UNC Center for Galapagos Studies and Universidad San Francisco de Quito researchers hosted workshops to teach participants how to assemble and annotate genomes de novo. The workshop required high-powered linux environments for participants from twelve institutions and six countries. ITS and SOM-IT collaborated to deliver resources on-time and cost-efficiently.
Between May 22-25, 2022, UNC Center for Galapagos Studies researchers Corbin Jones and Alan Jones, alongside Universidad San Francisco de Quito (USFQ) colleagues Maria de Lourdes Torres and Hugo Valdebenito, hosted the first of two workshops to teach participants how to assemble and annotate genomes de novo.
This workshop, held at North Carolina State University, was made possible by a $1.2m NSF grant awarded in May 2021 to better understand the genetic characteristics of grasses across Ecuador – including the Galapagos, and how the genes within these grasses allow them to respond to changing light environments. This work began with a seed grant from UNC Center for Galapagos Studies, with part of the project being conducted at the Galapagos Science Center.
The 30 students who participated needed a high-powered Ubuntu Linux environment and came to the workshop with a variety of IT support at their home institutions. Corbin Jones and Hemant Kelkar engaged with IT experts at Information Technology Services (ITS) and School of Medicine IT to provide the appropriate computing environment to the students.
Collaborators from ITS, including Chuck Crews, Bruce Messick, and John Godehn, and School of Medicine IT, including Ken Langley and Charles Thayer, met with Hemant on May 17 to better understand the resource needs and costs involved.
The team quickly decided to provide the Ubuntu Linux environments within the Google Cloud Platform (GCP). Each Linux system provided 16 CPUs, 104 GB RAM, and 500 GB of attached disk space to meet the computational need. Hemant Kelkar developed a custom Linux image with the tools needed for the class including R, conda, and jupyter. Final configuration and testing was completed just days prior to the start of the workshop with 30 identical custom Ubuntu Linux systems ready for student use.
Charles Thayer attended the first day of the workshop to help students overcome any IT problems connected to the cloud-based Linux systems.
“Having Charles on-site was huge” and contributed to the program’s success, Corbin Jones said.
“I felt that the solution was perfect for our needs,” Kelkar said.
The team met at the conclusion of the workshop to discuss improvements for delivering this type of environment in the future.
More about the workshop can be found online, and to learn more about how cloud resources can be used to support research or educational work, please contact School of Medicine IT: Research IT.