Parallelizing Code in the Cloud

August 08, 2011

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Dutch company Vector Fabrics has released a new cloud-based tool they're claiming will allow developers writing HPC or scientific computing software to easily parallelize code for multicore x86 architectures.

The vfThreaded-x86 cloud-based tool has the ability to examine cache hit/miss effects, data bandwidth to memories and bandwidth between individual code sections. The tool can be accessed through the Vector Fabrics website with a standard web browser while the development tool itself runs on Amazon's EC2 cloud.

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Senate Takes up NIH Funding
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This Week in PNAS

GenomeWebinars

Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

On-demand recording is available here.

Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows

Sponsor: New England Biolabs

Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

Available here.
Young Investigator Profile

Alex Pearlman

Instructor
Albert Einstein College of Medicine

Prostate Cancer Metastases Predictions

Alex Pearlman hopes his discoveries will affect the way prostate cancer patients are treated. With other researchers, he has developed a genomic copy-number alteration-based prognostic model to predict, at the earliest stage possible, the likelihood that a local prostate cancer will metastasize.

The model was featured in a recent issue of the Journal of Probability and Statistics, a paper that he calls the "culmination of 10 years of work" and the "methods paper" for what he hopes will soon be a clinical test. "The finish line is pretty clear," says Pearlman, who is at New York City's Albert Einstein College of Medicine. "It is to develop a US Food and Drug Administration-approved kit to predict prostate cancer metastases and to alleviate men of needless surgeries and radiation treatment."
Blog

Senate Takes up NIH Funding

A Senate committee hears of sequestration woes at NIH.

May 17, 2013

A Diverse Collection

The Natural History Museum is amassing tissue samples from around the world to analyze with genomic tools.

May 17, 2013

Polling the Public on Science

A survey suggests that public interest in biomedical research is high, but knowledge is not as high.

May 17, 2013

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May 17, 2013
Papers of Note

Variation and genetic control of protein abundance in humans
Wu, Candille, et al. Nature

Stanford University scientists publish a study demonstrating high-throughput human proteome quantification, and its combination with DNA variation and transcriptome information to add a "new dimension" to the characterization of gene expression regulation. The investigators used isobaric tag-based quantitative mass spectrometry to determine relative protein levels of 5,953 genes in lymphoblastoid cell lines from 95 diverse individuals genotyped in the HapMap Project. They found that protein levels are heritable molecular phenotypes and have considerable variation between individuals, populations, and sexes. Additionally, the investigators found protein quantitative trait loci, including variants not detected by previous transcriptome studies.

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
Supple, Hines, et al. Genome Research

A group from the US, UK, and Colombia describes findings from a comparative genomics-based study on a form of adaptive variation in butterflies known as mimetic wing coloring. By sequencing co-mimicking Heliconius butterflies from two species and a handful of hybrid zones, researchers narrowed in on a color pattern-associated site near a gene already implicated in red color variation — an apparent regulatory region suspected of evolving by convergence in the two species distantly related species. "Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius," they write, "and gained important insights into the evolution of novel adaptive phenotypes in natural populations."
People on the Move

Kevin Hrusovsky is resigning his post at PerkinElmer as senior VP and president of the Life Science and Technology division. Hrusovsky will serve as a consultant to the company for up to one year, beginning in June. He joined PerkinElmer through the company's acquisition of Caliper Life Sciences, where he was CEO and president.

Hologic has appointed former Beckman Coulter head Scott Garrett to its board of directors, where he will serve on the corporate development committee.
Garrett currently is an operating partner with Water Street Healthcare Partners, a private equity firm. Garrett spent 10 years at Beckman Coulter, where he was chairman, president, and CEO.

Gina Costa is now senior director of genomic applications at Illumina. She joins Illumina from Life Technologies, where she was senior director of genetic analysis, working on development of the Ion Torrent and SOLiD sequencing technologies. She has also held positions at Agencourt Bioscience and Roche's 454 Life Sciences.

Bioinformatics firm Golden Helix has hired Andreas Scherer to be its new president and CEO. Scherer has managed large global software services businesses, and he started his executive career at AOL/Netscape. He will replace Former CEO Christophe Lambert, who will take on the new role of company chairman.
Upcoming Events

Conferences, Meetings & Deadlines

2013 Mid-Atlantic Genetic Epidemiology and Statistics (MAGES) Conference: Methods and Applications in the Next Generation Sequencing Age
May 17 / Philadelphia
University of Pennsylvania

ASM 113th General Meeting
May 18-21 / Denver
ASM

National Advisory Council for Human Genome Research meeting
May 20-21 / Rockville, Md.
National Advisory Council for Human Genome Research

2013 ASCO Annual Meeting: Building Bridges to Conquer Cancer
May 31-Jun 4 / Chicago
American Society of Clinical Oncology

European Human Genetics Conference 2013
Jun 8-11 / Paris
European Society of Human Genetics

Abstract & Registration Deadlines

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Science
An international team has sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba. Their findings suggest that the carnivorous plant has ditched virtually all its non-coding DNA, retaining a set of sequences that's almost exclusively genic. "What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the ['junk' DNA]," said co-corresponding author Victor Albert.
Business
Agilent Technologies announced a restructuring program expected to reduce its headcount by about 450 employees and save the company $50 million annually in operating expenses. CEO Bill Sullivan said that the focus of the restructuring will be on Agilent's Electronic Measurement Group and that the company will explore opportunities "to streamline our organization around the world." The firm also announced that its Q2 revenues were flat year over year.
Funding
The US Department of Energy's Joint Genome Institute has funded six new initiatives to develop technologies that will help JGI and its users conduct their research efforts into microbiology, metagenomics, and plant genomics. The projects will be supported under the Emerging Technologies Opportunity Program with a total of around $3.5 million over the next two years. Among the researchers receiving funding are Stephen Quake and Jay Shendure.
GenomeWebinars
GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

GenomeWeb and EMD Millipore invite you to view an archived webinar discussing new approaches to detect RNA at the single-cell level as well as new probes for the direct quantification of circulating miRNAs. In this free online seminar, recorded April 25, 2013, our expert panel shares protocols for improved RNA and miRNA detection.

On-demand recording available here.

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