliverables. I am also preparing for the presentation on Friday. Also, my happy hour group is in charge of this weeks happy hour, so we are going to prepare that for Friday.

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Self Assessment 3

Concise Overview of Things Learned

  • Technical Area: New R packages (for example: limma), object manipulation in R, data annotation
  • Tools: More RStudio experience, Asana
  • Soft Skills: Presentation skills, leading team building (happy hour), working in a team of new people

Three Achievement Highlights

  • Object manipulation in R: Sometimes functions don’t work with specific object formats, I have learned how to deal with that
  • Better understood the volcano plots and how to set thresholds
  • Successful organization of Happy Hour

List of Meetings/ Training Attended Including Social Team Events

  • Team meetings
  • Technical webinars (R training, Bioinformatics Overview)
  • Organized and led Happy Hour

Tasks Completed
I completed all steps of the Week 4 assignment using the Troubleshooting Forum and Bioconductor package documentation to help solve issues. I had an issue with the functions not being compatible with my objects, but I learned how to sort it out. I played around with volcano plots a lot to better understand them.

Goals For The Upcoming Week

I am focusing mainly on learning R at this point so that I can fully understand each step and what it does in the overall project. I plan to catch up on Github and Python soon.

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Self Assessment 4

Concise Overview of Things Learned

  • Technical Area: New R packages (topGO, cluserProfiler), Gene Ontology Enrichment (enrichGO and groupGO), KEGG and DAVID enrichment analysis
  • Tools: More RStudio and Asana experience, DAVID (new tool learned)
  • Soft Skills: Further improvement of presentation skills, Time management

Three Achievement Highlights

  • Technical deliverable completed on my own (team mates left)
  • Improved ability to debug issues with code
  • Improved ability to understand how each step connects to the overall pipeline

List of Meetings/ Training Attended Including Social Team Events

  • Team meetings
  • Technical webinars
  • Happy Hour

Tasks Completed
I completed all steps of the Week 5 deliverable, consisting of the groupGO, enrichGO, KEGG, and DAVID functions / tools for data enrichment. I had some issues initially because I did the first step in a slightly different way than intended and, therefore, had an object which the GSEA analysis would not take, but after playing around with the vectors, I managed to sort it out. I also had an issue with the dotplots not showing up, but some debugging helped me realize that I didn’t have enough data because I started with the wrong data set (I had started with the Top 100, not the full table).

Goals for The Upcoming Week

Further research DAVID analysis for presentation.

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Self Assessment - Final (last 2 weeks)

Concise Overview of Things Learned

  • Technical Area: R Bioinformatics functions: DEG Analysis and Quality Control (affyQCReport, PCA, rma, limma, pheatmap), Gene Ontology Enrichment (enrichGO and groupGO), KEGG (EnrichKEGG and Pathview) and DAVID enrichment analysis
  • Tools: RStudio, Asana, DAVID, Gsuite, STEM-Away Platform
  • Soft Skills: Presentation skills, Time management, Collaboration/ Communication

Three Achievement Highlights

  • Bioinformatics programming in the context of a scientific goal
  • Increased programming knowledge and ability to debug issues
  • Collaboration with peers and leads to effectively execute steps of the colorectal cancer paper

List of Meetings/ Training Attended Including Social Team Events

  • Final Presentation
  • Team Meetings
  • Happy Hour

Tasks Completed
For these last two weeks, all of the tasks I completed were for my final presentation. I applied each step of the programming pipeline to the new data set we were tasked with, and things went smoothly for the most part, as I learned how to efficiently deal with any coding issues the first time around. Initially, I forgot to remove some of the files that were of data that we didn’t need to use, so R kept saying that the functions wouldn’t work on such a big data set, but luckily, I figured out that error rather quickly. Also, I had removed only 3 samples to start during quality control and only realized that it would be better to have removed a fourth sample afterwards, but that was also an easy fix. Details of steps and plots are in the attached presentation:
Final presentation.pdf (2.1 MB)

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