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eBioinformatics to Acquire Life Sciences Data Integration Co. Empatheon for $11M


Bioinformatics application service provider eBioinformatics of Pleasanton, Calif., has agreed to pay $11 million for Empatheon of Sunnyvale, Calif., a privately held life sciences data integration company that offers real-time access to public and private genomics and proteomics information.

According to eBioinformatics, the deal will help the company increase the range of data analysis options and boost the performance of its BioNavigator service by improving the way it stores and retrieves data.

Empatheon’s data management and access technology will be integrated into BioNavigator before year’s end to transition away from a data warehouse approach that can slow down scientific inquiry.

Under the data warehouse model, researchers have to call up data from a number of disparate sources using separate data-specific software to query any existing data important to their research, said eBioinformatics.

To examine one area, a scientist might have to go to several different databases of genetic, proteomic, bibliographic, and patent information, often using separate software applications to query each database.

The data warehouse method also thwarts real-time access to ever growing biological databases because database managers have to collect, reformat, and assimilate the new biological data and republish their databases periodically.

According to eBioinformatics, Empatheon’s technology avoids the difficulties presented by incompatible life science data by using Java-based applications to replace a data warehouse and to coordinate real-time access between scientists and the multiple sources of data they need.

Using this strategy, researchers can access all current data relevant to their studies from a single, browser-based graphical user interface, said eBioinformatics. Java applications also upgrade the user interface automatically to inform users that new life science databases have been added to the application service.

That technology will allow eBioinformatics customers to do more data analysis functions such as cross database comparisons, said eBioinformatics vice president of product marketing James Nelson.

The acquisition of Empatheon should enable eBioinformatics to streamline the way it manages data in its databases, said Nelson. This includes updating the databases, some of which have to be completely duplicated using compact disks when updates come in.

The company maintains mirror versions of databases such as GenBank and Swiss-Prot on its server structure. This is done primarily for intellectual property reasons because pharmaceutical companies are worried that if they submit their proprietary sequences to a public domain site like GenBank for matching purposes, they could lose their claim to the proprietary sequence, said Nelson.

“But if you copy the same databank as we do – take the GenBank records and mount them on our server, which is account and password protected, then the IP is protected,” said Nelson.

Empatheon’s technology will allow the company to do some of this data addition work through Web-based updates that will not require entire databases to be duplicated. This method will compare only the items that have changed between the two databases, which will speed the process, said Nelson.

“This is a technology that will make [things] that much more efficient for us to do,” said Nelson.

Nelson declined to discuss the details of Empatheon’s offerings because patents on the technology have not been filed yet. He did say that the technology goes much deeper than just the use of Sun Microsystem’s Java programming language.

When the acquisition closes, eBioinformatics will have about 67 employees with the majority being in Australia where eBioinformatics originated. Empatheon has about 12 employees in the United States and about eight in India. No layoffs are expected.

Assuming the Empatheon acquisition closes, eBioinformatics will have development sites in Australia, India, and the United States.

Both companies’ employees are already working side by side in California after eBioinformatics moved its staff to Empatheon’s office in Sunnyvale, said Nelson. EBioinformatics decided to relocate to Empatheon’s facility because of its better information technology infrastructure such as wiring and network access capabilities.

Empatheon CEO and chairman Bala Manian will take over as eBioinformatics’ chairman from Geoff Brooks, the company’s current chairman, who will remain on the board.

Manian, who declined comment until the acquisition closes, founded Digital Optics, Lumisys, Molecular Dynamics (now owned by Amersham Pharmacia Biotech), and Biometric Imaging.

EBioinformatics is hoping Manian will be an important addition. The entrepreneur is well known and respected in Silicon Valley, said Nelson, who first worked for Manian back in 1989 at Molecular Dynamics.

“Manian is not going to be a figurehead chairman of the board by any means. He’s going to be a strong contributor to the company and to the direction of the company,” said Nelson.

Empatheon’s Harry Vlahos will join the company as vice president of new ventures and will assess which other technologies should be brought into the company. Nelson declined to say which ones are under consideration.

The search for new technologies is what led eBioinformatics to Empatheon in the first place. The company, which had been looking for new technology to license to expand its capabilities, came across Empatheon and the two companies discussed their businesses, they eventually decided an acquisition would be better than a licensing agreement, Nelson said.

Founded in 1998, eBioinformatics provides Web-based, per-use access to bioinformatics and biotech-related e-commerce for life scientists in pharmaceutical, biotech, agricultural, government, and university laboratories.

—Matthew Dougherty

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