Pranhav Sundararajan - BI Pathway - Self Assessment

I have learned a lot about bioinformatics as entering this program I had no experience with manipulating datasets and normalizing them to plot the genes and figure out which ones are the most different. The tasks I have completed are that I have done the deliverables by myself slowly to see if I get the same results as the task leads so that I can check their work and also mine to make sure it is accurate. I faced many challenges as I initially did not know in some steps what to do, especially after normalization and in batch correction. However, with the help of others in my group, I was able to correctly program using the datasets.

7/28 - Self Assessment

Technical Area - I learned about R and how to manipulate methods in R to get the results and models that I need. I have learned a lot about how to normalize and do quality control on datasets.

Tools - I learned how to use and load packages in R as I used multiple different packages, causing me to use multiple different methods.

Soft Skills - I learned how to not only work with my group but mainly ask questions as I am new to R and bioinformatics.

Highlights - I conducted quality control, normalized the dataset, and conducted batch correction while also plotting all the necessary plots.

I attended the presentation meetings and Monday meetings.

Goals - Go back through the deliverables and really understand them more and also build an atmosphere of teamwork and cooperation in my team.

I finished every task in the deliverables but I had initial problems to get started due to my inexperience in R so I had to ask around and truly understand R before proceeding.

8/4 - Self Assessment

Technical Area - I learned more about using the various functions in R and I got comfortable with different arguments and functions to sort through the genes.

Tools - I learned how to use all the various packages and format each type of plot

Soft Skills - I was able to work with my group and ask questions so we were all able to finish the deliverables

Highlights - I finished the plots that were required, I was able to sort through the data and make a final data set, and I was able to convert this into the top 100 differentially expressed genes.

I attended the presentation meetings and Monday meetings.

Goals - Finish the deliverables, get to know my group more, learn more about R

I was able to finish every task in the deliverables but I had some initial problem with sorting through the data because I was not sure if it was in the document. I had to learn that the loops in R are the same as Java and then I was able to proceed.

8/11 - Self Assessment

Technical Area - I learned more about the different packages in R and I learnt more about how to manipulate the plots.

Tools - I learned how to use the new GSEA plots.

Highlights - So far I have done all of the enrich results and the plots for the functional analysis, for example the cnetplots. Also was able to use the gene vector well and extract symbols and IDs when necessary.

I attended the Monday meeting so far.

Goals - Finish the deliverables and learn more about how to analyze and understand the plots.

I had some problems initially with the gene vector as I did not know how to have a named vector but I was able to figure out using RStudio. I also had some trouble with reading the enrichKEGG into setReadable but I had to change the key type in the argument which I later found out.

8/18 - Self Assessment

Technical Area - I was able to learn more about the different normalization methods on my own project.

Tools - I learned how to use the same methods but in a better and more organized way.

Highlights - So far I have gotten the DEG table and am working on GSEA analysis.

Goals - Finish my project and work on the presentation
I had some problems because this is my project all on my own and it has been difficult as we are all working on different datasets and i do not have that much experience with R. But I am working through what I did for the other deliverables and I am adapting that to the current project.

8/27 - Self Assessment

Technical area -Starting this internship I had no knowledge with R and bioinformatics. I had experience with Java but this is still a much different experience. After all I learned, I know how to manipulate and use data to figure out the most dysregulated genes. Furthermore, I learned how to plot using different types of plots such as heatmap and boxplot and cnetplot. I also learned how to conduct differential gene and functional analysis which are all crucial in analyzing our data and gene samples.

Tools: I learned all about R, its main packages, and the various methods and arguments I can use to analyze data.

Soft skills - I worked well with teammates who continuously helped me throughout the internship as I had no prior experience. We made an amazing atmosphere of teamwork and we were all respectful and gracious towards one another.

Highlights - Learned about R and bioinformatics, networked to find friends and colleagues throughout the internship, improved my technical skills and critical thinking to deliver results.

Meetings - I attended all presentations except 1, and I attended all meetings until the last week due to appointments I could not miss.

Goals - Continue to learn and develop my skills to better myself and do meaningful work to help others.

I did the deliverables and completed them but I did have to ask for help periodically throughout the internship and especially at the start. However, I was able to figure these out and work through my problems, giving me a valuable experience I will never forget.