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AMDeC Greenlights Iobion s GeneTraffic for First Piece of Microarray Integration Project


AMDeC, a consortium of 39 New York medical schools and research institutions, said last week that it had selected Iobion’s GeneTraffic Multi software to serve as a key building block in an effort to integrate its microarray data.

A total of 20 GeneTraffic servers will be installed across the AMDeC network, which supports an estimated 19,000 researchers. AMDeC’s microarray resource center, based at the University of Rochester, will coordinate the project and plans to use GeneTraffic Multi to handle microarray data from both Affymetrix GeneChip and spotted array experiments.

Andrew Brooks, director of the Functional Genomics Center at the University of Rochester Medical Center and the head of the microarray resource center, said AMDeC’s long-term plans include developing its own MIAME-compliant gene expression database, which may use the EBI’s ArrayExpress as a central repository and would be capable of contributing data to the NCBI’s Gene Expression Omnibus.

“The very first step to that was to find a central analytical tool that will be available to investigators throughout the AMDeC consortium, that will allow them to store their raw data files, in addition to having access to other sites’ data sets to expand their analysis,” said Brooks.

Brooks said the consortium considered building a similar system on its own, but that option was cost-prohibitive.

The group also investigated “some of the popular informatics products” that compete with GeneTraffic and found “there are things that the Iobion package does now that nobody else offers.”

One particular advantage Brooks cited is the open source underpinnings of Iobion’s product, “which is going to allow AMDeC to develop it specific to our goals beyond even what Iobion is offering.”

GeneTraffic is built on the PostgreSQL database, Apache server, and Red Hat Linux, and includes two open source components for probe-level analysis, the RMA algorithm developed by Rafael Irizarry, and MBEI developed by Cheng Li and Wing Hung Wong.

Stephen Sharp, director of marketing for Iobion, noted that “Iobion’s pricing structure is based solely upon the software components we create, with the open source components being freely available from their respective foundations.”

The company, which contributes any source code changes it makes back to the respective open source project, is thus able to offer GeneTraffic at a substantially lower price than many competing products.

As for the value of the AMDeC deal, Sharp was unable to provide details, but said “the AMDeC representatives were able to negotiate deep discounts and unique value-add components for their member institutes. The outcome is that both AMDeC and Iobion are extremely pleased with the financial aspects of this deal.”

— BT

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