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December 15, 2010

A new grid application may help biologists solve the structures of mystery proteins.

December 15, 2010

Imagine living next to a busy highway operating 24 hours a day for 365 days per year. That’s what life is like for ocean animals living next to busy shipping lanes.

December 1, 2010

Read about how the EpiCollect application can help field researchers gather data.

November 17, 2010

Feature - Life at the extreme at the Pierre Auger Observatory The Pierre Auger Observatory has a detection area of 3,000 km², so large that it is best seen by airplane. A space-based sucessor with a detection area hundreds of times greater is already being planned: the JEM-EUSO will be attached to the International Space Station in 2013. It will use large volumes of the earth’s atmosphere to detect and observe particles colliding with planet’s magnetic field. All images courtesy Pierre Auger Observatory Some people enjoy living life at the edge, such as participants in extreme sports. At the other extreme are those who relish watching rare events.Among the latter are astronomers at the Pierre Auger Observatory, a multi-national collaboration to detect the 'light-signature' given off as these cosmic rays hit particles in our atmosphere. Based in Argentina, the observatory monitors ultra-high energy cosmic rays —  spectacular examples of some of nature

November 3, 2010


Project Profile - From grids to clouds and beyond: GRNET supports Greek researchers

The Acropolis from Philipapou Hill at sunset, Image courtesy Tim Rogers, stock.xchng

All Greek universities get their internet from one source: GRNET (Greek Research and Education Network), a company supported by the Greek state, which connects them both to each other and to the larger pan-European academic network, GÉANT.
GRNET’s mission is to get universities on line, to provide computing power and storage, and to develop services for researchers. Not the least of which is providing technical know-how and supporting schools and universities in Greece. “GRNET is actually a human network — this is the most important thing about it,” says Kostas Koumantaros, member of GRNET in Athens. “We transfer know-how between universities throughout Greece. It is a good vehicle to both promote research in Greece and for us to learn from our international collabora

October 20, 2010

Announcement - ESFRI and e-IRG publish ‘Blue Paper’ on e-Infrastructure

Photo courtesy  ESFRI

The European Strategy Forum on Research Infrastructures (ESFRI) and e-Infrastructure Reflection Group (e-IRG) has just released a report about the current trends, issues and policy areas for users of Europe's e-Infrastructure services.
Topics that are covered include:

e-infrastructure services to support scientific research.
e-infrastructure as a European service.
Digital research infrastructure for the Arts and Humanities.
e-science and technology infrastructure for biodiversity data and observatories.
And much more . . .

The full report can be downloaded in pdf form.

October 20, 2010

Feature - Climate model tackles clouds

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Animation from the NICAM model simulation of 21 May - 31 August 2009, showing cloudiness (based on outgoing long-wave radiation) in shades of gray and precipitation rate in rainbow colors, based on hourly data from the simulation. The cloudiness is shaded in brighter gray for thicker clouds, and the colors range from shades of green, indicating precipitation rate less than 1 mm/day, to yellow and orange (1 - 16 mm/day), to red (16-64 mm/day) and magenta (> 64 mm/day). The animation begins zoomed in over India and the Bay of Bengal, showing the fact that tropical cyclone Aila, which in reality made landfall near Calcutta killing dozens of Indian and Bangladeshi citizens and displacing over 100,000 people from their homes, was very accurately predicted in the simulation.
Video and caption courtesy NICS

Few areas of science are currently hotter than clima

October 20, 2010

Feature - New physics in space

A C5 Supergalaxy, one of the world’s largest planes, loading the AMS-02 experiment at Geneva Airport. Image courtesy CERN Bulletin

New life was breathed into the International Space Station (ISS) this year after NASA announced it will extend the ISS from 2015 to at least 2020.The new deadline extends opportunities for science experimentation in the largest space research laboratory ever constructed. One of these experiments is the Alpha Magnetic Spectrometer (AMS-02), a detector that may help scientists understand why our universe exists and why there is more matter than anti-matter.Most space-grade electronics are about ten years old, so the AMS-02 represents the newest and most advanced physics experiment in outer space to date. Currently, it is being tested and due to launch in February 2011. AMS-02 was shipped via Geneva airport to NASA this August in one of the largest planes in the world, a US Air Force C5 Super Galaxy.Once aboard the ISS, A

October 6, 2010

Feature - A lasting ocean observatory

A map indicates the location of the four major ocean arrays, as well as the two minor ones. Click for a larger version. Image courtesy of OOI - CEV at University of Washington.

Agile architecture is essential if a large-scale infrastructure like the Ocean Observatories Initiative is to last three decades, as mandated.
“The Ocean Observatory has been in planning for fifteen years and more,” said Matthew Arrott, OOI’s project manager for cyberinfrastructure. “It is our anticipation, over a 30 year lifespan, that we need to account for user needs and the technology that we are using all changing.”
That’s why they’ve focused their attention on creating an infrastructure that can interface with a wide variety of software packages and computational resource providers.
“The observatory supports a broad range of analysis with the expectation that the majority of the analysis capability will be provided a

October 6, 2010

Feature - Achilles tendon a blessing, not a curse

Sprinters lining up for the start of the Women’s 100-meter at the Beijing Olympics. Image courtesy LIM CK, under Creative Commons license.

Compared with other runners on this planet, humans are feeble.
If Olympic sprinters competed against mammals of comparable size, they would never even qualify for the finals. The top speed for an in-shape male human is normally between 15 and 18 miles per hour (24 to 29 kilometers per hour). The world record is 27 mph (43kmh), and that was sustainable for only a few seconds.
Meanwhile, horses have been clocked at about 48 miles per hour, wolves about 42, and the speed champion — the cheetah — at 70 miles per hour. (That’s about 77 kmh, 68 kmh, and 113 kmh, respectively.)
Even warthogs are faster than us.
But in the field of endurance racing however, we leave everyone else in the dust. Over long distances, a well-trained human can outrun a horse.
What is the ke

September 22, 2010

Feature - Surfing for earthquakes

Aftermath of Haiti earthquake. Image courtesy UN Development Program

A better understanding of the ground beneath our feet may come from research by seismologists and an organization called RAPID—a group of computer scientists at the University of Edinburgh.
The very structure of the Earth controls how earthquakes travel and the amount of damage they cause. Therefore, a clear picture of this structure would be extremely valuable to earthquake planners — but it requires the analysis of huge amounts of data.
To help, the RAPID team developed a system that performs the seismologists’ data-crunching, and have made it easy to use by relying on an interface familiar to all scientists: a web browser.
Seismologists measure vibrations in the Earth at hundreds of observatories across Europe, which allows them to study earthquakes as they travel across countries and continents. By measuring the speed and strength of the vibrations at d

September 22, 2010

Project profile: PL-Grid

Legacies of older architectures exist along side the new in Poland, and not just in research computing: Here contemporary architecture in Warsaw reflects the past. Image courtesy Jaime Silva, Flickr, under Creative Commons license

Beyond being at the geographic center of Europe, Poland plays a central, leading role in Europe’s grid community. In 2009, Poland became the first country to form an independent and autonomous National Grid Initiative — an operational unit, based in a single country, set up to run a national computing infrastructure to support the European Grid Infrastructure (EGI).
With the close of the Enabling Grids for E-sciencE project, the health of the EGI is dependent upon such NGIs — and the technical process developed by Poland to move away from the parent EGEE ROC is a model other countries will look to. PLGrid itself is one of a series of NGIs to form as legal entities over the last few years, particularly in South Eas

September 8, 2010

Feature - BiG Grid’s big idea

Image courtesy BiG Grid

With the EGI Technical Forum coming up next week, iSGTW thought ths would be a good time to learn more about one of the Forum’s sponsors, BiG Grid.
Modern detectors, medical imaging instruments and micro-arrays produce huge volumes of data, far beyond the storage capacities of conventional computing — thus calling for ever-increasing enlargement of infrastructure.
To help solve this problem, the Netherlands-based BiG Grid project is turning to the grid as a place to combine data, analyze it and allow scientists to conduct research in a wide range of disciplines. BiG Grid is a collaborative effort between Nikhef (the National Institute for Sub-atomic Physics), NBIC (Netherlands Bioinformatics Center) and NCF (the National Computing Facilities foundation). “Our goal is to build and roll-out a nationwide, grid-based, e-science infrastructure,” said Arjen Van Rijn, chairman of the BiG Grid executiv

September 8, 2010

Profile - People behind the European Grid Initiative: Tiziana Ferrari

Image courtesy EGI

The European Grid Infrastructure’s role is to support research and collaboration across the continent by providing seamless, instant access to computing resources. But who has the job of making sure things actually work? Meet EGI’s Chief Operations Officer, Tiziana Ferrari. She spoke recently with iSGTW to tell us what is rewarding about her job, what is challenging and why it is important.
iSGTW: Describe what you do for EGI.Ferrari: I am responsible for coordinating the operations of the infrastructure across Europe. The user doesn’t care whether a resources is in Spain or in France, they just need it to work — that is my job. In EGI though, every country is responsible for its own operations.
But EGI needs to coordinate this and ensure that everyone is using the same protocols. That is my role. I need to make sure the production and accounting infrastruc

August 25, 2010

Feature - OSG and TeraGrid join forces for ExTENCI

Image courtesy of Jayanta Behera.

Last week marked the kick-off for ExTENCI, the first major technical collaboration between TeraGrid and Open Science Grid.
“The idea is to have Open Science Grid and TeraGrid work together on a joint project as an experiment,” explained Paul Avery, the principle investigator for ExTENCI (which stands for Extending Science Through Enhanced National CyberInfrastructure). Although the two infrastructures have worked together to agree on principles and attend each others’ meetings, ExTENCI marks the first time that they will work together, sharing milestones and goals.
In order to make the partnership possible, the National Science Foundation’s Office of Cyberinfrastructure and Math and Physics Directorate each awarded ExTENCI approximately one million U.S. dollars over two years, for a grand total of just over two million U.S. dollars.
The limitations imposed by a small budget

August 11, 2010

Feature - NetLogo: A low threshold, no ceiling language

Two fifth grade students use NetLogo to learn about electrical current. Image courtesy Pratim Sengupta.
Front page image: Tiling with squares whose sides are successive Fibonacci numbers in length. Courtesy Wikipedia under Creative Commons license.

Elementary school students may not be able to decipher mathematical models such as Maxwell’s Equations. But given the right visualization and computational modeling tools, they can learn the underlying concepts.
Meet NetLogo, a multi-agent programmable modeling environment authored in 1999 by Uri Wilensky, a learning sciences and computer science professor at Northwestern University, and founder of the Center for Connected Learning and Computer-Based Modeling.
Remember the turtle?
A generation of adults were introduced to functions and programming through Logo and the “turtle” - an on-screen triangular cursor - that accompanied it. Logo was first created in 1967

August 11, 2010

Feature - The sky’s the limit

Image courtesy Simon Langton Grammar School

Becky Parker, head of physics at the Simon Langton Grammar School in Kent, UK, is introducing her students to outer space. In 2007, Becky organized a trip to CERN for her 16 to 18 year-old students. There, they were introduced to the Timepix computer chip, a sensitive light-detector used for medical imaging. Back in Britain, one of her students came up with the idea of using the chips to measure cosmic radiation. Parker’s response: “Brilliant!” A Timepix chip has 65,536 pixels over a 2 cm² area. An event occurs when a particle strikes a pixel and is converted into an electrical signal, which can be measured. Her students wanted to use Timepix chips to detect particle type, energy and possibly, the directionality.Consequently, her students entered and won a space experiment competition with their design made from adapting readouts of the chip. Their instrument, called LUCID (Langton

August 11, 2010


Link of the Week - A new twist on summer camp: computing classes in the wild

Image courtesy Carlos Jaime-Barrios Hernandez

We’ve all heard of summer camp.But SuperComputing Camp (or SSCAMP, as it is known by its acronym in Spanish) is a little different.
Starting on the 15th of August, 46 undergraduates and masters students will learn about high performance computing, grid computing, volunteer computing and cloud computing — while staying in a hacienda near Panachi National Wildlife Park, just outside the small town of Piedecuesta, Colombia.The organizer, Carlos Jaime-Barrios Hernandez, says the idea is for students to learn in a natural environment, where they can explore and enjoy the great outdoors while having access to fully up-to-date facilities, including digital resources, projectors and live-video feeds to keynote speeches and online lectures. They will remotely connect to the grid infrastructure via the web. Hernandez — a research scient

August 11, 2010

Video of the week - Learning with multi-touch

Multi-touch technology has been around longer than you might think; experimental implementations have been surfacing since the early 1980s. This technology really hit the big time, however, when Apple released the first iPod Touch.
In 2008, the Renaissance Computing Institute at University of North Carolina-Chapel Hill unveiled a multi-touch table that has since become an invaluable tool in the scientific visualization toolbox. At the same time, learning scientists, computer scientists, and psychologists from Virginia Tech and the University of Chicago formed itemL – interactive technologies for embodied mathematics Learning – and began investigating how young children (three to eight-years-old) interact with a multi-touch play table.
“We are collecting extensive data on the commercially available SMART Table while developing our own technology, TanTab,” explained Michael Evans, assistant professor of learning science and technologies at Vir

July 14, 2010

Feature: Fruitfly + flight studies + grid = flying robots?

The GUI pre-processor used to generate the geometry of the fly wings. (Click on image to enlarge.) All images courtesy Diego Scardaci, INFN

The study of the flight of a fruit fly may one day lead to the development of autonomous ‘Micro-air vehicles’ (MAVs), or independent ‘flying robots,’  if scientists in Argentina have their way.
Working in conjunction with the Italian Institute of Nuclear Physics (INFN) under the EELA-2 initiative, they are conducting the study to understand the flight mechanisms of insects and small birds. Their hope is that someday, 'flying robots' could be developed with maneuvering capabilities similar to insects — the most agile flying creatures on Earth.
MAVs could be used to study and explore places that are too dangerous or inhospitable for humans to tread; examples include search-and-rescue teams exploring buildings to detect fires, or scientists investiga

July 14, 2010

Feature - RadiotherapyGrid Gamma-ray map for treatment. Image courtesy BEinGRID Cancer is Europe’s second largest cause of death. One of the most common and effective treatments is external radiotherapy, where a Linear Accelerator (Linac) attacks the cancerous tissue with radiation delivered from several different directions. The treatment plan — the direction, size and length of dosages — has to be carefully calculated to avoid damaging healthy tissue. These calculations can take a long time — speeding up this process would allow earlier treatment and more patients to be treated.RadiotherapyGrid is a solution based on grid technology that helps hospitals plan the best possible treatment for each patient. It has two core functions: verification of plans using accurate — but computationally expensive — techniques; and searching for the optimal treatments. These tools improve the efficiency and effectiveness of planned treatm

June 30, 2010

Feature - Project profile: ESFRI

Image courtesy GridTalk

So, just what is ESFRI?The European Strategy Forum on Research Infrastructures (ESFRI) is a European Commission initiative whose role is to guide policymaking on Research Infrastructures (RIs) in Europe. ESFRI projects span social and biomedical sciences, earth and physical sciences, energy, infrastructures and analytical facilities.
The ESFRI projects are detailed in the ESFRI Roadmap, which was last updated in 2008. A new version of this document is due to be released in 2010 and will include also input from the e-Infrastructure Reflection Group (e-IRG), a body which defines and recommends best practices for pan-European e-Infrastructure efforts.
But with such wide scope and vision, the ESFRI projects will place large demands on the storage, processing and networking services of Europe’s e-Infrastructures. To address this, the European e-Infrastructure Forum (EEF) has released a report addressing the future requiremen

June 23, 2010

Video of the week - When your visualization wall isn't enough

Getting a good sense of your data on a mere large HD screen isn’t easy. And, sure, your friendly neighborhood visualization wall is an improvement, at about 13 million pixels projected across 84 square feet.
But wouldn’t it be better to stand in the center of a 2800 square foot sphere, interacting with your data in three dimensions at a resolution of 24 million pixels? Not to mention listening to audio cues in surround sound, projected from 500 individual speakers plus subwoofers.
Welcome to the AlloSphere, the visualization jewel of the California NanoSystems Institute at the University of California, Santa Barbara. Construction on the facility was completed in 2007, but the team behind the AlloSphere has continued to roll out additional features since then.
In this week’s video JoAnn Kuchera-Morin, the woman behind the AlloSphere, speaks to the audience at TED 2009 about five different research projects that

June 16, 2010

Back to Basics – Q&A on meshes

The geometry and adapted mesh for a patient-specific abdominal aorta aneurysm. Image courtesy of Min Zhou, Onkar Sahni, H. Jin Kim, C. Alberto Figueroa, Charles A. Taylor, Mark S. Shephard and Kenneth E. Jansen.

The word “mesh” seems to pop up all over the place. What exactly is a mesh? How about an adaptive mesh? Who uses them, and for what? This week, iSGTW interviewed Mark Shephard to learn more about meshes. Mark Shephard is the director of the Scientific Computation Research Center (SCOREC) at Rensselaer Polytechnic Institute. His primary area of interest is the development of techniques to reliably automate multiscale simulations..
iSGTW: So, what is a mesh? When do you use these?
Shephard: In the context of modeling physical behavior over complex geometric domains that can be modeled by partial differential equations (PDEs), meshes are used to support the application of methods that can provide approximate but accurate sol

June 9, 2010

Feature - Seeing particles with VPM

VPM Interview from Renaissance Computing Institute on Vimeo.

Before we can make use of data, we need to make sense of it. But with complex concepts such as particulate air pollution, you could just as easily drown in the data.
And that’s exactly what was happening when NASA first approached Uma Shankar, an atmospheric scientist at the Institute for the Environment at UNC Chapel Hill, to ask what sort of advanced visualizations the particulate matter research community needed.
After some thought, Shankar suggested an application to visualize particulate matter across the range of sizes in which it occurs.
“Particulate matter has such important impacts on a variety of air quality issues, especially human health” Shankar explained. “Now we better understand the connection between particulate matter and climate, so its importance is even greater than we originally understood.”
Despite this better understanding, the existing visu