Snehasharma - Bioinformatics (Level 1) Pathway

Certificates Summer 2021 Certificates Bioinformatics Workflow 2021
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Week 1 Self-Assessment:

Overview:

Technical Area:

  • Installing RStudio, along with packages in R
  • Familiarizing myself with basic R fundamentals, such as: coding, debugging, and syntax
  • Understanding how to read scientific papers
  • Getting a brief understanding of R Shiny and its features

Tools:

  • STEM-Away
  • RStudio
  • R
  • R Shiny

Soft Skills:

  • Time Management - learning how to efficiently progress through the module, while still being able to get a good grasp of the material.
  • Perseverance - Since I had no prior knowledge using RStudio or coding in R, I had to learn to persist in completing the module with the help of STEM-away and my basic coding knowledge.

Achievement Highlights:

  • Successfully downloaded R v4.0.0, RStudio, and the two packages needed
  • I wad able to learn and practice navigating R.
  • Able to get a basic understanding of bioinformatics and reading scientific papers.
  • I was successfully able to get a little bit familiar with R Shiny

Difficulties Completing Tasks:

  • I had a little bit of trouble using the STEM-away website and locating different pathway hubs, but I eventually was able to get the hang of using this site.
  • While trying to download R, I was initially downloading R v4.1.0, as it is the latest version. Eventually, I was able to figure out the issue and download to correct version, R v4.0.0.
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Week 2 Self-Assessment

Overview:

Technical Area:

  • Understanding the purposes of the GEO Database
  • Learned how to input and manage data in the GEO Database

Tools:

  • STEM-Away
  • RStudio
  • R
  • R Shiny
  • GEO Database
  • Github
  • Trello
  • Slack

Soft Skills:

  • Time Management - Once again, I was able to figure out how to understand the material from the module at a quick pace
  • STEM-Away Website - Learning how to use the STEM-Away website for future purposes
  • Communication - It took a while, but I was able to organize myself and get familiar with the different communication tools we will be using and what we will use them for

Achievement Highlights:

  • I was able to easily download the dataset needed for this week
  • Learning how to navigate the GEO Database and Github
  • Got more familiar with the STEM-Away website
  • Getting comfortable to reach out to the leads for help

Difficulties Completing Tasks:

  • I had a little bit of trouble organizing and setting myself up to complete tasks, as I was a little bit unsure about what tasks I needed to complete and how to achieve them.
  • At the start, I was confused on how to put data into Rstudio, but after a lot of trouble shooting, I was able to get it loaded
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Week 3 Self-Assessments:

Overview:

Technical Area:

  • Installing multiple necessary libraries
  • Creating a QC plot with the GSE 19804 dataset
  • Using the GSE 19804 Dataset to create a PCA Plot and Correlation Heatmap

Tools:

  • RStudio
  • R
  • R Shiny
  • Github
  • Trello
  • Slack
  • Bioconductor website
  • Simpleaffy

Soft Skills:

  • Time Management - being able to efficiently manage completing all of the tasks, while still
  • Perseverance - It took me a very long time to understand how to use the functions needed to complete this weeks tasks, but I was able to achieve goals with perseverance
  • Communication - after having some problems with my QC Stats output, I was able to reach out to a team lead to get some advice

Achievement Highlights:

  • I was successfully able to create a QC Stats output, correlation heatmap, and a PCA plot
  • I was able to understand how, using the outputs created, I could determine potential outliers and identify influential data points
  • Understanding the output of the heatmap and how it compares raw and normalized data

Difficulties Completing Tasks:

  • I ended up spending a lot of time looking up how to use the different functions needed to graph the plots, but at the end I was successfully able to figure it out
  • I had some problems with my QC Stats output, and it took me a long time to figure out how to correct it. With the help of a team lead, I was able to solve the issue.
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Week 4 Self-Assessments:

Overview:

Technical Area:

  • Installing multiple necessary libraries
  • Normalizing data
  • Limma Analysis
  • Volcano Plot

Tools:

  • RStudio
  • R
  • R Shiny
  • Slack
  • Websites for research

Soft Skills:

  • Time Management - being able to efficiently manage completing all of the tasks
  • Presentational Skills - Creating a insightful presentations in a limited amount of time
  • Communication - Working with group members to complete shared tasks in a timely manner
  • Research Skills - Finding important and relevant information

Achievement Highlights:

  • Although it took me longer than expected, I was successfully able to complete all the module tasks
  • I was able to take initiation for collaboration and communication among my subgroup
  • Contributing to group calls by presenting my ideas and findings.

Difficulties Completing Tasks:

  • I had a lot of trouble following the instructions for the module tasks, so I spent a lot of time researching the steps to find more information about the tasks we were completing
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Week 5 Self-Assessments:

Overview:

Technical Area:

  • Module 5 Tasks such as creating a GSEA plot to understand DEGs, gene ontology using Transcription factor analysis, and KEGG analysis
  • Met with Ashlesha and Mark to understand some web based tools for functional analysis (such as EnrichR, David, and Metascape)

Tools:

  • RStudio
  • R
  • R Shiny
  • Web based tools (EnrichR, David, and Metascape)
  • Slack
  • Websites for research
  • STEM-away website for resources

Soft Skills:

  • Time Management - being able to efficiently manage completing all of the tasks
  • Perseverance - It took me a very long time to understand how to use the functions needed to complete this weeks tasks, but I was able to achieve goals with perseverance
  • Research Skills - Finding important and relevant information

Achievement Highlights:

  • Successfully created a GSEA plot, after a little bit of troubleshooting with my code
  • Got a better understanding of R syntax
  • Met with team 2 to discuss web based tools we could use for functional analysis

Difficulties Completing Tasks:

  • I was struggling with understanding the functional purposes of the web based tools, but after Mark shared a list of basic uses, I was able to do more research and get a better understanding.
  • The module took me much longer than expected, with unfortunately left me a bit behind the rest of my teammates, but with their help, I was able to catch up.
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Final Bioinformatics Presentation:

Final Bioinformatics STEM-Away Sneha.pdf (318.3 KB)