ChloeLi - Bioinformatics Pathway

Certificates July 2020 Certificates Bioinformatics Workflow Self-Assessments
1

Self assessment for week 7/19 - 7/25

Things learned:

  • Technical area: I reviewed the procedures to perform quality control, normalization and PCA plot on microarray data and looked into new functions such as simpleAffy and mas5. I also learned how to correct the batch effect among sample sets and make heatmaps using the pheatmap package.
  • Tools: R, GEO database, Slack, Google Suite, STEM-Away forum.
  • Soft skills: I actively reached out to and connected with team members on the STEM-Away forum as well as on Slack. I also made sure to promptly address the problems my peers are facing with my experience in the June session.

Achievement highlights:

  • Re-familiarized myself with essential initial steps in handling the data.
  • Learned to perform batch effect correction and make nice-looking heatmaps.
  • Connected with new team members and tried to help them out with coding problems.

List of training and meetings attended:
7/20 team meeting, 7/21 biology webinar, 7/23 group meeting, 7/26 group meeting.

Tasks completed:
Completed all the deliverables on my own.

Goals for the upcoming week:

  • Work as a task lead of the group and streamline the working process by properly assigning deliverables and helping out members.

  • Further connect with the team members and other participants.

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2

Self assessment for week 7/26 - 8/1

Things learned:

  • Technical area: I reviewed the procedures for annotation, gene filtering, limma analysis and volcano plot. I explored new functions to achieve the same objective, such as collapseRows() and na.omit().
  • Tools: R, Slack, Google Suite, STEM-Away forum.
  • Soft skills: I volunteered to be the task lead this week and I created documents for the deliverables and presentation so that the group could collaborate. I also actively communicated with my group members and addressed their confusions on the forum and Slack.

Achievement highlights:

  • Re-familiarized myself with differential gene expression analysis.
  • Worked as a task lead to streamline cooperation among the group members.
  • Completed all deliverables despite I was in an urgent moving situation.

List of training and meetings attended:
7/27 team meeting, 7/28 team presentation.

Tasks completed:
Completed all the deliverables on my own and created deliverables & presentation documents.

Goals for the upcoming week:

  • Look into new areas that were not covered in the June session (survival analysis, etc).
  • Get to know my group members and other participants better.
3

Self assessment for week 8/2 - 8/8

Things learned:

  • Technical area: I re-familiarized myself with the purposes and procedures for gene ontology analysis, KEGG pathway analysis, and PPI network construction using STRING. I also learned to construct gene-concept network and gsea plots, as well as to interpret them. Finally, I used external tool GEPIA to perform survival analysis of the differentially expressed genes.
  • Tools: R, Slack, Google Suite, STEM-Away forum, STRING, GEPIA, GitHub.
  • Soft skills: I led the group presentation for differential gene analysis as a task lead. I actively connected with participants from STEM-Away on LinkedIn and got to personally know some of them.

Achievement highlights:

  • Dived deeper into functional analysis by performing more types of analysis and interpreting their results.
  • Took the lead to produce the presentation slides.
  • Completed the deliverables early by researching and asking questions on the forum.

List of training and meetings attended:
8/3 team meeting, 8/4 team presentation, 8/5 deliverables webinar.

Tasks completed:
Completed all the deliverables on my own; created and submitted the deliverables document and R script on GitHub; created presentation slides for cooperation.

Goals for the upcoming week:

  • Start working on my independent final project by looking into the context of the data.
  • Apply the procedures I learned during the internship to the project.
4

Self assessment for week 8/9 - 8/15

Things learned:

  • Technical area: I reviewed the procedures for QC, DEG analysis and functional analysis. I learned to download and arrange metadata for the microarray data from GEO. I looked into new functions to perform these procedures such as gcrma(). I researched about AML and learned its basic mechanism.
  • Tools: R, Slack, Google Suite, STEM-Away forum, GEO, STRING, GEPIA.
  • Soft skills: I actively communicated with my teammates and leads when situations came up and I was not able to attend the meetings.

Achievement highlights:

  • Applied skills learned with colorectal cancer to AML.
  • Grasped the fundamentals of AML.
  • Challenged myself to work with data of not AML and normal samples, but MYC wildtype and MYC mutant samples.

List of training and meetings attended:
8/10 team meeting.

Tasks completed:
Looked into new datasets for AML and picked a research theme; researched about AML and MYC; performed all required procedures on the selected data.