Reha_Matai - Bioinformatics Pathway

  • Concise overview of things learned
    -Technical Area: We went over the basics of Python, including print statements, variables, data structures, and applications in math. Also, the R trainings have covered the basics about R and how to work with R studio. Yves taught an introduction of data visualization and covered ggplots, heatmaps, histograms, scatterplots, and volcano plots.
    -Tools: R programming (data visualization), Python programming(basics)
    -Soft skills: By attending team meetings, the welcome session with Erin, and the welcome chat with Debeleena, I have had the chance to communicate and get to know my team members. It was a great idea to get to know the leads and team members before starting the project to know who we’re working with and to feel comfortable asking for help/anything else.
  • Three achievement highlights
    -As I haven’t had much prior programming experience, I’m that that I was able to understand the basics of both R and Python.
    -Attending and/or watching all team meetings and webinars to keep up to pace with everything that is going on
    -Attempting to understand the scientific paper we’re using for the project and researching terms/understanding concepts that I’m unfamiliar with
  • List of meetings/ training attended including social team events
    -I have attended or watched all the Bioinformatics meetings, which includes all of the R trainings with Yves, the Python trainings, the webinars, welcome chat with Debeleena, and the get to know everyone meeting with Erin. I didn’t attend the paint happy hour, but will definitely attend the upcoming happy hours to not miss out on a fun hour to socialize and get to know everyone.
  • Goals for the upcoming week.
    -I am going to be sure to make a schedule for the week to not miss out on any team meetings
    -Get started on the R exercises and go through what was taught in the 4th training because I was having trouble with one part.
    -Attend the happy hour this week to get to know everyone better
1 Like

Self Assessment - 6/23

  • Concise overview of things learned
    -Technical Area: I learned to visualize data through PCA, visualize analysis reports from quality control methods, create multiple plots such as histograms and boxplots, and why we should normalize data.
    -Tools: R studio and R
    -Soft skills: I attended the happy hour on Friday and got to know my team better. I also communicated and worked with my partner for the week 3 deliverables. We helped eachother out and I learned a lot from her.

  • Three achievement highlights
    -was able to understand and create the PCA plot with some help
    -made many new Linkedln connections from sharing my linkedln with other stem away members
    -worked through the Week 3 deliverables through communicating with my partner, not doing it alone

  • List of meetings/ training attended including social team events
    -went to Asana training, 2 of the team meetings, the technical training, and the happy hour

  • Goals for the upcoming week.
    -complete the Week 4 deliverables ahead of time and not wait till last minute
    -continue to attend the happy hours
    -since I’m not doing much this week, attend all the meetings and keep up with everything

  • A detailed statement of tasks done
    -From week 3 deliverables, I completed steps 1-3 without much trouble. I used the technical trainings and completed it with my partner
    -Steps 4 and 5, especially step 5, were harder for me to do and I came across a few hurdles. I tried plotting PC1 and PC2 but my code for this didn’t work. When talking to my partner (Disha) about this, she showed me her code and I was able to find my error. I also had some trouble with the data visualization for plots. I used some online resources to figure it out as well as talked to Disha about it.
    -We submitted the assignment first and have started reaching out to the other team to discuss our presentation. This week, I joined Asana and slack as well as filled out the feedback forms.

1 Like

Self Assessment (6/29)

Concise overview of things learned
-Technical Area: I learned how to analyze data using the limma package in R, improve making volcano plots, and annotate as well as filter genes through functions in R.
-Tools: R studio and R, Python Jupyter notebook
-Soft Skills: I attended a happy hour to play a game and worked with my team for deliverables

Three achievement highlights
-learned how to analyze using Limma
-made more stem-away connections on LinkedIn
-completed the assignment on time and used help from others

List of meetings/ training attended including social team events
-I attended the team meetings last week, but will look at the meeting notes for todays meeting. I attended the fireside chat, python trainings, and Webinar with Ali. I also went to the happy hour with my team.

Goals for the upcoming week.
-complete the phenotypic analysis
-get started on Week 5 deliverables soon
-continue practicing and improving my Python skills

A detailed statement of tasks done
-I joined the teams github, attended meetings, and finished the week 4 deliverables which includes the volcano plot, model matrix, data set annotation, and limma analysis.

1 Like

Comprehensive Self-Assessment (leaving on 7/3)
Concise overview of things learned

  • Technical Area: I learned many data analyzation and visualization methods using Python. I also learned how to visualize data and create many plots in R such as histograms, boxplots, heatmaps, and volcano plots. I gained knowledge and how to use a variety of packages and functions in R to filter data, annotate genes, and for normalization.
  • Tools: R studio and R, Jupyter Notebook for Python, Github, Asana
  • Soft Skills: In these 5 weeks, I have improved on my communication and teamwork skills by working with other people to complete the deliverables and create presentations together. I have also expanded my network and created a Linkedln. I got to know my teammates better through the happy hours.

Three achievement highlights

  • With no experience in R and a little experience in Python, I have learned and improved a lot in both of these programming languages.
  • I created a Linkedln and added many people from stem away
  • I attended/watched all meetings

List of meetings/ training attended including social team events

  • I attended most meetings live, and watched/looked at notes for those I couldn’t make it to. These are the webinars , team meetings, R trainings, Python trainings, Asana/Github trainings, fireside chats, and the calls with my deliverables team.

A detailed statement of tasks done

  • I finished the deliverables for weeks 3,4, and 5. Week 3 includes the background normalization and correction, visualization from quality control methods, and creating histograms/boxplots. Week 4 includes analyzing data from the Limma package, gene filtering, and creating a volcano plot/model matrix. For week 5, I did the phenotypic analysis. I also joined Asana and Github.

I really learned a lot from this internship, especially with R and Python. Thank you to all the leads for organizing such great meetings and webinars! I appreciate all the time and hard work they spent to be sure we had the best experience. I loved meeting and working with a few new people and expanding my network as well!

1 Like