Share |

Content about Project Profile

April 1, 2009

From Martinique to Marseilles to Medaka: profile of bioinformatician Mirana Ramialison The Medaka fish is a simple model organism, amenable to genetic techniques, easily grown in the lab, but at the same time sharing many molecular processes with higher vertebrates. This image, taken with a newly developed microscope called a Digital Scanned Laser Light Sheet Fluorescence Microscope, shows a 5mm-long juvenile at the age of 10 days. The glowing green areas show its developing brain, eye and spinal cord.  Image by Philipp Keller, from the lab of Ernst Stelzer at EMBL Editor's note: As part of an ongoing series, iSGTW presents profiles of women researchers in grid computing.   What do you do? In our research group, led by Jochen Wittbrodt of the European Molecular Biology Laboratory in Germany, we are studying Medaka (alias "the-small-fish-with-big-eyes" in Japanese) to understand how an eye forms in an embryo. Since Medaka eyes are similar to human ones, we can have a better understanding of human eye dis

April 1, 2009

Feature - For the love of movies: recommendations from the grid Cary Grant in “North by Northwest.” Image courtesy of MGM Alfred Hitchcock once said, “A good film is when the price of the dinner, the theatre admission and the babysitter were worth it.” Tired of wasting your time sifting through DVDs at the rental store only to end up with a mediocre film? Help is on the horizon for all interested in movie recommendations. In a one-man project, Leandro Neumann Ciuffo, offers grid-powered film recommendations through a simple algorithm, his Web portal and EELA-2, the E-science grid facility for Europe and Latin America. “This is a very simple application,” he said. “It’s not going to cure cancer, but it does show that average people can use the grid.” Marilyn Monroe gets fitted for a scene with the help of Hollywood costume designer William Travilla, who custom-made Monroe’s outfits for eight of her films. Image courtesy of  The Travilla Tour Custom-tailored suggestio

March 4, 2009

Feature - Get it all with GridGuide Click on the map above for an interactive guide.  Image courtesy of GridGuide Want to know what science is on the grid, who the scientists are and where they work? Help is at hand with a new website launched today. GridGuide is an innovative introduction to the sites — and sights — that contribute to global grid computing, a technology that connects computers from around the world to create a powerful, shared resource for tackling complex scientific problems. The launch of GridGuide comes as part of the Enabling Grids for E-sciencE (EGEE) User Forum.While still a work-in-progress, the GridGuide website already allows visitors to explore an interactive map of the world, visiting a sample of the thousands of scientific institutes involved in grid computing projects. Sites from 23 countries already appear on the GridGuide, offering insider snippets on everything from research goals and grid projects to the best place to eat lunch and the pros and cons of their jobs. GridG

February 18, 2009

Feature - Help create an earthbound sun A view of the International Thermonuclear Experimental Reactor (ITER), showing its main components, with a person for size reference. One of the pilot applications running in Ibercivis is devoted to ITER simulations. Image courtesy of ITER The dream of fusion power sounds so fantastic that one’s initial reaction might be to dismiss it as science fiction. Yet  scientists hope to bring the power that emblazons the sun, fusion, to earthbound reactors. In this type of reaction two atomic nuclei bind — or fuse — together to form a heavier atom, triggering a monumental release of energy. The International Thermonuclear Experimental Reactor (ITER) is a joint international research and development project seeking to build a prototype fusion power plant. (The finished machine will be located in the south of France.) Aiding ITER in its computational load is Ibercivis, a volunteer computing project centered in Spain, which allows computer users citizens to donate unused computing

February 18, 2009

Feature - The magic of GENI: Building networks for the future It may look like a galaxy, but is actually a map of the Internet, showing the hardware that serves as its 'skeleton' or infrastructure of the Internet. Colors indicate geographic location. Despite its obvious complexity, this map represents just a fraction of the whole network - the rest is simply impossible to accurately represent. Image courtesy of Barrett Lyon, The Opte Project The Internet may be a powerful tool. But researchers trying to extend the Net's capabilities want to test their ideas for improving network design, distributed systems and cyber-security without disrupting or breaking it.  Recognizing this, the National Science Foundation started the Global Environment for Network Innovations (GENI) project. GENI will provide an infrastructure for a large-scale experimental network, where researcher can build test versions of the Net to safely study networking in ways never before possible.Some of those participating in the first phase of th

February 4, 2009

Feature - Anticipating "The big one" Click here or on image  to view the animation.The detailed, perspective views show the ground shaking from a viewpoint two miles (three kilometers) above the earth looking towards each location. The left panel shows a map view of the area with the fault rupture highlighted in red, the epicenter (location where the rupture starts) identified by the red ball, and the location shown in the right panel labeled in yellow. In the right panel the deformation of the ground associated with the propagation of the seismic waves is exaggerated by a factor of 1000. Simulations developed by the Southern California Earthquake Center ShakeOut Simulation workgroup. Animations courtesy of the U.S Geological Survey and the Southern California Earthquake Center. At 10 a.m. on November 13, 5.3 million people in Southern California participated in the largest earthquake preparedness activity in U.S. history. The Great Southern California ShakeOut — an earthquake drill that was a collaborati

February 4, 2009

Feature - G-eclipse: easier interface to both grids and clouds The g-Eclipse interface in action.Image courtesy of g- Eclipse Consortium The g- Eclipse Consortium released the g- Eclipse framework, which developers claim will provide an easy-to-use workbench for accessing both grid and cloud infrastructures. The software provides a graphical workbench that enables seamless access with the same simplicity as accessing the Internet from a browser. "This enables interoperabilty between different grid and cloud infrastructures on the client side," said Harald Kornmayer, a researcher at NEC Laboratories Europe, who led the project.It currently supports EGEE's gLite grid middleware (aimed for scientific domains), and the GRIA middleware (used by industry and commerce), as well as AmazonWeb Services' cloud computing and storage offerings.A key feature of the g- Eclipse workbench is its independence from the underlying grid and cloud technology. "We started with the goal of accessing available scientific grid infra

February 4, 2009

  Image of the week - ThIS cancer therapy  ThIS is an acronym for Therapeutic Irradiation Simulator for cancer therapy, which simulates the irradiation of a patient with carbon ion beams in order to allow clinicians to compute the 3D dose distributions inside the patient for a computer-aided tomography (CT) scan.Such simulations are very computing intensive, requiring thousands of hours on a single CPU. But by putting ThIS on the EGEE Grid, one simulation can be split into independent sub-simulations executed concurrently on different CPUs, speeding up the job.The project is now being integrated into the OpenGATE project. The developers — Sorina Camarasu, Tristan Glatard, Laurent Guigues, Thibault Frisson and David Sarrut, of CNRS in Lyon, France — say “The results are promising and we are confident that this advanced submission method will help the simulator to reach a larger research and medical community. Moreover, since most users need a higher-level graphical user in

February 4, 2009

Opinion - Grids for optimizing cancer radiotherapy treatment (The author, Dimitri Dimitroyannis, is a board-certified, clinical medical physicist at Kansas City Cancer Centers, who trained in experimental high-energy physics. This summary is rewritten from his longer article in Medical Physics Web.) Transverse slice from an actual computer-aided tomography image of a patient with cancer at the base of the tongue. Soft tissue appears as light grey, while bone is whitish. Red area is the cancerous target that needs to be irradiated. The three yellow areas correspond to uninvolved tissues that need to receive as little radiation as possible — the spinal cord (center) and the two parotid glands (left and right). Image courtesy of Dimitri DimitroyannisAbout 4 million European and North American citizens will be diagnosed with cancer this year. More than half of these new cancer patients will receive radiotherapy for the treatment of their disease, along with surgery and chemotherapy as appropriate. However, treating cancer patient

January 21, 2009

Observing the grid Peer through Grid Observatory to explore the world of the grid.  Image copyright © 2005-2008 David Opie What was once lost has now been found—and stored.Thanks to the Grid Observatory, people in the esoteric field of studying the behavior of large, distributed systems have been given a gift: a trove of data. Like astronomers who peer through a telescope to explore the solar system, researchers in grids and complex systems are able to examine Grid Observatory’s data repository to find new patterns in the global behavior of the grid. The Grid Observatory, a sub-set of Enabling Grids for E-sciencE’s applications group, opened its doors—via a Web portal—this autumn. Through the portal, researchers can access anonymous grid traces, collected and stored through the Grid Observatory application, and information about those traces, for an overall picture of the grid. Grid traces, explains Cécile Germain of Grid Observatory, are signatures of grid usage. These take many f

January 21, 2009

Feature - Rough waters: fighting modern-day pirates with technology

Map of reported pirate incidents in the Gulf of Aden, off the coast of Somalia. (Click for large, high-resolution version.) Image above courtesy of UNOSAT; image on front page courtesy of sxc.hu

In the past year, maritime shipping has suffered a resurgence of piracy, at a level that the world has not seen since the early 18th century. Sailors working off the Horn of Africa have been particularly hard hit: last year, records show that 125 ships were attacked and 45 seized.
Real numbers are likely much higher, as piracy is believed to be widely under-reported. One of the world's busiest shipping lanes, about 20,000 ships annually pass through the Gulf of Aden on their way to and from the Suez Canal — carrying a tenth of world trade.
Unlike the popular image of pirates seen in movies and books, modern pirates are more likely to wield machine guns than muskets; and the crime remains as difficult to fight as it ever

January 7, 2009

Feature - Divide and conquer: distributed graphics rendering   A still from Nano Factor, a game-like toolkit designed to give junior high school students the opportunity to perform virtual experiments based on real-world micro and nano technologies.Image courtesy of Nicoletta Adamo-Villani, Purdue Rendering frames in a complex animation can tie up workstations for days or weeks. A two-minute animation at 30 frames per second will typically take over 100 hours to render on a single computer. Sharing the load among hundreds or even thousands of machines dramatically reduces a job’s run time—and the time required to complete a project.Enter the Distributed Rendering Environment, or DRE, developed at Purdue University five years ago for computer graphics students. It draws on the Purdue Condor pool, a system for sharing unused computing time on more than 20,000 linked processors in computers at Purdue and its partner campuses. This pool is part of both the TeraGrid and the Open Science Grid. DRE has become a staple in

January 7, 2009

India gets its “passport” to the grid GARUDA had linked 45 institutions in 17 cities via a high-speed network to promote science and computing in India. Image courtesy of GARUDAOn the 5th of November, 2008, the Indian Grid Certification Authority (IGCA) was granted accreditation by the Asia Pacific Grid Policy Management Authority, also known as APgridPMA.Indian researchers can now request user and host certificates to the Center for Development of Advanced Computing (C-DAC), which is located in Bangalore, and get access to worldwide grids.(C-DAC spearheads the Indian National Grid Initiative and is a project partner of EU-IndiaGrid, which joins European and Indian grids.)Grid Certificates provide a secure key that allows researcher to access the grid, much the same as a passport allows you to enter a country. They are fundamental to guarantee worldwide grid access.For this reason, supporting the creation of an internationally recognised National Grid Certification Authority represented one of the main goals o

January 7, 2009

  Image of the week - GlobAerosol Aerosols are tiny particles suspended in the air, and they are a fundamental component of the Earth's atmospheric chemistry. Knowing their distribution and density is vital to improving the accuracy of air quality forecasting and predicting. But tracking where aerosols come from, where they tend to collect, and where they tend to “sink” on a planetary scale is a tricky busines. (Due to wind and weather patterns, sometimes the most pristine, remote areas accumulate the most aerosols.) However, by coordinating European Space Agency satellite data through BeinGrid, researchersat GMV are able to make maps such as the one above as part of the GlobAerosol project. (Black represents no aerosols, purple is some aerosols, and red is the most aerosols.)  Image courtesy of GlobAerosol    

January 7, 2009

Opinion - UK grid researchers aid efforts to understand climate change Then and now: The way Muir Glacier looked back in August, 1941, when it was photographed by W.O. Field on White Thunder Ridge, Muir Inlet, Glacier Bay National Park and Preserve, Alaska. (See photo at bottom of page for comparison.) Image courtesy of National Snow and Ice Data Center/World Data Center for Glaciology, Boulder, Colorado. (Our latest opinion piece comes from a team of researchers at the Natural Environment Research Council Datagrid (NDG), and OMII-UK.) To learn about climate change and its effects, climate researchers have to play detective. And as detectives, they need access to a wide variety of clues, on everything from the rate of coral growth in the Great Barrier Reef to the amount of carbon in the atmosphere since the dawn of the Industrial Revolution. For instance, one climate researcher—Beate Liepert at Columbia University—has floated above the greater New York City area in a hot-air balloon, in order to collect aerosol sampl

December 10, 2008

Feature - Massive new digital storage library for atmospheric research  The Nested Regional Climate Model is an initiative of the NCAR in collaboration with university, government and private-industry colleagues. With added support the NRCM will be able to simulate a variety of 21st-century climates, from which statistical portraits of the future atmosphere can be produced. The simulations can give a better idea of how and where weather patterns are likely to shift from decade to decade and how specific high-impact weather events, such as hurricanes, may change in frequency, intensity, size and rainfall. Images courtesy of UCAR;NASA-GSFC, NOAA GOES The National Center for Atmospheric Research (NCAR) recently installed a massive new digital storage library planned to hold nearly 30 petabytes of data— the equivalent of more than 6 million DVDs. The new system, AMSTAR (Augmentation of the Mass Storage Tape Archive Resources), will be one of the largest archives in the world dedicated to geoscience research, and will store

November 26, 2008

Fight AIDS at home, via unused computer time World Community Grid is helping “FightAIDS@Home” by completing computational calculations related to molecular structures of potential anti-HIV drugs..  Image courtesy of World Community Grid Starting on World AIDS Day on 1 December, the World Community Grid will sponsor a month-long challenge via its FightAIDS@home project, with the goal of increasing the number of computers and computer cycles available to researchers conducting HIV/AIDS research.Like all molecules, HIV—the virus that causes AIDS—is dependent upon its three-dimensional shape to attack the human immune system, in much the same way that a key must fit into a lock in order to gain entry. If the lock can be blocked—with a drug, for example—then the key cannot fit, and the virus is prevented from maturing. Such blockers, known as “protease inhibitors,” are one way of avoiding the onset of AIDS.Researchers have been able to determine by trial-and-error the shapes of a

November 12, 2008

Feature - Security through collaboration, part II: a framework for investigations Image courtesy of NCSA. Last week, Randal Butler of NCSA, University of Illinois, discussed cyber security in today’s world of cross-domain computing, trust relationships and sophisticated cyber attacks. This week, he follows up with a discussion of collaborative cyber security and a prototype framework for cyber investigation developed by NCSA.   In today’s cyber-climate, a single attack can affect multiple organizations, increasing the need for security professionals to collaborate in both incident prevention and response.   The challenges that cyber investigators face are very much like those of their counterparts in academic research. The data they collect often comes from many sites and in a variety of formats, making it difficult to analyze.  Cyber security at academic sites is often underfunded and understaffed. They also share benefits. In both research and security, the combination of unique problem-solvi

November 12, 2008

Feature - Where are they now? Interconnected computers for high performance operations call for strong interoperability. Image courtesy of cordis.europa.eu Updates from the three projects covered in iSGTW’s inaugural issue, 16 November 2006.Building the global gridISGTW led its first issue with a feature on the possibility of and progress toward achieving one seamless global grid.  At the time of writing, basic interoperation between Open Science Grid and Enabling Grids for E-sciencE had been achieved, according to Laurence Field of EGEE. “Scientists using either infrastructure can now submit jobs to both and copy data between the infrastructures,” Field said. “And if another grid interoperates with either, they’ll see the other grid’s resources. Through activities like these we hope to build up a homogenous grid landscape.”Where are they now?Morris Riedel of the Jülich Supercomputing Centre in Germany, and chair of the Grid Interoperation Now (GIN) group within the Open Grid F

October 29, 2008

Feature - A fine-grained approach to “cool” simulations A snapshot of a simulation examining the interactions of six water molecules. Image courtesy of Andrew Schultz. When deciding how best to design equipment in a chemical plant that produces liquid nitrogen, designers must know the properties of a mixture of nitrogen and oxygen gas at various stages as it cools and compresses. Researchers at the State University of New York at Buffalo have developed a new simulation technique that makes calculating these properties much more efficient.OSG is “the ideal workhorse”The new technique involves running simulations on the grid unfeasible on a single computer because they require large amounts of computing power. Andrew Schultz, a SUNY-Buffalo chemical and biological engineering researcher, said Open Science Grid (OSG) is “the ideal workhorse” to run these simulations. Schultz and his team have run more than 60,000 jobs on OSG resources since January—an order of magnitude jump in productivity.

October 29, 2008

Feature - Cycle-harvesting around campus in Singapore The NUS Grid Project Team: (from left) Yeo Eng Hee, Wang Junhong (Project Lead), Grace Foo, Tan Chee Chiang (Manager), Zhang Xinhuai. Image courtesy of NUS Grid At the National University of Singapore (NUS), researchers  in the areas of bioinformatics, financial simulation and data-mining had a problem: It was taking days, if not weeks, to run a computation.  The situation encountered by one researcher at the NUS Business School, Dr Ding, was typical. He found that each simulation he needed to do took over ten days to execute on a desktop computer. Clearly, something had to be done.Then came the NUS Grid (also known as Tera-scale Campus Grid or TCG@NUS), overseen by the Computer Center team at NUS. By using technology similar to that of well-known community grids  such as SETI@HOME, FOLDING@HOME and World Community Grid, the team found that they could dramatically cut down computation time. “With the NUS PC grid, we can finish one execution of our pro

October 15, 2008

  Image of the week - CMS CMS In the world of physics, “compact” is a relative term. Here is a view of the “Compact” Muon Solenoid, or CMS, as shot by Peter McCready, who has been creating a series of panoramic views of all the large experiments. Last in the series, this shows CMS in a 360-degree, rotating view, with natural sound, when you click on the picture above. For each image, 102 separate, individual photos were shot,  then stitched together into one seamless 40MP spherical image, much like an old-fashioned cyclorama. Each image takes as much as four weeks to complete in the his digital darkroom. When coupled with ambient sound that he recorded at the site, the user gets what McCready calls a  “Virtual Reality” experience. Image courtesy of Peter McCready    

October 15, 2008

Feature - Volunteer computing helps track malaria Thousands of volunteers are contributing to the project from all over the globe. Image courtesy of Nicolas Maire How do you predict the results of a malaria vaccine? With the grid, and volunteer computing.A research team at the Swiss Tropical Institute, or STI, in Basel studied the use of computer simulations to predict the epidemiological impact of potential malaria vaccines.  These predictions were obtained with the help of thousands of volunteers who made their computers available to Malariacontol.net, a volunteer computing project based on the Berkeley Open Infrastructure for Network Computing (BOINC).Malaria is one of the world’s leading public health problems, estimated to cause over a million deaths per year. Mathematical modeling of malaria, such as that done on computer, can help public health experts predict the epidemiological impact and cost effectiveness of vaccines and other malaria control interventions.Because running such simulation models is computatio

October 15, 2008

  Opinion - Reaching for the Exa-scale, with volunteer computing Over the last few years, GPUs green) and CPUs (blue) have increased exponentially in speed, but the doubling time for GPUs has been about 8 months, while it has taken 16 months for CPUsImage courtesy of NVIDIA (Editor's note: David Anderson is the founder of the popular volunteer computing platform known as BOINC, or the Berkeley Open Infrastructure for Network Computing. Here, he peers into his crystal ball to predict the direction of volunteer computing, especially as new, high-speed graphics processing units come into the market.)Remember your prefixes? Kilo, mega, giga, tera, peta . . . exa? Each denoting a thousand times more than the one before? Today, the average personal computer can do a few GigaFLOPS (the acronym refers to doing one billion FLoating-point Operations Per Second). A modest cluster might do one thousand GigaFLOPS, or 1 TeraFLOPS. And for several years, one thousand TeraFLOPS, or one PetaFLOPS, was the Holy Grail

October 15, 2008

Link of the Week - LHC Inauguration Day Specially commissioned by CERN for the ceremony to inaugurate the Large Hadron Collider, ORIGINS is a 20-minute adaptation of the original, one-hour, multimedia production LIFE: A Journey Through Time, featuring Frans Lanting’s photographs and Philip Glass’s music, choreographed by Alexander V. NicholsImage courtesy of LHC Fest Imagine that in a few days (the 21st of October, to be exact), you are hosting the formal, invitation-only, LHC Inauguration, in front of several notables, 11 heads of state, and VIPs from many nations.What, exactly, do you serve your honored guests, and how do you entertain them? For one thing, you give them ice cream cooled by liquid nitrogen. It's all part of the philosophy of  “Molecular Cooking,” which chef Ettore Bocchia said consists of foodstuffs pushed to similar extremes, in order to keep everything at its absolute, flavorful best.All accompanied by music composed for the occasion by Philip Glass, and performed by the Orchest