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Ariadne, U of Oklahoma, NCI, GeneGo, NIHS, LBNL, OpenHelix, InforSense

Ariadne, U of Oklahoma Partner on Cancer-Related Pathway Collection
Ariadne Genomics said this week that it has partnered with the University of Oklahoma to develop a cancer-related pathways collection.
The collection will become available to Ariadne customers as an add-on to its pathway-analysis product line.
The University of Oklahoma has already deployed Ariadne’s Pathway Studio software tool to develop the collection of cancer-related pathways.
Dee Wu, associate professor at the University of Oklahoma Health Sciences Center, said that the university will “perform scientific evaluation of pathway expansion and microarray data analysis algorithms available in Pathway Studio” in order to build the collection of cancer-related pathways.
The university will also use Ariadne’s ResNet database and pathway reconstruction and literature mining tools.

NCI Awards GeneGo $1M Phase II SBIR Grant to Discover Breast Cancer Biomarkers
The National Cancer Institute has awarded GeneGo a phase II SBIR grant worth $1 million over two years to help it discover breast cancer biomarkers.
The research program includes a large-scale gene-expression and genotyping study to be conducted at the Mayo Clinic. GeneGo will use its MetaCore data-mining program for data analysis.
In phase I of the SBIR, GeneGo performed a network analysis of previously published microarray expression data.

Simulations Plus Licenses Compound Classification Software to Japan's NIHS
Simulations Plus has sold a five-year license for its ClassPharmer software to the National Institute of Health Sciences in Japan, the company said this week.
Japan’s NIHS will use ClassPharmer to generate chemically relevant compound classifications, Simulations Plus said. The organization had been using an earlier version of ClassPharmer, previously sold by Bioreason, which Simulations Plus acquired last year.
Financial details of the new ClassPharmer license were not disclosed.

LBNL and OpenHelix Launch VISTA Training Program
Lawrence Berkeley National Laboratory has contracted OpenHelix to provide training and outreach programs for its free web-based genomics resource, VISTA (visualization tools for alignment), OpenHelix said this week.
“VISTA is making a difference in many aspects of research, with important outcomes for medical applications,” said Inna Dubchak, principal investigator for the VISTA project, in a statement “But to make it even more valuable and accessible, we wanted to provide the best training material possible.”
LBNL has contracted OpenHelix to create several outreach and training programs, including a self-run tutorial, exercises, and a PowerPoint slide set and handouts that can be used by professors, teachers, and trainers.

InforSense to Provide Tech Platform for EU-Funded Semantic Grid Project
InforSense said this week that it has been selected as a technology partner for ARGUGRID, a grid computing project supported by €2 million ($2.5 million) in funding from the European Union’s 6th Framework program.
The project, a collaborative effort between eight partners from five countries, aims to develop a service-oriented computing platform for scientific and business applications based on semantic web and agent-based technologies.
InforSense KDE workflow technology will provide the “central mechanism” for computing services composition in the project, the company said. The workflow engine will be enhanced by logical reasoning technology that will be developed in the project.
The company said that it will integrate technology developed in the project into its upcoming product releases.

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The Scan

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.

Seagull Microbiome Altered by Microplastic Exposure

The overall diversity and the composition at gut microbiome sites appear to coincide with microplastic exposure and ingestion in two wild bird species, according to a new Nature Ecology and Evolution study.

Study Traces Bladder Cancer Risk Contributors in Organ Transplant Recipients

In eLife, genome and transcriptome sequencing reveal mutation signatures, recurrent somatic mutations, and risky virus sequences in bladder cancers occurring in transplant recipients.

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.