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August 26, 2009
Feature - Improving Alzheimer's research a million scans at a time

Feature - Improving Alzheimer’s research, a million scans at a time

Alzheimer’s is one of the most feared diseases associated with aging. Fortunately, early detection can slow its development. Image courtesy stock.xchng

As you read this, your brain is busily working. In a complex but unconscious process, it scans the pixels on your screen, analyzes the images and turns them into meaningful information.
This week, a similar work began, neuGRID, that might help keep our minds whirring wonderfully as we (alas) age.
This massive scanning project will feed 6,300 magnetic resonance (MR) scans from more than 700 patients — a bit less than 200 images per patient, making for an impressive total of 1,260,000 images — through an automated series of calculations. This “pipeline” will analyze the cortical thickness of the brain (a measurement aligned with brain health) and its deterioration over time. The images are from the Alzheimer’s Disease Neur

August 26, 2009
Feature - The Lost Sounds Orchestra

Feature - The Lost Sounds Orchestra

An audience experiences “the sonic scenario of the past.” Image courtesy Luca Petrella  

Last September, iSGTW reported upon the return of the epigonion, an ancient Greek wooden stringed instrument resembling a harp. Ancient instruments can be lost because they are too difficult to build, or too difficult to play, but the epigonion was heard again after ASTRA (Ancient instruments Sound/Timbre Reconstruction Application) recreated its sound using grid-enabled computer modeling.
More ancient instruments are to be heard soon, after the organization’s official Lost Sounds Orchestra finishes its preparations for a unique performance towards the end of summer.
Having successfully reconstructed the sound of the epigonion, ASTRA is working on a whole host of other lost instruments including the barbiton (an ancient base guitar), the syrinx (a pan flute), an ancient lower Mediterranean frame drum, the salpinx (a kind of ancien

August 19, 2009
Feature - Grid helps to filter LIGO data

Feature – Grid helps to filter LIGO’s data

Workers at LIGO adjust the optic suspensions in situ. The suspension system is one of the physical measures LIGO takes to isolate the detector from false signals such as seismic activity. Courtesy of LIGO Lab.

Tiny ripples in the fabric of space-time may provide scientists with a way to study cosmic processes that are invisible to optical telescopes, such as the collision of two black holes.
In his theory of general relativity, Einstein predicted that such ripples, called gravitational waves, would be created when a mass accelerates. However, gravitational waves are so small – about one thousand times smaller than a proton – that even the relatively large ones generated by massive astrophysical events are very difficult to detect.
The Laser Interferometer Gravitational Wave Observatory (LIGO), which has sites in Washington and Louisiana, uses lasers to search for these minute cosmic ripples that carry information abou

August 12, 2009
Feature - Academia Sinica watches global carbon

Feature - Academia Sinica watches global carbon

Chi-Lan Flux Tower is located on one of the long-term ecological research sites in Taiwan, in the northeast part of the island and close to Yuan-Yang Lake nature preserve. At 1400 - 1800 m above sea level, the area of the Chi-Lan Mountain site covers approximately 310 hectares, with a high frequency of fog and cloud year-round. The climate is temperate, heavy and moist, and the trees are mainly Taiwan Cypress. Image courtesy Jia-ying Jiang, Chi-Lan Mountain
Front page: Polarized light reveals the state of the atmosphere thousands of years ago, in a slice of glacial ice containing bubbles of atmospheric gases trapped eons ago. Image courtesy UCAR

With the help of data standards and computing resources, Academia Sinica Grid Computing Center (ASGC) has developed an innovative, grid-enabled approach to tackle carbon flux observation.
The carbon cycle — in which the carbon from the greenhouse gas carbon dioxide (CO2) travels fro

August 12, 2009
Video - Health-E Child video documentary

 

Video of the Week: Health-e-Child documentary

Athenaweb, one of the hosts for the Health-e-Child video, can be thought of as “the YouTube of science,” with hundreds of films and videos available. Image courtesy Athenaweb 

The Health-e-Child project (See iSGTW 28 May, 2008 and the 8 July, 2009 HealthGrid roundup) has video documentaries about its work that can now be seen as broadcasts on the Euronews website. (Click on the “Science-Tech” banner up on the right.) The first broadcast is entitled “New frontiers of imaging the human body.”
All European public televisions and main private ones receive the broadcasts, and some of them will be re-aired during the summer. 
They are also accesible on YouTube and other smaller, regional streaming online websites. The reports will be also broadcast on athenaweb.org, a website specializing in Worldwide Research TV reports.
A special broadcast has also been scheduled for Friday, September

July 29, 2009
Feature - Burning down the house

Feature - Burning down the house (with FireGrid)

Fire at a warehouse. Image courtesy London Fire Brigade

About noon on 29 October 2008, a fire broke out in a small apartment in the town of Watford, UK.
The fire had been deliberately started in a sofa in the living room. With no intervention, the sofa soon started to burn fiercely, allowing the fire to spread to a nearby table and TV. The temperature within the room increased to such a high level that the walls and other furnishings burst into flames, a phenomenon known as “flash-over” that would have been potentially fatal to anyone in the apartment. As the flash-over occurred, a ball of fire coursed down the hallway, creating a plume of flame that curled around the front door. At this point, the fire was calmly extinguished.The fire was actually a test, run in a state-of-the-art “burn hall facility” — essentially a large hanger in which the apartment rig was assembled — at the Building

July 29, 2009
Feature - Common cheap chips get jobs done faster

Feature - Common cheap chips get jobs done faster

Although much of today’s most interesting research requires immense amounts of computational power, many scientists don’t have the funds to access expensive supercomputers or clusters. Now, a commonplace computer chip may provide a thrifty way to get those jobs done.
Graphics processing units (GPUs) are found in most computers and are designed to render 3-D computer graphics. They contain hundreds of processing cores on a single chip, and several chips can fit into a single desktop. Computational geneticists Marc Suchard of the University of California Los Angeles and Andrew Rambaut of the University of Edinburgh were able to use GPUs to speed up their computations by a factor of 100.

This tree shows how a population of viruses evolved over a 10-year period within an infected patient. The branch colors reflect relative rates of evolution along each branch.
Courtesy of Marc Suchard of UCLA.

Suchard and Ramba

July 29, 2009
Link of the Week - Gaia

 

Link of the Week - Gaia

Image courtesy ESA

This week’s Link is the Gaia project — a global space astrometry mission. Its goal is to make the largest, most precise three-dimensional map of our galaxy by surveying an unprecedented number of stars, more than a billion. The data- handling is done with a combination of grid and cloud computing.
Gaia will monitor each of its target stars about 70 times over a five-year period, precisely charting their positions, distances, movements and changes in brightness. It is expected to discover hundreds of thousands of new celestial objects, such as extra-solar planets and failed stars called brown dwarfs. Within our own solar system, Gaia should also identify tens of thousands of asteroids.Additional scientific benefits include detection and characterization of tens of thousands of extra-solar planetary systems, a comprehensive survey of objects ranging from huge numbers of minor bodies in our solar system, through galaxies i

July 8, 2009
Feature - A solid production demonstration of the LCG

Feature - A solid production demonstration of the CMS role in WLCG

Last fall’s unplanned shutdown of the Large Hadron Collider was a disappointment for physicists around the world. But for organizers of the computing grid supporting the collider’s detectors, it was also an opportunity to keep working hard. For the first two weeks of June, instead of flooding the grid with data from actual particle collisions, experiment collaborators at CERN and remote computing sites in Europe, Asia, and North America joined up to test the ability of the collider’s Worldwide LHC Computing Grid (WLCG) to record, transfer and analyze simulated data in a step-by-step “production demonstration.”
Scientists conducted a series of challenges, collectively called the Scale Test of the Experimental Program 2009 (STEP09). All four LHC experiments participated in the test. For example, at the CMS experiment (see earlier iSGTW story, CMS readies network links for LHC data) they first tested the archivin

July 1, 2009
Feature - Cancer knowledge cloud for a new generation of medicine

Feature - Cancer Knowledge Cloud for a new generation of medicine

Kenneth Buetow, shown speaking at a conference in 2005.Image courtesy of NCRI.

Kenneth Buetow is the National Cancer Institute’s Associate Director of Bioinformatics and IT, and Director of the Center for Biomedical Informatics and IT, where he initiated and oversees the caBIG (cancer Biomedical Informatics Grid) program. He spoke last April at the Bio-IT World conference on caBIG: An interoperable IT framework for uniting research and care.
Thinking BIGKen Buetow thinks BIG.  He envisions what he calls a Cancer Knowledge Cloud — an IT environment designed to foster information connectivity among cancer patients, cancer researchers and clinical care providers. This environment, powered by caBIG tools and infrastructure, would enable a continuous and accelerated cycle of discovery, diagnostic and pharmaceutical product development, and improved clinical care.Cancer care and research still operate on a lin

July 1, 2009
Feature - Grid makes a SPLASH in underwater archaeology

Feature - Grid makes a SPLASH in underwater archaeology

Up to 3.2 million square kilometers of the European continental shelf (about 40 per cent of Europe’s land mass) was exposed as dry land during the periods of lower sea level that persisted throughout the Ice Ages. These now-submerged coastal regions probably played a key role in the survival and dispersal of Europe’s earliest Stone Age inhabitants, the extinction of the last Neanderthals, their replacement by modern humans originating from Africa, and the initial dispersal of agriculture from the Near East. (Insets show local river patterns on the shelf.) Image courtesy Nic Flemming/SPLASH

Submerged beneath the waves lies a large part of human history. For our ancestors, the ancient coastlines were attractive places to settle and experiment with what became the foundations of civilization. As the major glaciers melted between sixteen and six thousand years ago, these sites — where people first began to make fishin

June 24, 2009
Feature - Plenty more fish in the sea?

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

June 24, 2009
Feature - Watch near real-time earthquake simulations

Feature - Watch near real-time earthquake simulations

(Click image for more information on the topographical map and to see cross-sectional diagrams of compressional wave speed.)
Every time an earthquake occurs in Southern California, thousands of seismograms are recorded at hundreds of seismic stations. The Caltech team collects these seismic recordings automatically from the Southern California Seismic Network (SCSN) through the internet. They subsequently simulate the seismic waves generated by the earthquake in a 3-D  southern California seismic velocity model using the source parameters determined by the seismic network. At periods of about 4 seconds and longer, the resulting wave motion simulated at most stations closely match the gathered data recorded at these stations. Image courtesy of Caltech; image previous page courtesy of Nate Brelsford, stock.xchng

When an earthquake rumbles through southern California, seismometers at almost 400 sites jump into action. They s

June 24, 2009
Opinion - The age of citizen cyberspace

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

June 10, 2009
Feature - TeraGrid's Campus Champions: connecting campuses to national HPC

Feature - Campus Champions: Users get help from a familiar face

A few words from Kay Hunt, pictured above . . .In the fall of 2007, Scott Lathrop asked me to work on a new effort to support campus representatives (Champions) across the nation who would become the local source of knowledge about high performance computing opportunities for researchers and educators.After working on the design and development of the project I really became enthused about making contacts all over the United States and developing a network of folks who could learn and grow with each other for the common goals of the group.Now, as lead of the Campus Champion program, I recruit Champions and provide them with timely information, user support, training, resource allocations, and outreach support. There are many who help with these activities — I coordinate the people and the process and do the bulk of the recruitment. I am like the head coach of a basketball team.Off the job, I am a “sportsaholic”

May 27, 2009
Feature - Gridding the aerosol problem

Feature - Gridding the aerosol problem

Image courtesy BEinGRID

It can be difficult to measure the number of aerosols – tiny particles suspended in the air – that are in our planet’s atmosphere.Such knowledge is important in a number of ways, as aerosols can have an effect upon everything from short-term  air-quality forecasting to predicting the effects of aerosols on global warming. At least one climatologist says that on a long-term, global scale, aerosols will make India’s monsoons more intense, and Australia’s droughts hotter and longer. So, wet areas will be wetter, and dry areas drier. (See 7 January 2009 iSGTW, “Opinion - UK grid researchers aid efforts to understand climate change.”) Tracking where aerosols come from, where they tend to collect, and where they tend to “sink” on a planetary scale is a tricky business as well . Due to wind and weather patterns, sometimes the most pristine, remote areas accumulate the most

May 27, 2009
Feature - Volunteer computing against childhood cancer

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

May 20, 2009
Feature - Countdown: World's most sophisticated thermometer blasts off into space

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

May 13, 2009
Feature - EDGeS helps us all talk to each other

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

May 13, 2009
Feature - PKU protein structure

Feature - Peking University advances protein research

At top: Superimposition of 20 structures of hPHPT1. At bottom: Ribbon diagram of the mean structure of hPHPT1. Red: alpha-helix, blue: beta-sheet, white: random coil. Image courtesy of Weibin Gong

Researchers at Peking University’s Beijing Nuclear Magnetic Resonance Center (BNMRC) can determine 3D protein structures 1000 times faster, thanks to the grid. 
Function follows form in the protein world, so their work contributes to scientists’ understanding of the roles that individual proteins play. This in turn should lead to advances in drug discovery and health care.The Peking University team uses Nuclear magnetic resonance (NMR) spectroscopy to determine protein structures. NMR works well, but the calculations involved are time-consuming and computationally demanding. Scientists have so far learned the structure of only about 50,000 proteins out of the millions that exist in nature.
The Peking team has calculat

April 29, 2009
Feature - Engaging UK researchers

Opinion - Engaging UK researchers

Some of the things that ENGAGE has been involved in include software for the Aladin2 project, which allows for a simple, fast-running model of the Earth’s climate system. Image courtesy National Snow and Ice Data Center/World Data Center for Glaciology, Boulder, Colorado

It is risky to second-guess your users. There can be a difference between what we think our users need, and what they actually need. This is especially the case when trying to create technological platforms that enhance researchers’ ability to generate, collect, share, analyze, store and retrieve information; this is a young technology with a multi-disciplinary research base that can change focus with lightning speed. To counter this problem, the UK’s universities of Southampton, Edinburgh and Manchester (represented by OMII-UK, of which I am a part) and the National Grid Service  began the ENGAGE project. The goal was to create a picture of the computational need

April 29, 2009
Link of the Week - The Epigonion is heard once more

 

Link of the Week - The Epigonion is heard once more

Music historians believe that the Epigonion's closest relative, was a "psaltery," shown above, a musical instrument that was plucked or hammered. Image courtesy of Wikimedia Commons/Public Domain Image.

As we reported last September in "Ancient musical instrument comes back to life," a harp-like instrument from ancient Greece can now be heard again for the first time in centuries, due to the grid and a computer modelling project known as ASTRA (Ancient Instruments Sound/Timbre Reconstruction Application).In the first week of March, after the EGEE User Forum in Catania, Sicily, BBC Radio 4 treated its listeners to an interview with Domenico Vicinanza of ASTRA, in which he described the process of reconstructing this long-lost instrument. 
And you can now hear a full-blown “concert” done in Naples, using virtual epigonions on the grid.  (Note: This may be slow to load, depending on software configuratio

April 15, 2009
Feature - Grid sails to the aid of shipbuilding

Feature - Grid sails to the aid of shipbuilding New FSG ships anchored next to the factory building where they were constructed. Image courtesy of FSG Shipyards in Europe cannot compete on price alone against overseas competitors, especially those based in the Far East.Consequently, European shipbuilders must  concentrate on high-quality construction projects that are specially tailored to their customer's requirements. Each ship is a unique product, produced only once or in a very small run. To improve their competitive position, modern European shipyards must harness the most advanced simulation and design tools to produce complex structures cost effectively, in order to reduce the technical and economic risks at a time when orders for new ships are down worldwide.The goal? The complete, virtual design of a ship. The solution: the grid. At the Flensburger Schiffbau Gesellschaft (FSG) shipyard, managers wanted to find ways to design their ships so that they used less of costly materials such as steel — while r

April 15, 2009
Feature - PanDA lets scientists stay cool

Feature - PanDA makes huge job sets more bearable

Simplified view of core PanDA architecture. Click on image to see the complete diagram in a larger size. Image courtesy of BNL.

Keeping track of huge job sets processed on hundreds of compute clusters around the world through the LHC Computing Grid might send the most organized of logical thinkers into a tizzy. The PanDA (Production and Distributed Analysis) system, developed for the ATLAS collaboration at the Large Hadron Collider, lets scientists stay cool while it takes charge of distributing jobs, collecting results and managing workflow.An important feature of PanDA is that it allows the user to submit one job, called a pilot job, which coordinates a series of jobs that the user has put together and configured. When launched, the pilot job contacts the PanDA server, which in turn locates available resources and sends the collected jobs to run based on their relative priorities. The pilot system manages the workflow efficiently,

April 15, 2009
Image of the Week - Los Alamos' "Map of Science"

 

Image of the week - Los Alamos’ “Map of Science”

The Map of Science illustrates, in real time, the online behavior of scientists accessing different scientific journals, publications, aggregators, etc. Colors represent the scientific discipline of each journal, based on disciplines as classified by the Getty Research Institute's Art and Architecture Thesaurus, while lines reflect the navigation of users from one journal to another when interacting with scholarly web portals. Image courtesy of Los Alamos National Laboratory.

Scientists at Los Alamos National Laboratory (LANL) in New Mexico have produced what they call the world's first “Map of Science” — a high-resolution, graphic depiction of the virtual trails scientists leave behind whenever they retrieve information from online services.
The research, led by Johan Bollen of LANL, and his colleagues at the Santa Fe Institute, collected usage-log data gathered from a variety of publisher