Skip to main content

Student researchers collaborate virtually with help of open-source software

July 29, 2015

A summer research internship for undergraduates is not only helping them learn to build new lifesaving drug molecules and create new biofuels—it’s also testing the concept of a virtual research community.

The Johns Hopkins Institute for NanoBioTechnology—with the help of a $200,000, two-year grant from the National Science Foundation—has launched a first-of-its-kind training program in which students study vaccine design, create biofuels, and build protein circuits in living cells, all with the help of specialized software that lets them collaborate from distant host university labs.

A typical summer research program—the institute’s Nanobio Research Experience for Undergraduates, for example—brings students together to one host university, where they work in different laboratories on various projects. In the new pilot training program on Computational Biomolecular, students use an open-source software called Rosetta to work together on problems in computational biology and are mentored by faculty who are part of a global collaborative team known as the Rossetta Commons. The software gives users the ability to analyze massive amounts of data to predict the structure of real and imagined proteins, enzymes, and other molecular structures.

Chemical and Biomolecular Engineering professor Jeff Gray (standing) confers with Rosetta Commons undergraduate intern Morgan Nance (left) and her mentor, undergraduate research assistant Rebecca Alford, during a video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University. IMAGE: WILL KIRK / HOMEWOODPHOTO.JHU.EDU

Chemical and Biomolecular Engineering professor Jeff Gray (standing) confers with Rosetta Commons undergraduate intern Morgan Nance (left) and her mentor, undergraduate research assistant Rebecca Alford, during a video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University.
IMAGE: WILL KIRK / HOMEWOODPHOTO.JHU.EDU

“Computational biologists study known macromolecules or design new ones and use computers to predict how these molecules will fold in 3D and how they might interact with cells or other molecules,” says Jeffrey Gray, professor of chemical and biomolecular engineering at Johns Hopkins and the INBT affiliate who spearheaded the program. “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 their research experience with a weeklong boot camp at the University of North Carolina at the end of May. The following week, students traveled to their host universities, which include Johns Hopkins; University of California, Davis; Scripps Research Institute; Stanford University; New York University; Rensselaer Polytechnic Institute; and Vanderbilt.

Excerpted from The Hub. Read the complete story here.

Back to top