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 to make a significant impact in a relatively short time. Partly this impact has been technological, thanks to increased sharing of data storage and processing power between participating institutions in the region. This has happened through a concerted effort by the project to encourage adoption of EGEE’s gLite middleware in the region.

As Marco Paganoni, who heads EUAsiaGrid and is based at INFN and University of Milan-Bicocca, points out, “this technological push has enabled researchers in some of the participating countries to become involved in international science initiatives like CERN’s LHC, that they otherwise might not be able to afford to participate in.”

Fifth graders tour Asia as they find landmarks on the map and on the globe. Image courtesy Karen Mabry, Flickr

Building links

The project has had many regional research benefits, too. “We realized that identifying and addressing local needs was the key to success in this region,” says Paganoni.

From the outset, capturing local e-Science requirements was an important component of the project’s objectives. And comparing those requirements revealed a great deal of common ground amidst all the regional diversity.

The region’s propensity to natural disaster, and the ability of grid technology and related IT solutions to help mitigate the consequences of such disasters, was one common theme.

For example, EUAsiaGrid researchers have helped to build links between different national sensor networks, such as those of Vietnam and Indonesia. Researchers in the Philippines are now benefitting from grid-based seismic modeling experience of partners in Taiwan. Sharing data and grid know-how like this means that scientists involved can better tune local models of earthquake and tsunami propagation.

Another common thread of the research sponsored by EUAsiaGrid has been searching for cures to diseases that plague the entire region, such as dengue fever. A series of in-silico drug design challenges, achieved by pooling regional as well as European grid resources, have been a highly visible outcome of the project.

But it is not just hard sciences like geology and biology that benefit from grid know-how. Indeed as Paganoni notes, “modeling the social and economic impacts of major disasters and diseases is a grid computing challenge in itself, and is often top of the agenda when EUAsiaGrid researchers have discussions with government representatives in the region.”

An important legacy of the EUAsiaGrid project, reckons Paganoni, will be the links it has helped establish between researchers in the natural sciences and the social sciences, both within the region and with European institutions. These links trace their origin to a common interest in exploiting grid technology.

—François Grey, for EUAsia Grid

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 that for a long time, scientists believed that they might be massless.

Since then, we’ve learned a lot about these elusive particles. We know that there are three types of neutrinos – the electron neutrino is the smallest, the tau neutrino the largest, with the muon neutrino caught in the middle.

We also know that when no one’s looking, neutrinos go ‘fuzzy.’ Just as Schrodinger’s cat is both dead and alive while it is still sealed in its box, an unobserved neutrino is all three types of neutrinos at the same time. As an example, imagine that a scientist has just measured a subset of a neutrino beam, and found that it is 99 percent muon neutrinos, with one percent electron neutrinos. In between measurements, the neutrino beam reverts to a fuzzy state, where it is all three types of neutrinos at once. According to one theory, when the scientist measures the beam again in order to bring it back into focus, the scientist may find that the ratio of neutrino types has changed to include more electron neutrinos.

The likelihood that a scientist will see a particular type of neutrino changes periodically over time, oscillating like the rise and fall of a merry-go-round. Three different constant angles determine the rate at which those probabilities oscillate. Scientists have already seen muon and tau neutrino oscillation, and measured two of the three angles. The third angle, theta13, is much tricker to measure, however, because it is very small. And that’s where the Tokai-to-Kamioka (T2K) experiment in Japan comes into the picture.

A schematic of a neutrino's journey from the neutrino beamline at J-PARC, through the near detectors (yellow dot) which are used to determine the properties of the neutrino beam, and then 295 km underneath Japan to Super-Kamiokande. Image courtesy of T2K.

Measuring the unknown

At the Japan Proton Accelerator Research Complex in Tokai, protons are accelerated to extraordinarily high speeds before striking a fixed target. The collision with the target produces positively charged pi mesons, or pions for short.

The pions don’t last for long before they decay, but while they do, magnets direct them into a beam pointing westward, towards the Super-Kamiokande detector in Kamioka, 295 km away.

When the pions do decay, 99.9877 percent of them decay into a muon and a muon neutrino. These are recorded by the Near Detector in Tokai for later comparison with the neutrinos observed at Super-Kamiokande. By measuring the change in the percentage of electron neutrinos, scientists will be able to calculate the value of theta13, confirming that the electron neutrino percentage oscillates.

Because neutrinos rarely interact with other particles, they don’t need a tunnel to travel through the ground to Kamioka. But by the same token, they cannot be shaped into a straight beam. The neutrinos spread out, much like the light from a flashlight. By the time they get to Kamioka, the beam is spread thin, so that only a fraction actually reach the Super-Kamiokande detector. And, since neutrinos rarely interact with other particles, only a fraction of those will be detected at Super-Kamiokande.

A cutaway drawing of the Super-Kamiokande Detector. The detector is a 40 meter diameter by 40 meter high cylinder filled with ultrapure water and surrounded by more than 10,000 50 centimeter phototubes, each sensitive enough to see a single photon. Image courtesy of Super-Kamiokande.

Scintillating at Super-Kamiokande

Super-Kamiokande is, in essence, a giant cylindrical tank filled with 50,000 tons of pure water located 1,000 meters underground. The inside walls of the tank are covered with photomultiplier tubes, which detect any sparks of light that occur inside the tank.

The lepton is ejected, traveling at extremely high speeds. Although it does not travel as quickly as light does in a vacuum, it does travel faster than light does in water, creating Cerenkov radiation – the visual equivalent of a sonic boom. The photomultiplier tubes detect the scintillating light of the Cerenkov radiation, and in so doing, they indirectly detect the neutrino.

In the control room at Super-Kamiokande, physicists monitor the experiment around the clock, watching for potential events.

“It is set up in such a way that if a candidate event arrives, it notifies that there is a candidate event,” explained Chang Kee Jung, US spokesperson for T2K. “So in some ways it is in real time that it is detected, but it is analyzed a couple of days later.”

Super-Kamiokande events are analyzed on site in Kamioka using local computational resources. But to answer the question of how rapidly neutrinos change from muon neutrinos into electron neutrinos, they need a basis for comparison.

Drawing comparisons

Back in Tokai, the Near Detector recorded a great deal of information on the outgoing muon neutrinos. That data is transmitted to a computer cluster at KEK in Tsukuba, Japan.

“A lot of processing will be done at KEK,” said Ian Taylor, a researcher with the US T2K collaboration. “The file output from that will be distributed to the Tier 1 and Tier 2 sites.”

Taylor and Jung caution not to confuse their tier system with the more familiar LHC Computing Grid (LCG) system. Within T2K, Tier 1 sites are distinguished by the fact that they have complete copies of the raw data, the reconstructions, and even the calibrations data. Tier 2 sites will not have the calibration data, and Tier 3 sites will have to download data as needed.

The North American Tier 1 site is located at TRIUMF, a subatomic physics laboratory in Vancouver, Canada. In Europe, the Tier 1 site is located at the Rutherford Appleton Laboratory in Didcot, UK.

“The different countries have taken different approaches,” Taylor said. “It’s a lot of work to set up our software on the grid, and for the amount of monte carlos we need to do, it's just not worthwhile” for the US collaboration.

The Europeans have chosen a different approach, however. The multinational T2K collaboration is already using a global EGEE virtual organization, t2k.org, to authenticate and distribute data.

“Collaborators all over the globe are accessing this data using LCG grid tools and processing small amounts locally,” said Ben Still, a researcher with the UK T2k collaboration. In other words, at the moment, the grid is being used to distribute data, but not to process it.

In the UK, there are plans for that to change. “I am developing scripts for running over data and producing monte carlo simulation data,” Still said. “We hope to be up and running on the Grid in time for the next physics data taking beam runs.”

—Miriam Boon, iSGTW

Close-up of the Aedis aegypti mosquito that carries dengue. Image courtesy

First, you get a bad headache. Then your joints feel like they are being crushed. This is followed by fever and a bright red rash on your legs and chest. You may also start vomiting or have diarrhea. This is dengue fever, and it affects two-fifths of the planet’s population. Thanks to the EUAsiaGrid project, grid technology is doing its part to help reduce the burden of this devastating disease.

For most, dengue fever passes after a very unpleasant week, but for some it leads to dengue haemorrhagic fever, which is often fatal. Like malaria, dengue is borne by mosquitoes. Unlike malaria, though, it affects people in cities as much as in the countryside. As a result, it has a particularly high incidence in heavily populated parts of South–East Asia, where it is a significant source of infant mortality in several countries.

As yet, there are no drugs that specifically tackle the dengue virus. So the goal of an initiative called Dengue Fever Drug Discovery, launched last July, was to start a systematic search for such drugs, by harnessing grid computing to model how huge databases of chemical compounds would interact with key sites on the dengue virus, potentially knocking it out of action.

This is not the first time that grid technology has been used to amplify the computing power that can be harnessed for such ambitious challenges: malaria and avian flu have been targets of previous massive search efforts, dubbed by experts “in-silico high-throughput screening.”

Leading the effort for dengue at Academia Sinica in Taipei is researcher Ying-Ta Wu, of the Genomics Research Center. He and his colleagues prepared some 300,000 virtual compounds to be tested in a couple of months, using the equivalent of over 12 years of the processing power of a single PC.

Map showing prevalence of dengue around the world, and the mosquito associated with it. Image courtesy

Benefits of research

The goal of this exercise, though, was not just to get the processing done quickly. It was also about encouraging partners in Asia to collaborate on sharing the necessary hardware.

These included Universiti Putra Malaysia and the MIMOS Berhad Institute in Malaysia, the Institute of Applied Mathematics and Informatics in Vietnam and the Hydro and Agro Informatics Institute of Thailand, as well as CESNET, an academic network operator in the Czech Republic.

The successful collaboration is a testament to efforts by the EUAsiaGrid project, led by Academia Sinica Grid Computing in Asia and INFN in Italy, to attract new partners in South-East Asia to grid computing, and to train them in how to deploy and run the necessary middleware in their own institutes. In this case, the GAP-based Virtual Screen Service (GVSS) was used — an application package that combines the EGEE gLite middleware with a drug docking simulation package called Autodock.

“We will have to wait a while to judge the final result of this effort,” says Ying-Ta Wu. Indeed, after sorting out the most promising drug candidates, researchers must now begin the arduous task of testing these drugs on real viruses. And even if successful candidates are found, there is still a long way to a product that can be safely administered to people suffering from dengue.

But at least, thanks to grid computing, an important first step has been taken down that road.

—François Grey, for EUAsia Grid

Gridcast bloggers take you live, behind the scenes at ISGC 2010. Image courtesy Gridcast

All this week, GridCast, the blog that takes you behind the scenes of some of the most exciting events in grid computing, will be coming to you live from Taipei in Taiwan, where we’re at  ISGC 2010.

This year ISGC (International Symposium on Grid Computing), organized by TWGrid, is focusing on data driven e-Science.

With plenty of use cases and scenarios there’ll be a lot to blog about!

We’ve put together a team of bloggers from around the world to bring you the latest news and views right from Taipei. From blog posts on sessions, to photos of speakers and videos of demos, you’ll feel like your right here with us!

So head on over to the GridCast website to check out what’s going on...

—Manisha Lalloo, GridTalk

Image courtesy GridTalk

It’s hard to get a sense of Asia, but thanks to GridTalk’s GridCast you’re not too far removed from the International Symposium on Grid Computing 2010.

Get some feedback from the conference room floor, hear the word on the street via twitter, see podcasts (available soon).

Held from 5 March to 13 March, the event promises to showcase grid technologies and connect developers, users and newcomers to distributed computing in Asia. Come along and check out the benefits of grid computing for business and research, now and in the future.

Can’t make it? The GridCast team will be there to blog the latest on all that's happening!