The Rosetta REU: software lets students collaborate at a distance

Johns Hopkins Institute for NanoBioTechnology (INBT) has launched a summer research undergraduate internship to train students to build new lifesaving drug molecules and create new biofuels, while testing the concept of a virtual research community. With the help of a $200,000, two-year grant to INBT from the National Science Foundation, Jeffrey Gray, professor of chemical and biomolecular engineering, spearheaded a first-of-its-kind training program where students collaborate with others from distant host university labs and use computer software to build vaccines, biofuels, and protein circuits in living cells.

Typical summer internships bring students together to one host university, but students in the Computational Biomolecular training program use an open-source software called Rosetta to work together on problems no matter where they are. Participants are mentored by members of a global collaborative team known as the Rossetta Commons, and users analyze massive amounts of data to predict the structure of real and imagined proteins, enzymes, and other molecules.

ChemBE professor Jeff Gray (standing) confers with Rosetta Commons undergradutate intern, Morgan Nance (seated left), and her mentor, Rebecca Alford (seated right), undergraduate research assistant, as they video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University.

ChemBE professor Jeff Gray (standing) confers with Rosetta Commons undergraduate intern, Morgan Nance (seated left), and her mentor, Rebecca Alford (seated right), undergraduate research assistant, as they video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University. Photo by Will Kirk/Homewood Photography

“Computational biologists study known macromolecules or design new ones and use computers to predict how these molecules will fold in 3D and interact with cells or other molecules,” said Gray. “For example, researchers create computational algorithms to design a new drug molecule or use the Rosetta software to predict how molecules might behave in a living organism. And because the work is done using a computer, researchers can easily collaborate at a distance.”

The students in the pilot program began with a week-long boot camp at the University of North Carolina at the end of May. Then, they traveled to host universities, which included Johns Hopkins; University of California, Davis; Scripps Research Institute; Stanford University; New York University; Rensselaer Polytechnic Institute; and Vanderbilt.

Morgan Nance, a biochemistry and molecular biology major from the University of California, Davis, worked in the Gray Lab. “I hope to become more familiar with Rosetta to the point that I am able to utilize it in my home lab,” Nance said. “I want to gain the technical skills of how to use this new software and the knowledge of how to develop it further. “

With the pilot program, students quickly expand their skill set. “Each lab has different expertise,” Gray said. “One lab might specialize in protein docking, another in RNA structure and design, another in vaccine design or protein function. When students cross train in these laboratories, they learn to recognize the common themes. “

Each week, Nance and her colleagues “met” via video chat to discuss current published papers and to present updates from host labs. At the end of 10 weeks, the Rosetta cohort convened at the annual RosettaCON in Leavenworth, Washington. Though Nance was on her own at Hopkins, INBT staff included her in activities organized for their other summer research interns.

“If this distributed model works just as well as the traditional one, we would then be able to accept this kind of model and access the best labs in the country for doing research,” said Sally O’Connor, the NSF program director.

Story by Mary Spiro

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

Leave a Comment

*