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:
- Completed the Python exercises.
- Learned about the importance of bioinformatics from the webinar.
- 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:
- Uploaded to GitHub for the first time
- Signed up to host office hours for incoming interns
- 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:
- Held office hours and helped someone who is transitioning to the BI team from a different team.
- Helped analyze results of analyses and compared these results to our hypothesis from Week 4.
- 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:
- Got an early start on the final deliverables and completed the volcano plot and heat map.
- Created a great presentation with my group for the GT meeting.
- 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:
- I completed weekly deliverables with my group, which led to an analysis of differentially expressed genes and possible prognostic markers of colorectal cancer.
- 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.
- 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!