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Bioinformatics Briefs: Apr 10, 2009


Dana-Farber to Launch Computational Biology Center

Dana-Farber Cancer Institute said this week that it is opening a Center for Cancer Computational Biology that will offer researchers access to data-analysis and -interpretation services.

According to a statement, the fee-for-service CCCB will offer tools, equipment, and the expertise necessary to evaluate the large, complex datasets associated with -omic studies.

"Our goal is to provide the infrastructure necessary to address the needs of 'omic
scientists and to establish the capacity to tackle the next generation of questions arising from the application of new technologies across the range of biological research," John Quackenbush, CCCB director, said in a statement.

Quackenbush is a professor in the department of biostatistics and computational biology at Dana-Farber and at the department of computational biology and bioinformatics at Harvard School of Public Health.

The center will offer a wide range of analytic services including gene expression, copy number variation, ChIP-seq, SNP analysis, and second-generation sequencing data.

GenoLogics Integrates Geneus with ABI SOLiD; Hopkins Deploys Proteus

GenoLogics said this week that it is partnering with Life Technologies' Applied Biosystems group to integrate its Geneus lab- and data-management solution with the ABI SOLiD sequencing system.

Geneus provides sample and workflow management. automates pipelines, and enables reporting. The company signed a similar integration agreement for Illumina's Genome Analyzer last fall [BioInform, Nov. 14, 2008]

"Our relationship with GenoLogics helps ensure that scientists using the SOLiD System are fully supported with an end-to-end lab and data management solution, enabling efficient management of their growing volumes of next-generation sequencing data," Roger Canales, senior manager of ABI's SOLiD Software Development Community, said in a statement.

Separately last week, GenoLogics said that the Technical Implementation and Coordination Core of the Johns Hopkins National Heart, Lung and Blood Institute Proteomics Center has deployed its Proteus software.

Proteus automates data capture from instrument and software integrations and tracks projects, samples, and results.

AstraZeneca to Use BioWisdom Data-Mining Services

AstraZeneca has selected BioWisdom to provide customized vocabulary and meta-data from toxicological reports gleaned from its development compounds, BioWisdom said in a statement this week.

Under the agreement, BioWisdom will convert documents to machine-readable formats, and provide entity extraction and derivation, semantic normalization, mapping, and meta-data.

BioWisdom Chief Scientific Officer Julie Barnes said in a statement that the project "will enable AstraZeneca to harness value from both public and now private repositories of safety-related information."

Financial terms of the agreement were not released.

Physionomics Lands Lilly License

Physiomics announced that Eli Lilly has licensed a customized version of its ModelPlayer software to perform in silico simulations of unspecified anticancer drugs.

According to Physiomics, ModelPlayer incorporates a range of features that drug developers need to calibrate models and simulate anticancer drugs.

Financial terms of the agreement were not released.

Golden Helix Hires Spinco Biotech as Distributor for India

Golden Helix said this week that it has tapped Spinco Biotech to distribute its genetic-analysis software in India.

Under the exclusive agreement, Spinco will provide sales, marketing, and first-level customer support for Golden Helix's analysis and visualization software and services.

Bozeman, Mont.-based Golden Helix struck the agreement in response to "a continual increase in the volume of inquiries from leading Indian research organizations," Andy Ferrin, VP of sales and marketing, said in a statement.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.