Refreshing my knowledge of biology and diving deeper into molecular biology
Tools
Google Calendar has been a life-saver! It’s easier to attend more meetings because all the times and links are in one place
Getting more comfortable with the STEM-AWAY platform, though the user experience is still a bit unintuitive to me
Slack and Google Drive have been working perfectly for me
Excited to learn how to use ASANA, that’s a new platform I have no experience with
Soft Skills
Developing my ability to be patient and compassionate
Recognizing that things are super hectic and rather than complaining about the things that aren’t going well, offering solutions to the problems I point out
Being mindful of other people’s time
Being grateful for the amount of behind-the-scenes effort that us participants may not see, but which is clearly happening
Three achievement highlights
Attended almost all mandatory meetings in real time (I missed one R training session on Tues, July 9)
Completed assignments on time
Being proactive about asking questions and clarifying things I don’t understand
List of meetings/ training attended including social team events
Week 1
Fri 6.29: Internship Kick-off
Mon 7.1: Bioinformatics Webinar
Mon 7.1: Team Meeting
Tues 7.2: R Training
Wed 7.3: Bioinformatics Webinar
Fri 7.5: R Training (only attended first hour)
Fri 7.5: Happy Hour
Week 2
Mon 7.8: Team Meeting
Tues 7.9: Python Training
Wed 7.10: Logistical Training (only attended 1.5 hours)
Wed 7.10: Technical Training
Thurs 7.11: Office Hours
Thurs 7.11: Gene Team Meeting
Fri 7.12: Welcome Session
Fri 7.12: R Training
Fri 7.12: Happy Hour (only attended first 15min)
Goals for the upcoming week
Complete and self-correct all assignments
Meet with my smaller team and go over what our assigned tasks are
Detailed statement of tasks done
Assigned R Tasks from Book (3.2.4, 3.3.1, 3.7.1)
Had questions about the difference b/w geom_bar and geom_col . Went over the entire assignment during our team meeting on Thurs 7.11 and this hurdle was clarified
Couldn’t figure out how to install certain packages and did my own research and realized I needed to update my version of R
R Exercises from June 5 and June 9 Training
I’m still confused about the metadata and will raise this question during our next team meeting
R Exercises from June 12 Training
I’m still confused about the relationship between differentially expressed genes, upregulated and downregulated genes, so I had trouble answering exercise 2. I will ask Yves during our next training session
Unsure how to change the data for the volcano plot. I will clarify this during our next training session
Read the paper Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer
Unclear about figures. We went over the first four during our team meeting on Mon 7.15, which was incredibly helpful
Python Exercises
Problem 2: Write a function where when given an integer n , perform the following conditional actions
– During office hours on Mon 7.15, Goral helped me understand that I couldn’t but n in square brackets
Problem 6: Write conditional statements to check the following statements
– During office hours, Goral helped me with the notation ( 4 in x) for checking whether an integer is in a list
Problem 10: String Repetition and String Length
– During office hours, Goral helped me understand the notion print (len(“Hey!” * 10)) for printing the length of the string “Hey!” , which has been repeated 10 times.
Mine microarray data to extract biological meaning to understand underlying mechanisms relating to colorectal cancer
Read Affymetrix Array data obtained from GEO using Affy package in RStudio
Check Quality Control using the simpleaffy and affyPLM packages
Normalize the raw dataset using RMA normalization technique
Gene expression analysis and identification of differentially expressed genes
Apply linear model to the normalized dataset using the limma package
Explore the relationship between threshold values, log fold change, and p-values
Analysis of genes and their biological functions using DAVID, wikipathways, and Gene Ontology (GO) Analysis
Visualization of microarray data such as bar plots, dot plots, hierarchical clustering maps, heatmaps, Principal Component Analysis, and volcano plots
Tools
Asana
DAVID
GEO database
GitHub
Slack
STEM-Away
RStudio and BiocManager Packages
Soft skills
Teamwork: I worked with Group 5. We had an extremely supportive work environment. We tried the deliverables on our own and then met up multiple times during the week to share different ways of doing things and helping each other out with concepts and code.
Communication: I communicated well with my group members, reaching out with questions when I had them and helping them out when they needed my support. I was a very active participant during the technical training sessions and always asked questions to clarify any misunderstandings and confusing concepts. I proposed various organizational strategies to the Gene Team Leads, such as using GoogleCalendar, in order to help our entire team remember deadlines and find links to all of the various meetings.
Flexibility and adaptability: I was initially very uncomfortable going into this internship due to my lack of experience with Bioinformatics. Over the course of the internship I attended office hours and did some research on my own to better understand the biological mechanisms we were studying.
Curiosity: Overall, this internship sparked my interest in Bioinformatics and I am excited to delve deeper into this field.
Achievement Highlights
I have a solid foundation in Bioinformatics. I am comfortable performing quality control, normalization, DEG and functional analysis on raw files from the GEO database. Over the course of this internship I learned how to mine microarray data. This was done to extract biological meaning of the data in order to better understand the underlying mechanisms of colorectal cancer.
Future Goals
I’d like to combine my paleontological research with genome analysis and study human evolution during the Pleistocene epoch. I have plans to pursue a Master’s Degree in Archaeo- and Paleogenetics. I am excited to conduct genomic research on ancient DNA to better understand our ancestors.