Samfenske - Bioinformatics Pathway

Certificates June 2020 Certificates Bioinformatics Workflow Self-Assessments
1

  • Concise overview of things learned

    • Technical Area: The R training has been very helpful in learning the general format of RStudio and the packages that we’ll be using for this project. I am familiar with python and have gone through the Jupyter notebooks to make sure I’m well-versed in the code provided.
    • Tools: RStudio, specifically ggplot2 and DESeq packages
    • Soft Skills: The past week I have been working on my management and communication skills, as there are multiple platforms for information and communication. Also, interacting with new teammates virtually is a new challenge to me, but I have enjoyed the team happy hours and I look forward to getting to know my teammates.

  • Three achievement highlights

    • I have completed all of the R trainings and feel confident completing exercises/assignments in R.
    • I have gone through all of the webinar notes and recordings and have a firm grasp on the project goals.
    • Been to all of the meetings since I moved from observer to participant (last Thursday).

  • List of meetings/ training attended including social team events

    • I have been to all of the team meetings after last Wednesday.
    • I attended the first two R trainings and have watched all of the other recordings.
    • I attended the painting happy hour and enjoyed it very much!

  • Goals for the upcoming week

    • My goal is to thoroughly read the paper and its referenced/related research to have a greater understanding of research in bioinformatics. Now that I have a good grasp of all of the platforms, I plan to make all team meetings/happy hours and technical training unless I have a valid excuse.
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2
  • Concise overview of things learned
    • Technical Area: Over the past week, I have greatly improved my understanding of how different datasets and data types are used in RStudio. I was confused why my PCA plot was so jumbled, but I had not realized that there were cell line files in the raw dataset- this made more sense when I saw the actual files on the GEO2R website. I have gone back and reviewed the slides from last weeks webinar and am starting to understand the main bioconductor methods we’ve been using.
    • Tools: I am becoming familiar with the RStudio format, especially how to teach myself different methods or data types by consulting bioconductor or other online resources
    • Soft Skills: Engaging in a project that is entirely virtual has been a bit challenging, but I feel much better going in to next week. It’s important to have office hours on my radar so that I can uncover any issues beforehand. I think my communication has been consistent, and will improve the more comfortable and familiar I am working through the virtual platforms. The earlier one communicates, the better!
  • Three achievement highlights
    • My team submitted the week 3 deliverables on time.
    • My team’s submission had some errors in not removing the cell line data and having a messy PCA graph, but I have gone through Yves’ solutions and now understand where our errors were.
    • Feel confident working with new team members and incorporating their insight into the team’s work.
  • List of meetings/ training attended including social team events
    • Attended all of the team meetings.
    • I attended all of the training sessions for the week.
    • I was unable to make the happy hour this week- but I look forward to the next one!
  • Goals for the upcoming week
    • Work on week 4 deliverables before office hours so that I can ask questions before deadlines approach.
    • Gain a greater understanding of the biocunductor functions, to the extent that I could explain them to someone else without having to look at notes.
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3
  • Concise overview of things learned
    • Technical Area: Interpreting the different data types in bioinformatics and how to interpret plots/visualizations. I also learned a lot about the bioinformatics and data science fields from Ali and Alex’s webinars.
    • Tools: How to really code on my own rather than just copy and paste methods that I know I’m supposed to use- how to modify data to look a certain way.
    • Soft Skills: I’v been communicating well and frequently with my teammates! It’s been a unique experience to work with students from so many different backgrounds and apply our different skills to contribute to a team effort.
  • Three achievement highlights
    • Finishing the week 4 deliverables after much work was an accomplishment.
      *Working with new team members to finish phenotypic deliverables.
    • Attended the two webinars on about different fields in industry.
  • List of meetings/ training attended including social team events
    • Attended all of the team meetings.
    • I missed the R training, but have watched the recording.
    • I was unable to make the happy hour this week- but I look forward to the next one!
  • Goals for the upcoming week
    • This week will conclude my time with bioinformagic- it has been a great experience!
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4
  • Concise overview of things learned
    • Technical Area: Coming in to the program, I really did not know much about bioinformatics other than it was the intersection of biology and computer science. Getting a dense introduction to the bioinformatics tools that are used for research will serve me as I continue down the bioinformatics path.
    • Tools: I did not have much understanding of R beforehand, but now I feel as confident tackling tasks in R as I do in languages I’ve known for a while. I also understand the significance of R and the packages/methods that are available.
    • Soft Skills: Collaborating on difficult technical assignments virtually was a challenge, but I learned to embrace the environment and learn from my teammates. Each member of a team possesses unique skills or knowledge that can be shared in order for the team to achieve a greater understanding or product. I feel confident, especially virtually, managing technical projects and accomplishing group work effectively.
  • Three achievement highlights
    • Working with new teammates from all over the country/world, coming from different academic backgrounds to achieve group projects.
      *Learning a and applying new coding language ®, as well as software programs such as Bioconductor and RStudio.
    • Performing microarray analysis to examine differential gene expression in normal vs. colorectal cancer patients.

This has been a tremendous all-encompassing learning experience! There are so many technical tools, industry knowledge, networking strategies and knowledge, as well as personal connections that I have gained over the last five weeks. I want to thank Isha, Yves, Erin, and everyone else who helped put this program together!

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