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Feature - Ecological forecasting in NEON

TOP: NEON's proto-tower just north of Boulder, Colorado, where the project is testing equipment. The site is already producing a real-data stream.
BOTTOM: Hongyan Luo conducts tests at the base of NEON's test proto-tower.
Images courtesy of NEON, Inc.

Massive independent networks of environmental and ecological data stations distributed across the globe could launch environmental science into the petascale era, transforming the way scientists look at our planet.
In the United States, the National Ecological Observatory Network is poised to begin construction later this year.
“What NEON is about is measuring the effects of climate change, land use change, and invasive species on continental scale ecology. And we’re doing that in order to enable ecological forecasting,” said Michael Keller, the chief of science at NEON.
Ecological forecasting, like weather forecasting, uses extensive data sets over large areas and pe

Feature - Q&A: Grid Colombia warms up

A group photo at an Open Science Grid-sponsored Grid Colombia workshop, which took place in October 2009. Image courtesy of Open Science Grid.

With a little help from colleagues at Open Science Grid and EGEE (via EELA-2), Colombia is on the cusp of launching its first national grid infrastructure. iSGTW caught up with Jose Caballero to learn more about the present and future of this promising project. Caballero currently does software development for ATLAS, and serves as the OSG liaison to South America. Previously, he spent five years working with the gLite grid software for the CMS experiment.
iSGTW: How did Grid Colombia get started?
Caballero: EELA-2 (E-science grid facility for Europe and Latin America) chose Colombia to host one of its main conferences in 2008, and that brought the worldwide grid movement to the attention of both academia and government in Colombia. After that, universities started to study the creation of a national

Feature - OSG All Hands Meeting

Attendees visited vendor tables to network and watch demonstrations at the first ever vendor and e-demonstration session to run at an OSG All Hands Meeting.
Image by Miriam Boon.

Last week, 183 researchers and vendors gathered at Fermilab in Batavia, Illinois for the Open Science Grid’s annual All Hands Meeting.
In addition to hosting workshops for CMS and ATLAS computing meetings, sessions covered a variety of topics, including security, virtualization, cloud computing, biology applications, reports from European colleagues, and the future of US cyberinfrastructure. This year also marked the first vendor and e-demonstration session.
Several people expressed pleasure at the dynamic discussions that occurred during the panel-style sessions, said Paul Avery, a researcher at the University of Florida and co-chair of the OSG Consortium Council. Kent Blackburn, Avery’s fellow co-chair and a researcher with LIGO Caltech, suggested that the inc

Feature - A neutrino's journey: From accelerator to analysis

The first T2K event seen in Super-Kamiokande. Each dot is a photo multiplier tube which has detected light. The two circles of hits indicate that a neutrino has probably produced a particle called a π 0, perfectly in time with the arrival of a pulse of neutrinos from J-PARC. Another faint circle surrounds the viewpoint of this image, showing a third particle was created by the neutrino. Image courtesy of T2K.

Neutrinos are the introverts of the particle physics world. They travel through the universe largely unnoticed, except for the very rare interaction. Every day, neutrinos pass through you, and you don’t even notice. Don’t panic – they can’t hurt you, because they don’t interact with your body’s matter.
Neutrinos are neutral – free of charge. That means that electricity and magnetism can’t draw them out and force them to interact. Likewise, they have so little mass tha

Opinion - EUAsia Grid makes a virtue of diversity

Seventeenth-century Dutch map of Asia. Image courtesy Flickr

EUAsiaGrid, a two-year project to promote grid awareness in South-East Asia, is entering its final phase.  Time to take stock of some of the unique aspects of running such a geographically and culturally diverse grid project, and the opportunities it has created for closer scientific collaboration.
More than half the world lives in Asia.
Even putting aside the two titans of India and China, there are some 600 million inhabitants – 100 million more than the entire EU - in the region commonly referred to as South-East Asia, which stretches nearly twice the width of the continental United States from Burma in the West to Indonesia’s Papua province in the East.
Most of the Asian partners in EUAsiaGrid are from areas prone to natural disasters such as earthquakes, volcanoes, typhoons and tsunamis.
Despite the challenging circumstances, EUAsiaGrid has managed

Nice to meet you, authentically

Famed Australian cricket player Neil Harvey (right) shaking hands at the start of the 1950/51 Test series between England and Australia. Image courtesy Wikimedia Commons

We all know that authentication is a must when using grid resources but how much do we really know about it? Jens Jensen from the UK's Science and Technologies Facilities Council Rutherford Appleton Laboratory (STFC RAL) explains, using as a case history his own experience in working as part of that country’s Certificate Authority — one of the largest in the world.
 
If you have ever used the grid, then you know that you “shake hands” with a resource using a certificate — a “digital passport” which identifies you to the resource. In turn, the resource also sends a certificate of its own to you (but which you will most likely see only if something goes wrong).Why authenticate?
When you access any valuable resource, whether it’

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

Q & A: Larry Rudolph talks about pervasive computing, virtualization, and science

Image courtesy of Larry Rudolph.

We’ve all heard about how pervasive computing will change the way we connect and compute in our everyday lives. But what about the way we do science? How is that going to change?
Larry Rudolph joined VMware in 2008 to help start a project on mobile phone virtualization, after five years as part of Project Oxygen: Pervasive Human-Centric Computing at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). Read on to find out what he had to say about pervasive computing, virtualization, and science.
iSGTW: How would you define virtualization or virtual machines?
Rudolph: A virtual machine is a computer made out of software. It is just like a regular computer. It can run programs, and it has a file system, mouse, keyboard, and display. Virtual machines run on physical computers, but it can be easily moved from one physical machine to another an

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

Playstation goes from games to grid

Playstation: more than just fighting aliens on distant planets. (Click to enlarge.) Scene from Halo 3 courtesy of wallpaperez.net

Now, a Sony PlayStation 3 doesn’t just let you pretend to be the Beatles in ‘Rock Band’ or fight in alien ring-worlds in ‘Halo.’
The PS3 is the latest piece of hardware to get on the grid. A mini-cluster of PS3s in Ireland is running software which can screen for new and potentially life-saving drugs.  
Eamonn Kenny, portability coordinator for the Enabling Grids for E-sciencE project, and Peter Lavin, a grad student at Trinity College Dublin, have ported the EGEE-supported gLite middleware, specifically the worker node software (performing the majority of the computational work on the Grid) to eight connected PlayStation 3’s.
gLite, the middleware which connects 13,000 researchers world-wide to the computing resources of the EGEE grid, is mostly run from multi-core processors

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