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SDSC's Swami Revamps Decade-Old Biology Workbench; Plans Fall Launch

The San Diego Supercomputer Center’s Biology Workbench is getting a makeover as it approaches its tenth birthday.
Mark Miller, principal investigator for the redesigned system, called Swami, said that the new version should be available the end of summer. Swami will fully replace the Biology Workbench to serve the approximately 32,000 users currently registered for the platform, which allows biologists to search a number of protein and nucleic acid sequence databases through a single web-based interface.
The original Biology Workbench is the work of Shankar Subramaniam, who began developing the system at the National Center for Supercomputing Applications at the University of Illinois, Urbana-Champaign in the late 1990s. He brought the system with him when he joined the University of California, San Diego, in 1999.
Miller told BioInform that the concept of an integrated bioinformatics system was a “novel idea” at the time. “There are about 66 tools and 33 databases and the idea was to provide people with a toolkit that [meant] they didn’t have to go to 33 websites to get their tools or even four websites to get their tools,” he said. “There wasn’t anything like it at the time, and there isn’t now.”
As the Swami development team redesigns the interface, Miller said it will keep the integrity of this vision alive, but on a larger scale. The improved system, also called the Next-Generation Biology Workbench, will add support for additional types of data other than sequences, such as protein structures, as well as a number of other features expected to be of interest to users.
The goal of Swami “is to completely reproduce the function of the existing Workbench with some additions to make sure that people using it as a teaching tool don’t get lost in the shuffle,” he said.
“We want to make it possible to add new tools easily and that, even by itself, creates something of a problem for the user — if you give someone 100 tools, that’s not very useful [if] they have to scroll down to find the one they want.”
Swami co-developer Rami Rifaieh discussed the system at last week’s Data Integration in Life Sciences conference in Philadelphia. Rifaieh explained that the Swami developers solicited input for the redesign from the Biology Workbench user community, 29 percent of its users of which are internationally-based.
Among the US contingent, nearly half are academics and 15 percent are non-profit institutes, as determined by user e-mail accounts. The remaining user base is divided between personal or business accounts, with just a fraction, about one percent, being governmental agencies. There are about 40 countries in the user base.

“The idea was to provide people with a toolkit that [meant] they didn’t have to go to 33 websites to get their tools or even four websites to get their tools. There wasn’t anything like it at the time, and there isn’t now.”

Miller said that the Swami developers are using improved ontologies under development at the National Institutes of Health to help users more succinctly locate the information they need.
Other changes include building upon the two data types that the current Workbench handles – sequences and sequence alignments – by adding protein structure data, small molecular data, and genome data.
“One thing the old Workbench has is that when one sends a piece of data it is sent back via text response, but for protein structures you really want something interactive, to be able to call up that protein data and make changes to it and save that change data to our environment,” Miller said.
In addition, Swami will enable users to store data in a secure environment. “You can download it to your area, but the idea is you don’t have to install anything and you can get all these things and a little storage space too so you can have a little private area where you work,” Miller said.
Miller said that Swami will be geared toward bench biologists who don’t have access to sophisticated computer equipment. “It’s not a beautiful application, but it’s useful,” Miller said. “If you can meet the needs of 32,000 you should go home proud.”
Further information on Swami is available here.

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