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Actuaries and Epidemiologists: Same Data, Different Interpretations

October 5, 2011 10:14 am | by Sandy Weinberg, Ph.D. and Ronald Fuqua, Ph.D. | Comments

Interaction of two computing modeling fields provides critical disease mitigation tools Sandy Weinberg, Ph.D. and Ronald Fuqua, Ph.D. While neither may qualify as “the world’s oldest profession,” at least in risqué jokes, both professional actuaries and epidemiologists have long histories, with an interesting modern intersection. The Old Testament describes a variety of diseases in great detail: arguably Moses was, in addition to his other skills, an effective epidemiologist. And, as for actuaries, didn’t Noah count off the animals in his ark two-by-two? However, it is in the modern analysis of health trends that these two modern professions emerge to provide a scientific basis for research and application.

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Implementing Electronic Lab Notebooks Part 5

October 5, 2011 8:04 am | by Bennett Lass Ph.D., PMP | Comments

Systems Integration Bennett Lass Ph.D., PMP Web Exclusive This is the fifth article in a series on best practices in Electronic Lab Notebook (ELN) implementation. This article discusses the fourth core area: System Integration.

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HPC Democratization

October 4, 2011 10:46 am | by Steve Conway, IDC Research VP, HPC | Comments

Be Careful What You Wish For Steve Conway, IDC Research VP, HPC In 1995, the global market for high performance computing (HPC) servers, a.k.a. supercomputers, was worth about $2 billion. By 2010, that figure nearly quintupled to $9.5 billion, thanks to the rise of HPC clusters based on commercial, off-the-shelf (COTS) technologies.

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Competing with C++ and Java

October 4, 2011 10:13 am | by Rob Farber | Comments

    Everyone’s a winner in the race for a common application language that can support both x86 and massively parallel hardware Rob Farber Commercial and research projects must now have parallel applications to compete for customer and research dollars. This translates into pressure on software development efforts that have to control costs while supporting a range of rapidly evolving parallel hardware platforms. What is needed is a common programming language that developers can use to create parallel applications with a single source tree that can run on current and future parallel hardware.

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What Constitutes a Good Forensics LIMS?

October 4, 2011 8:53 am | by John R. Joyce, Ph.D. | Comments

While it is common for users in various laboratories and industries to feel that their processes are unique, in many ways, they all have common needs. Similarly, in many respects, all laboratory information management systems (LIMS) are alike, or at least they should be. All must perform basic functions, such as track the users entering data, track the samples arriving at the laboratory and their processing through it...

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Considerations for Software Expansions and Upgrades

September 30, 2011 11:21 am | by Peter J. Boogaard | Comments

Before you decide to rock the boat, several key decision-making steps can help to ensure a smooth and successful upgrade Peter J. Boogaard The upside of upgrading the IT infrastructure will give many organizations the ability to eliminate barriers to enable cross-functional collaboration between research, development, quality assurance and manufacturing. Standardizing workflows and operating procedures and applying best industry practices throughout operations also are key drivers. Quick advantage occurs when the implementation is fast and when it results in strategic value. This article will highlight key decision-making steps to be considered when upgrading your software.

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Maple 15: How do they do it?!

September 29, 2011 10:31 am | by John A. Wass, Ph.D. | Comments

For those new to this software, perhaps a little background is in order. Maple is mathematical software that is constantly being improved as to breadth of the calculation routines, optimality of the algorithms, speed of computation, and ease-of-use. The last is one of the most useful features, as the new user can quickly come up to speed by testing the menu items, going through the tutorials and reading the pertinent sections of the manuals

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Data Traffic is about to Explode: Don’t Get Caught in the Blast

September 28, 2011 11:13 am | by Dan Joe Barry, Napatech | Comments

Using what you have in a smarter way Dan Joe Barry, Napatech Web Exclusive If you like theory, then you’ll be interested to know that many are predicting that data center traffic is set to sharply increase. As cloud computing centralizes, more computing resources and more devices, such as mobile phones, tablets and TVs, are being used to exchange data.

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Seven Tips for Staying on the Right Side of the Ethical Line in Tough Times and Beyond

September 23, 2011 9:34 am | by Christopher Bauer, Ph.D. | Comments

Avoiding the consequences of cutting corners Christopher Bauer, Ph.D.  Web Exclusive Times are tough in business right now, certainly including laboratory informatics, and any sane business person is trying to cut corners in any way possible. Scaling back on your attention to ethics, however, can have catastrophic consequences. Between the possible fines, legal fees and reputational damage to you and your company, you could lose anything from thousands to millions of dollars as well as your career or business. No matter how tough the times are, that kind of risk is simply not worth taking. Unfortunately, though, tough times can easily make it seem worth trying to cut ethical corners if it looks like there might be some financial gain from it.

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How Data Tiering Can Lower IT Storage Costs

September 20, 2011 10:14 am | by Will McGrath | Comments

Solving the problems of “big” data growth Will McGrath Web Exclusive The explosion of data growth created by next-gen instruments has caused tremendous challenges in handling and storing those files. While growth in structured and semi-structured data — like e-mail and databases — continues to grow, it is really unstructured “big” data growth that is causing the biggest problems. This is true in verticals like oil and gas with upstream seismic and interpretation applications or in life sciences with a number of newer instruments being introduced for electron microscopy, high content screening / high throughput screening and flow cytometry — or especially, next generation sequencing (NGS).

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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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