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Bioinformatics Briefs: Feb 6, 2009


GSK Taps Entelos for Anemia Research Project

Entelos said this week that it has signed an agreement with GlaxoSmithKline to conduct in silico research using its Hematopoiesis PhysioLab platform.

The Hematopoiesis PhysioLab platform simulates the biology of anemic patients and patient populations to predict responses to drugs. According to Entelos, the technology has "already been used successfully with other pharmaceutical partners to assess the safety and efficacy of biologics, find the best doses for specific patient types, and optimize complicated, adaptive clinical trial designs to better position products in the highly competitive market for anti-anemia drugs."

James Karis, president and CEO of Entelos, said in a statement that the agreement is the third project that Entelos has conducted for GSK "across multiple therapeutic areas" over several years.

Financial terms of the agreement were not provided.

NIGMS Awards Insilicos $400K Grant to Develop Statistical Method

Insilicos said this week that it has been awarded a grant worth around $400,000 from the National Institute of General Medical Sciences to develop a statistical method called least angle regression, or LARS.

LARS is a technique for producing "stable predictions from data with a large number of dimensions," Insilicos said.

Chris Fraley, who joined Insilicos as senior scientist earlier this year from Insightful, is the principal investigator on the grant [BioInform Jan. 2, 2009].

The work is a continuation of Fraley's work at Insightful with Tim Hesterberg, who is now at Google. Fraley and Hesterberg began working on LARS several years ago under an NIGMS grant [BioInform Nov. 17, 2006].

Fraley's current LARS research "emphasizes biomarker discovery applications," Insilicos said.

Insilicos president Erik Nilsson said in a statement that the company is taking a systems biology approach to diagnosing disease,"where we see disease as breakdown of molecular communication in the body. When you measure this breakdown, you have lots of different signals to choose from, different molecules you can measure."

The company views LARS "as a way of selecting the most promising signals and using these signals to predict disease," Nilsson said.

Insilicos said that it has received more than $3 million in NIH grants to date.

E&K to Resell Sciformatix SciLIMS in California

Sciformatix, a startup providing laboratory information-management systems via a software-as-a-service model, said this week that it has tapped laboratory supply firm E&K Scientific to distribute and resell its SciLIMS products in California.

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"In our customer base we have seen a huge need for people to find a way to get control over their samples and storage in a less labor-intensive way," Brian Ruf, CEO of E&K Scientific, said in a statement. "This is the first software product we have ever sold in our 35-year history, but it has proven to be an extremely easy addition to our catalog."

Sciformatix recently launched its first product, SciLIMS Samples & Storage Management [BioInform Jan. 23, 2009], which is currently available in limited distribution, but will be available for general distribution in March.

Pricing for SciLIMS SSM begins at $50 per month per user.

EMBL Genomics Core Purchases Genomatix's Software


The European Molecular Biology Laboratory's Genomics Core Facility has installed genomics data mining and analysis tools from Genomatix Software, the company said this week.

The Munich-based company said that EMBL purchased its Mining Station, which provides SNP detection and genotyping, copy number analysis, and small RNA analysis; and Genome Analyzer, which enables deep biological analysis of data from the GMS. Together, the systems offer an integrated solution for analyzing raw next-generation sequencing data.

EMBL's GeneCore is focused on studying the benefits and utilization of new technologies developed at EMBL, and on improving the quality, efficiency, and relevance of lab data.

Financial terms of the agreement were not released.

Fox Chase Licenses Bioinformatics Tools from BioDiscovery

Fox Chase Cancer Center's Keystone Program in Blood Cell Development and Cancer has acquired a site license for two bioinformatics software programs from BioDiscovery.

The El Segundo, Calif.-based bioinformatics firm said that the Keystone Program will use its Nexus Copy Number and Nexus Expression tools for DNA copy number and RNA expression analysis from microarray data.

"The Nexus Suite enables us to be less dependent on in-house bioinformatics support as we attempt to identify the subset of genes regulating development and transformation from among the larger cohort whose altered expression or copy-number is merely correlated with these processes," David Wiest, co-leader of the Keystone Program, said in a statement.

BioDiscovery noted that the two software products support all array platforms including Agilent, Affymetrix, Illumina, Roche NimbleGen, and custom arrays. It said the tools can integrate data from thousands of arrays in a single project and provide a streamlined interface for data exploration.

Roche Extends License for Genedata's Refiner Module

Roche has extended a license agreement with Genedata for the Refiner mass spectrometry module of the Expressionist biomarker platform, Genedata said this week.

The Refiner MS module is aimed at supporting large-scale proteomics and metabolomics programs, and it performs automated preprocessing of data, which it then delivers ready for analysis or for storage.

Financial terms of the agreement were not released.