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IntegrationConundrum?GeneticXchange Promotes New Method for Solving the Riddle


GeneticXchange says it has developed a way to look at the problem of integrating data through a different lens, an approach that has reaped the company rewards in the form of corporate and academic partnerships and a recently announced extension of a previous deal.

Jeff Edwards, chief operating officer at GeneticXchange of Menlo Park, Calif., said that while many of today’s bioinformatics solutions involve taking all of the heterogeneous data from the various sources, wedging it, however awkwardly, into relational tables, and then joining it all back together again, GeneticXchange extracts data from its existing structures using software that knows how to deal with the information.

“With CPL [the Collection Programming Language], we can treat data and algorithms all the same way, which no one else can do at this point,” said Edwards, referring to the company’s proprietary language.

GeneticXchange is built upon concepts pioneered by Limsoon Wong, currently deputy director of the Bioinformatics Center at the National University of Singapore. Working on a DOE-funded project at the University of Pennsylvania to look for an efficient way to seek homologous genes in disparate species, Wong set out to prove mathematically that any data, no matter how it is structured, could be described in a common way.

Having accomplished this feat, and with $3 million in funding from Singapore BioInnovations, a government-sponsored venture capital firm, Wong helped start GeneticXchange in 1998. He remains involved as a scientific advisor to the company, which now has partnerships with biotech company Signature Biosciences and several academic research institutions, including Stanford University.

Last week, GeneticXchange got another nod of approval as Genomics Collaborative extended its one-year non-exclusive license for GeneticXchange’s gX-Engine, a data access and integration software, for an additional five years. In addition, GCI executives will now sit on the product board of GeneticXchange to help direct software development and integrate the two companies’ R&D.

The gX-Engine product, based on Wong’s research, uses dozens of “drivers” to access varied databases, as well as interface with software suites such as Blast and HMMer. The CPL, a proprietary superset of XML, can be used to build chains of data retrieval and algorithms, creating packaged workflows. The GeneticXchange software can be tailored to a particular customer, becoming a layer in their infrastructure.

Software developers at GeneticXchange are having a busy spring. Additional drivers are being written, including one that will access dbSNP. The company’s first applications package, gX-PathVision, for visualizing and annotating biological pathways, is targeted for release in mid-April.

A new user interface for CPL queries, incorporating an editor, on-line help, and the ability to save and combine scripts, is currently in alpha test and ports of the gX-engine, which was first developed for Solaris 7, are underway.

The company, which hopes to increase its staff to 40 from 17 within the year, is currently seeking a second round of financing. GeneticXchange also plans on using the funds to expand its operations to Singapore and the United Kingdom.

— SCC with additional reporting by JSM

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