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Gene-IT: RNAi, Primer-Design Modules for GenomeQuest in Beta Testing at Two Pharmas

Gene-IT executives said this week that two undisclosed pharmaceutical customers are beta-testing two new modules for its GenomeQuest sequence search platform.

The company expects to launch the new modules — one for RNAi and the other for primer design — in around three months, according to Ron Ranauro, CEO.

Ranauro said that the company is collaborating with the two pharmas under early-access agreements to evaluate and validate the new capabilities.

The firm began developing the new modules in December, when it raised $4 million in VC funding [BioInform 12-05-05].

Ranauro said that the RNAi module offers customers "insight into the off-target effects" of RNAi probes by classifying off-target hits into "meaningful buckets" that relate to stringency.

The module, which enables searching across RNAi sequences in the US Patent and Trademark Office database — both for issued patents and patent applications — enables companies to immediately determine their freedom to operate around a particular sequence, Ranauro said. In the case where another party holds the IP on a sequence, the software can also be used to design a non-infringing probe, he said.

Gene-IT is currently working with a pharmaceutical partner to validate the results of the company's approach in the wet lab, he said.

The primer-design module is in beta testing at a separate pharmaceutical firm, he said.


Teranode Demos Semantic Web-Based App; Product to Launch at End of Quarter

In a session on the semantic web, Matt Shanahan, chief marketing officer at Teranode, gave a brief demonstration of some of the new capabilities that semantic web technologies are contributing to the upcoming version of its XDA system.

In order to demonstrate "the difference between the web and the semantic web," Shanahan explained how semantic technologies enable the creation of "lenses" that allow different users — such as a biologist or a chemist — to look at the same data in many different ways. If a user annotates a data point in one lens, a different user viewing the information from a different lens can link directly back to the one in which the original annotation was made in order to see the full data set.

Shanahan told BioInform that the company has just begun beta-testing the new semantic web-based product, which is due out by the end of the second quarter.


Stone Bond's EE-LIMS Gains Affy GeneChip Compatibility

Stone Bond Technologies announced at the conference that its Enterprise Enabler integration platform and EE-LIMS data-management system have achieved GeneChip-compatible status with Affymetrix.

As a result, laboratories can use EE-LIMS to automate data import and result outflow to and from the Affymetrix GeneChip Operating Software.

Jawad Pashmi, application scientist at Stone Bond, said that the company is initially targeting microarray core facilities for EE-LIMS, but added that the company can customize the system for other experimental platforms.


InforSense Signs Matrix Science for Partner Network; First OEM Deal on the Horizon

InforSense said that proteomics software firm Matrix Science has become the 19th member of its Open Workflow Partner Network.

Matrix Science will integrate its flagship Mascot search tool and its newer data management product, called Mascot Integra, with InforSense's KDE workflow-based analytics platform.

The integration will enable researchers to query proteomic data using KDE's visual workflow interface and also to integrate proteomics data analysis with other types of experimental data.

Jonathan Sheldon, chief scientific officer of InforSense, told BioInform that Matrix Science is the company's first proteomics software partner, and that the agreement "enables us to build a powerful bridge between proteomics and other data."

Sheldon said that InforSense has also signed its first OEM deal, though he was unable to disclose the company's partner, noting that InforSense plans to announce the agreement formally in a few weeks.

KDE "lends itself" to the OEM model, Sheldon said, so the company plans to pursue similar deals in the future.

 

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