Nivedha_J - Bioinformatics Pathway

Certificates June 2020 Certificates Bioinformatics Workflow Self-Assessments
1
  • Concise overview of things learned
    • Technical Area: We went over the basics of data visualization with R and the different uses of various R packages. We also went over tools such as ggplot2 to construct things such as heat maps or volcano plots. In addition to that, we have learned how R is applied in bioinformatics and our project specifically.
    • Tools: R packages (ggplot2, DESeq2)
    • Soft Skills: After attending the weekly meetings, I have learned how to better communicate with other team members. In addition to that, the importance of connections was also emphasized, which therefore lead me to update my LinkedIn account and connect with people from our group.
  • Three achievement highlights
    • Learned about various R packages and their uses
    • Learning how to efficiently read a scientific paper
    • Better communicating with team members and connecting with them on LinkedIn
  • List of meetings/ training attended including social team events
    • I have attended all the team meetings, as well as the R trainings and technical training meetings. Aside from that, I attended the Bioinformagic Happy Hour last week as well.
  • Goals for the upcoming week
    • Attend more of the happy hours in order to get to know the team members better
    • Practice and get better at using R
    • Research and learn more about the project topic
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2

Self-Assessment #2:

  • Concise overview of things learned
    • Technical Area: We started learning Python as well as developing more skills and techniques in R.
    • Tools: R packages, Python
    • Soft Skills: We worked with a group on the deliverables and learned how to best communicate in a group setting as well as collaborating with other groups.
  • Three achievement highlights
    • Learned about more skills on R
    • Got to know my group better, and therefore increasing our team efficiency
    • Learning Python
  • List of meetings/ training attended including social team events
    • I have attended all the team meetings, as well as the R trainings and technical training meetings. Aside from that, I attended some of the Python sessions as well.
  • Goals for the upcoming week.
    • Attend more of the happy hours in order to get to know the team members better
    • Practice and get better at using R
    • Complete more of the Python exercises
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • I completed all the tasks for the Week 3 deliverables with my team (Team Enchanted). At first, the coding was confusing but it helped a lot to communicate with my group as well as other members from different teams. The troubleshooting forums and office hours were helpful to get help as well.
    • For the Week 3 deliverables, we installed and loaded the necessary R packages and created a csv file of the data. We then implemented a quality control method, normalized the data, and created a PCA plot. For each of the steps, we worked on them separately then collaborated with our group in order to compare our results and fix any issues we may have had.
    • We also completed the presentation for the Week 3 deliverables with Team Hufflepuff and collaborated well with them.
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3

Self-Assessment #3:

  • Concise overview of things learned
    • Technical Area: We developed more skills on R and implemented them into our data analysis process.
    • Tools: R packages
    • Soft Skills: We worked with a group on the deliverables and learned how to best communicate in a group setting as well as collaborating with other groups.
  • Three achievement highlights
    • Learned about more skills on R (creating volcano plots and performing a phenotypic analysis)
    • Learning how to collaborate efficiently in a group, and improve some things that may not have worked last week
    • Used the office hours and other resources more effectively
  • List of meetings/ training attended including social team events
    • I have attended all the team meetings, as well as the R trainings and technical training meetings. Aside from that, I also attended some of the office hours and one of the fireside chats.
  • Goals for the upcoming week.
    • Attend more of the happy hours in order to get to know the team members better
    • Practice and get better at using R
    • Stay up to date on Asana
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • I completed this Week 3 and Week 4 deliverables with my team (Team Enchanted). The code this week was a little more difficult, but with the help of my team, the troubleshooting forums and office hours we were able to complete all the tasks.
    • For the Week 4 deliverables, I completed all the tasks. First, I had to annotate the normalized data. Then, we used gene filtering to filter out the lower 4% of the data. We then used limma analysis, then created volcano plots from this data. During this process, as well as after finishing, I compared and consulted with the rest of my team members if any of us had questions or ran into problems.
    • We also completed the phenotypic analysis and presented the deliverables with Team Hagrid.
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4

Self-Assessment #4:

  • Concise overview of things learned
    • Technical Area: We developed more skills on R and implemented them into our data analysis process. We also learned how to use external tools to analyze our data such as EnrichR and STRING.
    • Tools: R packages, EnrichR, STRING
    • Soft Skills: We worked with a group on the deliverables and learned how to efficiently manage the work in a group setting.
  • Three achievement highlights
    • Learned about more skills on R (gene ontology analysis, KEGG analysis)
    • Further analyzing the purpose of the functions performed in our Week 4 deliverables through the presentation
    • Used the office hours and other resources more effectively
  • List of meetings/ training attended including social team events
    • I attended some team meetings, but wasn’t able to attend some, so I either watched the recordings or got the information from other group members instead. Aside from that, I also attended some of the office hours and R trainings.
  • Goals for the upcoming week.
    • Attend more of the happy hours in order to get to know the team members better
    • Practice and get better at using R
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • We presented the Week 4 Deliverables and phenotypic analysis with Team Hagrid and completed the Week 5 Deliverables.
    • For the Week 5 deliverables, I completed all the tasks. First, we prepared the ordered data, defined the threshold and used the bitr function. We then completed the gene ontology analysis with the groupGO and enrichGO functions in order to produce bar plots, dot plots, and plot GO graphs. After doing this, we performed a KEGG analysis by producing a dot plot. In addition to the tools we used on R, we used some external tools such as EnrichR and STRING in order to analyze and compare our data.
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5

Self-Assessment #5:

  • Concise overview of things learned
    • Technical Area: We performed Gene Ontology analysis, KEGG analysis, WikiPathways analysis, EnrichR analysis, and STRING analysis during the Week 5 Deliverables.
    • Tools: R packages, KEGG analysis, WikiPathways analysis, EnrichR analysis, STRING
    • Soft Skills: We continued to communicate effectively in our group and collaborate with other groups.
  • Three achievement highlights
    • Learned about more skills on R (gene ontology analysis, KEGG analysis, WikiPathways analysis)
    • Used external tools (STRING, EnrichR)
    • Used the office hours and other resources more effectively
  • List of meetings/ training attended including social team events
    • I attended the team meetings and one of the Python training sessions.
  • Goals for the upcoming week.
    • Attend more of the happy hours in order to get to know the team members better
    • Practice and get better at using R
    • Gain a better overall understanding of what we have done so far so I can complete the individual deliverables
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • I completed the Week 5 Deliverables, and for that we performed Gene Ontology (GO) analysis, enriched GO analysis, KEGG analysis, and WikiPathways analysis. In addition to that, we also used external tools such as EnrichR and STRING. At first, I had some trouble interpreting some of the analysis but after collaborating with my group and doing more research on each method, I was able to gain a better understanding and interpret the analysis.
    • For the team presentations on the Week 5 Deliverables, my team worked with Team Ravenclaw. The biggest challenge was due to the fact that we had differing results and our teams used different methods in certain areas. In order to overcome this, we compared our code and our results to determine what may have caused the variation in the results.
    • Overall, our team communicated really well and efficiently. We worked independently at first, but had frequent meetings to discuss any issues we came across and worked them out.
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6

Self-Assessment #6:

  • Concise overview of things learned
    • Technical Area: I used several skills we have learned so far such as creating heatmaps and volcano plots for the Week 7/8 Deliverables.
    • Tools: R packages
    • Soft Skills: Despite having individual deliverables, I still managed to collaborate with team members or go to office hours if I ran into any problems.
  • Three achievement highlights
    • Used everything we learned so far to analyze the new data set (GSE21510)
    • Still kept in touch with my team
    • Completed Week 7/8 Deliverables and worked on the presentation
  • List of meetings/ training attended including social team events
    • I attended all the team meetings and one of the office hours.
  • Goals for the upcoming week.
    • I was able to gain a better understanding of everything we learned as a whole, and I aim to successfully summarize it all in the presentation for the end of the week.
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • For Week 7/8 Deliverables, I performed several of the skills we learned up till now on the new data set, GSE21510. I used quality control metrics such as Array Quality Metrics, then normalized the data using mas5. I also annotated the data set, performed gene filtering, and LIMMA analysis. After that, I made the volcano plot and heatmap similar to what was shown on the paper. In addition to the part on R, I analyzed the paper and compared it to what we learned throughout this internship.
    • Despite not having to work with a team, we still communicated effectively to compare our results or help each other with any problems we came across.
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7

Final Self-Assessment:

  • Concise overview of things learned
    • Technical Area: During the team meetings and technical webinars, we learned a lot about the field of bioinformatics and the paper we were studying. In addition to this, during R trainings and through completing the deliverables, we also learned a lot of skills in R. Prior to this, I had never used R, however, throughout the course of this internship I was able to learn a lot and become comfortable with using R to analyze data sets.
    • Tools: R Studio, R packages, EnrichR, STRING, STEM-Away platform, Slack, Asana, Zoom and Google Meets
    • Soft Skills: Throughout the course of this internship, we frequently worked in groups and this allowed me to learn how to effectively and efficiently work in a group setting. In addition to this, we also had weekly group presentations on the deliverables for that week which helped me develop my presentational skills. Aside from the activities in the internship itself, we also learned the importance of networking and I was able to build my LinkedIn account more.
  • Three achievement highlights
    • Despite not having any prior experience in R, I was able to successfully complete all the deliverables and analyze the results. We learned several new concepts and new methods to analyze the data which were interesting to learn and connect back to the original paper.
    • I was able to effectively work with my group and developed good connections with my team members. We communicated really well, and aside from the efficient communication to complete our deliverables, we also all got along really well, and I was lucky to have such a great team.
    • I was able to develop my presentation skills through presenting the work we did for each deliverable. I generally struggle with presenting, but I found that once I understood the material really well, and with the support of my team, the presentations weren’t too difficult.
  • List of meetings/ training attended including social team events
    • I attended the majority of the team meeting, and caught up with any of the ones I didn’t attend by either watching the recording or asking my team members.
    • I also attended a majority of the R trainings, technical trainings, and Python trainings.
    • I also attended some of the other sessions such as the fireside chats, and a few of the happy hours.
  • Goals for the upcoming week
    • I aim to continue developing both the technical and soft skills I’ve learned throughout this internship.
  • Detailed statement of tasks done. State each task, hurdles faced if any and how you solved the hurdle. You need to clearly mark whether the hurdles were solved with the help of training webinars, some help from project leads or significant help from project leads.
    • Throughout this internship as a whole, we used data sets collected through the use of microarrays comparing normal and cancer cells, for colorectal cancer.
    • For the Week 3 Deliverables, I started off by installing and loading the necessary R packages and creating a csv file of the data. I then implemented a quality control method, normalized the data, and created a PCA plot.
    • For the Week 4 Deliverables, I annotated the normalized data. Then, I used gene filtering to filter out the lower 4% of the data. I then used limma analysis, and then created volcano plots from this data.
    • For the Week 5 Deliverables, I prepared the ordered data, defined the threshold and used the bitr function. I then completed the gene ontology analysis with the groupGO and enrichGO functions in order to produce bar plots, dot plots, and plot GO graphs. After doing this, I performed a KEGG analysis by producing a dot plot. In addition to the tools I used on R, I used some external tools such as EnrichR and STRING in order to analyze and compare our data.
    • For the individual Week 7/8 Deliverables, I performed several of the skills we learned up till now on the new data set, GSE21510. I used quality control methods such as Array Quality Metrics, then normalized the data using mas5. I also annotated the data set, performed gene filtering, and LIMMA analysis. After that, I made the volcano plot and heatmap similar to what was shown on the paper. In addition to the part on R, I analyzed the paper and compared it to what we learned throughout this internship.
    • Throughout this process, we presented the deliverables each week with our own group and another group. We communicated effectively within our group to compare data and support each other whenever someone ran into a problem. We also communicated well with other groups when creating the presentations for the deliverables.
    • At times, I also came across issues or problems with R, however, I was able to work through them with the help of my group or by attending office hours and getting help from the leads.

Final Presentation Slides

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