Chai - Bioinformatics Pathway

Overview of things learned:

  1. Technical:
  • Systematic way to understand a biology paper, understand figures and critique

  • Coding in Python and R studio

  • Improved understanding of plots in R

  1. Tools:
  • R studio, tools related to visualization and organizing data

  • Python bioinformatics tools


  • Slack

  • STEM-away platform

  1. Soft skills:
  • Etiquette in a virtual classroom
  • time management
  • Raising relevant questions

Three achievement highlights:

  1. Ability to read a scientific research paper in an organized way
  2. Getting comfortable with R visualizations
  3. More organized in understanding meeting schedules, deadlines

Meetings attended:

  • Technical Webinars [3]

  • R Training Workshop [2]

  • Python Trainings [2]

  • Logistical Webinar

  • Gene Team Meetings

  • Asana Training

Goals for next week:

  • improve background knowledge on CRC and prognostic markers

  • attend social meetings

  • complete all assignments


  1. Technical:
    getting more comfortable with R.
    Learnt to import data, pre-processing, generate QC report, exclude outliers, normalize with mas5, PCA plotting and interpretation, annotation, gene filtering, limma package, normalization methods, QC report
    Tools pertaining to Asana, Slack, StemAway

  2. achievement highlights

  • understood figures in the paper-
  • participated in coordinated presentations with another team
  • asked relevant questions in different webinars
  1. Meetings Attended:
    All team meetings
    Fireside chats with mentors [2]

  2. Goals for next week

  • Develop deeper understanding of the biological concepts such as differential gene expression
  • timely work on week 5 deliverables
  • attend social meetings

SELF-ASSESSMENT [FINAL]: Chaitra Sreenivasaiah

I joined STEM-Away’s online internship in June as an observer, with a strong background in medicine and biology, and almost no experience in R and data analysis. My aim was to develop a greater understanding of the growing field of Bioinformatics, through immersion and working on a hands-on project. Simultaneously, I also hoped to interact with many students from diverse backgrounds and draw inspiration from the experienced mentors.

My main take-aways:

  • Technical:

    • Strategies for dissecting salient aspects of a scientific paper, and the utility of figures in conveying the information.
    • Beginner-level understanding of the BioConductor and related packages in R Studio, concepts of Differential Gene Expression and Gene Ontology, the stepwise pipelines available to perform pre-processing, Quality control, Normalization and analysis of both kinds of data.
    • Improved my ability to code in R, and Python.
    • Improved ease while working with platforms GSuite, STEM-Away, LinkedIn, Slack, Asana and GitHub.
  • Soft Skills:

    • Actively participated in all Training sessions, Gene team meetings and group meetings. Tried to ask relevant questions, and contributed to group presentations.
    • Began working on networking on the LinkedIn Platform.
    • Learned the importance of formatting my Resume, making a good elevator pitch, maintaining positive body language, and cultivating cultural competence.

Final thoughts:

  • Training sessions were extremely useful to get me up to speed with the background knowledge and skills needed for the various tasks.
  • The work was well organized over many weeks, with periodic deliverables and reminders.
  • Unfortunately due to the lockdown, many other responsibilities encroached on my time. This impacted my performance during this internship.
  • Nevertheless, I am very thankful to everyone at STEM-Away, the organizers and leads who put together this online program, and thus facilitated me to gain valuable Bioinformatics experience during these troubled times.
  • I hope to return in November as a Participant!