# Ethanlau - Bioinformatics Pathway **URL:** \ **Category:** Bioinformatics Workflow Self-Assessments\ **Created:** [June 16, 2020, 7:44pm UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501 "2020-06-16T19:44:15Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Ethanlau](https://d2nat51eddc6b4.cloudfront.net/letter_avatar_proxy/v4/letter/e/8a9e4e/32.png) [@Ethanlau](https://stemaway.com/u/Ethanlau)\ **Post date:** [June 16, 2020, 7:44pm UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501/1 "2020-06-16T19:44:15Z")
**Things Learned** Technical Area: I learned the main idea of the paper and the basic skills of coding in R. I also brushed up on my python skills. Tools: R, Jupyter Notebook, Slack, Asana Soft Skills: Learning how to work in groups on an online platform. **Achievement highlights** Read through the paper and understood the fundamentals of it. Completed all assignments in a timely manner. **List of training and meetings attended:** 6/1 Team meeting, 6/2 R training, 6/5 R training, 6/9 R training, 6/9 Python training, 6/10 logistical meeting, 6/10 technical webinar, 6/11 Office Hours, 6/11 team meeting, 6/12 welcome session, 6/12 R training, 6/12 Happy Hour, 6/15 Team Meeting, 6/15 Python Office Hours, 6/16 Asana Training **Goals for the upcoming week:** Continue to build my skills in R and Python and apply what I learned to the data. Further my understanding of the paper and produce results. **Tasks Completed** All R Exercises All Python Exercises. Read the paper _Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer_. One of the main hurdles I faced when completing the tasks was the difficulty of understanding many of the figures and what those figures represented. I solved this problem by asking questions and looking up what those figures represent. ---
**Author:** ![Ethanlau](https://d2nat51eddc6b4.cloudfront.net/letter_avatar_proxy/v4/letter/e/8a9e4e/32.png) [@Ethanlau](https://stemaway.com/u/Ethanlau)\ **Post date:** [June 25, 2020, 4:21am UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501/2 "2020-06-25T04:21:00Z")
**Things Learned** Technical Area: I learned how to create PCA plots and quality control plots in R. I also learned how to conduct normalizations and preliminary analysis. Tools: affy, affyPLM, and affyQCReport, Asana Soft Skills: Learning how to work in groups on an online platform. **Achievement highlights** Completed Week 3 Deliverables and learned how to use Asana. **List of training and meetings attended:** 6/16 Asana Training, 6/16 Python and Pandas Webinar, 6/17 Technical Training Webinar, 6/18 Gene Team Meeting, 6/19 Gene Team Happy Hour, 6/19 Office Hours **Goals for the upcoming week:** Continue to build my skills in R and Python and apply what I learned to the data. Starting the week 4 deliverables ahead of time. **Tasks Completed** Completed PCA plot Completed NUSE and RLE boxplots and histograms of medians. One of the main hurdles I faced when completing the tasks was the difficulty of getting the code to work due to my inexperience in R. I overcame this by asking questions and googling. ---
**Author:** ![Ethanlau](https://d2nat51eddc6b4.cloudfront.net/letter_avatar_proxy/v4/letter/e/8a9e4e/32.png) [@Ethanlau](https://stemaway.com/u/Ethanlau)\ **Post date:** [July 9, 2020, 5:35pm UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501/3 "2020-07-09T17:35:44Z")
**Things Learned** Technical Area: Learned how to annotate genes in R Preliminary understanding of Limma (package in R) Tools: Limma, Annotation Packages, Pandas, Seaborn, Matplotlib, Github Soft Skills: Learning how to work in groups on an online platform. **Achievement highlights** At first, I was very confused on how to complete the week 4 deliverables. After communicating with my group, we collectively completed the Week 4 Deliverables. **List of training and meetings attended:** 6/24 Office Hours, 6/24 Fireside Chat, 6/25 Bioinformatics Webinar, 6/25 Gene Team Meeting, 6/29 Gene Team Meeting, **Goals for the upcoming week:** Continue to build my skills in R and Python and apply what I learned to the data. Starting the week 5 deliverables earlier so I can ask questions. **Tasks Completed** Completed Week 4 Deliverables Presented on Week 3 Deliverables Compiled Phenotypic Data ---
**Author:** ![Ethanlau](https://d2nat51eddc6b4.cloudfront.net/letter_avatar_proxy/v4/letter/e/8a9e4e/32.png) [@Ethanlau](https://stemaway.com/u/Ethanlau)\ **Post date:** [July 27, 2020, 7:03am UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501/4 "2020-07-27T07:03:16Z")
**Final Self-Assessment** **What I Have Learned:** - Understanding scientific writing (figures and methodology) - Analysis of microarray data using R - Downloading GEO datasets from online databases - Running quality control assessments in R - Understanding and creating PCA plots, heat maps, and volcano plots using microarray data - Differential expression analysis - Determining gene ontology - Creating plots in python using seaborn and matplotlib - Other packages in R (affy, affyPLM, etc.) **Tools:** - Asana - G-Suite - Jupyter Notebook - R Studio - Github - STEM-Away forum - Slack **Soft Skills:** - Connecting with people on linkedin - Working in both small and groups in an online environment - Improving my presentational skills - Helping others perform tasks **Achievements:** Over the course of this 8-week internship, I learned many things related to field of Bioinformatics. I learned how to extract and analyze data using R packages, despite my limited prior knowledge of the topic. I learned how control the quality of data and how to find trends in differentially expressed genes. On top of the technical skills I learned at this internship, I gained valuable soft-skills involving communication and teamwork. I hope to use the skills and knowledge I learned from this internship to future positions in the classroom and in the workplace. [EthanLau.pdf](https://stemaway.com/uploads/short-url/aVqZaVhkfzOSU2XqVx8N5gvceyV.pdf) (65.2 KB) ---
**Author:** ![Ethanlau](https://d2nat51eddc6b4.cloudfront.net/letter_avatar_proxy/v4/letter/e/8a9e4e/32.png) [@Ethanlau](https://stemaway.com/u/Ethanlau)\ **Post date:** [October 12, 2020, 7:08am UTC](https://stemaway.com/t/ethanlau-bioinformatics-pathway/3501/5 "2020-10-12T07:08:30Z")
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