Community Highlight: An Nguyen and Dinh Phan
An Nguyen (AN) and Dinh Phan (DP, pictured below) are high school students who conducted summer research with KBase as part of Oak Ridge National Laboratory’s Next Generation STEM Internships (NGSI) program.
Dinh Phan, Farragut High School
For their project, they worked in KBase to sequence 4 bacterial genomes isolated from the rhizosphere of Populus trichcocarpa, commonly known as poplar or black cottonwood trees. These isolates were provided by the Plant-Microbe Interfaces (PMI) SFA.
How Has KBase Supported Your Research or Project?
(AN) KBase is an extremely easy platform to navigate and it helped me with my job of sequencing my isolates. I used tools for quality assessments of sequenced reads and trimming them, as well as assembling them together for later use such as determining taxonomy and functions.
(DP) KBase has been integral to my work. I have used the apps that KBase houses; from sequencing the genome to annotating it and building a species tree, I have used KBase in every step of my analysis and research.
What is your favorite part about using KBase?
(AN) I think my favorite part was the DRAM app. It is very useful for determining the isolate’s functions.
(DP) My favorite part about KBase is its user-friendly interface and the variety of apps that it houses. It is very easy to understand as a first-time user, and all the workflows and the overall design of the platform makes sense. As a user, I also appreciate the diversity of apps that KBase houses. It is very convenient to have all of my workflows, and be able to display all of my data on one platform.
What role do you see KBase having in open science principles (related to your work)?
(AN) I believe that KBase could open up doors for easier access to high quality works, such as genome sequencing. In my work, KBase enabled reproducible workflows for genome sequencing, annotation, and metabolic modeling. It also allowed me to share my findings with other researchers and improve communication.
(DP) KBase embodies the core values of open science by making data, tools, and workflows accessible and shareable. This promotes transparency and collaboration across all institutions and disciplines. As a student researcher, KBase gave me access to professional-grade tools without having to cross the border of paying expensive fees, and I was able to share my work in a way that contributes to the broader scientific community.
Special thanks to Delaney Beals, PMI post-doc who provided the isolate data for this project.
