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Entelos, Genstruct, Genbank, Natural Selection, Blue Gene, TeraGrid, Socabim, Emphron


Unilever Taps Entelos to Build Computer Model of Skin Allergy

Entelos said last week that it is collaborating with Unilever to develop an in silico model for the study of skin allergy.

The platform, dubbed the Skin Sensitization PhysioLab, is "part of an on-going Unilever program to develop alternative approaches for risk assessment for assuring the safety of consumer products," Entelos said in a statement.

Under the terms of the agreement, Entelos will transfer the PhysioLab technology to Unilever for continued advancement of the model and research in skin sensitization. Entelos will retain full rights to use the platform, including rights for all pharmaceutical applications.

Financial terms of the collaboration were not disclosed.

The platform will "represent the dynamics of skin sensitization, and be used to identify the biological drivers of its induction," the company said.

Genstruct Meets Data-Analysis Milestone for Pfizer

Genstruct said last week that it has reached its first performance milestone in a multi-year data-analysis agreement with Pfizer that began in 2004.

The company developed causal system models to "investigate mechanisms of toxicity and develop biomarkers for compounds in development," Keith Elliston, president and CEO of Genstruct, said in a statement.

The milestone entailed the delivery of a scientific report to Pfizer "that elucidates the potential mechanisms of toxicity that led to the identification of rational mechanism-based biomarkers," the company said.

Genbank, EMBL, DDBJ Hit 100-Gigabase Milestone

The three primary public repositories for DNA and RNA sequence data — Genbank, the EMBL Nucleotide Sequence Database, and the DNA Data Bank of Japan — have surpassed the 100-gigabase mark, according to a statement from the National Library of Medicine last week.

This sequence data represents both individual genes and partial and complete genomes of more than 165,000 organisms, NLM said.

Submitters to GenBank currently contribute more than 3 million new DNA sequences per month, NLM said.

Representatives from all three resources declared the event a significant milestone.

"As we enter the era of systems biology and researchers begin to exchange complex types of information such as the results of experiments that measure the activities of thousands of genes, or computational models of entire processes, it is important to celebrate the achievements of the three databases that pioneered the open exchange of biological information," said Takashi Gojobori, director of the Center for Information Biology and DNA Data Bank of Japan.

NSF Awards $400K SBIR to Natural Selection to Develop MicroRNA Analysis Software

Natural Selection said last week that it has won a $406,000 Small Business Innovation Reserch grant from the National Science Foundation to develop software for microRNA detection and analysis.

The Phase II SBIR will support the company's development of neural network architectures to predict functional RNA genes, including microRNAs, the company said.

The company's Phase I research supported the development of machine learning approaches for discriminiating fRNA coding regions from noncoding regions in four model eukaryotes. The Phase II effort will "focus on the refinement of evolved neural networks for ten key eukaryotes capable of discriminating fRNA coding from noncoding sequence information and experimental validation of predicted fRNA coding regions in humans and mice," said Gary Fogel, vice president of Natural Selection, in a statement.

"We envision rapidly translating these products to market," Fogel said.

Argonne to Provide Use of Blue Gene for Protein Simulation, Other Projects

The US Department of Energy's Argonne National Laboratory has added a 91-teraflop Blue Gene supercomputer to the computational resources it makes available to scientists under the DOE's INCITE (Innovative and Novel Computational Impact on Theory and Experiment) program.

Argonne and IBM are "developing a plan for researchers to request computation time on the IBM Blue Gene system," IBM said. The system, nicknamed BGW, is located at IBM's Watson Research Laboratory.

According to the DOE, the INCITE program "The program seeks computationally intensive research projects of large scale… that can make high-impact scientific advances through the use of a large allocation of computer time and data storage." Proposals are accepted from industry as well as academic research groups, and can be for one to three years.

Prospective uses for the supercomputer capability include applications in aerospace, automotive engineering, biotechnology, chemistry, energy, and physics, the DOE said.

A protein-folding project at the University of Washington was among three INCITE awards last year [BioInform 12-24-2004]. The project was granted 2 million processor-hours on a 6,656-processor 7.3-teraflop IBM supercomputer at the DOE's National Energy Research Scientific Computing Center.

Information about the 2006 INCITE program is available at

NSF Awards $150M for TeraGrid Development

The National Science Foundation said last week that it has awarded a five-year, $150 million grant to operate and enhance the Extensible Terascale Facility, a nationwide IT infrastructure of scientific computing that is more commonly referred to as the TeraGrid.

According to a statement from NSF, US researchers are currently using TeraGrid for genome analysis and disease diagnosis, as well as a broad range of other scientific applications such as real-time weather forecasting.

The new award includes $48 million to provide overall architecture, software integration, operations, and coordination of user support, an effort led by the University of Chicago. An additional $100 million will support TeraGrid resources at eight provider sites.

The award also supports the development of "science gateways" — web portals and desktop applications targeted at specific scientific user communities. An initial set of 10 gateways is planned, including a bioinformatics gateway, NSF said.

The TeraGrid project kicked off in 2001 with an initial award of $53 million from the NSF [BioInform 08-27-01].

Bruker AXS to Acquire X-Ray Analysis Firm Socabim

Bruker AXS said last week that it will acquire privately held Socabim, a Paris-based software firm focused on X-ray analysis.

The sale is expected to close in the first quarter of 2006.

Socabim, founded in 1977, supplies software for X-ray diffraction and X-ray fluorescence analysis to Bruker AXS.

Bruker AXS said it will merge Socabim with its French subsidiary Bruker AXS SA near Paris. All of Socabim's employees are expected to join the merged company.

Polyclone and Emphron to Jointly Provide Data Analysis, Experimental Design

Polyclone Bioservices of Bangalore, India, and Emphron of Queensland, Australia, are teaming up to provide services in data analysis, data mining, and experimental design for proteomics and genomics, Polyclone said last week.

The companies plan to combine Emphron's bioinformatics data-analysis capabilities and Polyclone's microarray core facility, which is being set up at the University of Agricultural Sciences in Dharwar. The new facility will focus on developing new arrays and provide analysis tools to researchers.

Note to Subscribers:
BioInform will not publish on Aug. 29 or Sept. 5. The next issue of the newsletter will appear on Sept. 12.

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.