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PANTHER s Release in Public Domain is First Step in Web Portal Overhaul, ABI Exec Says


Applied Biosystems last week made good on a promise to release its PANTHER (Protein Annotation Through Evolutionary Relationships) classification system into the public domain, with the launch of version 5.0 and a pledge to integrate the system with EBI’s InterPro database by February.

An earlier version of the system, PANTHER 4.1, was made freely available through the company’s website last fall [BioInform 10-04-04], but was not widely publicized. Ramin Cyrus, senior director for marketing for ABI’s services and systems solutions group, told BioInform that last week’s announcement kicks off a broader strategy underway at the company to modify its informatics business following its reorganization last July.

At that time, ABI restructured its business units into four divisions: molecular biology; proteomics and small molecules; applied markets; and services [BioInform 07-19-04]. Cyrus said that informatics — a group of “a couple hundred” employees — now falls under ABI’s services business unit, which has been charged with taking a “solutions-oriented approach” to its customers. This entails making informatics “more accessible,” Cyrus said, “because it’s becoming part of the experiment now. It used to be this unique set of skills, kind of limited to the high-end labs, and now it’s just becoming prevalent at every facet, so we have to move with our customers.”

Cyrus said that ABI will be revamping its web-based informatics offerings over the year to include a still-unnamed “community” site — of which PANTHER is the first example — as well as some subscription-based services, such as the Celera Discovery System. In addition, the company plans to upgrade its e-commerce portal — currently dubbed MyScience — “to make purchasing easier and more intuitive to our customers,” he said.

“We’re planning to evolve it so that the e-commerce site and the community site are much better defined and clearer to the customer,” Cyrus said. “So you can go to the community area … and freely browse, run some analysis and so forth, while the e-commerce area will be very specific to helping you find the right product and buying it.”

ABI’s strategy is in line with that of other instrumentation and reagent vendors in the market, such as Invitrogen and Affymetrix, who have added more freely available analysis tools to their online portals as a service to their customers [BioInform 09-13-04]. These efforts are beginning to blur the line between bioinformatics and e-commerce — a trend that Cyrus said could potentially complicate matters for customers.

“Bioinformatics and bioinformatics tools are part of the commerce now,” he said. “You can’t just use a traditional search engine to find your assays, because sometimes people don’t even know what assay they need.” However, he said, “We’re trying to make it more intuitive” by clearly delineating the commercial site from the community site.

PANTHER, freely available at, is ABI’s “first foray” into the community portal, and researchers can expect “a lot more things being added to that over time,” Cyrus said. He declined to provide details on specific content or tools — or offer a timeline for their release — but did rule out the possibility that the Celera Discovery System will be made freely available through the public site.

However, he said, since the “value proposition” for CDS has evolved from proprietary sequence data towards curation and annotation, there is a possibility that some portions of CDS would be released publicly, while the “value-added curation pieces will be made available to our customers through a subscription or potentially bundled with some or our analysis tools.”

CDS is currently available for $875 per month for commercial subscribers and $175 per month for academic subscribers.

In addition to the web-based strategy, Cyrus said that ABI is ramping up its on-site services capabilities to include more informatics expertise, in order to advise customers on the best combination of instruments and software to help answer specific research questions. This approach is targeted toward large, multi-site research labs and pharmaceutical companies, and Cyrus said the company is already engaged in several deals based on this model that it will announce in the coming months.

These customers often require a more customized approach than the web-based platform can provide, Cyrus said, and have requested the company’s help in assessing their experimental pipelines, to ensure that they are running the right protocols and instruments and software in the most optimal way. Cyrus said that ABI’s customers in this area so far “are using not just our instruments, but other third-party instruments and software, and they’re telling us they need help across the spectrum” — a fact that the company is prepared to address. “We don’t have the hubris to think their labs only have AB instruments and AB software,” he said.

In order to expand the services group’s informatics capabilities to tackle this challenge, Cyrus said that AB is collaborating with “a lot of world-class partners to work collaboratively to fill out that portfolio of solutions our customers need.” He declined to identify these partners, but said that information would be forthcoming in the next few months.

— BT


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