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Inpharmatica to Add Structural, Functional Data to Celera Database for Joint Biopendium Product


Celera Genomics and London-based Inpharmatica plan to develop a joint product built around Inpharmatica’s structural bioinformatics technology and Celera’s genomic data. Among other things, the effort marks the first time Celera has released its entire mammalian database to a third party for processing and structural/functional annotation.

The new product — called Celera Edition Biopendium — will be a premium version of Inpharmatica’s existing Biopendium database, which currently is built around public domain sequence data. The first release of the Celera Edition should be ready around the end of the first quarter of 2002, said David Ricketts, vice president, business development, at Inpharmatica.

Inpharmatica was founded in 1998. Its key technology is software that predicts protein structure and function — including putative protein-protein interactions — from sequence data. The technology was originally developed in Janet Thornton’s lab at University College London. Since July, Thornton has been research director at the European Bioinformatics Institute in Hinxton.

For 90-person Inpharmatica the Celera deal represents an important validation of its technology. “We are delighted that Celera has chosen Inpharmatica as its partner in the application of structural bioinformatics,” said the company’s chief executive, Malcolm Weir.

Inpharmatica builds the current Biopendium database by pumping the public sequence data through its software, a process that takes about three months and requires a large amount of raw computing power. Customers receive updates quarterly. The Celera Edition will include the same public data but also Celera’s human and mouse information. Ricketts expects the first version to contain around a billion predicted protein-protein interactions.

Celera and Inpharmatica will jointly market the new product and share revenue on a formula weighted toward Inpharmatica in the early days but reaching parity after certain revenue targets are hit, said Ricketts. An annual license for the database is expected to cost around $2 million for a mid-sized pharmaceutical customer. Customers who do not already subscribe to the Celera Discovery System will also be required to purchase a minimal Celera license, he said.

The Celera Edition Biopendium will be delivered to customers like the basic Biopendium, installed on-site on a stand-alone Sun platform with updates arriving via tape. Thus there is no immediate opportunity to integrate the new product with the Web-based Celera Discovery System. But Ricketts says the agreement doesn’t preclude further integration efforts should Celera be willing to allow customers to store its database on-site or Inpharmatica become interested in delivering its product over the Web.

As a starting point, both companies are expected to try to upgrade their existing customers to the new product. Inpharmatica’s largest customers for the existing Biopendium are Pfizer, Genentech, and Serono, of which the first two are also Celera Discovery System users. Ricketts, however, says he wouldn’t be surprised if the first sale is made in Japan, where Yamanouchi and Takeda are both Celera customers.

In order to build the Celera Edition Inpharmatica will have to upgrade its compute farm, said Pat Leach, the company’s chief information officer. The company currently has two data facilities, one at its London headquarters adjacent to the UCL campus and the other in suburban Hemel Hempstead. The first is a 1,400-processor Linux cluster built around Intel Pentiums that is used chiefly for internal research. The other runs 500 Sun Sparc processors under Solaris and is used for Biopendium production.

In order to have enough capacity to build both the old and new versions of Biopendium, Inpharmatica will add a Linux cluster of 400 Intel processors to its current production site, said Leach. Among other things, this will make it one of the world’s largest Solaris-Linux facilities.

Since Celera and Inpharmatica both run internal drug discovery programs, the companies have also cross- licensed each other’s databases for internal use.

Ricketts said the companies have been in serious negotiations since the first of the year. The Inpharmatica negotiating team was headed by Edith Cookson, business development manager. On the Celera side, responsibility for the joint Biopendium product will fall to Tony Kerlavage, senior director of product strategy.

— DW

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