When Purdue Professor Ashlie Martini wants to explain how force variations cause ribbon-like protein molecules to change shape, which governs their myriad functions in the body, she can bring up the webite nanoHUB.org and a web-based application called Forced Protein Unfolding.
The simulator allows visitors to nanoHUB.org to yank on a virtual protein and see what happens, something they certainly can’t do with a microscope. Proteins are too small to view let alone pull, even with tweezers.
Martini, an assistant professor of mechanical engineering, has another application on nanoHUB.org that simulates the role of friction in molecular dynamics, her research focus. She’s also posted course lectures and multimedia slides on the site, an international resource for nanotechnology research and education with more than 100,000 users. The repository is the first stop for her new graduate students, but viewable by any visitor to nanoHUB.org.
“It’s a great tool,” she said of the nanoHUB.org site.
It also is a tool now available to anyone, thanks to the free, open source release of the software package — called HUBzero — underlying nanoHUB.org. The open source package became available in April 2010 on the HUBzero Web site.
Developed at Purdue, HUBzero is the YouTube of simulation tools — sort of a Swiss Army knife for deploying and accessing computational research codes, and visualizing and analyzing results, all through a familiar Web browser interface. Built-in social networking features akin to Facebook create communities of researchers and educators in science, engineering, medicine and almost any field or subject matter while facilitating online collaboration, distribution of research results, training and education.
The open source release has all the software developed in setting up 20 hubs and growing. Besides nanotechnology, the existing hubs enable a wide spectrum of projects in science and engineering, health care research, social science and education. The hubs deliver hundreds of research tools, seminars and other materials to nearly a half million users each year, while helping to satisfy National Science Foundation and other grant-funder cyberinfrastructure requirements.
“Hubs have become successful in a variety of diverse disciplines, including cancer research, thermal engineering, pharmaceutical manufacturing, and earthquake science, to name just a few,” says Gerry McCartney, Purdue’s vice president for information technology and chief information officer. “These new open source tools are going to allow dozens of additional science and engineering hubs to spring up over the next few years. These tools accelerate the development of research communities and provide real benefit to research impact and discovery.”
The open source package includes:
• HUBzero Web, social networking and research publishing elements.
• Middleware that makes it easier to connect to supercomputing clusters and other grid-computing infrastructure.
• Middleware to manage online research and educational tools and tool sessions, along with HUBzero’s Rappture tool kit, which helps turn research codes into web-enabled, graphical applications.
That’s everything needed to build a hub for use by researchers, educators and others at single or multiple institutions with the full ability to host, deploy, use and collaborate with real research codes, which is the most prominent feature of HUBzero, says Michael McLennan, senior research scientist and hub technology architect at Purdue.
“It’s kind of a hub-in-a-box,” McLennan says.
Purdue will continue to offer a hub hosting service. But the open source release allows users to host a hub themselves, whether on a server farm or a Linux PC under a graduate student’s desk.
What those using the open source software will get is a hub without content — no tools, seminars, tutorials, populated message boards and the like. McLennan likens it to a fully equipped library whose shelves have to be stocked.
Hub builders wanting to use commercial software that can work within HUBzero, such as MATLAB and Adobe Presenter, also will have to do their own licensing of that software.
HUBzero is supported by a consortium of universities including Purdue, Indiana, Clemson and Wisconsin. A major motivation for the open source release is to enlist an even larger pool of developers who will help further advance the technology.
“We’re hoping to build a vibrant community around this,” McLennan says.
The open source version of HUBzero is covered by a GNU Lesser General Public License. The license commits developers who make changes in the existing core software to returning those changes to the community as open source. New system software and research codes aren’t covered by the license. But nothing prevents them from being made available either, and there will be a mechanism, something like an “app store,” for doing so, McLennan says.
McLennan says developing for HUBzero ranges in degree of difficulty from familiar Web development with PHP scripting and similar tools, to more complicated, system-level programming in the middleware, to specialized research codes.
Forced Protein Unfolding was developed by a summer undergraduate intern in Martini’s Purdue lab. A graduate student built Atomic Stick-Slip, the molecular dynamics simulator.
“They thought it was pretty fun,” Martini said of building tools in HUBzero.
HUBzero was originally developed to power nanoHUB.org, but the underlying technology proved so attractive that Purdue extracted and tailored it for application in other fields. Other hubs now link researchers transforming laboratory discoveries into new medical treatments; working to revolutionize cancer prevention, detection, treatment and care delivery; promoting assistive-technology innovations for those with disabilities; and engineering earthquake-resistant buildings, bridges and related structures, among other things. A hub will be at the center of the Network for Earthquake Engineering Simulation (NEES), a $105 million NSF program announced in 2009.
Writer: Greg Kline, science and technology writer, Information Technology at Purdue (ITaP), (765) 494-8167 (office), (765) 426-8545 (mobile), firstname.lastname@example.org
Sources: Michael McLennan, (765) 494-6495, email@example.com
Gerry McCartney, (765) 496-2270, firstname.lastname@example.org
Last updated: Jan. 10, 2011