Dan Binderman - Bioinformatics Pathway - Self Assessment

Concise Overview:
Over the course of Week 2, my ability to code with R greatly improved. Considering that I had never previously worked with R, I expected getting thrown straight into a bioinformatics pipeline reliant upon usage of R would be very difficult; and although I faced some syntax challenges at first, I believe I caught on relatively quickly by watching videos and using the help feature in R Studio.

Achievements:

  1. I gained a comprehensive understanding of the bioinformatics pipeline that we will be performing. While this may seem basic, I believe it is crucial to have a firm understanding of our goals ahead of time so that we can connect with the project more.
  2. I improved my programming knowledge by working with R and making sure to write out effective comments to help out my team members.
  3. I managed to produce a wide variety of graphs in R Studio when performing quality control and normalization. By taking the time to look at the graphs and truly understand them, I managed to improve by analytic skills as well.

Meetings Attended:
I attended the overall group meeting where we engaged in team-building activities and introductions to our purpose in performing quality control and normalization techniques. Additionally, I joined some of the office hour meetings throughout the week to ask some questions.

Upcoming Goals:
I would like to collaborate with my team more because I believe that part of what I can take out of this internship is experience in working with a group on a programming project.

Tasks Completed and Challenges Faced:
This week I successfully completed quality control, normalization, and batch correction of the datasets. Nevertheless, I faced some errors throughout the coding process, specifically an error “cannot allocate vector of size ___”. After trying several different solutions, the one definitive one was to expand the memory limit with memory.limit(size = 100000).

Concise Overview:
Week 3 went much better than the prior week because my team and I collaborated with each other much more effectively, making the completion of the deliverables easier and more efficient. Furthermore, I learned the fundamentals of differential gene analysis, a concept that I believe has an infinite amount of applications in the real-world.

Achievements:

  1. I greatly improved my communication and team-building skills because I was the task lead for this week, which meant that I was responsible for ensuring our group’s timely completion of the deliverables. Together, we learned what it means to be successful collaborators on not only a coding project but really any project in which the members have a like-minded objective.
  2. I additionally improved my leadership skills because of my role as the task lead. Through effective communication and being receptive to my groups needs (as they were receptive to mine in previous weeks), I made sure that we all not only finished the deliverables and presentation but also understood the bioinformatics concepts.
  3. I performed differential gene analysis on a large dataset for the very first time and I learned to analyze the results and graphs, thus improving my ability to describe technical visuals. I also learned how to perform limma analysis to obtain a set of differentially expressed genes.

Meetings Attended:
I attended the overall group meeting where we engaged in team-building activities and an overview of the differential gene analysis process. Additionally, my group and I scheduled several meetings throughout the week to collaborate. Working with my group was very fun on a social standpoint and helpful on a technical standpoint.

Upcoming Goals:
Although I believe my ability to describe what is going on improved, I would like to improve next week in terms of a less-technical delivery. I want to be able to explain technical concepts in a way that nearly everyone can understand.

Tasks Completed and Challenges Faced:
This week I successfully completed the differential gene analysis on the dataset and analyzed the corresponding visuals. Some challenges I faced were, in fact, with understanding some of the more complex plots that I had never seen before, but I quickly learned the meaning behind these plots by asking the project leads.

Concise Overview:
Week 4 consisted of functional gene analysis on the significantly differentiated genes that we observed from the results of the differential gene analysis. I continued learning more about R applications for bioinformatics, analysis of obscure visuals, and new, useful databases.

Achievements:

  1. This week I was successfully able to apply my knowledge of the central dogma theory that I learned in high school for the purposes of the functional gene analysis. This, essentially, helped our group in finding several effective protein-protein interactions to target for a potential treatment of colorectal cancer.
  2. I continued to improve my R programming capabilities by playing around with various functions, including the enrichGO function to display the cellular functions of the top differentially expressed genes and GSEA analysis to determine how extraneous conditions may have influenced gene expression.
  3. I continued working with my group and we even worked with some more challenging Bioconductor packages, like DOSE, enrichplot, and WGCNA to perform the functional gene analysis. Additionally, we successfully identified useful hub genes.

Meetings Attended:
I attended the overall group meeting where we engaged in team-building activities and functional gene analysis examples. Additionally, I collaborated with my group in various meetings throughout the week.

Upcoming Goals:
The upcoming week is the one of the final project and so I hope to be able to successfully complete it and learn a lot from the process.

Tasks Completed and Challenges Faced:
This week I successfully completed various functional gene analysis techniques. Most of the errors I faced were minor syntax errors, but they were all relatively easy to fix once they were spotted.

Concise Overview:
During Week 1 of the bioinformatics internship and in the days leading up to it, I taught myself the basics of R, was introduced to bioinformatics pipelines, and learned about the applications of bioinformatics in the real-world.

Achievements:

  1. After having taught myself R through videos and the provided tutorials, I successfully completed the assessment. For example, I learned about the various data types, such as vectors, matrices, and data frames.
  2. I became more accustomed to using the stemaway platform by submitting posts with questions and answers to other questions.
  3. I learned how to use GitHub to collaborate on code, such as how to merge different programs, use pull requests, and create repositories.

Meetings Attended:
I attended the overall group meeting where we engaged in team-building activities and introductions.

Upcoming Goals:
I would like to challenge and expose myself to the world of bioinformatics in a way that I cannot in the school setting.

Tasks Completed and Challenges Faced:
Although it proved challenging at first, I managed to teach myself R and how to utilize GitHub.

Concise Overview:
Week 5 was the most challenging because I was largely on my own, however it was also the most rewarding because I was proud of my accomplishment in going from being a beginner to bioinformatics and R to developing my independent pipeline in a span of one month.

Achievements:

  1. Via an independent bioinformatics pipeline, I explored the gene networks that vary among breast cancer patients of different molecular subtypes (Her2, LumA, LumB, TN).
  2. I managed to help some of my peers with their own bioinformatics projects by answering their questions. This was a fun challenge because I was completely new to their program (seeing as how we were studying different diseases), but I had to come up with creative solutions to aid them. Some were simpler, such as using a different quality control metric, while others were more challenging, such as amending functions.
  3. I improved my presentation skill because I ended up presenting my final results to the leading panel of the internship. Not only did I improve my delivery skills, but also my presentation-creating skills.

Meetings Attended:
I attended the overall group meeting and several group meetings to discuss our results and practice presenting. I also listened to some of my peers’ presentations to support them.

Upcoming Goals:
With the useful information I learned over the course of this internship, I look to continue to pursue my love of learning and feel more confident in my future computational biology endeavors.

Tasks Completed and Challenges Faced:
I successfully completed my final research project for the internship and it is definitely a milestone I am proud of because of the amount of time I put into learning and troubleshooting.