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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

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 (EGI.eu), 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

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-

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

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

Feature - Doing science on the hub

Michael McLennan demonstrates a visualization tool hosted on nanoHUB.org 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

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

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 LDAustinArt.com

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

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

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

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 Globus.org.
Take a 10 terabyte transfer using GridFTP as an example. “On a typical network it takes about two days,” said

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