Erin Doyle, a biology professor at Doane University, says Jetstream cloud computing in the classroom gives computational biology students an opportunity to understand the scope of bioinformatics.
Covering data manipulation, sequence data, as well as reading and writing files, Doyle’s goal is to give students experience with the tools of the trade.
“I think it’s important for computational biologists to have some basic coding skills,” said Doyle. “And that’s where Jetstream comes in because I require them to learn basic Python programming.”
“With Jetstream, I want them to understand what’s happening between clicking the button and the output appearing like magic,” said Doyle.
Starting with the basics, Doyle’s students learn to read and manipulate code, starting with variables and, later, string variables. “They can interact with Jetstream at whatever level they want,” said Doyle. “It acts like a desktop but what’s actually happening is the job is run on a supercomputer.”
Before Jetstream, Doyle’s students accessed virtual machines that often took up too much memory on their laptops. Now, it’s easy.
I can just create a virtual machine, everyone logs into the web browser so it’s not using a lot of memory. Jetstream makes it so much easier to get everybody up and running ~ Erin Doyle, Doane University
As part of a small university located in Crete, Nebraska, Doyle says Jetstream gives students a chance to explore the wide world of bioinformatics. “They can start to think of how big some of these computations can get,” said Doyle.
“We’re talking about protein structure modeling—how if you tried to model all the interactions and forces between all of the atoms, that computation is so big it won’t finish before your laptop’s battery dies,” Doyle added.
Jetstream may also have an impact on Doyle’s work in agriculture. She compares the structure of rice genomes, and also considers the roots of corn plants. Both projects require large files containing genomic data, along with the ability to share data among researchers at other institutions.
Given how well Jetstream has worked in the classroom, Doyle is considering it for her own work. “We have all of these images on Google Drive, and some of them are on another server, and the code is somewhere else. It really becomes a problem when these projects get big.” Having data and code on Jetstream, like in her classrooms, “would really help the collaboration process,” said Doyle.
"Research and education support is a core tenet of Indiana University (IU). We're pleased to support Doane University through the Jetstream project to train the next generation of scientists through access to leading-edge resources," said Dave Hancock, director for advanced cyberinfrastructure in IU's Research Technologies division.
Jetstream, led by the Indiana University Pervasive Technology Institute (PTI), is funded by the National Science Foundation, and is accessible to researchers and educators free of charge. The system also fosters reproducible, shareable computing with a geographically isolated cloud located at the Texas Advanced Computing Center.