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Feature - Jamie Shiers on the STEP'09 postmortem

Image courtesy Jamie Shiers 

Recently, CERN conducted the STEP’09 test, a full- scale assessment of all the computing resources which will be used to process experiment data from the Large Hadron Collider. Those computing resources include sites all over the world which are organized into different levels, or “tiers.”
Jamie Shiers leads the grid support group in the IT department at CERN, and is responsible for the coordination of the worldwide LHC Computing Grid (wLCG) service. He organized the postmortem for STEP’09 at CERN. iSGTW caught up with him to find out how it went.
iSGTW: What is the STEP’09 postmortem?
Shiers: It’s the workshop to review the results from the STEP (Scale Testing for the Experiment Program) test. The big difference between STEP and other tests we’ve done is that it’s supposed to emphasize that we are in full production. It’s a test of readines

Feature – Superlinks to identify genetic culprits

A graphic map of a particularly complex family tree. The squares represent males, while the circles represent females. Individuals affected by a genetic mutation are represented with red squares or circles. Yellow lines indicate a marriage between relatives. Image courtesy of Kwanghyuk (Danny) Lee, Baylor College of Medicine.

Once scientists know which mutation causes a disease, they can apply that knowledge in their search for a cure. Likewise, doctors can recommend lifestyle changes that will alter the course of the disease. But the computer analysis used to identify these mutations would take years to complete on a single computer.
Superlink-online, a distributed system developed at the Technion-Israel Institute of Technology, helps researchers perform their analyses in a matter of days by distributing the computations over thousands of computers worldwide. Geneticists submit their data through the web portal with a single click

Feature - The Lost Sounds Orchestra

An audience experiences “the sonic scenario of the past.” Image courtesy Luca Petrella  

Last September, iSGTW reported upon the return of the epigonion, an ancient Greek wooden stringed instrument resembling a harp. Ancient instruments can be lost because they are too difficult to build, or too difficult to play, but the epigonion was heard again after ASTRA (Ancient instruments Sound/Timbre Reconstruction Application) recreated its sound using grid-enabled computer modeling.
More ancient instruments are to be heard soon, after the organization’s official Lost Sounds Orchestra finishes its preparations for a unique performance towards the end of summer.
Having successfully reconstructed the sound of the epigonion, ASTRA is working on a whole host of other lost instruments including the barbiton (an ancient base guitar), the syrinx (a pan flute), an ancient lower Mediterranean frame drum, the salpinx (a kind of ancien

Feature - Recovery Act funds speed up high-speed ethernet

Photo courtesy of Phil Edon, stock.xchng.

ESnet will build the world’s fastest supercomputing network and test subnetwork for future technology using $62 million in American Recovery and Reinvestment Act funds.
ESnet, which is based at Lawrence Berkeley National Laboratory, described their plans for the network in an announcement on the 10 August. Dubbed the Advanced Networking Initiative, it will serve as a pilot for 100 gigabit per second ethernet technology.
“We’re moving to 100 gigabits because the standard today is 10 gigabits, and we already have individual streams of data that are bumping against that limit,” said Steve Cotter, ESnet department head, in a recent interview. “We’d like to have a system out there that can handle more.”
The Initiative will build 100 gigabit connections between the National Energy Research Scientific Computing Center at Lawrence Berkeley National Labo

Feature - Academia Sinica watches global carbon

Chi-Lan Flux Tower is located on one of the long-term ecological research sites in Taiwan, in the northeast part of the island and close to Yuan-Yang Lake nature preserve. At 1400 - 1800 m above sea level, the area of the Chi-Lan Mountain site covers approximately 310 hectares, with a high frequency of fog and cloud year-round. The climate is temperate, heavy and moist, and the trees are mainly Taiwan Cypress. Image courtesy Jia-ying Jiang, Chi-Lan Mountain
Front page: Polarized light reveals the state of the atmosphere thousands of years ago, in a slice of glacial ice containing bubbles of atmospheric gases trapped eons ago. Image courtesy UCAR

With the help of data standards and computing resources, Academia Sinica Grid Computing Center (ASGC) has developed an innovative, grid-enabled approach to tackle carbon flux observation.
The carbon cycle — in which the carbon from the greenhouse gas carbon dioxide (CO2) travels fro

Opinion - New funding for new ideas

Image courtesy owaisk_4u, stock.xchng

A common complaint heard in Europe is that funding for research and development lags far behind that of the United States. In particular, the US public sector spends $50 billion per year in procurement for R&D, which is 20 times higher than in Europe, and accounts for 50% of the investment gap between the US and Europe. Even taking into account large investments in defense, the US expenditure in R&D is still four times higher than that of Europe.One of the engines behind this R&D expenditure in the US is the Small Business Innovation Research (SBIR) program. SBIR, established in 1982, reserves 2.5% of federal funds from the research budgets of 11 different federal agencies for use in encouraging small businesses to maximize their technological potential. These projects comprise feasibility studies and early prototype development — often the riskiest and most expensive stage of a start-up or

Feature – GridFTP accelerates traffic on the World Wide Grid

Image courtesy of the Washington State Department of Transportation.

The standard system for transferring data online can’t handle the data-intensive needs of today’s larger scientific collaborations, resulting in delays and data loss. However, the GridFTP data transfer system is changing all that.
“There is a great need for bulk data movement in almost all areas of science,” said Raj Kettimuthu, technology coordinator of the GridFTP project at Argonne National Laboratory. “Collaborative science experiments have large volumes of data in their repositories, but the data must be distributed among researchers all across the world for analysis. With GridFTP, researchers can move the bulk data quickly and save a lot of time.”
GridFTP, which builds on the widely used File Transfer Protocol, transfers data 20 to 30 times faster than FTP, with speeds of up to 200 megabytes per second. It achieves the speedup by

Feature - A week at CERN

Ilaria (second from left) lunching with the EGEE project office. Image courtesy Ilaria Marchese

In mid-June, the Enabling Grids for E-sciencE project office hosted Ilaria Marchese, a student from the International School of Geneva, on work-experience for a week. Ilaria, who will be 15 in August, shares her thoughts on her week, women in science and research, and life at CERN. What did you think about spending a week in the EGEE project office?
“It was really interesting. I hadn’t heard of the project before, so I was amazed at the reach of EGEE’s work — it’s practically everywhere. It’s in more than 50 countries and helps all types of research. I was also impressed by how much work goes into the project to help people use this service.” What interests you about science?
“Science is fascinating — I love understanding how and why things work. I recently wrote a report on holograms for school . . . they seem

Feature - Common cheap chips get jobs done faster

Although much of today’s most interesting research requires immense amounts of computational power, many scientists don’t have the funds to access expensive supercomputers or clusters. Now, a commonplace computer chip may provide a thrifty way to get those jobs done.
Graphics processing units (GPUs) are found in most computers and are designed to render 3-D computer graphics. They contain hundreds of processing cores on a single chip, and several chips can fit into a single desktop. Computational geneticists Marc Suchard of the University of California Los Angeles and Andrew Rambaut of the University of Edinburgh were able to use GPUs to speed up their computations by a factor of 100.

This tree shows how a population of viruses evolved over a 10-year period within an infected patient. The branch colors reflect relative rates of evolution along each branch.
Courtesy of Marc Suchard of UCLA.

Suchard and Ramba

Feature - Supercomputing promises super-insight into human evolution

Visualization by John L. Moreland.

Humans and chimpanzees are closely related – even closer than mice are to rats. That’s why the slight differences between the two species could provide valuable insight into the origin and evolution of humans.
But it isn’t always easy for researchers to get access to the data they need to see those differences. Researchers at the Center for Academic Research and Training in Anthropogeny are using San Diego Supercomputer Center resources to change that. They are in the process of digitizing an extensive collection of skeletons and medical records from more than two dozen chimpanzees; eventually, the results will be made available to researchers for study.
The specimens and records were donated to CARTA by the Primate Foundation of Arizona, which cares for retired zoo primates and primates whose owners can no longer care for them. Jo Fritz, PFA’s director,

Feature - Conserving bio-diversity at Peru’s CIP

A few of the many varieties of potatoes. CIP maintains the world’s largest genetic bank of potatoes, including 1500 samples of 100 wild species collected in eight Latin American countries, as well as samples of 3800 traditional Andean cultivated potatoes. The collection is maintained under the auspices of the UN’s Food and Agricultural Organization, and is available to plant breeders worldwide free upon request. (Click to enlarge.) Image courtesy International Potato Center

What do the objects at right have in common?
They’re all potatoes.
And their continuing variety will be partly because of the grid.The International Potato Center (known by its Spanish acronym, CIP) seeks to ensure the genetic diversity of this staple food crop. The organization also seeks to reduce poverty and achieve food security on a sustained basis in developing countries through scientific research and related activities —

Profile - Craig Lee, president of Open Grid Forum

Craig Lee
Image courtesy Craig Lee

iSGTW and BELIEF-II (Bringing Europe’s eLectronic Infrastructures to Expanding Frontiers - Phase II) teamed up to find out what the speakers at the 4th BELIEF International Symposium think about the state of e-infrastructures in Latin America. Here, we interview Craig Lee, who is giving a presentation on “Future Trends and e-Infrastructure application: towards sustainable development.”What is your job?I’m serving as president of the Open Grid Forum. In this capacity, my role is not only to be the “public face” of OGF, but more importantly to understand all of our stakeholders’ requirements, and to promote all possible synergies among our current — and new — stakeholders.How is your job related to the development and application of grids and e-infrastructures?Obviously my job is to promote the development and use of all manner of distri