Vaidehip - Bioinformatics Pathway

Concise overview of things learned.
Technical Area: I have gained knowledge about R and R studio which I had never used. I have watching all R training to better understand about R programming. Also, I have gained experience on using R packages and libraries such using ggplot to create a plot or graph for data visualize. Also, python training were helpful with understanding basic of python programming

Tools: Data visualization in R and python programming.

Soft Skills: I am working on knowing more people in the team and learning to be able to communicate more openly.

Three achievement highlights

  1. Understand the scientific paper more in depth as we will be using the paper for this project.
  2. Learning R programing and basic knowledge of Python
  3. Have added people on LinkedIn and asked for help when I needed. Trying to get in touch with people in my team.

List of meetings/ training attended including social team events
I have attended webinar and meeting whenever I can but I haven’t been able to attend all meetings and happy hour because I started working three weeks ago so I had work training ongoing .However, I have been watching most webinars and trainings when it were posted so I m up to date with what is going on.

Goals for the upcoming week. Next self-assessment will be due on the following Tuesday 06/23;
My goal for this week is to attend most of the meeting and training because I have tried to adjust my work schedule so I will try to attend most of it. I also have made a to-do list for assignment which are due this week and next week. I also want to get to know more people in my team and get connected to them on LinkedIn.

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Concise Overview of things Learned( week 3)
Technical Area: I learned to visualize data by PCA and also plot quality control plot by using packages from bioconductor. Also, learned why PCA is important and quality control step is essential.
Tools: R studio, Bioconductor.
Soft skills: I worked with my team member and tried to help each other.

Three achievement Highlights

  1. I was able to create qc plot and PCA plot by trying multiple codes and learned so much about R.
  2. New Linkedin connection with stem-away team members and some professional connection
  3. I worked through week 3 deliverable and ask for help to Vyes when I got coding error.

List of meeting/training attended
I have attended webinar and team meetings but couldn’t attend happy hour( working at that time). I have been watching webinar and team recording if I missed any. I m up to date with what is going on and when assignments are due.

Goals for the upcoming week.
My goal is to start working on week 4 deliverables and ask questions if I need any help with anything. I would try to attend all team meetings.

Task completed( week 3)
I completed all steps for week 3 deliverables but I have make some changes. I was able to do step 1 and step 2 easily. Also, I was able to plot qc plot with the code. However, I struggled a little bit with step 4 which was write a file .csv. I had to try different codes to able to get the excel file at the end. Also, I tried code multiple ways to produce my PCA plot. I learned so much R this week as I don’t have any coding background. I intend to work with my team to make presentation for Friday.

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Concise Overview of things learned (Self-assessment)

Technical Area : I learned how to do annotation, gene filtering and Volcano plot. I learned to use more packages such as Limma. Also, I learned how to produced volcano plot from output of previous steps. I had problems with producing volcano plot but I was able to learn.
Tools: R studio, Github, R packages( Bioconductor)
Soft skills: Worked with team member from different team when encounter problems with some steps.
Three Achievement Highlights:

  1. I learned how to use Limma package and also gene filtering.
  2. I Communicated with team members and other team’s by using slack. I also tried to reach out first if I have any question.
  3. I learned more about R and also created Github account.
    List of meetings/training attended including social team events
    I have attended webinar and team meetings last week but I couldn’t attend happy hour last Friday. I couldn’t attend R training on Friday but I have watched the recorded video.

Goals for the upcoming week.
I have chosen to end my internship on July 3rd. I learned a lot about R and bioinformatics in past 5 weeks during my internship. My goal for this week is I will be doing my presentation on Thursday and submit phenotypic analysis deliverable on Wednesday on time.

Task completed
I completed all the steps for week 4 and submitted it to GitHub. Both of the team (Sam and I) worked together to finish the week 4 deliverable. We were late to submit because we had issue in R. We both worked together well and were able to help each other even though we are in different team (we worked as team).

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Concise Overview of things learned ( Comprehensive Self-assessment-5 Weeks)
Technical Area: During 5 weeks of my internship at STEM-AWAY, I learned a lot about R programming, scientific research paper and Bioinformatics. I learned how to use packages from Bioconductor, PCA plot, quality control of samples, ggplot to create a plot or graph for data visualization. I also learned how to annotation, gene filtering and volcano plot.
Tools : R studio, Github, R packages, Python
Soft skills: Worked with different team member and try to communicate with them well before presentation and deliverable due date

Three Achievement Highlights:

  1. I learned R programming and many bioinformatics techniques
  2. I have try to communicate with my team and team that I had to do presentation with. I was the first person to email each team if we were working on presentation or deliverables. I got comfortable with communicating especially approaching them first.
  3. linkedin connection

Task completed
I have completed all tasks and presentation except the week 4 deliverables presentation. I participated and worked with all my team members to finish the deliverable and presentation. I think that it could be better if I had same team members from Week 2 to Week 5. Changes in team such as team members makes it difficult sometimes. I was working almost full time and managing my internship so I had to manage my time. I was able to learn a lot about R programming as I had never used R before.

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