Content about Data management

The trivial has become critical when it comes to the role of data transfer in genetic research, argues Brigitte Raumann from the Initiative in Biomedical Informatics at the University of Chicago.

Telescopes are not usually dual-purpose instruments – except for the KM3NeT underwater detector. Occupying a cubic kilometer of the Mediterranean, this device will focus on watching cosmic and underwater events.

New computing tools could save graduate students from thousands of hours spent visually inspecting historical maps, quilts, medieval art, and manuscripts.

Humanities researchers use laborious visual inspection of historical materials to determine authorship and artistic lineage for manuscripts, maps, and quilts. A typical research project could take the time of several graduate students two or more years.

“We are interested in understanding how to support these domain scientists so they are more efficient,” said Peter Bajcsy, principal investigator for the Digging into Image Data to Answer Authorship-Related Questions (DID-ARQ) project at the National Center for Supercomputing Applications. He added, “We are giving them tools that will automate the visual inspection process.”

Those tools are the product of extensive collaboration between humanities researchers and Bajcsy’s team. To create them, the computer experts engaged in lengthy discussions to determine what questions the humanities researchers seek to answer, and exactly how they would answer them using traditional methods. Their inquiries sought out details such as which image features researchers use – consciously or unconsciously – to identify the author or artist. Then the computer scientists developed algorithms that could rapidly identify those features automatically.

Announcement - e-Science Talk is coming to ERIN4Africa, Helsinki, 9-10 December Due to the success of e-Concertation in Geneva this month, e-Science Talk has been invited to become a media partner at the 2010 Euro-Africa Week on ICT Research and e-Infrastructures, to be held in Helsinki, Finland on 7-10  December 7-10, 2010.  We will be blogging live on GridCast from this four-day conference, which is  supported by the European Commission, the African Union Commission and the Finnish government’s ministries for foreign affairs, employment and economy. The agenda is: •    7-8, Dec, 2010 — “3rd Euro-Africa Cooperation Forum on ICT Research” •    9-10, Dec, 2010 — “2010 Euro-Africa e-Infrastructures Conference”  •    10, Dec, 2010 — Lab Visits Registration is free of charge, but pre-registration is required. Registration forms are available at the following l

Announcement - StratusLab releases open source cloud solution for grid

Photo courtesy of OpenNebula.org

StratusLab has released the first open-source cloud solution designed for the grid.
The StratusLab project has released the first version of its cloud computing software, which aims to provide a full cloud solution for grid and cluster computing.
The release is a technology preview (beta test) and not production-ready yet, but it will give system administrators and users a chance to try out the new features of what will become an integrated solution for cloud management and running grid services within clouds.
The software is based on the OpenNebula open-source toolkit for cloud computing management and can be used as an interface for managing cloud sites. It also provides a range of tools and services specifically designed to facilitate integration of cloud and grid technologies. These include automatic configuration of sites and integration with fabric management tools such as the

Feature - LHC open to all

An actual recorded event from the Compact Muon Solenoid experiment—this event shows radiation and charged particles spilling into the detector from the beam colliding with material in the beam pipe.
Image courtesy Carl Lundstedt

Occasionally, iSGTW runs across stories in other publications related to the fields we cover. Below is an excerpt from Linux Journal, containing one person’s view of the whole process.
One of the items at the heart of the Large Hadron Collider (LHC) experiments is open-source software. The following will provide a glimpse into how scientific computing embraces open-source software and its open-source philosophy.
The LHC at CERN near Geneva, Switzerland, is nearly 100 meters underground and produces the highest-energy subatomic particle beams on Earth. The Compact Muon Solenoid experiment is one of the many collider experiments within the LHC. One of its goals is to give physicists a window into the universe fractions

Feature - Rethinking scientific data management

The reading room of the George Peabody Library at Johns Hopkins University.
Image courtesy Leafar / Raphael Labbe, CC 2.0.

Despite all the good that science has wrought over the years, the way we manage scientific data is fundamentally flawed.
Sir Isaac Newton once said, “If I have seen further it is only by standing on the shoulders of giants.” Scientists stand on the shoulders of their peers and predecessors via peer-reviewed literature. The idea is that the literature is reliable by dint of being peer-reviewed, and thus researchers can safely build upon what they learn from it. Yet neither the reviewers who admitted those papers into the annals of scientific canon nor the scientists who wish to build upon it have access to the data used to produce those papers.
That means that they cannot ensure that they stand on solid ground by examining the data and doing their own analysis. They cannot analyze the data using altern

Announcement - ISC Cloud '10, Frankfurt, Germany: 28–29 October 2010

Photo courtesy of ISC

The inaugural  International Science and Cloud conference (ISC 10) will have over 29 international speakers from academia and industry sharing their own ‘hands-on’ experiences of cloud computing with approximately 300 attendants. Wolfgang Gentzsch, the DEISA (Distributed European Infrastructure for Supercomputing Applications) consultant is general-chair of the event.
The conference topics includee:

Cloud Technology
Implementation Experiences
Governance & Security in Cloud
Business Models & Cloud Economics
HPC & Cloud
Cloud Research
And...

Panel on ‘How to start with Cloud Computing’
Debate on Pros and Cons of Clouds

The cost to attend is 325 euros (plus government-required tax) and includes full catering, evening event and the conference proceedings.
More information can be found here.
 

Feature - Astronomical computing
Supporting the Large Synoptic Survey Telescope means thinking big

A visualization of the LSST.
Image credit: Todd Mason, Mason Productions Inc./LSST Corporation

The Large Synoptic Survey Telescope to be constructed in Chile will incorporate the world’s largest digital camera, capable of recording highly detailed data more quickly than any other telescope of comparable resolution.
For the scientists working on the project, that all amounts to an exciting opportunity to learn more about moving objects (including monitoring asteroids near the Earth), transients such as the brief conflagrations of supernovae, dark energy, and the structure of the galaxy.
For computing specialists, it means more data. A lot more data.
The LSST will take between 1000 and 2000 panoramic 3.2 gigapixel images per night, covering its hemisphere of the sky twice weekly. Along with daytime calibration images, this will amount to 20 terabytes of data stored every 2

Feature - HPC adds a spark to EDF’s computing capacities

Image courtesy Zsuzsanna Kilian, stock.exchng

Jean-Yves Berthou is responsible for IT in the research and development area of Electricite de France — a major energy company in Europe. EDF’s 2,000 researchers use computing to work on a number of different projects, including areas such as minimizing CO2 emissions, alternatives to fossil fuels, and ensuring the security of electricity grids. Here, he describes the use and impact of high performance computing (HPC) at the company.
Why do you use HPC?
Berthou: In many cases physical experiments and testing are not possible, for example in the simulation of fuel assemblies and crack propagation in nuclear reactors, or in optimizing electricity production and trading. Even when experimentation is possible, numerical simulation can go beyond what is physically possible. However, experimentation still remains an indispensable tool.
 
In what application

Just what do you think you’re doing, Dave?

Anyone who has seen the movie 2001: A Space Odyssey remembers the phrase “Just what do you think you’re doing, Dave?” While it looks similarly futuristic, ATLAS (above) is the setting for something completely different — the ‘Dave’ dataset. Photo courtesy CERN

What is 45 days old, has visited 22 countries and already has close to 500 children but will outlive them all?
Dave the ATLAS dataset.
Born on the 30th of March, 2010 to his proud parents, the ATLAS detector and the LHC, Dave weighed in at just over 3 Terabytes. Very soon after that, he was sent to the Rutherford Appleton Laboratory (RAL) grid operations center,  and the team there have been tracking his progress through the grid world ever since.Dave is the result of accelerating two beams of protons in the Large Hadron Collider (LHC) and colliding them in the center of the ATLAS detector.
He is a selection of the collisions chosen by

Announcement - e-IRG releases new Roadmap on e-Infrastructure

Image courtesy e-IRG

Since the publication of the previous e-IRG Roadmap in 2007, the e-Infrastructure field has undergone several fundamental changes. Networking, grid, data, high performance and commodity computing services are witnessing major organizational and technical changes. The ongoing expansion of the e Infrastructure user communities is also already producing new and updated requirements for the common e Infrastructure.
To help deal with this, the e-Infrastructure Reflection Group — an inter-governmental policy body comprising national delegates from more than 30 European countries — has released the e-IRG Roadmap for e-Infrastructures, (Publications/Roadmap).
Rather than looking at these changes independently, the Roadmap analyzes their impact from the points of view of users, service providers and the society as a whole. Ultimately, the document makes several recommendations aimed at max