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New complex algorithm speeds up genetic computation

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April 23, 2014

Scientists and university researchers have built DNA genomes for many years, but applying what we already know about genetics to everyday medicine is a difficult and rather daunting task.

Crafting treatments from genes is so complex that IBM recently entered a partnership to get its Watson supercomputer learning to help the medical profession tailor personalised treatments for cancer.

Part of the issue that researchers want to solve is gene expression. In all the complexities of how genes interact, what interactions are expressed in a physical trait? Whether that trait is blue eyes, or why one individual dies of a cancer that's arrested in someone else.

What's needed is a method to accurately predict gene expression, and one angle of the research is based on RNA sequencing (RNA-seq) data.

The problem is that analysing RNA sequencing is a very slow process, and that's where the research out of Carnegie-Mellon University and the University of Maryland comes in.

Their so-called Sailfish algorithm dramatically accelerates estimates of the likely outputs of RNA sequence. To explain why this is so important, the researchers' release says-- “Though an organism's genetic makeup is static, the activity of individual genes varies greatly over time, making gene expression an important factor in understanding how various organisms work and what occurs during disease processes. Gene activity can't be measured directly, but can be inferred by monitoring RNA, the molecules that carry information from the genes for producing proteins and other cellular activities.”

But analysing the RNA-seq reads (short sequences of RNA) traditionally results in huge datasets that have to be mapped back to their original genetic processes.

The Sailfish algorithm completely skips this painstaking mapping step, thereby increasing the speed of the process by a wide margin.

Instead, the university researchers found they could allocate parts of the reads to different types of RNA molecules, much as if each read acted as several votes for one molecule or another.

Think of it as upvoting posts in a forum-- individual votes bestow a kind of consensus on which reads or posts carry the greatest significance.

Getting what might be a 15-hour analysis down to just a few minutes is important, the researchers believe. There are already huge repositories of RNA-seq data, but turning data into insight is held back by computational effort.

Fifteen hours for each analysis really starts to add up, particularly if you want to look at 100 experiments, explains Carnegie-Mellon associate professor Carl Kingsford.

“With Sailfish, we can give researchers everything they got from previous methods, but faster,” he said.

In other IT news

VMware reported stronger earnings and revenue yesterday that beat analysts expectations. The Palo Alto-based company made $1.368 billion in sales in its first quarter, up 14 percent on the previous year's quarter.

VMware reported an operating income of $241 million, up 51 percent on the $160 million it reported in Q1 of 2013. Non-GAAP earnings per share was $0.80, versus expectations of $0.79.

VMware made $561 million from licenses in the quarter versus $799 million in maintenance, representing a growth-heavy start to a year that VMware executives believe will lead to significant growth for the company.

"Our strong financial results reflect VMware's unique position in helping customers transform their IT infrastructure," said VMware's CEO Pat Gelsinger.

"As the industry shifts from client server computing to the mobile-cloud era, customers are choosing our solutions because we have the most complete vision and offering for navigating this evolving world," added Gelsinger.

During the 1st quarter, VMware spent $77 million on additions to property and equipment, compared with $78 million in the same quarter last year.

Those purchases support the infrastructure that goes into VMware's strategically important vCloud Hybrid Service, which launched in August 2013 and is meant to compete with rivals Amazon, Microsoft and Google.

But it's important to note that VMware's competitors have been spending a lot more on capital expenditures in the last year, and that's something that VMware needs to look into if it wants to continue growing at the same pace.

VMware's COO Carl Eschenbach said that the company's cloud services grew greater than 100 percent year-on-year, including both the vCHS service and VMware's service provider partner program.

Toward the end of its last quarter, VMware acquired mobile management and security company AirWatch, which executives on the call following the earnings release said they expect will become a multi-million dollar per quarter business for VMware in 2014.

AirWatch is one of VMware's big bets, alongside software-defined data center acquisition Nicira, whose technology is now known as NSX, that it can not only make money from virtualization, but the next one-- mobile devices and software-defined data centers.

VMware said it expects its full 2014 revenues to be between $5.94 and $6.10 billion, or up 14 to 17 percent year-on-year.

In other IT news

Microsoft said earlier this morning that it has been given the green light to build a $1.1 billion data center just outside Des Moines, Iowa which, when taken together with its existing data center infrastructure, will raise the company's investment in the area of close to $2 billion.

On Friday, the Iowa Economic Development Authority (IEDA) approved a $20.3 million sales tax rebate on construction materials for the project, available until 2021, a sum that's in addition to $18 million in infrastructure improvements already promised by the city.

But naturally, Microsoft isn't getting off that easily. In return for those improvements, Nadella & Co. have agreed to a minimum taxable assessed value of $255 million once the project is completed – an amount that The Des Moines Register reports will bring the city of West Des Moines an annual tax revenue of about $8 million.

The state of Iowa also will require Microsoft to create 84 permanent jobs when the project is completed, and that 66 of those jobs must pay at least $24.32 per hour.

The data center will be built on a 154-acre site, with the facility comprising 1.16 million square feet. The data center project has been finding its way among the appropriate decision-makers, but under the code name of "Project Alluvion" – it wasn't until last Friday's meeting that Microsoft was revealed to be the company behind the development.

Project Alluvion was originally scheduled to have been on the IEDA's agenda in Mid-March, but was pushed forward to last Friday's meeting at the last minute.

The delay was caused by Willow Creek needing more time to ensure that it could acquire enough land. We'll keep you posted on this and other stories as they happen.

In other IT news

Now that Windows XP's end-of-life support is behind us, system admins will soon have another critical date to watch out for, this time it will be next year.

If you're still using Windows Server 2003 R2, Microsoft's product lifecycle advisories say that support for that operating system expires on July 14, 2015. That's only 449 days from today.

Both the Standard, Enterprise and Datacentre versions of the operating system, in 32-and-64-bit versions, will receive their last Windows security update on that date.

However, the obsolescence of Windows Server 2003 won't be as big an issue as the EOL (end of life) of Windows XP, and for two main reasons.

The first is that servers tend to be be upgraded more often than PCs, because the former are cared for by knowledgeable and skilful server technicians who understand the need to migrate from decade-old operating systems and have therefore probably already made the move.

The second reason is that there are many fewer servers than PCs. Gartner estimates that about 2,581,724 servers shipped in 2013's 4th quarter.

Source: Carnegie-Mellon University.

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