Shanya - Bioinformatics Pathway

Certificates June 2020 Certificates Bioinformatics Workflow Self-Assessments
1

Week 2:

Things Learned:

Technical Area:

  • Python and R: basic coding skills, creating different kinds of plots from large data sets, customizing plots, ggplot library ®
  • Data analysis and analysis of different data plots
  • Background information on the experiment (review on interpreting microarray data)
  • Role of genetics and DNA on the project

Tools:

  • G-suite
  • Stem-Away Forum
  • Google Colab (I am still working on running Jupyter Notebook as I ran into issues with installation)
  • R studio

Soft-Skills:

  • Collaborating with small and large groups of peers
  • Learning through virtual meetings
  • Effectively communicating with others online
  • Asking for assistance when running into issues

Three Achievements

  • I understand the background information on the project and the experimental portion with microarrrays
  • I attended most of the webinars and watched the recordings of all the ones that I was unable to attend and have a clear understanding of most of the technical skills (especially R and Python)
  • I met the two other members of my group and we have all established methods of communication through Slack and the Stem-Away Forum

List of Meetings/Trainings attended

  • Informal Team Meeting (6/1) to set up mentorchains on gmail and Slack account
  • R training workshops (6/5 and 6/12)
  • Python training sessions (Beginning and Advanced)
  • Technical Training Webinar (6/10)
  • Welcome Session on Leadership and Program Management (6/10)
  • Gene Team Meeting (6/11)
  • Gene Team Meeting (6/15)
  • Python Office Hours (6/15)
  • Asana Training (6/16)

Goals

  • Fix technical issues and Install Jupyter Notebook
  • Complete 6/12 R Exercises and get a more clear understanding of R
  • Attend all upcoming webinars and training sessions
  • Learn more about the tasks for Week 3

Tasks Completed/Hurdles Faced

  • I attended and learned from the trainings and webinars
  • I read and understood the research paper
  • I faced difficulties installing Jupyter Notebook so I attended the Python Office Hours (6/15) and received help and hope to resolve the issues by the end of this week and also be able to complete the Python exercises that I was unable to do
2

Week 3:

Things Learned:

Technical Area:

  • Bioconductor packages: simpleAffy
  • Normalization Methods: RMA, GCRMA, MAS5
  • Unzipping Raw.tar files
  • Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE)
  • Principal Component Analysis (PCA)
  • Plotting Histograms and Scatterplots through RStudio

Tools:

  • Asana
  • G-suite
  • STEM-Away Forum
  • Jupyter Notebook
  • RStudio
  • Slack

Soft-Skills

  • Speaking comfortably in groups with a large and small amount of people
  • Successfully troubleshooting with a team
  • Asking questions when faced with an issue and solving problems effectively
  • Working through team meetings productively

Three Achievements:

  • I was able to complete the deliverables for Week 3 on time with the help of my group members
  • I now have a more clear understanding of how to use RStudio
  • I fixed the issues with installing Jupyter Notebook and was able to download Anaconda and Jupyter Notebook so I was able to complete the Python exercises from last week

List of Meetings/Trainings Attended:

  • Python and Pandas Webinar (6/16)
  • Technical Training Webinar (6/17)
  • Gene Team Meeting (6/18)
  • Team 7 Group Meetings (6/21 and 6/22)
  • Gene Team Meeting (6/22)

Goals:

  • Work with Team 6 and Team 7 (my team) to create a presentation comparing our results
  • Begin working on the Week 4 deliverables
  • Attend all upcoming trainings and webinars

Tasks Completed/Hurdles Faced:

  • Completed analysis of the assigned data set
  • Ran into issues with unzipping the files my group helped me figure out how to fix it
  • Had issues creating the histogram of RLE and NUSE median values and the PCA scatterplot but consulted with my team and figured it out
3

Week 4:

Things Learned:

Technical Area:

  • Creating Heatmap in R
  • Annotation using Bioconductor package: hgu133plus2.db
  • Gene Filtering using quantile() function
  • Analyzing data using limma
  • Creating volcano plot in R

Tools:

  • Asana
  • G-suite
  • STEM-Away Forum
  • Github
  • RStudio
  • Jupyter Notebook
  • Slack

Soft-Skills:

  • Presenting in front of a large group of people
  • Successfully communicating issues with team and solving them effectively
  • Productively collaborating with other teams
  • Networking with people through Linkedin

Three Achievements:

  • My group and I finished the deliverables for this week’s (Week 4) tasks
  • I was able to network with different people in Linkedin
  • I was able to present with my group as well as group 6 to The Gene Team on our Week 3 Deliverables and the comparison of our data

List of Meetings/Trainings Attended:

  • Team 7 Meeting (6/22)
  • Gene Team Meeting (6/22)
  • Python Training (6/23)
  • Team 6 and 7 Meeting (6/24)
  • Gene Team Meeting (6/25)
  • Introduction to Bioinformatics Webinar (6/25)
  • R training (6/26)
  • Office Hours (6/26)

Goals:

  • Finish Phenotypic Data Tasks
  • Create presentation for Gene Team Meeting on Thursday and discuss with Team 2 about Gene Filtering
  • Finish Week 5 Deliverables
  • Attend all upcoming trainings and webinars

Tasks Completed/Hurdles Faced:

  • Completed Week 4 Deliverables with my group
  • Completed Presentation on Week 3 Deliverables with Team 6
  • Had trouble creating the model matrix
  • Ran into issues with using limma but attended Office Hours on Friday and resolved issue
  • Ran into issues with the Phenotypic Data Tasks and planning on attending Office Hours
4

Week 5:

Things Learned:

Technical Area:

  • Creating different types of plots in R (barplots, dotplots, plotGOgraph)
  • Using enrichGO, enrichKEGG, and DAVID
  • Interpreting data from different plots
  • Using Limma
  • Using GitHub
  • Using Python to create different plots

Tools:

  • GitHub
  • G-suite
  • RStudio
  • Asana
  • STEM-Away Forum
  • Jupyter Notebook
  • Slack
  • LinkedIn

Soft-Skills:

  • Troubleshooting with two teams
  • Asking questions and learning with the help of my team and the mentors
  • Collaborating and presenting with multiple teams
  • Networking

Three Achievements:

  • Completed Phenotypic Data Tasks
  • Successfully created plots for Week 5 Deliverables
  • Presenting with Group 2 to the Gene Team on Week 4 Deliverables

List of Meetings/Trainings Attended:

  • Group 6 and Group 7 Meeting to Compare Results (6/29)
  • Gene Team Meeting (6/29)
  • GitHub Webinar #2 (7/1)
  • Office Hours (7/1)
  • Group 2 and Group 7 Meetings (7/1 and 7/2)
  • Gene Team Meeting with Presentations (7/2)
  • Gene Team Meeting with Mentors (7/6)
  • BI Office Hours (7/7)

Goals:

  • Complete Week 5 Deliverables and submit by the end of today
  • Continue to Network on LinkedIn
  • Attend all upcoming Trainings and Webinars

Tasks Completed/Hurdles Faced:

  • Ran into issues while working through Week 5 Deliverables and also processing Limma analysis but was able to get help from my Team and the mentors
  • Had difficulty working through the Python Exercises
5

Week 6:

Things Learned:

Technical Area:

  • Using enrichGO, enrichKEGG, and DAVID
  • Interpreting data from the plots created from enrichKEGG, enrichGO, and DAVID
  • Using GitHub
  • Using Python

Tools:

  • GitHub
  • G-suite
  • RStudio
  • Asana
  • STEM-Away Forum
  • Slack

Soft-Skills:

  • Collaborating and creating a presentation with multiple teams
  • Effectively troubleshooting with multiple people
  • Networking with people on LinkedIn
  • Resume-building skills
  • Creatively thinking with small groups

Three Achievements:

  • Completed Week 5 Deliverables
  • Completed Week 5 Presentation with Group 1
  • Uploaded all past work onto GitHub

List of Meeting/Trainings Attended:

  • Group 7 Meeting (7/7)
  • Gene Team Meeting (7/8)
  • Group 1 and Group 7 Meetings for Presentation (7/10)
  • Gene Team Meeting (7/13)

Goals:

  • Start working on new deliverables
  • Continue to network on LinkedIn
  • Attend upcoming Webinars and Team Meetings

Tasks Completed/Hurdles Faced:

  • Had difficulty creating plots because different group members had different results
  • Creating this week’s presentation presented a few issues because of all the plots and the varying results
  • There was confusion as to whether or not we needed to split the up regulated and down regulated genes
6

Week 7:

Things Learned:

Technical Area:

  • Limma package
  • Reading and identifying pipeline in scientific paper
  • Creating heatmap in R
  • Creating volcano plot in R

Tools:

  • Github
  • G-suite
  • RStudio
  • Asana
  • STEM-Away Forum
  • Slack

Soft-Skills:

  • Learned how to troubleshoot on my own
  • Working through deliverables on my own without the assistance of my team
  • Networking and making connections on LinkedIn
  • Speaking in front of the team

Three Achievements:

  • Completed the final deliverables
  • Attended the last Gene Team Meeting
  • Networked with new people on LinkedIn

List of Meetings/Trainings Attended:

  • Gene Team Meeting (7/15)
  • R Office Hours (7/17)
  • Gene Team Meeting (7/21)

Goals:

  • Present the final deliverables
  • Network with more people on LinkedIn
  • Complete Final Assessment for this session

Tasks Completed/Hurdles Faced:

  • I had a little confusion surrounding the data set and the wording of the paper when starting the final deliverables but I resolved the issue with the leads and the mentors
  • I had some trouble using limma on my own without the assistance of my group but I was able to figure it out and complete the deliverables
7

Final Self Assessment:

Things Learned:

  • Reading and identifying the pipeline of a scientific paper
  • Analyzing microarray data
  • Analyzing large and smaller data sets using R
  • Creating different plots using R
  • Basic coding skills using Python
  • Using several different packages in RStudio

Tools:

  • RStudio
  • G-suite
  • Jupyter Notebook
  • Github
  • Asana
  • Slack
  • STEM-Away Forum
  • LinkedIn

Soft Skills:

  • Connecting and networking with new people on LinkedIn
  • Troubleshooting with a small team
  • Effectively working with a small and large team
  • Resume building skills
  • Presentation skills

Achievements:

  • I was able to complete all the deliverables on my own and was able to troubleshoot with my team
  • I was able to present each week with my team and another team
  • I was able to complete a set of deliverables and present on my own in front of a lead and a mentor
  • I was able to network with new people and received new opportunities
  • I attended all the Gene Team meetings and attended several webinars to learn technical skills and soft skills
  • I learned how to use many different platforms over the course of these 8 weeks
  • I was able to learn a lot from being part of the Gene Team and from my teammates in my smaller team

Shanya Sanof Final Deliverables.pdf (925.4 KB)