Sydneymcmahon - Bioinformatics Pathway

Self Assessment 6/15

  • Concise overview of things learned
    • Technical Area: I have attended and/or watched all the R Trainings given by Yves so far. These have included learning the basics about how R and R Studio work (what the four panes do, how to import data, basic commands), as well as getting into more complicated practices with graphing and data visualization (using ggplot to create bar graphs, scatter plots, heat maps and volcano plots and visualize various patterns).
    • Tools: R Programming Language, Python basics from previous experience.
    • Soft Skills: Through team meetings, happy hours and chats with Debaleena, I have already practiced team communication and a little bit of networking. It certainly helps to get to know the team in the beginning of any project so that as issues and complications arise, it’s easy to work things out.
  • Three achievement highlights
    • Staying on top of all the R Trainings and finding success in the exercises since I have never really considered myself someone who loves programming.
    • Putting in the effort to get to know my Leads and teammates and further networking through LinkedIn.
    • Reading and really trying to understand the scientific paper we will be using for our project.
  • List of meetings/ training attended including social team events
    • I have attended all team meetings–Team 1 and now Bioinformagic (I believe there have been 3 so far).
    • I have attended all training webinars (2 during week 1, 1 during week 2).
    • I attended 3 of the R Trainings and watched the 4th that I couldn’t attend live afterwards.
    • I attended both of the happy hours with my team.
    • I also attended the Welcome Chat with Debaleena.
  • Goals for the upcoming week
    • Since the pace of the project will be ramping up this week, I am setting the goal for myself to stay on top of all my meetings and assignments. I am organizing all my “To-Do’s” so that I know exactly what is expected of me. I am going to start the first R assignment early and ask for help when necessary. I also hope to get to know all of my teammates and leads a little bit better this week!
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Another really well written self-assessment. Covers all important points in a concise way. And perfectly formatted!

Your team rocks :slight_smile:

Self Assessment #2 (6/23)

  • Concise overview of things learned
    • Technical Area: Through the recent R Trainings and Week 3 Deliverables guide, I learned how to deal with microarray data and visualize that data through principal component analysis (PCA). I also learned how to interpret various plots and figures that are produced by quality control and the importance of normalizing data to more accurately analyze it.
    • Tools: R Programming Language & R Studio.
    • Soft Skills: I have continued to attend team meetings and happy hours to get to know my team better. Since splitting into smaller teams for the weekly deliverables, I have worked with that team and communicated regularly with them. I have also continued to network through LinkedIn.
  • Three achievement highlights
    • Through help at Office Hours last week I was able to produce all the necessary deliverables for Week 3.
    • I helped another team work through their code and understand where they may have made an error so that they could produce the deliverables themselves.
    • I made 10+ new LinkedIn connections in my field, in the STEM-Away network and more.
  • List of meetings/training attended
    • I attended the two team meetings last week and the one we had yesterday.
    • I attended the Asana Training and Technical Training last week.
    • I attended Office Hours last week.
    • I attended our “Family Feud” Happy Hour.
  • Goals for the upcoming week
    • This upcoming week is a busy week for me aside from the STEM-Away program, so I want to make sure I am prioritizing tasks and making good use of my time so that I can complete what is asked of me. I will make sure to regularly communicate with my teams and leads and check emails and tasks assigned.
  • 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.
    • There were 5 steps for our Week 3 deliverables. I completed Steps 1-4 with the help of the Week 3 Deliverable guide on the GoogleDrive as well as the Technical Training from 6/17. These steps included installing all necessary libraries in R, loading the gene data, performing quality control on the data to assess the quality and normalizing the data.
    • Step 5 (visualization) was trickier for me, so I sought help from the project leads and mentors at Office Hours this past week. They walked me through their code so that I could better understand the necessity of each step to produce the final PCA plot. Before going to Office Hours, I did a lot of searching online and found great resources as well.
    • My team and I produced and submitted the Week 3 deliverables on time. We used resources from online and from the 6/17 Technical Training to understand our data better and explain our results.
    • I joined Slack and Asana.

Self Assessment #3 (6/30)

  • Concise overview of things learned
    • Technical area: This past week I have learned how to perform gene annotation, filtering, and analysis with the limma() R package in order to conduct differential gene expression analysis. I read documentation for several R functions to better understand them and how they contribute to DE.
    • Tools: R Studio, GitHub, Asana, Slack
    • Soft Skills: I have continued to communicate with my smaller team as well as the other team we worked with for our first deliverables presentation. I have also tried to communicate well with my leads. I have also continued my LinkedIn networking.
  • Three achievement highlights
    • I was able to produce results for my Week 4 Deliverables with the help from others on the forums and in separate chats, as well as from the leads.
    • I stayed on track with assignments and attended the meetings, even with other priorities going on.
    • I learned about several new R packages that will be able to help me down the line.
  • List of meetings/training attended
    • I attended the GitHub Webinar #1, Ali’s Bioinformatics Webinar and our two Bioinformagic team meetings last week and this yesterday.
    • I was not able to attend as many meetings and trainings as I wanted, but did what I could due to family traveling and work outside STEM-Away.
  • Goals for the upcoming week
    • I am choosing to stay in this internship for the next 3 weeks because I am enjoying the work and learning a lot; however, I am starting a new intensive internship next week so I want to make sure I am setting aside time for both internships. I will make sure to communicate extremely well with my leads and team members so they know where I am at.
  • Detailed statement of tasks done.
    • Team Hufflepuff and Team Enchanted successfully presented our Week 3 Deliverable results and I believe we did a great job! Communicating about when to meet beforehand was tough at first, but we were able to meet up to discuss how to set up our presentation slides and practice presenting.
    • I was able to complete all the Week 4 Deliverables: gene annotation (adding gene symbols as row names), gene filtering (removing any data below a certain percentile) and creating volcano plots (to show the log fold changes and adjusted p-values of the differentially expressed genes). I used resources found on Google, as well as the Google Drive and Trainings. I also communicated with my teammates and Team Enchanted to compare our data, and while we did not get the same results, I tried my best to figure out what I had done differently and how I could fix my code. Even though I was not able to produce the correct volcano plots, I have continued to go back in my code and seek help from other students about how to adjust my code. I plan on going to office hours this week and rewatching some of the R Trainings to see where I may have gone wrong.
    • I am working on setting up GitHub and being able to upload my future deliverables there.
    • I have communicated well with my teammates through GroupMe, email and video calls.
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Self Assessment #4 (7/7)

  • Concise overview of things learned
    • Technical Area: Through following the Week 5 Deliverables doc, I have learned about Gene Ontology (GO) analysis, KEGG analysis, WikiPathways analysis and external tools that can be used on the gene data.
    • Tools: R Studio, GitHub, Metascape, STRING
    • Soft Skills: I am continuing my communication with teams and leads, networking through LinkedIn and other places, and management of time and my other internship.
  • Three achievement highlights
    • I took the time to sort through my Week 4 code that was incorrect and figure out where I went wrong and how to fix the code. I ended up producing the correct results and presenting with my team.
    • I figured out how to use GitHub to upload code and deliverables.
    • I am having success with the Week 5 deliverables and am excited to present them next week.
  • List of meetings/training attended
    • I attended the second GitHub webinar last week.
    • I attended our Bioinformagic team meeting (presentations) last week and the mentor meeting yesterday.
    • I attended Office Hours earlier today.
  • Goals for the upcoming week
    • I have moved teams due to some people leaving after the 5 weeks, so I hope to communicate with my new team about the tasks for the week and communicate with my presentation teams. I will consistently check the forums and Asana and make sure I’m on top of my work. I also hope to compare my Week 5 deliverable results with teammates and create a great presentation.
  • Detailed statement of tasks done.
    • I completed the Phenotypic Data Analysis by downloading a series matrix file from GEO, accessing the phenodata and adding it to the original expressionSet (normalized, no outliers)
    • I successfully corrected my originally-incorrect Week 4 deliverable results before presentations by troubleshooting using online resources (GEO2R) and help from other teams.
    • Team Hufflepuff and Team Hagrid presented our Week 4 deliverables in a collaborative presentation. We met beforehand to discuss and compare our results and create the presentation/delegate slides.
    • I have almost finished the Week 5 deliverables as detailed above. I am working on communicating with my new team and the teams I will present with next week.
    • I made sure to upload R files to GitHub that I hadn’t uploaded yet.
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Self Assessment #5 (7/14)

  • Concise overview of things learned:
    • Technical Area: After finishing up the Week 5 deliverables, I continued to explore the Metascape external tool to really figure out the uses and what it has to offer. I also went back through the other weeks’ deliverables and ran through all the code to recap my understanding of all the steps I’ve learned.
    • Tools: R Studio, GitHub
    • Soft Skills: Through my last week of this program, I made sure to keep my teammates and leads in the loop of my decision to leave STEM-Away. I also made sure to completely finish my presentation and any other tasks so that I could leave on a strong note.
  • Three achievement highlights
    • I completed the Week 5 deliverables and checked them with a mentor and confirmed I had the right code and results.
    • I communicated with my team/other teams and my leads about changes to the teams so that things were clear for the deliverables and presentation.
    • I successfully presented my last set of deliverables for this program!
  • List of meetings/training attended
    • The BI team meetings last week and yesterday (presentations)
    • My last happy hour on Friday
  • Goals for the upcoming week
    • I am leaving the program, but will reflect on my awesome experience here!
  • Detailed statement of tasks done.
    • I completed the Week 5 deliverables which included performing Gene Ontology (GO) analysis, enriched GO analysis, KEGG analysis and WikiPathways analysis. I also made use of external tools such as Metascape and STRING. I found a lot of help for these deliverables online, but made sure I understood the code and method for every step I was taking. I ran into a bit of an issue at the beginning with the format of my data; however, I was able to use a different method than described in the deliverables doc and still complete the necessary steps.
    • Team Slytherin (the team I moved to), Team Magic and Team Wand worked together nicely to present out results for the Week 5 deliverables.

Cumulative Self Assessment (7/14)

  • Concise overview of things learned:
    • Technical Area: Through reading and analyzing a scientific paper and attending technical training webinars, I learned about what bioinformatics really is on a deeper level, what bioinformaticians do, and how coding languages are used to analyze not only gene data, but really any type of biological data. Through the R trainings and practicing on my own, I grew from not ever using R before to feeling very comfortable coding in R and being able to use outside resources when I get stuck. Learning about microarray analysis to determine differentially expressed genes in a dataset was really interesting and something I want to continue to look into in the future.
    • Tools: R, R Studio, Zoom, Slack, Asana, GitHub, STEM-Away forums
    • Soft Skills: STEM-Away made sure to emphasize the importance of soft skills and I certainly came to understand this through LinkedIn connecting and networking, communicating with my team and leads and time management of the several things I had to balance.
  • Three achievement highlights
    • I am proud of myself for coming into the program having never coded in R before (but coded a little bit in a few other languages) and picking up the syntax, functions, methods, how to seek help, etc. Thanks you to @yvesgaetan for his wonderfully helpful R trainings!
    • Building on the previous highlight, I successfully completed all the deliverables that were assigned. Even if I didn’t get things working perfectly right away, I was always able to troubleshoot through online resources or the forums. Additionally, submitted everything on time and stayed on track with everything.
    • Lastly, I am proud of myself for staying engaged in the program throughout its duration. I felt as though I always spoke up during meetings, whether it was a comment about the work itself or just chatting with the leads/others. I posted on the forums frequently and tried to help others, in addition to asking my own questions. I also attended as many happy hours as I could to get to know my teammates and leads outside of the work-aspect of the program.

Thank you to @egunduz, @Isha and @yvesgaetan for all their help and dedication to making this program a success! I have truly learned a lot and am excited to see what is next for me in the bioinformatics field!

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It was so wonderful getting to know you @sydneymcmahon!! All the best :smiley:

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Well done @sydneymcmahon!! You did a great work during the whole session and I’m really happy that the other leads and I helped you achieving your goals. All the best :clap:t5: :clap:t5: :clap:t5:

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