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May 26, 2010

Image of the week - Traffic visual

This visualization of traffic flow in downtown Chicago was created using data generated by TRANSIMS, the TRansportation ANalysis and SIMulation System.
TRANSIMS is a regional transportation modeling and simulation software environment, used in this case to generate data that represents car paths. In order to bring that data to life, those car paths were converted into trajectories. Next, the trajectories were read into a data visualization plug-in called Maya, which was developed by Alex Betts at the National Center for Supercomputing Applications’ Advanced Visualization Laboratory. The finishing touch was to add accurate models of buildings.
TRANSIMS is part of the US Department of Transportation’s Travel Model Improvement Program. In order to create the Chicago version of TRANSIMS, AVL has been collaborating with the Argonne National Laboratory TRACC Center.
What next? According to the AVL website, “AVL’s Matt Hall is creating an

May 19, 2010


Link of the Week: The sound of science — electrons in your left ear, muons in your right

ATLAS — World’s largest musical instrument? Image courtesy CERN

On the iSGTW Nature Networks Forum the other day, reader Lily Asquith mentioned the “LHC Sounds” project, which just started this past January.
Intrigued, we found that there is a whole community of particle physicists, composers, software developers and artists, who are working together to convert raw data from the ATLAS detector into sound. It can be a useful scientific analysis technique . . . and the source of a cool new art form.
The LHC Sounds’ website explains how such ‘sonification’ is done. Essentially, software on ATLAS takes silicon detector hits and energy deposits — or ‘objects’ — and converts them into streams of ones and zeroes, which can then be rendered step-by-step into two or three columns of numbers, known as a &l

May 5, 2010

CLARIN: A project that speaks to you

Wee-Ta-Ra-Sha-Ro, Head Chief of the Wichita. Painted by George Catlin in 1834. Image courtesy

The creation story of the Wichita people tells of a creator, “Man-never-known-on-Earth,” who formed the world, land, water and the first man and woman: “Man-with-the-Power-to-Carry-Light” and “Bright-Shining-Woman.” This couple brought to the Earth light, corn-growing, deer-hunting, game-playing and prayer, before becoming the morning star and the moon. While the story itself is preserved in literature for antiquity (e.g., in George Dorsey’s 1904 book The Mythology of the Wichita), fewer than 10 people today can tell the story in the Wichita language, nearly all of whom are elders living on tribal lands in Oklahoma, USA. It’s a pattern repeated around the world; many languages are endangered or dying. Preserving these languages is vital for groups seeking to revitalize and maintain their

May 5, 2010

Feature - From EGEE to EGI: Plain talk with Bob Jones and Steven Newhouse At the Uppsala Gala Dinner, Bob Jones of EGEE handed over to Steven Newhouse of EGI his most prized possession — a crown made from all the name tags he collected from conferences in the past six years. Image courtesy GridTalk After six years, on 1 May, EGEE will hand over responsibility for the world’s largest grid infrastructure to a new organization dedicated to its coordination and development (, and its newly elected director, Steven Newhouse. During its lifetime, EGEE — Enabling Grids for E-SciencE — assembled a world-wide infrastructure of CPU cores, hosted by computing centers around the world. Each month, about 13 million jobs are executed on the EGEE Grid. This massive multi-disciplinary production infrastructure was led until now by Bob Jones who initially, like Steven, held the position of technical director at EGEE, and quickly advanced to project director. Du

April 28, 2010

Image of the Week - Earthquake comics

Image courtesy PHIVOLCS

In the EUAsiaGrid Disaster Mitigation Workshop at ISGC 2010, Bart Bautista of the Philippine Institute of Volcanology and Seismology (PHIVOLCS) reminded delegates that it is not enough to simply detect earthquakes and the tsunamis they produce with sophisticated sensors, or simulate them with grid computing. Countries in earthquake-prone regions must also invest heavily in preparing the population to cope with major natural disasters. This starts in schools, where outreach material like the comic book shown above is used to raise awareness among children.
— Francois Grey, EUAsia Grid

April 21, 2010

Feature - Stem cell research goes Boolean with BooleanNet

Image courtesy of Rodolfo Clix.

To make use of the human genome in our quest to understand genetic disorders, we need to learn more about what each gene accomplishes. Unfortunately, connecting a specific gene to the formation of a specific cell can take years of hard work and thousands of dollars.
An algorithm that could cut that time down from years to hours has passed its first litmus test, however, according to a paper recently published in the Proceedings of the National Academy of Sciences.
The paper’s lead author, Debashis Sahoo, had his eureka moment during an immunology class. Sahoo, who was working on a doctorate in electrical engineering at the time, observed that although many biological relationships are asymmetrical, biologists tended nonetheless to look for symmetrical relationships. Sahoo and his advisors quickly realized that these asymmetrical relationships can be found using Boolean logic, such as if-

April 21, 2010


Link of the Week: EGEE Screencasts on grid computing


Just in time for the User Forum at Uppsala, the Direct User Support group  produced some educational screencasts that answer common questions about the grid. They are available for viewing here on YouTube and at Vimeo.
Alternatively, you can download them directly to your laptop.
A few samples are
[1] Introduction to Grid Computing[2] Credential management[3] Job submission[4] Data management(An index of such “Use Cases” can be found here.)

April 21, 2010

Opinion: Africa Grid?

Official ribbon-cutting for “Blue Gene for Africa” last year. This supercomputer is the fastest scientific computer on the African continent, capable of 11.5 teraflops (11.5 trillion floating point operations per second). Image courtesy Center for High-Performance Computing

At the EGEE User Forum in Uppsala, the author, Bruce Becker of the Meraka Institute and coordinator of the South African National Grid, called for making an AfricaGrid a reality. Here he outlines the reasons why now is the opportune time for work on this to be starting in earnest.
For some years now, many have been hinting at an “AfricaGrid.”
In the Mediterranean basin, we have seen many African countries participating directly in EUMedGrid (and more recently EUMedSupport).
In the southern region of Africa, we have seen much activity over the last couple of years that allows to envisage at least a “Sub-Saharan Grid.”
This prospect is very appealing to the r

April 7, 2010

Lights, camera, action: FilmGrid

Image courtesy FilmGrid

Film-making is a very labor-intensive craft, relying upon the work of many people.
This is especially true of the part known as “post-postproduction” — traditionally, that portion of the process when all the raw film has been shot and is “in the can.” During this phase, all the editing, natural sound, music, background painting, voiceovers, montages, special effects, and everything else take place.
Because so much of post-production is manual, and because so many hands are involved — and because post-production often involves widely scattered individuals and companies — it can often be very difficult to maintain an up-to-date picture of the status of a film production, leading to inefficiencies, unwanted duplication of effort, and complications. In addition, couriers sometime lose hard disks containing footage with terabytes of information, and security can often be difficul

February 24, 2010

Feature: Virtualization - Key for LHC physics volunteer computing

BOINC is versatile enough that even mobile phones can do volunteer computing. Image courtesy BOINC

In 2006, the team that built LHC@home was given a challenge by Wolfgang von Rueden, then IT Division Leader at CERN: look at the use of the volunteer computing project BOINC (Berkeley Open Infrastructure for Network Computing)  for simulating events of interest in the Large Hadron Collider. It presented a demanding problem.
The software environments used by the experiments such as ATLAS, ALICE, CMS and LHCb are very large.
Furthermore, all LHC physics software development is done under Scientific Linux, whereas most volunteer PCs run under Windows. Porting the large and rapidly changing software is not practical, so another approach was needed.
The solution?
Marrying volunteer computing with the CernVM virtual image management system under development. It would enable the practical use of thousands of volunteer P

February 17, 2010

Feature - Doing science on the hub

Michael McLennan demonstrates a visualization tool hosted on in his office at Purdue University. Image courtesy Miriam Boon.

The HUBzero platform will be released as open source for the first time at the HUBbub 2010 workshop, 13-14 April. The release of this powerful platform could change the way you research, collaborate, and teach.
HUBzero has been described as a cloud, a content management system, and “FaceBook for scientists.” In a way, these are all true. Yet none of them adequately convey the capabilities of this platform.
It all began with a web infrastructure called PUNCH, which was developed in 1995 at Purdue University in order to deploy simple science gateways. Scientists could use PUNCH to create a web form that, when filled out and submitted, would run batch jobs.
At the time, this was pretty revolutionary. But by 2002, it was time for an update. So they began work on the now well-known nanotechnology resource

February 17, 2010

Feature - Forecasting weather on the grid

This image shows the 10 meter wind field on 24 April 2006 at 1300 UTC (1400 h local time). During the early afternoon, a sea breeze flow reached its maximum intensity. Over the land, the wind is rather irregular due to very complex topography. Wind speeds mostly varied in the range of 3.5 m/s to 5 m/s along the Adriatic coast (e. g., Šibenik, Split, Makarska, Dubrovnik). At the land measuring sites, the sea breeze was developing from the southwest direction. The island’s measuring sites, however, showed the significant influence of the northwesterly large-scale wind. Image courtesy of Davor Davidovic.

The Weather Research and Forecasting prognostic model (WRF) is an atmospheric simulation system that runs on parallel computing platforms. It is designed with the goal of being flexible, portable, and efficient.
Within the field of meteorology, the Advanced Research WRF (ARW) is one of today’s best-known weather research an

February 17, 2010

OSCAR understands the language of chemistry, naturally

When it comes to chemistry terminology, one person’s sodium chloride is another’s salt. Image courtesy Snack/stock.exchng

Like any other language, the language of chemistry lacks uniformity.
New words are invented, old words fade out of use, styles of writing change and some writers suffer from less-than-perfect grammar.
What’s more, there is no single way of referring to a chemical: one person’s salt is another’s sodium chloride (and yet another’s NaCl). To search for a specific word in a chemistry text, a researcher must take into account every permutation of that word and every possible mistake in representing it.
This is highly inefficient, and with more sources of chemistry information becoming available every day, it’s not getting any easier to find relevant information.
But now, there’s OSCAR to help. Also known as “Open Source Chemistry Analysis Routines,” it

February 10, 2010

Bringing LHC data to US Tier-3s

Computer racks at the Fermilab Grid Computer Center. Image courtesy of Fermilab.

It’s a challenge for smaller research groups to get set up on a grid, but that’s exactly what physicists at over 40 sites across the United States need to do to get access to data from the Large Hadron Collider.
The new US Tier-3 centers – evenly split between the ATLAS and the Compact Muon Solenoid experiments – have each received about $30,000 in funding as part of the American Recovery and Reinvestment Act. Physicists scattered around the country will be able to use them to do their own analysis of data generated by two of the LHC experiments.
To get these sites online, a great deal of expertise will be needed. And that’s where the US LHC Tier-3 support group comes into the picture.
“What we are trying to do is to help them get their systems set up and connected to the grid, to make it easier for them to get access to data and addi

January 27, 2010

Answering a truly big question: how did dinosaurs move?

Dinosaurs such as this therapod (“beast-foot”) are  believed to be the ancestors of modern birds. Image courtesy

In a memorable scene from Steven Spielberg’s Jurassic Park, a Tyrannosaurus rex gallops behind a jeep, close to overtaking it, lunging to take a bite out of Jeff Goldblum — to the horrorified delight of millions of thrill-seeking movie-goers. 
Assuming dinosaurs could be resurrected, how realistic would this situation be?
Not very, according to Karl Bates, a researcher in dinosaur locomotion. In fact, our scrawny-armed, prehistoric friend would probably have trouble outrunning a bicyclist. Depending on how fast you run, you may or may not be in trouble if you were on foot.
How does Bates know this?
Because he is a member of the Animal Simulation Laboratory at the University of Manchester, UK, which for over five years has made computer models of prehistoric an

January 27, 2010

Feature: The grid that sifts for dark matter

Cryogenic Dark Matter Search detectors. The CDMS experiment uses five towers of six detectors each. Photo credit: Reidar Hahn.

Think of grid computing as a sieve that physicists use to sift out those rare events that might just be signs of dark matter — the mysterious substance that appears to exert gravitational pull on visible matter, accelerating the rotation of galaxies.
FermiGrid, the campus grid of Fermilab and the interface to the Open Science Grid, recently helped researchers from the Cryogenic Dark Matter Search experiment do just that: identify two possible hints of dark matter.
Dark matter has never been detected. And although the CDMS team cannot yet claim to have detected it, their findings have generated considerable excitement in the scientific community.
“This is a very intriguing result,” said Lauren Hsu, a CDMS researcher at Fermilab who announced the experiment’s results at a talk last Dec

January 27, 2010

Feature: Grids and clouds - reaching for the next phase

A composite image of the Cat’s Eye Nebula with data from NASA’s Chandra X-ray Observatory (blue) and Hubble Space Telescope (red and purple). This cloud of dust and gas is about 3,000 light-years from Earth. The hybridization of grids and clouds seems considerably closer than that. Image courtesy Smithsonian Astrophysical Observatory

“This is not a replacement technology,” says Ignacio Llorente, “This is the next phase of evolution for grids.”
Llorente coordinates ‘virtual machine’ management  for RESERVOIR, an EC-supported project standing for Resources and Services Virtualization without Barriers, that works to enable deployment and management of complex IT services across different administrative domains. This project began collaborating with EGEE in June 2009 to marry the advantages and practicalities of cloud computing with grid technology.
After starting in February 2

January 27, 2010

Image - Satellite maps aid Haiti earthquake relief

Click on map for full-screen, PDF version. Original courtesy UNOSAT

Emergency response teams in Haiti are getting a helping hand from UNOSAT, the UN Institute for Training and Research (UNITAR) Operational Satellite Applications Program. Operating out of  CERN, UNOSAT is supplying maps of the roads in Port-Au-Prince to help humanitarian aid workers avoid road blockages. The maps show the location of debris that is blocking roads and bridges outright (shown in red) or partially restricting access (shown in orange).
The computer-intensive raw images from UNOSAT are transferred to EGEE, where programs compress the satellite images for transmission over low-bandwidth connections, allowing users to access the latest maps from devices as simple as mobile phones — essential in areas where land-lines are down and infrastructure destroyed. The location of the debris is captured by the GeoEye-1 satellite and placed on top of the c

January 20, 2010

PEGrid gets down to business

This image depicts a simulation of the water saturation changes in a quarter of a homogeneous oil reservoir over time, as water is injected. The water increases the pressure in the reservoir, pushing the oil to the surface. Because the reservoir is symmetrical, researchers were able to save time by simulating only one quarter of the reservoir.
The colors indicates the water saturation, with purple being highly saturated and red being least saturated. Each of the six slices represents a snapshot in time.Image courtesy of Shameem Siddiqui.

Although Petroleum Engineering Grid officially started up in late 2009, it is already a classic example of how research projects can have unexpected benefits.
PEGrid came into existence using techniques and tools created by TIGRE (Texas Internet Grid for Research and Education), a state-funded project based on the use of federally funded middleware such as Open Science Grid’s Virtual Data Toolkit.
When TIGRE ende

January 13, 2010

Feature - Keeping an eye on the skies with LifeWatch, poster winner of EGEE 09

Bird encounters jets. According to the photographer, “This was not done in Photoshop. The bird was certainly a lot closer than the planes, but the depth of field was deep enough to capture everything in focus.” Image courtesy Flickr/Kent Smith

Reports of ‘bird strikes’ in recent years are on the rise. According to Scientific American, in 1990 there were only 1,750 incidents in which birds struck a plane, whereas the number for 2008 was close to 8,000. While these encounters never work out well for the bird, normally the plane and passengers escape unharmed — although sometimes a lot of luck is involved. A small percentage of the time, the plane becomes seriously damaged and its engines fail, forcing an emergency landing (as happened last January with US Airways Flight 1549).
Several factors are contributing to the rise in bird strikes. For one thing, migratory bird popu

January 13, 2010

Feature - Transferring FTP to the cloud: Off of desktop, out of mind

Kettimuthu’s team chose the 10 terabyte data set shown in this image for the Bandwidth Challenge. The data, which comes from the World Climate Research Program Coupled Model Intercomparison Project, simulates temperature change at the Earth’s surface and zonally-averaged throughout the atmosphere from 1900-2100. Image courtesy of Rajkumar Kettimuthu.

Don’t shut down. Don’t reboot. Don’t disconnect. And don’t even think about closing the window. Securely and rapidly transferring large amounts of data with GridFTP comes with a lot of “don’ts.”
That’s why the Globus Alliance team led by Steve Tuecke, a researcher at Argonne National Laboratory and the University of Chicago, decided to create a hosted data movement service dubbed
Take a 10 terabyte transfer using GridFTP as an example. “On a typical network it takes about two days,” said

December 16, 2009

Feature - GRAPPAling with evolutionary history

This figure illustrates how gene order changes among the eight species. Each thin line represents a single gene and its position in the different species. Most genes are conserved on the same chromosomal arm or Muller element, but gene order is shuffled between species. This figure appeared in the July 2008 issue of Genetics. Image courtesy of Arjun Bhutkar, Stephen Schaeffer et. al., with permission from The Genetics Society of America.

We’ve known for several years now that chimpanzees share 96 percent of our DNA. Our technology tells us how closely humans and chimps are related. But it doesn’t tell us how we’re related. We need new technology for that.
Enter GRAPPA – or Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms if you want a mouthful. GRAPPA has already been used to analyze the evolution of organelles such as chloroplasts and mitochondria, running on cluster computers with

December 9, 2009

Case study: The GeoChronos web portal

Surface reflectance and ocean temperature, an example of Earth observation science. Image courtesy of Jacques Descloitres, MODIS Land Rapid Response Team, NASA/GSFC.

When GeoChronos launches, it will serve up a buffet of scientific and social networking ingredients that together empower Earth observation scientists to collaborate and make new discoveries.
The GeoChronos recipe didn't come out right the first time, however. The path the GeoChronos team has followed provides valuable insight into the process of creating a scientific web portal.
“The idea is that scientists can come to a portal where they process and share their data without having to worry about the overall technical details of how that’s being done,” said Cameron Kiddle, a research fellow for the Grid Research Centre at the University of Calgary in Alberta, Canada.
Social networking features and collaborative tools are a must for the project, and so the first GeoC

December 9, 2009

Feature - Observing oceans online Overview map of the NEPTUNE Canada observatory off the west coast of Vancouver Island, British Columbia. The network, which extends across the Juan de Fuca plate, will gather live data from a rich constellation of instruments deployed in a broad spectrum of undersea environments. This system will provide free Internet access to an immense wealth of data, both live and archived throughout the life of this planned 25-year project. Image courtesy NEPTUNE Canada. Although the Earth is mostly water, scientists know relatively little about the ocean floor. But with the creation of ocean observatories such as NEPTUNE Canada, all that could change. Until recently, scientists had to use cruise ships, satellites, and temporary probes to study the world’s oceans. This allowed them to take occasional snapshots of the ocean for later study. Ocean observatories are made up of more permanent installations of instruments directly on the ocean floor, along the co