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Feature - FOOTWAYS takes its first steps

Footways started quite literally in the back of someone’s garage. Image courtesy Igor Dubus

Google, Hewlett Packard and Apple all had humble beginnings in the back of someone’s garage. Could the same be true in the back of a garage in Orleans, France?
“I had never seen a router/switch in my life, I had to get into VPN, network, perl scripting. I also had problems with electricity supply and consumption — this was my home, not a dedicated IT room,” says Igor Dubus.
This was only the beginning. Having built a 96-node cluster in his garage to run computer models as the coordinator of the FOOTPRINT project (iSGTW ran an article about FOOTPRINT earlier this year,) Dubus launched his own start-up company, called FOOTWAYS. His goal is to develop this “garage-cluster” into a 12,000-node high performance computing center dedicated to pesticide modeling.
FOOTPRINT, an EU project, seeks to minimize water contam

Feature - Vietnam welcomes three new grid sites; hospitals get new ‘HOPE’

Participants from ACGRID school at Institute for Francophone Informatics (IFI) in Hanoi, October 2009. Image courtesy ACGRID. Image of Vietnamese flag on front page courtesy Wikipedia/Creative Commons

Vietnam hosts some of the world’s most biodiverse areas — with six biosphere reserves — along with one of the lowest unemployment rates in the third world and, as of last month, three of the newest grid sites to join the world’s largest grid computing infrastructure.EUAsiaGrid was launched in April of 2008 to foster grid computing technology within Asia, and to create ties between the e-Infrastructure communities of Asia and Europe. Last month, EUAsiaGrid partners co-organized with the French research institute Centre National de la Recherche Scientifique (CNRS) the second ACGRID school, or Advanced Computing and Grid Technologies for Research, to train current and up

Feature - In case of emergency, call SPRUCE

A part of the complete synthetic social contact network of Chicago obtained by integrating diverse data sources and methods based on social theories. This sort of simulation can bring insight into how a virus will transmit through a population. Check out this SciDac Review article for more information about this research. Image courtesy of Madhav Marathe and SDSC.

When disaster strikes, simulations could give authorities the information they need to save lives. But simulations are computationally intensive, and during a crisis, there’s no time to wait in line for access to computer resources. That’s where urgent computing comes in.
“What you really want is to be able to hook together or have access to all the supercomputers that you need, wherever they are,” said Pete Beckman, project lead for TeraGrid’s Special PRiority and Urgent Computing Environment, or SPRUCE. “The purpose of this sort of urgent com

Feature - Clearing the air: solving an atmospheric controversy with DEISA

The PINNACLE project tests climate models. Image courtesy UCAR

Scientists seeking to develop models for predicting weather, climate and air quality have long been confronted with the fundamental problem of how to accurately forecast the height of the atmospheric boundary layer (ABL) as it develops during daytime heating.
In an attempt to solve this controversy, a team of scientists from the Delft University of Technology in the Netherlands, together with Imperial College London and the National Center for Atmospheric Research in Colorado, initiated the PINNACLE project, using the resources of the DEISA grid of supercomputers.
The ABL is the lower layer of the atmosphere, the part which we live in. Its height grows throughout the day, from a few hundred meters in the morning to one kilometer or more in the afternoon. The ABL has a large Reynolds number (a measure of the turbulence of the system), which me

Feature - A new test bed for future cyberinfrastructure

Image courtesy of jaylopez at stock.xchng.

Grid, cluster, and cloud developers will have somewhere new to test their software before letting it loose on the world, thanks to a new initiative called FutureGrid.
“I think people found that it was pretty hard to test early grid software on the machines that were available, because the machines that were available didn’t like being experimented on,” said Geoffrey Fox, principle investigator for FutureGrid. “FutureGrid is trying to support the development of new applications and new system software, which are both rapidly changing.”
The FutureGrid collaboration, which will be headquartered at Indiana University, had its first all-hands meeting 2-3 October.
“We will have early users throughout the first year,” said Fox. A small number of users are already signed up, but there remains room for more on the FutureGrid roster.
“We would like

Feature - Supercomputing code helps develop new solar cells

Image courtesy of Patrick Moore.

If scientists could use simulations to zoom in on the atomic level of solar cells, the insight they gain could launch solar power into the next energy orbital.
Unfortunately, those simulations would require an exorbitant amount of computational power.
“Typically we need to simulate tens of thousands of atoms,” said Lin-Wang Wang, a scientist at Lawrence Berkeley National Laboratory. “For the conventional code, if the number of atoms increases by a factor of ten, the computational load increases by a factor of a thousand.”
In fact, the same problem arises with nano-scale simulations of a wide variety of materials. That’s why Wang and his research team came up with the LS3DF code.
“We were thinking about how to improve the algorithm and have linear scaling,” said Wang. When an algorithm scales linearly, the computational cost increases at the same rate

Feature - An unexpected bounty of Near Earth Objects

Image of a near-earth object detected by the Sloan Digital Sky Survey. The blue, red and green streaks show the object as it moves through three of the five SDSS filters over a period of five minutes. The two white objects are distant stars. Image courtesy Stephen Kent.

While scanning through images from the Sloan Digital Sky Survey, Fermi National Accelerator Laboratory researcher Stephen Kent noticed something unusual — a few extended streaks scattered among the millions of point-like stars and galaxies.
Kent realized the streaks were produced by Near Earth Objects (NEOs), asteroids or extinct comets whose orbits bring them close to Earth — close enough that they could collide. They appear as streaks because the closer an object is to Earth, the more quickly it moves across our sky. That’s why the patterns of distant stars appear unchanged over the course of our lifetimes, whereas our closest neighborin

Feature: MANGO-NET - Helping to bring African ICT up to speed

Mangoes are cultivated in African countries such as Nigeria, MANGO-NET aims to cultivate an ICT infrastructure. Image courtesy Amr Safey, stock.xchng 

While computing technology is ubiquitous and increasingly powerful, its availability in developing nations remains limited. African universities struggle to participate in cutting-edge research because they do not have access to a widespread computer infrastructure, so their ability to conduct experiments and share results is compromised. As more science becomes “e-science,” the problem gets worse.
To help solve this, MANGO-NET (Made in Africa NGO NETwork), was launched. This project seeks to boost information and computing technology (ICT) throughout Africa, by establishing a network of schools and production labs to train ICT students to build their own computers. Because components are bought in bulk, it should reduce hardware costs, decreasing African depe

Feature – New organization shakes up earthquake consortium

Earthquake engineers at University of Nevada, Reno test a 110-ft bridge model to failure. Image courtesy of Joan Dixon/University of Nevada, Reno.

We cannot stop earthquakes and tsunamis from happening. But with well-engineered buildings, we can prevent some of the death and damage these natural disasters leave in their wake.
First, however, engineers must understand how buildings react when shaken by earthquakes or pummeled by tsunami waves. To accomplish that goal, researchers use a combination of specialized equipment: giant tables that shake, wave tables filled with water, and high-end computing resources that can simulate just about anything.
To find out how sound a building will be during an earthquake, researchers can build a model on top of a large shake table. But most of the shake tables in the United States are not large enough to accommodate an entire building. Instead, they accommodate individual building com

Feature - The digital story behind the mask

Mak Yong dancer in a 3D body scanner. Courtesy Info Com Development Centre (IDeC) of Universiti putra Malaysia.

Capturing culture in digital form can lead to impressive demands for storage and processing. And grid technology has a role to play in providing those resources. For instance, a 10-minute recording of the movements of a Malay dancer performing the classical Mak Yong dance, using motion-capture equipment attached to the dancer’s body, can take over a week to render into a virtual 3D image of the dancer using a single desktop computer. Once this is done, though, every detail of the dance movement is permanently digitized, and hence preserved for posterity.
The problem, though, is that a complete Mak Yong dance carried out for ceremonial purposes could last a whole night, not just ten minutes. Rendering and storing all the data necessary for this calls for grid computing.
Faridah Noor, an associate professor at the University of

Feature - Visualizations go big in planetarium show

An image from Toomre and Brown's visualization of the magnetic field of the solar convection zone. Here, the sunspot is magnified for better visibility, and is not to scale relative to the sun. © 2009, American Museum of Natural History

"Journey to the Stars" is currently showing at the American Museum of Natural History’s Hayden Planetarium in New York City, US
The stars are writ large in all their majesty in “Journey to the Stars,” a planetarium show that uses grid-generated simulations to take audiences deep under the surface of the sun.
With Whoopi Goldberg as a guide, viewers embark on a journey through the lifespan of stars and the origin of life. Visualizations of the universe, projected onto the 87-foot seven-million-pixel dome of the Hayden Planetarium in New York City, explain how stars first formed and then exploded to produce the chemical elements that make life possible.
The 25-minute journey culm

Feature - A SLiM chance for viruses

Viruses hijack the replication machinery of cells. Image courtesy Simon Hettrick

Viruses have evolved a clever way of reproducing. They hijack the replication machinery of their host cell, which is controlled and regulated by a variety of signaling pathways, and fool them into producing copies of the virus.
Richard Edwards, head of the Bioinformatics and Molecular Evolution group at the University of Southampton, UK, is trying to better understand signaling pathways in order to develop treatments for viruses — and for diseases that operate similarly.  This is an enormous task, because to understand signaling pathways in the human body requires studying the interactions between the 20,000 or so proteins contained within the cells.
To do so, Edwards is focusing on short, linear motifs known as SLiMs. “A protein can be thought of as a sequence of amino acids, like beads on a string” explains Edwards. “[SLiMs] consist o