Aditi_3 - Bioinformatics (Level 2) Pathway

Certificates Summer 2021 Certificates R Shiny Transcriptomics App 2021
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1

Module 1

Overview:

Technical Area:

  • R programming (reviewing visualization, coding, and debugging on RStudio)
  • Process of reading and understanding research papers, highlighting key points and evaluating results
  • Getting better informed about Bioinformatics

Tools:

  • RStudio
  • STEM-Away

Soft Skills:

  • Effectively navigating through the STEM-AWAY website
  • Using things I previously learned in an efficient manner

Achievement Highlights

  • Successfully downloaded RStudio and got it to run. I had to download RStudio again because I got a new computer. Nevertheless, because I had already done it once before, the process was smooth.
  • Revisited the basic understanding of how to display visuals and how to overall code on R.
  • Practiced reading research paper on a topic of my choice

Difficulties during Tasks

  • Figuring out the internship and where all the information was located was a challenge.
  • Reading the research paper on lung cancer for our project was also challenging because there were many complex terms. Luckily, the following kick off meeting helped clear some of the confusion. I think I still have a lot to work when it comes to reading research papers though.
2

Module 2

Overview:

Technical Area:

  • Practicing steps I learned previously to efficiently navigate different resources
  • Exploring the ins and outs of GEO database
  • Familiarizing myself with raw datasets and matrix datasets
  • Extracting metadata into Excel

Tools:

  • GEO Database
  • RStudio
  • STEM-Away

Soft Skills:

  • Organizing my directory by modules to make navigation easier
  • Using things I previously learned in an efficient manner
  • Improving involvement through active engagement, paying attention, and trying to make sense of things in my head (giving honest effort).

Achievement Highlights

  • Successfully downloaded the correct expression data from GEO
  • Being able to navigate and understand the matrix format a bit better than before
  • Learning how to change the orientation of information from horizontal to vertical in Excel. As well as swiftly gathering required data without being confused or overwhelmed.

Difficulties during Tasks

  • Because I was disconnected with my internship team, I was unsure if I had to do a self-assessment. After inquiring, I found out that I was missing a big task.
  • I had trouble unzipping my datasets because I lacked an application that would unzip files properly. I also accidentally clicked on an option that would open all gz. files as a PDF. I got all of this resolved with assistance from my dad.
  • I remember being confused with batches in the pathway and I encountered the same issue here. After some digging, I found out that batches were not necessary when using one dataset.
3

Module 3

Overview:

Technical Area:

  • Background correcting and normalizing data
  • Using R to conduct several quality controls and data visualizations
  • Analyzing plots to identify outliers

Tools:

  • RStudio/R
  • GitHub
  • Excel
  • Slack

Soft Skills:

  • Applying knowledge gained from pathway into the internship
  • Following instructions and looking at resources for more insights and extra help
  • Organizing files and code to improve efficiency

Achievement Highlights

  • Being able to follow the module and work through the code without struggling
  • Understanding the plots and visualizations and their purpose and results better than before
  • Officially joining the internship group after realizing that I was not fully involved in it

Difficulties during Tasks

  • I figured out that I was not part of the private internship channels which cause a lot of disturbances in my workflow and confidence. It was very overwhelming to navigate Slack and other platforms. In addition to above, my @mentorchains.com email was not working, so I reached out for help from Kelley, Ivan, Debaleena, and Sarah and got it resolved.
  • The QCReport function was giving me an error saying that it didn’t exist. I checked the documentation and it seemed that there was no error in my code. After some time, I figured out that I forgot to install the affyQCReport.
  • The vector size for both QCReport and arrayQualityMetrics were too large which introduced me to a new function, memory.limit(), that enlarged the memory size.

Goals for Module 4

  • I hope that I can work as well as I did in module 3 (without encountering major issues)
  • I also cannot wait to collaborate with my team
4

Module 4,5 & Group B2,C

Overview:

Technical Area:

  • Annotation/converting to SYMBOL/PROBEID/ENTREZIED
  • Filtering and setting thresholds on data
  • Visualizing the top 10 DEG and KEGG pathways

Tools:

  • RStudio/R
  • Figma
  • GitHub
  • Slack

Soft Skills:

  • Time management, making sure to complete all the deliverables before the deadline
  • Communication/collaboration, working with my group members to sort out any problems and to unify our code
  • Public speaking, presenting to group members

Achievement Highlights

  • Generating identical plots with other group members
  • Got a good grasp on the RShiny app groupings and began to work
  • Worked on public speaking by presented outputs, layouts, and documentations without choking up
  • Getting to know my team members better through comical chats and socials after the zoom meetings

Difficulties Encountered

  • I had trouble using my outlier omitted samples because the code kept using the raw samples. Later, I realized that the normalization was using the raw data, so once I replaced it with the new samples, the problem was resolved.
  • Our group was confused on if we had to use upregulated genes or downregulated genes for the KEGG pathway dotplot. The mentor contacted Anya and assisted on the matter.
  • I was having a hard time wrapping my head around the RShiny project and the different groups. I took some time to explore all the options and have finally decided on my groups.

Goals for Next Week

  • Possibly compile some documentations
  • Start coding on RShiny or begin brainstorming
  • Improve on presentation skills
5

Module 6 & Group B2,C

Overview:

Technical Area:

  • Gene ontology analysis using web tools (EnrichR and DAVID)
  • App layout using figma

Tools:

  • RStudio/R
  • Web Tools (EnrichR/DAVID)
  • GitHub
  • Slack

Soft Skills:

  • Presenting among team members about our findings
  • Organizing outputs and visualizations into sensible information
  • Researching with partner to get a deeper understanding

Achievement Highlights

  • Generated gene ontology using EnrichR and DAVID
  • Held a meeting with partner to navigate and explore the web tools as well as discuss importance of output
  • Got my first set of documentations for the RShiny project for Group C

Difficulties Encountered

  • I accidentally used a gene set worth of 300 genes instead of 125 genes which resulted in a different analysis compared to my partner.
  • Although EnrichR was easy to navigate and understand, DAVID wasn’t. Due to the complexity, I had trouble beginning my analysis. Collaborating with my partner Leila, made it much easier to understand.

Goals for Next Week

  • Start coding on RShiny
  • Hold a meeting with Group C
6

Week 7: Group B2, C

Overview:

Technical Area:

  • Coding/using RShiny
  • Exploring bs4Dash
  • Updating GutHub member list

Tools:

  • RStudio/R
  • Google Docs
  • GitHub
  • Slack

Soft Skills:

  • Presenting to other groups about recent updates and future goals
  • Asking questions and help immediately
  • Managing group member’s progress

Achievement Highlights

  • Held my first group meeting with a member. Discussed how to improve the documentation format, who will be in charge of tutorials, and GitHub updates
  • Formatted document to look more like a documentation and less like an essay by meeting with Disha for advice
  • Got different examples of tutorials from Samuel to brainstorm format for tutorial

Difficulties Encountered

  • Due to my incompetence, I could not run the RShiny app no matter how many times I tried. It was a week and a half long process, but I ended up being unsuccessful
  • Documentations were slow, so I didn’t have any task I could complete.
  • Members were inactive, so I had to figure out how to do some of their tasks myself.

Goals for Next Week

  • Start/complete tutorials and documentations
  • Run the app
7

Week 8: Group B2, C

Overview:

Technical Area:

  • Airtable to update GitHub
  • Complete documentations
  • Start tutorials

Tools:

  • RStudio/R
  • Google Docs
  • GitHub
  • Slack

Soft Skills:

  • Presenting to other groups about recent updates and future goals
  • Asking questions and help immediately
  • Taking over responsibilities when expectations are not met
  • Communicating with other groups for frequent updates on documentations and layout

Achievement Highlights

  • Began tutorials myself because I was in group B2 as well and because expectations were not met
  • Received complete documentations and formatted it
  • Prepared FAQs for group B2 using documentations
  • Became much better at presenting updates to the pathway wide meeting

Difficulties Encountered

  • There weren’t many difficulties this week, but figuring out if I should take over tutorials or not was a challenge. I ended up doing them myself which I am glad about
  • I still couldn’t run the app, so i decided to just contribute in B2 by doing tutorials and drafting many FAQs
  • While updating GutHub, I forgot where all the member’s info was listed, so I had to scout for it
  • Being told that I had to present the app to a company and STEM-Away coordinators was intimidating and I felt like I wanted to give my position away to escape it. I decided to present to get over my fears.