Purdue highlighting versatile HUBzero technology and more at international supercomputing conference
For researchers like Nick Marra, who’s studying genes in evolutionary adaptation, using BLAST, the standard software for DNA and other biological sequence searches, is now easier and faster with BLASTer, a Web-based version of BLAST sporting a friendly interface and seamless access to powerful computing systems.
Developed at Purdue, BLASTer is enabled by Purdue’s HUBzero platform, a ready-made cyberinfrastructure for research and education that makes it possible to access powerful computational tools right from a Web browser.
Purdue’s booth at SC12, the largest international supercomputing conference, will highlight the new open source version of HUBzero, along with BLASTer and other hub-powered tools and an array of other computing resources Purdue develops to advance groundbreaking research in science, engineering and other fields. SC12 is Nov. 10-16 in Salt Lake City.
“More than 40 virtual communities already use HUBzero in fields ranging from nanotechnology and cancer treatment to earthquake engineering and the bonds between human and companion animals,” says Michael McLennan, chief architect of HUBzero at Purdue. “They can all benefit from the features in this new version.”
A doctoral student in Purdue Professor Andrew DeWoody’s lab, Marra says his research benefits both from the ease of use of BLASTer and from DiaGrid.org, the HUBzero interface to Purdue’s DiaGrid distributed computing system. DiaGrid can make thousands of processors available at once for BLAST searches and reduce the time needed to set up computations and get results.
“DiaGrid is particularly suited for research using BLAST because it involves numerous serial computations that can be parceled out to any number of available processors,” says Carol Song, senior research scientist at the Rosen Center for Advanced Computing, ITaP’s research computing unit.
For Marra, BLASTer on DiaGrid has reduced the time for some jobs from days to hours. That gives him time to do more — and more complex — runs to get higher resolution results and to explore what-if scenarios.
“It makes it feasible to start tweaking to see what is possible,” Marra says.
A major HUBzero feature is its ability to deploy computational research codes, and visualize and analyze results, all through a Web browser. It makes posting tools about as easy as posting a YouTube video and eases access to high-performance computing systems. Moreover, the platform has a growing set of data management tools. Built-in social networking features create communities in almost any field and facilitate communication and collaboration, distribution of research results, training and education.
Other notable hub-based tools
WaterHUB.org, focused on the global issue of water, from availability, or lack of it, to the effects of climate change. The SWATShare tool on WaterHUB makes the U.S. Department of Agriculture’s Soil Water Assessment Tool (SWAT), a standard for modeling how land use changes affect watersheds, accessible literally to anyone.
- nanoHUB-U, a hub-based virtual nanotechnology school with Purdue faculty experts who are pioneers in the field teaching an international student body. Purdue also is in the process of employing HUBzero as the platform for Purdue HUB-U, which will offer interactive courses in a broader array of topics but on the same global basis.
- Purdue University Research Repository (PURR), an online solution for data management plans now required by the National Science Foundation and other funding agencies, which mandate that researchers publish not just results, but the data and tools used to obtain those results. PURR provides a hub where Purdue researchers can collaborate privately with colleagues to gather datasets, clean them up, and eventually publish the data as electronic resources others can access.
- Decades of data on proper levels of calcium intake for kids, now available to researchers, public health officials, nutritionists and physicians worldwide through IndianaCTSI.org, the HUBzero-enabled Web home of the Indiana Clinical and Translational Sciences Institute. The data have been collected by Professor Connie Weaver and her Purdue team as part of Camp Calcium, a fun and educational summer camp for children ages 11 to 15 that also monitors calcium metabolism and absorption rates to inform international health standards. Indiana CTSI is a collaboration between Purdue, Indiana University, the University of Notre Dame and public and private partners.
- The Infusion Pump Informatics Community, designed to improve the use of programmable infusion pumps that intravenously deliver nutrition, fluids and drugs like pain medications, insulin and cancer treatments. Purdue’s Regenstrief Center for Healthcare Engineering and hospitals in Indiana, Iowa, Illinois, Nebraska and Wisconsin partnered to create the online community where members can easily share data and analysis along with best practices. Highlights of the new open source version of HUBzero
A new project-management, collaboration tool for managing data, workflow and communication whether the task is working on a funding proposal or a research paper or developing an application. HUBzero projects include a file repository with version history keeping; wiki space for notes and documentation; to-do lists; and a Facebook-like microblogging tool providing a stream of project updates from team members with the ability to comment on activities.
- Federated identity allowing integration with social networking sites. Users can now log into a hub using their Facebook, Google or LinkedIn accounts, meaning one less password to remember.
- A hub email gateway that automatically processes forum posts and support tickets, making it easier for users to receive status messages and reply without leaving email to go to the hub.
- User interface and tag improvements including cleaner, configurable administrative and starter templates; a sleeker, better integrated user profile page; and tags with new categorization options, aliases and version histories.