Cloud Computing Helps Decode German E. Coli Strain

Cloud Computing Helps Decode German E. Coli Strain

When a nasty strain of E. coli flooded hospitals in Germany this summer, it struck its victims with life-threatening complications far more often than most strains — and the search for an explanation began.

Over a feverish weekend after the rogue bacterium’s genome was sequenced, scientists from all over the world submitted the E. coli genome to rounds of rigorous study. Thanks to a unique Argonne-developed computer program and cloud computing testbed, researchers mapped the strain’s genes — and came a little closer to understanding the bacterium’s secrets.

A team of Argonne scientists near Chicago, Illinois, developed the Rapid Annotation using Subsystems Technology (RAST) program in 2007. The program, which is free and open to any scientist, is designed to make sense of the jumble of letters that makes up an organism’s DNA.

A genome is a long, incomprehensible string of letters in a four-letter alphabet: G, A, T, C. Sections of the string are divided into genes. Each one describes how to build a protein, and proteins build all of the parts of the cell.

If we can figure out what DNA codes for which protein, and what that protein does, then we can look at any bug and have an idea of what it can do,” explained Ross Overbeek, an Argonne computer scientist who helped design RAST.

“For example, bugs with multi-drug resistance often turn out to have little pumps that drain the drug out of the cell as fast as it comes in,” Overbeek said. “Once you know what those pumps look like, you can think about how to get around them.”

RAST matches sections of the new string with its enormous catalogue of previously sequenced genes and proteins. At the end it spits out an annotated genome with a sort of ‘Cliffs Notes’ to the organism’s probable genes and proteins.

When scientists announced they had sequenced the genome to the E. coli strain that plagued Europe on June 3, researchers from around the world began sending versions of the genome to RAST for annotation. They wanted to compare the new strain with past strains to tease out its origins and vulnerabilities.

Genomes can vary even within a strain,” Overbeek said. “You can get slightly different genomes in the same outbreak, even from the same patient. You compare genomes to see how the organism is mutating even as it’s wreaking havoc.”

RAST servers were already overwhelmed by a flush of genomes and the new requests began to pile up — reaching more than 200 genomes an hour at one point. Its operators wanted to prioritize the E. coli work, so they turned to a resource designed for just such a possibility.

Magellan is a test cloud computing project, run by the U.S. Department of Energy, designed to boost research by making additional servers available on demand for scientific computing. The program, partially funded by the Recovery Act, has two sites — one at the Argonne Leadership Computing Facility and one at the National Energy Research Scientific Computing Center in California — but is designed to give researchers across the nation access to computing power in times of need.

The Argonne team duplicated the RAST server on Magellan, rapidly increasing the available computing power. “Our system is designed to use clusters, so we engineered it so that a piece of Magellan became part of the cluster that we use for RAST,” explained Bob Olson, an Argonne computer scientist who maintains RAST.

It worked — so well that even more submissions poured in. Argonne and Virginia Tech teams worked around the clock that weekend to keep the servers running smoothly.

They found exactly what they were looking for,” Overbeek said. “The difference between this new strain and older ones came down to just a few genes. Apparently, the new strain included a combination of virulence factors present in other studied strains.”

The operation was a perfect case for Magellan, Olson said, because each genome submission is an independent problem. Simply adding more processors to handle the extra jobs is easy — unlike many other computations, which often must solve successive problems; processors must wait to start their jobs until another processor finishes.

Overbeek remembered the early days of annotating genomes in the mid-1990s, when it took four or five scientists more than a year to analyze just one genome. “Now we can spit them out in a few hours,” he said, and the team has already tested the next generation of RAST — a version so fast that it cuts the time for annotating a typical E. coli genome from eight hours to just 15 minutes.

RAST is really revolutionary,” Overbeek said. “It’s turned a problem that used to be insurmountable into one that is trivial.”

There is even an iPhone app to submit and receive genomes from RAST servers.

Developed at Argonne, RAST is funded through the U.S. National Institutes of Health and run by the Pathosystems Resource Integration Center (PATRIC) at the Virginia Bioinformatics Institute. PATRIC keeps a publicly available database of sequenced genome information.

Contribution By Louis Lerner/http://www.isgtw.org/

version of this story first appeared on the ANL website.

About CloudTweaks

Established in 2009, CloudTweaks is recognized as one of the leading authorities in connected technology information and services.

We embrace and instill thought leadership insights, relevant and timely news related stories, unbiased benchmark reporting as well as offer green/cleantech learning and consultive services around the world.

Our vision is to create awareness and to help find innovative ways to connect our planet in a positive eco-friendly manner.

In the meantime, you may connect with CloudTweaks by following and sharing our resources.

View All Articles

Sorry, comments are closed for this post.

4 Cloud Technology Trends To Look Out For

4 Cloud Technology Trends To Look Out For

Cloud Technology Trends When you are reading articles on the future of tech on the Internet you cannot escape mention of the cloud: it is set to be the best thing that has ever happened to us, pundits assure us, and there is a promise of some serious money to be made. Reading these articles you can tell there is…

The Internet of Things And The Knowledge Revolution

The Internet of Things And The Knowledge Revolution

The Knowledge Revolution Think about a few things in your life right now. It really doesn’t matter what they are, as long as you interact with them daily. They could be your phone, your shoes, your watch, your car, your refrigerator, your garage door opener…you get the idea. What do all of these things have…

Cloud Computing – The Real Story Is About Business Strategy, Not Technology

Cloud Computing – The Real Story Is About Business Strategy, Not Technology

Enabling Business Strategies The cloud is not really the final destination: It’s mid-2015, and it’s clear that the cloud paradigm is here to stay. Its services are growing exponentially and, at this time, it’s a fluid model with no steady state on the horizon. As such, adopting cloud computing has been surprisingly slow and seen more…

The Collision of Cloud and Data Privacy

The Collision of Cloud and Data Privacy

Cloud and Data Privacy The “cloudification” of everything from data storage to applications to security services has increased the availability of free-flowing data, allowing business to access anything from anywhere. However, it’s raised serious concerns about the security of personally identifiable information (PII) collected and shared by businesses and government agencies across international borders, and…

Finally, The Time For Security Information Event Management (SIEM)

Finally, The Time For Security Information Event Management (SIEM)

The Time For SIEM Security Information Event Management (SIEM) tools have been around for a long time. My first encounter with a SIEM vendor was about twenty years ago while being courted to resell their product. To this day, I still recall two vivid memories from that meeting; the product was very complex and quite…

New Smartphones From Apple, Samsung and HTC Promise To Light Up 2016

New Smartphones From Apple, Samsung and HTC Promise To Light Up 2016

New Smartphones from Apple, Samsung and HTC (Sponsored post courtesy of Verizon Wireless) The launch of the Galaxy S7 Edge at the Mobile World Congress in Barcelona during February was the first shot in a vintage year for mobile phones. The S7 is an incredible piece of hardware, but launches from HTC and Apple later in the…

Featured Sponsored Articles
How Successful Businesses Ensure Quality Team Communication

How Successful Businesses Ensure Quality Team Communication

Quality Team Communication  (Sponsored post courtesy of Hubgets) Successful team communication and collaboration are as vital to project and overall business success as the quality of products and services an organization develops. We rely on a host of business tools to ensure appropriate customer interactions, sound product manufacturing, and smooth back-end operations. However, the interpersonal relationships…

Featured Sponsored Articles
How To Develop A Business Continuity Plan Using Internet Performance Management

How To Develop A Business Continuity Plan Using Internet Performance Management

Internet Performance Management Planning CDN Performance Series Provided By Dyn In our previous post, we laid out the problems of business continuity and Internet Performance Management in today’s online environment.  In this article, we will take a look at some of the ways you can use traffic steering capabilities to execute business continuity planning and…

Featured Sponsored Articles

CloudTweaks is recognized as one of the leading influencers in cloud computing, infosec, big data and the internet of things (IoT) information. Our goal is to continue to build our growing information portal by providing the best in-depth articles, interviews, event listings, whitepapers, infographics and much more.

Sponsor