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March 19, 2008
iSGTW Image of the week - Window to a molecular world

Image of the week - Window to a molecular world  The Vaccinia virus, a bundle of DNA comprising 250 genes, is a member of the poxvirus family and was key to World Health Organization efforts to eradicate smallpox. This image was produced using EGEETomo: grid-powered electron tomography.Image courtesy of Fernández, J.J.Electron tomography, also known as ET, provides researchers with a tiny window on to the alien world of molecular biology. The technology works by shooting electron beams through super-slim samples at different angles, producing data that can be pieced together to produce a three-dimensional structure. The technology is well suited to biological specimens such as chromosomes and viruses, providing nano-scale resolution for an all-new look at these target macromolecules.To achieve such resolution, ET demands sophisticated reconstruction algorithms. Where iterative algebraic algorithms yield high quality reconstructions, they are computationally expensive and their use requires high performance techniques.

March 19, 2008
iSGTW Link of the week - Defibrillation of the heart

Link of the week - Defibrillation of the heart What happens to the heart under the influence of electric shock? Defibrillation may be well used in hospitals, but the mechanisms behind it are still not fully understood.Image courtesy of National Grid ServiceStep inside the heart as part of the Integrative Biology Project, a consortium of researchers using e-science to combat fatal diseases.Members of this project, Blanca Rodriguez and her colleagues from the Computational Biology Group at the University of Oxford, are using the National Grid Service to power simulations of the application of electric shocks to both healthy and diseased hearts.Rodriguez hopes the simulations will help improve understanding of exactly how defibrillation, a common but poorly understood medical technique, works.The research involves running many sequential simulations, including parameter sweeps of variables such as shock strength and timing.250 milliseconds of data; 28 CPU hours of workTo obtain just 250 milliseconds of animated data, Rodriguez chu

March 12, 2008
iSGTW Feature - Building BRIDGEs between Europe and China

  Feature - Building BRIDGEs between Europe and China The BRIDGE project includes three case studies of interoperation between Chinese and European middleware, covering aerodynamics, meteorology and pharmaceuticals.Images courtesy the BRIDGE project Grid middleware has become a pervasive e-science technology and Chinese middleware is no exception, with technologies such as CNGrid GOS and CROWN Grid contributing to e-science efforts across the globe.Yet one of the remaining challenges in grid computing is interoperability, and more sustainable international co-operation must be accomplished to align middleware developments on a global scale.The EU ICT BRIDGE project (Transcontinental Workflows for Simulation, Engineering, and Design on heterogeneous Grid Platforms) is addressing these challenges using three case studies of interoperation between Chinese middleware CNGrid GOS and European middleware GRIA in the aerospace, meteorology and pharmaceutical sectors.Protein docking for disease controlThe first case study is a distrib

March 12, 2008
iSGTW Link of the week - How low can a Sudoku go?

Link of the week - How low can a Sudoku go? What is the minimum number of clues required to solve a Sudoku? The BOINC-powered Sudoku project is keen to find out.Image courtesy of the Sudoku project There are two ways to solve a Sudoku: by hand, or by writing a computer program to do it for you. For “ordinary” Sudoku—where you begin with 25 to 30 “clue” numbers—this is a relatively simple proposition. But what happens when you start with half as many clues? Can you still solve a Sudoku which begins with only ten clues? What about five clues? How low can a Sudoku go while still ensuring it has only one unique solution?Running the numbersSo far, all known minimal Sudokus with a unique solution begin with 17 “clue” numbers. Further, any puzzles with fewer than eight clues have resulted in at least two different solutions. Thus, minimal Sudokus are thought to require 8-17 numbers.A new BOINC-powered distributed computing project—Sudoku—is determined to close this gap, aiming

March 5, 2008
iSGTW Announcement - EC invests 2.5 billion in embedded computer systems

Announcement - EC invests 2.5 billion in embedded computer systems Ninety-eight percent of computing devices are embedded electronic equipment and machines. Over four billion embedded processors were sold last year and the global market is worth € 60 billion with annual growth rates of 14 percent. Forecasts predict more than 16 billion embedded devices by 2010 and over 40 billion by 2020.Image courtesy of ArtemisThe European Commission last week launched a major Joint Technology Initiative as part of ARTEMIS. With an unprecedented investment of € 2.5 billion, this initiative addresses embedded or “pervasive” computer systems that—while running almost unnoticed by users—improve the performance of all kinds of machines: from cars, planes and phones, to factories, washing machines and televisions. “Invisible computers embedded in all devices of industrial application can have a tremendously positive impact on Europe’s economy,” said Viviane Reding, EU Commissioner for Information Soc

March 5, 2008
iSGTW Announcement - NSF partners with Google and IBM

Announcement - NSF partners with Google and IBM Jeannette Wing, assistant director at NSF for CISE, says the NSF hopes the new relationship with Google and IBM may provide a blueprint for future collaborations between the academic computing research community and private industry.Image courtesy of Carnegie Mellon Last week the National Science Foundation’s Computer and Information Science and Engineering directorate announced the creation of a strategic relationship with Google Inc. and IBM. The Cluster Exploratory (CluE) relationship will enable the academic research community to conduct experiments and test new theories and ideas using a large-scale, massively distributed computing cluster.“Access to the Google-IBM academic cluster via the CluE program will provide the academic community with the opportunity to do research in data-intensive computing and to explore powerful new applications,” said Jeannette Wing, assistant director at NSF for CISE. “It can also serve as a tool for educating the next gener

March 5, 2008
iSGTW Feature - Introducing TRIUMF: Canada's Tier-1 on the worldwide grid

  Feature - Introducing TRIUMF: Canada’s Tier-1 on the worldwide grid Lead system administrator Denice Deatrich and networking administrator Chris Payne examining the dCache servers at the TRIUMF Tier-1 center.Image courtesy of TRIUMF When the Large Hadron Collider starts up at CERN in 2008, the world will be waiting to receive the data it produces. In Canada, researchers will be looking to TRIUMF, Canada’s particle and nuclear physics national laboratory. TRIUMF is host to one of eleven Tier-1 centers, forming an integral part of the Worldwide LHC Computing Grid collaboration and supporting the particle detector experiment, ATLAS, one of the LHC-powered experiments.With its experience supplying 24/7 service to international collaborations, TRIUMF provides the facilities required for the large-scale, data-intensive analysis that LHC data will require, while attracting expertise in the operation of the facilities as well as for user-support. High-density, liquid-cooled   Uniquely, TRIUMF’s Tier-1 cente

March 5, 2008
iSGTW Resources - Getting started with grid computing: engage with OSG

  Resources - Getting started with grid computing: engage with OSG The OSG Engagement team worked with the NanoWire community to grid-enable their research. This visualization—generated by the OSG-powered nanowire tool on nanoHUB—shows the electrostatic potential of a 26 nanometer long, 5nanometer thick nanowire.  Image courtesy of Gerhard Klimeck, NanoWire Grid computing can turbo-boost your research—many scientists are now aware of this fact. However, getting started in grid computing is not as easy as hitting the “warp-speed” button on your desktop. New users must adapt their applications and their mindset if they are to thrive in the grid environment. This process requires time, energy and qualified, dedicated help. So who’re you gonna call?Engage with OSG Hear from the users See eye-to-eye at CI days  Engage with OSG If you’re getting started in the U.S., Open Science Grid, with its fully supported “Engagement” activity, is a good place to start. &ld

February 27, 2008
iSGTW Feature - Les Robertson: six years at the head of the LCG

  Feature - Les Robertson: six years at the head of the LCG Les Robertson in 2001, “just before it [the LCG project] started,” and in 1974, when he first arrived at CERN.Images courtesy of Les Robertson In this special feature iSGTW chats to Les Robertson, who recently stepped down after six years at the head of the Large Hadron Collider Computing Grid.A hole in the funding bucket Democratic and global The Grid Challenges so far: the big three Our challenges for the future Countdown to startup In the beginning Les Robertson arrived at CERN in 1974 to fix a problem. The European physics research laboratory had just purchased a new supercomputer. The problem, says Robertson, was that it didn’t work.“At that time customers fixed their own operating systems,” he explains. “I arrived as an operating systems expert and stayed on.”Twenty-seven years later, Robertson began work on an entirely different problem: Preparations for the Large Hadron Collider were well underway, but the comput

February 27, 2008
iSGTW Image of the week - Grids help map salt in coastal aquifer

Image of the week - Grids help map salt in coastal aquifer The Korba aquifer in Tunisia is being studied using the grid-enabled CODESA-3D tool, a hydrological application deployed on the EUMEDGRID e-infrastructure.Image courtesy of EUMEDGRID Many of us love to live and vacation near the coast. But as coastal zones experience dramatic demographic and socio-economic development, there are also growing and conflicting demands on the natural resources of coastal areas. This leads to often irreversible degradation of natural resources, which severely limits the potential for further development. In parallel with this, expanding human activity is placing increased pressure on groundwater reserves, an issue heightened by seawater intrusion and salinization of coastal aquifers and soils, leading to major threats for food production and natural resources protection.To help manage these issues a team from the Center for Advanced Studies, Research and Development in Sardinia and the University of Padua, Italy, have developed CODESA-3

February 20, 2008
iSGTW Feature - CineGrid: lend some power to your pixels

  Feature - CineGrid: lend some power to your pixels RENCI’s tele-immersion room, which features a 10-foot by 5-foot rear projection display for stereoscopic viewing at four times HD resolution, will serve as its node on CineGrid. Image courtesy of Josh Coyle, RENCI High-resolution digital content. A 10-foot by 5-foot rear projection stereoscopic screen with four times high-definition resolution… Interested?If you’re into visual media, get an eyeful of CineGrid, a non-profit organization aimed at bringing together filmmakers, visualization specialists and digital media experts, using grid computing technologies for networked collaboration.Creating the futureCineGrid members work together to explore the feasibility of different networking approaches for emerging applications of media-rich forms of art, entertainment, distance learning, scientific visualization, remote collaboration and international cultural exchange. A new member of the CineGrid collaboration is the Renaissance Computing Institute, or RENCI,

February 20, 2008
iSGTW Link of the week - Kung Fu Panda digs grids

Link of the week - Kung Fu Panda digs grids Using grid computing, digital artists working on Kung Fu Panda are performing 75,000 to 100,000 batch-processing jobs each night, each ranging from a few minutes per frame to 15 hours per frame, depending on the rendering complexity of the digital frame sequence.Image courtesy of DreamworksGrid computing isn’t always about saving the world. It can be about creating a new world, in this case, the world of the Kung Fu Panda, a new animation feature by Dream Works to be released in June.Creating animation films like Kung Fu Panda typically requires around 25 million render hours from start to finish. The Dream Works computer farm comprises a 4000-processor Linux cluster, but when their digital artists are all simultaneously pinging the compute cluster to retrieve digital frame data, the system’s input-output comes under a lot of strain.Enter grid computing, in the form of Ibrix parallel file server software. DreamWorks added Ibrix to its animation system about six months ago,

February 13, 2008
iSGTW Image of the week - A map of all things science

Image of the week - A map of all things science Science-related activity on Wikipedia: Overlaid are 3599 math (blue), 6474 science (green), and 3164 technology (yellow) related articles. All other articles are shown as grey dots. This map is part of the Places & Spaces exhibition. An interactive version of the full Wikipedia visualization is also available. Image courtesy of InfoVis LabKaty Börner knows what Wikipedia looks like in English, all 2.1 million articles of it. Börner, a professor at Indiana University Bloomington, is director of the Information Visualization (InfoVis) Laboratory, and along with her InfoVis colleagues, Börner has analyzed and “visualized” the network of knowledge that is Wikipedia in English.The image on the right is a science-themed version of the same visualization, created using science-related Wikipedian activity. To construct it, the team laid out a sample of article images on a circular grid, positioning similar, linked articles close together. The result is a mo

February 13, 2008
iSGTW Link of the week - SHARE: who, what, when, how and in what order

Link of the week - SHARE: who, what, when, how and in what order Tony Solomonides speaks on behalf of the SHARE project at the opening plenary of this week’s EGEE User Forum in Clermont-Ferrand, France.Image courtesy of Yannick Legré, HealthGrid More than physics, more than astronomy, it is human health that captures the imagination of people across the planet. Whether it’s cancer or AIDS, aging or depression, health-related issues have an immediate and universal appeal that has powered the rise of several healthgrid-related projects. Now, a new project has arrived to bond and unite heathgrid projects from around the globe.SHARE and share alike  Called SHARE, or Structuring and supporting Healthgrids Activities and Research in Europe, the project unites collaborators working towards a common goal: better healthcare through the development of grid-powered e-science. “SHARE aims to develop a roadmap for the wide adoption and deployment of grid technology for health in Europe,” explain

February 13, 2008
iSGTW Technology - Taming the data deluge: the new open source iRODS data grid system

  Technology - Taming the data deluge: the new open source iRODS data grid system The iRODS team is working with a number of partners, including the U.S. National Archives. This image from the National Archives is a self-portrait of political cartoonist Clifford Berryman, who is credited with introducing the teddy bear into American vernacular after President Theodore Roosevelt famously refused to shoot an old, haggard bear during a hunting trip. Images courtesy of the National Archives The digital data we all love is growing explosively. In 2006, humanity produced 161 exabytes of digital data—that’s 161 billion billion bytes. This deluge of data is bringing with it unprecedented challenges in organizing and accessing digital information. To meet these challenges, the Data-Intensive Computing Environments group at the San Diego Supercomputer Center has released version 1.0 of iRODS, the Integrated Rule-Oriented Data System, a powerful new open-source approach to managing digital data. “iRODS is an innovati

February 13, 2008
iSGTW Technology - YAIM: herding gLite configuration

  Technology - YAIM: herding gLite configuration And why a yak? The yak logo was provided by David O’Callaghan, in reference to the concept of “shaving the yak.” This was subsequently adopted as part of YAIM’s motto.Images courtesy of YAIM Setting up a grid site can present a pretty steep learning curve, and with more than 250 EGEE sites and new administrators arriving all the time, anything that eases the transition to becoming a fully fledged grid administrator is a big plus. That’s where YAIM comes in. EGEE’s gLite middleware takes its components from a number of different sources, each of which has its own configuration paradigm. To save administrators from having to learn the details of each service, the YAIM configuration utility does all the hard work, providing simple and separable installation and configuration methods. Built on basic Unix technology, YAIM offers administrators a familiar and uniform interface, also adding transparency to the process. YAIM is installed on every

February 6, 2008
iSGTW Feature - Computing the unseen: the search for dark matter

  Feature - Computing the unseen: the search for dark matter Researchers are using the Collider Detector at Fermilab detector to help in the search for dark matter, hoping to observe a Bs particle decay, which could provide evidence of supersymmetry and dark matter. Image courtesy of FermilabThink you’ve seen it all? Think again. Everything we can see and detect makes up only four percent of the universe, according to Michael Weinberger, a physicist at Texas A&M University and member of the Collider Detector at Fermilab collaboration. Weinberger and his CDF colleagues are conducting a search that could shed light on the universe’s “dark matter”—material that doesn’t emit or reflect radiation but is predicted by astrophysical observations to outnumber visible matter by nearly six-to-one—and they are using grid technology to expedite their hunt. The elusive Bs decayThe key to the search is the ability to measure the rate at which Bs particles decay to form two muons. According to t

February 6, 2008
iSGTW Feature - DILIGENT: from digital libraries to virtual research environments

  Feature - DILIGENT: from digital libraries to virtual research environments Fires in Greece over August 2007 killed 64 people and destroyed half a million acres of vegetation, leaving a scarred battlefield. Thanks to continual collection of earth observation data, scientists have a detailed record of this event. Image courtesy of European Space Agency In August 2007, Greece saw more wildfire activity than any other European country in the last decade. The fires, which involved scores of separate blazes, killed 64 people and destroyed half a million acres of vegetation. Thanks to data collected by organizations such as the European Space Agency, we have a detailed record of this event.A drop in the proverbial data bucketSuch earth observation data is collected all the time, all around us. For instance, to continue the wildfire example, two European Space Agency satellites—ERS-2 and Envisat—are continually monitoring the Earth’s surface, sensing hot areas: spots exceeding 308 Kelvin at night are classified as

February 6, 2008
iSGTW Feature - Testing the waters: coastal ecologists look to open source software to manage distributed sensor data

  Feature - Testing the waters: coastal ecologists look to open source software to manage distributed sensor data Groundwater monitoring stations like these provide data on the quality and level of groundwater across the coast of South Carolina, allowing researchers to track any changes as commercial and residential developments go ahead.Image courtesy of PISCES Environmental Science graduate student, Samuel Esswein, is keeping a watchful eye on South Carolina’s changing coastline. With assistance from his graduate advisor, Christopher Post, Esswein and a team from Clemson University, U.S., are studying the impact of commercial and residential development along South Carolina’s traditionally forested coastal areas. Their work is funded by the Program of Integrated Study for Coastal Environmental Sustainability (PISCES). A system of sensors“Rapid coastal development has had a dramatic effect on the hydrologic and ecologic systems of South Carolina’s coastal areas,” Esswein says. “This has wid

February 6, 2008
iSGTW Image of the week - Real-time blood flow through the brain

Image of the week - Real-time blood flow through the brain GENIUS allows images of the blood flow around a patient’s brain to be visualized in real-timeImage courtesy of Centre for Computational Science, UCLPicture a clinician, standing at a terminal, watching a computer simulation of blood flowing through their patient’s brain, moving the model brain around to get a better look at the vessels they are about to operate on.Sound too futuristic? Not ifyou’re working on the GENIUS—or Grid Enabled Neurosurgical Imaging Using Simulation—project.“With GENIUS we’re aiming to make patient-specific treatment a reality for neurosurgeons, by developing an efficient system which fits in with current clinical practice,” explains collaborator Steven Manos.This system will allow conditions such as arterio venous malformations—abnormal tangles of blood vessels that can cause headaches, seizures, paralysis and haemorrhaging—to be better understood and treated, since studying patient blood f

February 6, 2008
iSGTW Link of the week - Weblin your way to cyber popularity

Link of the week - Weblin your way to cyber popularity See you on iSGTW?Image courtesy of weblin Tired of wandering cyberspace all alone? Give yourself a presence on the web using weblin, software that allows people browsing on the same Web page to see and communicate with each other.Apparently, having a weblin allows you to communicate with the different people you run in to while on your favorite sites, thus enriching the web surfing experience. According to the Web site, weblins can “help people to improve their virtual lives” and “secure their presence on the Web.”The free software allows you to choose an animated weblin character that “looks like you, or looks how you would like to appear.”Your weblin includes a public profile and “speaks” to other weblins using good old-fashioned cartoon-style speech bubbles. A weblin of few words? You can also rely on body language, including waves, smiles, frowns and evening a little dancing.If you’re no longer interested in chatting t

January 30, 2008
iSGTW Announcement - Louisiana Universities receive nine million to develop cybertools

Announcement -  Louisiana Universities recieve $9 million to develop cybertools Tulane University Health Sciences Center is one of nine Louisiana institutions participating in the cybertools project.Images courtesy of Louisiana EPSCoRA team of faculty researchers representing nine Louisiana universities has been awarded a US$9 million National Science Foundation (NSF) grant to develop new cyber tools aimed at enabling significant advances in science and engineering. With matching funds of $3 million from the Board of Regents Support Fund and $3.2 million from the participating institutions, the total of the three-year award is over $15.2 million.“This grant will allow Louisiana university researchers to capitalize on the state’s recent investments in cyberinfrastructure,” said Commissioner of Higher Education Joseph Savoie. “The project will take full advantage of the Louisiana Optical Network Initiative (LONI), the high-speed optic network that connects supercomputers at our major universities a

January 30, 2008
iSGTW Announcement - PRACE lays foundations for pan-European high performance computing

Announcement - PRACE lays foundations for pan-European high performance computing PRACE aims to provide European researchers with access to supercomputing capacities at a world-class level, transgressing those affordable at the national level.Image courtesy of PRACEOver 60 representatives from 14 European Countries participated in the kick-off meeting of the PRACE project at the Research Centre Jülich on 29 and 30 January 2008. PRACE aims to lay the foundations for a future European supercomputer infrastructure and recently received a grant from the European Commission towards a total budget of 20 million Euro for the coming two years. PRACE was established to create a persistent pan-European High Performance Computing service for research. In the preparatory phase, which will run until the end of 2009, the project will establish the basis of transnational organizational structure for scientific supercomputing in Europe. By bringing together the know-how and resources of the partners, PRACE aims to provide European research

January 30, 2008
iSGTW Feature - Editing, analyzing, annotating, publishing: TextGrid takes the a, b, c to D-Grid

  Feature - Editing, analyzing, annotating, publishing: TextGrid takes the a, b, c to D-Grid Using grid technology, scholars can access and re-use the work of their colleagues, opening new possibilities for collaborative and dynamic approaches to text science. Image courtesy of TextGrid A multitude of avid users are waiting to be introduced to grid technologies: scholars are semantically encoding and annotating texts, text scientists are researching the genesis of literature, digitization projects all over the globe are venturing to digitally capture our cultural heritage... Such projects can sometimes span years, working in isolation on a single text, and together they have already accumulated terabytes of data.Centuries of literature with just a few clicks  TextGrid is one of the early initiatives to make this data available to the wider community. Part of the German national grid initiative D-Grid, TextGrid establishes a virtual research environment for scholarly texts, synthesizing methods and technologies f

January 30, 2008
iSGTW Feature - Traveling salesman meets distributed computing

  Feature - Traveling salesman meets distributed computing The traveling salesman problem (TSP) is solved when the salesman travels through each of “n” cities while covering the least total distance. This shortest route is called a Hamiltonian circuit; however, there is no known general method for finding the TSP solution.Image courtesy of Wolfram Mathworld The traveling salesman problem (TSP) is a classic combinatorial problem: given a set of cities, what is the path that visits each city once and only once, while covering the minimum distance? For a small set of cities, the solution is trivial and can be discovered by simple inspection; however, the solution for even a moderate number of cities is out of reach for most home computers. For example, to exhaustively check all possible paths for a 48 city instance—assuming you could check one million paths a second—would take approximately 1047 years.     Despite all the research, there is still no known general solution to the TSP.