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Feature - SAGrid: A view from the coordinator’s chair

SEACOM is a 1.28Tbps, 15,000 kilometer-long undersea fiber-optic cable system that will provide high-speed communication between East Africa, South Asia and Europe. As of press time, its promoters expect the system to be up and running in less than three weeks. Image courtesy SEACOM

Bruce Becker of the Meraka Institute in Pretoria is the Coordinator for planning the upcoming South Africa Grid initiative — which will draw upon the resources of South Africa’s Center for High Performance Computing and the country’s high-speed network, SANREN. Here, he gives an update of the status of the project.After over a year of training sessions and technical workshops in multiple countries, preparations are under way for a move to full production readiness of the South Africa Grid, or SAGrid.The testing and incubation phase is coming to an end; the high-speed national research network SANREN is under way and already ac

Feature - EVO powers communication for global collaborations

Image courtesy caltech.edu.

For the Large Hadron Collider collaborators who are spread across the globe, staying connected presents challenges. The Enabling Virtual Organizations (EVO) system, a worldwide network designed for institutions participating in the LHC experiments and other high-energy physics collaborative programs, makes international collaboration easier by providing a reliable and secure system for real-time virtual meetings.
EVO, winner of the 2009 Internet2 IDEA award for applied advanced networking “at its best,” hails from the California Institute of Technology (Caltech). In 2008 it hosted more than 9,100 virtual LHC collaboration meetings with a total of over 4,200 users. The combined time each user spent in EVO LHC meetings last year totals more than 86,300 hours. Unlike commercial networks, EVO poses no restriction on the number of participants in a meeting. On September 10, 2008, about 1,250

Feature - Plenty more fish in the sea?

According to the UN’s Food and Agriculture Organization, over 70% of the world’s fish stocks are fully exploited, overexploited or depleted. Image courtesy nahpets/stock.exchng 

Once thought to be an endless source of bounty, the oceans’ supply of fish has plummeted dramatically. The biggest cause of this deterioration — bigger than pollution — is overfishing.
Rampant over-fishing around the globe has caused some of our favorite species to hover near collapse. There has been a 90 percent drop in the number of tuna, salmon, cod, swordfish, rays, pollack and haddock since the 1950s, wrote Jeremy Jackson, director of the Scripps Center for Marine Biodiversity and Conservation at the University of California, San Diego, in a paper published last year in the Proceedings of the National Academy of Sciences.
The effects of over-fishing are being exacerbated by global climate change, which changes the distribution of sp

Opinion - The age of citizen cyberspace

Using LHC@home, particle beam dynamics can be studied with volunteer computing. Image courtesy CERN

(François Grey, one of the key people behind the founding of the present-day iSGTW and a frequent contributor to these pages, argues that with volunteer computing, we are about to embark upon a new era of “citizen science.”)
I first met Rytis Slatkevicius in 2006, when he was 18. At the time, he had assembled the world’s largest database of prime numbers — those which are only divisible by themselves and one.
He had done this by harnessing the spare processing power of computers belonging to thousands of prime-number enthusiasts, using the internet. 
Today, Rytis is a mild-mannered MBA student by day and an avid prime-number sleuth by night. His project, called PrimeGrid, is tackling a host of numerical challenges, such as finding the longest arithmetic progression of prime numbers (the current record is 25). P

Feature - Grid-enabled virus hunting

3D replica of senecavirus, a pathogen discovered several years ago by researchers in Pennsylvania. UC San Francisco researcher Eric Delwart and his colleague Chunlin Wang of Stanford University use the RENCI-developed TeraGrid Science Gateway and the Open Science Grid to access grid computing resources in their search for new viruses.
Image courtesy of the Institute for Animal Health, UK

Researchers use distributed computing to make sequence analysis faster and easier.DNA sequencing and sequence analysis happens daily in many biological sciences laboratories, but analyzing large sets of genetic data increasingly requires computing resources beyond the capabilities of most labs. The search for the best hardware and software led Eric Delwart, a professor of laboratory medicine at the University of California, San Francisco, and a senior investigator at the Blood Systems Research Institute, and Chunlin Wang, a research associate at the Stanford Univ

Feature - Do more with MATLAB

Using MATLAB on EGEE middleware, researchers can make a better laser - such as this solid state Cornellium Cn3+ laser created by a sapphire crystal. Image courtesy MATLAB Central

Researchers from disciplines as far apart as lasers and finance have a new computing tool at their fingertips: MATLAB can now run on Enabling Grids for E-sciencE (EGEE) computing power. The software is a high-level language and interactive environment that enables users to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Widely regarded as a  powerful piece of simulation software, for use in everything from optimizing rocket launch control settings to vector analysis, it is now fully compatible with any grid computing system using gLite middleware.“Our motivation for incorporating this tool was rather straightforward. MATLAB is one of the most popular and important general-purpose scientific software

Opinion - Grids, clouds and communities: an Open Grid Forum perspective

Image courtesy BELIEF

(Editor’s note: Below, Open Grid Forum’s Paul Strong and Craig Lee give their view of the future of grids and clouds.)
OGF’s initial focus on grids has broadened over time, reflecting evolution in community needs and in technologies such as virtualization and cloud computing.
Grids have been widely adopted across academia and industry. Their evolution and deployment has been driven by several desires: to share data and computational resources, to get results faster, to improve efficiency and to collaborate.
Clouds are driven by different needs, primarily the desire for financial flexibility, offered by platforms such as “pay-per-use,” and business agility, such as reduced time to market and the ability to engage in fast, low-risk experimentation. The cloud model relies on the provider first achieving economies of scale, through sharing resources, and then offer

Feature - Clarity in clinial care: achieving fully interoperable databases

Werner CeustersImage courtesy of W. Ceusters.

Werner Ceusters, director of the  Ontology Research Group at the NYS Center of Excellence in Bioinformatics & Life Sciences, spoke at the Bio-IT World Conference in Boston this past April on the topic of "Do Healthcare IT Standards Hamper the Advance of Science?" 

“Swimming is healthy and contains eight letters.” Absurd? Of course — the real thing is confused with its symbolic representation. Absurdity, then, abounds in current Electronic Health Records (EHRs) according to Werner Ceusters of the New York State Center of Excellence in Bioinformatics and Life Sciences and the University at Buffalo. A polyp by any other name… A significant and universal problem with legacy EHRs, Ceusters says, is that software programs that access them cannot adequately differentiate between diagnoses for a given patient and link them prope

Feature - ETICS 2 offers help to software professionals

Image courtesy ETICS 2

Software professionals have been know to describe the task of building, configuring and integrating new software in as little as two words: “nightmare activity.”  But with E-infrastructure for Testing, Integration and Configuration of Software Phase 2, or ETICS 2, they have an all-in-one solution that helps configure and build software, and at the same time check its quality. The result of three years of project activities, this system provides tools and resources to build and test runs, thereby simplifying complex and often repetitive activities.
“By automating many day-to-day tasks, ETICS 2 supports software professionals obtain higher quality software, a shorter time-to-market, a lower risk on schedule and reduced project costs,” says Alberto Di Meglio, ETICS 2 project manager at CERN.
The ETICS 2 system exploits grid software and distributed computing infrastructures. It is

Feature - Volunteer computing against childhood cancer

Image courtesy of WCG.

Researchers from the Chiba Cancer Center Research Institute and Chiba University in Japan are launching a new World Community Grid project with IBM to discover a drug treatment for neuroblastoma, the most common cause of death in children with solid tumors. Help Fight Childhood Cancer, as the project is known, uses idle computational power from volunteers’ home and office computers to identify promising drug candidates.Most physicians believe that neuroblastoma is caused by accidental cell growth that occurs during normal development of the sympathetic ganglia and adrenal glands. This condition occurs most often the first two years of life, and poses a high risk for disease relapse with survival rates under 40 percent.The new Help Fight Childhood Cancer project uses volunteered computational power to identify which of the three million potential drug candidates prohibit growth of three proteins, TrkB, AL

Countdown! World’s most sophisticated thermometer blasts off into space

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Arianespace sent into orbit a scientific satellite known as the Planck scientific observatory, for the European Space Agency.  The launch process took the new instrument from the ground into space in less than an hour. Image courtesy ESA

On 1:12 pm on Thursday, May 14, the Planck satellite — arguably the world’s largest thermometer — lifted off from the European Space Agency’s launch pad in French Guiana.
The launch began with a 6-second vertical climb. The onboard computers optimized the motion of the rocket in real time, in order to minimize fuel consumption. The main stage engine took the launcher into an intermediate orbit before the end stage carried the payload into the final orbit. The main stage of the launcher fell back, just off the coast of Africa in the Atlantic Ocean. The launcher will remain at an altitude of about 852 kilometers travelling at about

Feature - EDGeS helps us all talk to each other

With AutoDock, biologists can predict how small molecules will interact with known larger molecules - vital to evaluating candidates for new drugs. Image courtesy www.YASARA.org

Like Bill Murray adrift in Japan in the movie “Lost in Translation,” things can go awry when service grids and volunteer grids try to talk to each other.
Service grids, such as EGEE, often involve large institutions whose work method is centered around collaboration — to the point where participants often know each other personally. To ensure security, resources and users pass through an accreditation process, and the resulting “certificate” provides proof that this occurred successfully. The certificate is key to allowing jobs to be submitted and completed.
On the other hand, volunteer systems — such as BOINC or XtremWeb-based desktop grids — consist of large numbers of personal computers linked together by individuals w