Kristen_15 - Bioinformatics Pathway

Week 3 Self Assessment

  • Concise overview of things learned:
    Technical Area: Analyzed the raw and normalized dataset, learned the importance of normalizing the data
    Tools: Used R to complete week 3’s deliverables, learned how to use Asana, practiced more Python and introduced to Pandas
    Soft Skills: Organized meetings with my team, reached out for help from mentors

  • Three achievement highlights:

  1. Initiated contact with my team members for us to start the deliverables.
  2. Completed Week 3 deliverables with help from my teammates and mentors.
  3. Completed most of the Linkedin professional tasks.
  • List of meetings/ training attended including social team events: 6/15 Gene Team Meeting, 6/16 Asana Training, 6/16 Python and Pandas Webinar, 6/17 Technical Training Webinar, 6/18 Gene Team Meeting, 6/18 Office Hours, 6/19 Gene Team Happy Hour

  • Goals for the upcoming week: I hope to create a good presentation with my teammates. I also hope to attend the Fireside chat.

  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    I worked on number 2 of the deliverables, then focused on the PCAs. This was my first time using R independently to code for bioinformatics, so I faced many challenges such as confusion on how to get the correct data into my environment and how to code for certain things. These hurdles were solved by asking questions to my mentors on Slack, attending office hours, searching the Internet and checking the troubleshooting page on the STEM-Away website.

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Week 4 Self-Assessment

Concise overview of things learned:
Technical Area: Learned about quality control and the normalization of data through the presentations of different Gene Team groups. Created a presentation with my group members.

Tools: Used R for annotation, gene filtration and the limma package. Used Python to complete the second set of exercises. Created a GitHub profile.

Soft Skills: Reached out to Team 8 to start working on our presentation, organized team zooms, created & shared documents for my team

Three achievement highlights:

  1. Completed the Python exercises.
  2. Learned about the importance of bioinformatics from the webinar.
  3. Created an informative presentation with my group and we were the first group to present.

List of meetings/ training attended including social team events: 6/22 Gene Team Meeting, 6/25 GitHub Training Webinar, 6/25 Webinar with Ali, 6/25 Gene Team Meeting, 6/26 Office Hours BI, 6/26 R training (recording)

Goals for the upcoming week: Complete phenotypic data tasks with my group and learn more about how we will use GitHub in the future.

Detailed statement of tasks done: Worked on the table for the first deliverable with help from teammate. Organized group meetings for my group and with Team 8. Completed the second set of Python exercises. I had some difficulty with the Python exercises because I am a Python beginner. I used the forums and Slack to ask questions, which helped greatly. I also went to office hours for the leads to further explain the deliverables.

Week 5 Self Assessment

Concise overview of the things I learned:
Technical Area: I completed the Python Exercises and fixed any errors after going to the training. I learned how to upload my work to GitHub. I used R to complete deliverables and phenotype task.

Tools: GitHub, Python, R, Google Slides, Slack, Asana

Soft Skills: Created Slack group for my team and team 1 because we were presenting together. Organized our Zoom meeting to work on the presentation. I connected with people on LinkedIn and followed a few hashtags.

Three Achievement highlights:

  1. Uploaded to GitHub for the first time
  2. Signed up to host office hours for incoming interns
  3. Came up with a future hypothesis in our presentation, and I am excited to see if it is accepted or rejected after analyzing the pathways

List of meetings/trainings attended: 6/29 Gene Team Meeting, 6/29 Python Training, 7/1 GitHub Webinar, 7/2 Gene Team Meeting

Goals for upcoming week: Practice using GitHub and Python

Detailed statement of tasks done: My team worked on deliverables and phenotype tasks separately, then we all came together to discuss. I coordinated working on the presentation with the other team by reaching out to them, scheduling a Zoom, and creating the Google Slides presentation. I worked on a few different slides in the presentation. I had trouble with some of the coding for the phenodata tasks, but after Yves sent out a message clarifying it, I was able to complete it. I had issues with one of the Python exercises, but during the Python training I was able to share my screen and we all went over the problem together.

Week 6 Self Assessment

Concise overview of the things I learned:
Technical Area: I learned more about GitHub in the Python Training. I learned more about the different analyses we can do with the data, listed in the Tools below.

Tools: GitHub, Python, R, Slack, GO analysis, KEGG analysis, WikiPathways, STRING

Soft Skills: Created Slack group for my team and team 5 for our presentation. Edited my resume with help from the presentation in our Gene Team meeting.

Three Achievement highlights:

  1. Held office hours and helped someone who is transitioning to the BI team from a different team.
  2. Helped analyze results of analyses and compared these results to our hypothesis from Week 4.
  3. I could not make my group’s meeting about the presentation, but I communicated effectively and worked on the slides ahead of time.

List of meetings/trainings attended: 7/6 my office hours, 7/8 Gene Team Meeting, 7/9 Python Training

Goals for upcoming week: Work on individual deliverables and come up with ideas for STEM-Away in the future. Get more LinkedIn connections before the internship comes to an end.

Detailed statement of tasks done: I had trouble creating the gene vector at first and I reached out to my teammates for help. I created the Google Slides presentation after initiating contact with the other group we were presenting with. In the Python training, I contributed thoughts to future Python exercises and projects.

Week 7 Self Assessment

Concise overview of the things I learned:
Technical Area: I used R to complete the volcano plot and heatmap for the final deliverables. I used Google Slides to create a presentation with my group for our deliverables and for my final deliverable presentation.

Tools: Python, R, Slack, Google Slides

Soft Skills: Learned public speaking and presentation tips in the Gene Team meeting.

Three Achievement highlights:

  1. Got an early start on the final deliverables and completed the volcano plot and heat map.
  2. Created a great presentation with my group for the GT meeting.
  3. Asked many questions to clarify and get a clear understanding of the final deliverables.

List of meetings/trainings attended: 7/13 Gene Team Meeting, 7/15 Gene Team Meeting

Goals for upcoming week: Finish my final deliverables and create a great presentation. Practice my presentation so I am ready for Thursday.

Detailed statement of tasks done: I presented with my group by describing our hypotheses and going over some of the results. I used R to analyze the other data set from Guo to get a volcano plot and heat map for the final deliverables. I asked questions on Slack about the directions for the final deliverables and the leads responded right away with answers.

Final Self-Assessment

Concise overview of the things I learned:

Technical Area: microarray data analysis using R, quality control of a large dataset, mas5 normalization method, creation of various visualization graphs (volcano plots, PCA plot, heat map), reading a research paper, forming new hypotheses from the previous week’s results, basic dataset analyses in Python

Tools: R, Python, GitHub, STEM-Away Forums, Asana, Slack

Soft Skills: LinkedIn/networking, communication within team, presentation skills, resume help, cultural competency, creative thinking

3 Achievement Highlights:

  1. I completed weekly deliverables with my group, which led to an analysis of differentially expressed genes and possible prognostic markers of colorectal cancer.
  2. After starting this internship with very limited R experience, I was able to complete the final deliverables all by myself, including the creation of a volcano plot and heat map from a new dataset.
  3. Throughout this internship, I was able to redefine my prior ideas of bioinformatics. I used to assume all bioinformaticians needed to be expert coders. However, bioinformatics requires scientists with many different specialties, such as biology, computer science and statistics to name a few.

Meetings Attended during the last week: 7/21 GT Meeting, 7/23 Presentation

Final Remarks:
I would like to thank all of my teammates, leads, and mentors for their help throughout this internship! I am very grateful I had this experience, and that I was able to make connections with all of you. I came into this internship with very little coding experience, but my confidence with R and Python has grown immensely during these 8 weeks. This internship has made me consider choosing a future path in bioinformatics!

Goodluck to everyone in the future!

Kristen Kelly - Final Deliverables (1).pdf (556.2 KB)

PDF of final deliverables!