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Caching in on Solid-state Storage

September 19, 2011 10:01 am | by Rob Farber | Comments

Intelligent use remains the best way to exploit speed and maintain the highest possible ROI Rob Farber Solid-state storage is revolutionizing computer storage. Unlike the currently ubiquitous rotating media disk drives, solid-state disk drives have no moving parts to waste power or delay data accesses. The fastest PCIe-based solid-state devices can perform over a million random disk accesses per second, while the fastest rotating media disk drives can deliver around 200 random disk accesses per second

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Four Months to Full NGS Output

September 16, 2011 9:31 am | by Mike Sanders | Comments

How the University of Washington scaled up with a LIMS Mike Sanders Web Exclusive When the University of Washington (UW) received a $23 million portion of a $64 million grant for the Large-Scale Exome Sequencing Project from the National Heart Lung and Blood Institute (NHLBI), investigators knew the clock was ticking. Grants generally have a limited shelf-life and this was no exception. The UW’s Northwest Genomics Center would need to sequence a total of 4,000 exomes over two years — an ambitious goal in a tight timeframe. Moreover, DNA would come from large cohort studies such as the Framingham Heart Study and the Women’s Health Initiative.

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InfiniBand Architecture Impact on CPU Utilization

September 13, 2011 8:47 am | by Joseph Yaworski | Comments

Joseph Yaworski Web Exclusive High performance computing applications require a tuned and efficient performance from the CPU, interconnect, MPI and communication library to achieve optimal performance. Conventional wisdom would have you believe that the host channel adapters (HCAs) with offload capability, where processing power for running the communication library is on a card, would require less CPU utilization than HCAs using an on-load method, where the communication library is run on the host CPU, thus, allowing more CPU cycles for applications

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Implementing Electronic Lab Notebooks Part 4

August 25, 2011 10:47 am | by Bennett Lass Ph.D. | Comments

Enabling Collaboration Bennett Lass Ph.D. Web Exclusive This is the fourth entry in a series on best practices in Electronic Lab Notebook (ELN) implementation. The first article identified five core areas which need to be managed to ensure a successful ELN deployment. This article discusses the third core area: collaboration.

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ELN Integration: Avoiding the Spaghetti Bowl

August 23, 2011 10:18 am | by Michael H. Elliott | Comments

Technologies are evolving to simplify integration and reduce long-term risk   Michael H. Elliott   Over the years, the desire to solve the myriad of data management problems in the laboratory has led to a plethora of point solutions. Not counting the vast number of instrument data management systems, it is not uncommon that a typical scientist has over 10 different systems to navigate. Despite all the sophisticated capabilities provided by these tools, over 20 percent of the average scientist’s time is spent on non-value-added data aggregation, transcription, formatting and manual documentation.

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Mathematica 8: An Easy Way to Compute, Develop and Deploy

August 19, 2011 6:11 am | by John A. Wass, Ph.D. | Comments

It’s always refreshing to see the latest version of an old friend and, in this case, delve into capabilities that go far beyond the simple algebra and calculus where the editor usually turns to this software (also to shed light on a biological process). Mathematica has expanded into so many areas, that it long ago ceased to be software that merely does math.

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One Step at a Time

August 18, 2011 9:34 am | by William L. Weaver, Ph.D. | Comments

While exciting, innovations in next-generation genome sequencing require painstaking development William L. Weaver, Ph.D. In 1898, Samuel P. Langley received a $70,000 grant from the United States War Department and the Smithsonian Institution to develop a piloted airplane. Langley invented a series of successful unmanned powered aircraft that were launched by a catapult system mounted on the roof of a houseboat anchored in the Potomac river — a system that would later serve as the basis for modern aircraft carriers.

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OriginPro Student Version Offers Useful Enhancements

August 18, 2011 8:28 am | by Jaclyn D. Wiggins-Camacho and Keith J. Stevenson, Ph.D. | Comments

This data analysis and graphing software is a truly comprehensive software package Jaclyn D. Wiggins-Camacho and Keith J. Stevenson, Ph.D. OriginLab offers a limited-time student personal use license for OriginPro 8.5, the latest version of their data analysis and graphing software. This is a fully-functional download from their Web site ( www.OriginLab.com ), requiring an online activation step to generate the license file for the individual student user.

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Implementing Electronic Lab Notebooks Part 3

July 28, 2011 8:58 am | by Bennett Lass Ph.D., PMP | Comments

Documenting experiments   Bennett Lass Ph.D., PMP web exclusive This is the third article in a series on best practices in electronic lab notebook (ELN) implementation. The previous article identified five core areas that need to be managed to ensure a successful ELN deployment. This article discusses the second core area: documenting experiments

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Primitive Restart Makes GPGPU Tech Sparkle

June 27, 2011 7:10 am | by Rob Farber | Comments

Exploiting the full computational power of the GPGPU to render high-performance, high-quality graphics Rob Farber   GPGPU technology is dramatically changing what is possible for data visualization, as well as computation. The orders-of-magnitude increased application performance reported in the recent literature succinctly conveys the computational power of GPGPU devices

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High-Fidelity Simulation of Landing Gear Noise

June 27, 2011 6:01 am | by Mehdi R. Khorrami, Ph.D. and Patrick J. Moran, Ph.D. | Comments

NASA aims to improve the sonic environment Mehdi R. Khorrami, Ph.D. and Patrick J. Moran, Ph.D. A key challenge in aircraft design is to minimize the noise radiated during take-off and landing. Increasingly strict U.S. regulations on noise pollution surrounding airports near major metropolitan areas mandate that aircraft that do not meet noise requirements be retrofitted or removed from service

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Finding the Right Tools for Energy Research

June 23, 2011 9:52 am | by Aaron Knoll | Comments

Visual analysis in this fast-growing, diverse field demands new ways of leveraging HPC resources Aaron Knoll The explosion of nanoscale research driven by computational chemistry is changing how materials are modeled, validated and synthesized. More than ever, research in energy storage, catalysis and alternative fuels is being conducted in a computational sandbox before it is validated experimentally and, ultimately, manufactured

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Arctic Snow Harbors Deadly Assassin

June 22, 2011 6:56 am | Comments

A new international study confirms that whilst snow has an insulating effect which helps plants to grow bigger, heavy and prolonged snow can, in certain circumstances, also encourage the rapid and extensive growth of killer fungal strains. The snowfall can bring about unexpected conditions that encourage fungal growth, leading to the death of plants in the Arctic

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Implementing Electronic Lab Notebooks Part 2

June 21, 2011 6:28 am | by Bennett Lass Ph.D., PMP | Comments

Building the foundation web exclusive Bennett Lass Ph.D This is the second article in a series on best practices in implementing an Electronic Laboratory Notebook (ELN). The previous article identified five core areas which will optimize return on investment (ROI) and ensure a successful ELN deployment. This article discusses the first core area: Establishing a Solid Foundation

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Implementing Electronic Lab Notebooks

June 2, 2011 9:35 am | by Bennett Lass Ph.D , PMP | Comments

How do you define and manage success? web exclusive Bennett Lass Ph.D In the past five years, the electronic lab notebook (ELN) has moved from nascent technology deployed mainly by early adopters and technology enthusiasts to a mainstream laboratory chemical informatics platform. Atrium Research and Consulting estimates that over 25% of the potential market for ELNs has either deployed or is in the midst of deploying an ELN

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