Fifth EGEE User Forum to focus on Health e-Grids and Grid technology coming to the iPhone and Sony PlayStation 3

Uppsala 14 April 2010Enabling Grids for E-sciencE (EGEE) is the world's largest multi-disciplinary computing Grid, supporting the research of thousands of scientists and bringing together to the processing power of hundreds of thousands of computers worldwide. The Grid and the software that glues it all together, known as middleware, is designed to run on a widely diverse range of computers. Cancer, heart and circulatory system diseases cause two thirds of all deaths in Europe. Three research projects at the Enabling Grids for E-sciencE (EGEE) User Forum in Uppsala, Sweden, have demonstrated ways in which modern computing techniques can investigate today's biggest killers. In addition, a team from Ireland has adapted the Grid software gLite to run on the Play Station 3. An Italian group has been able to use the iPhone to access Grid-enabled digital repositories.

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As it becomes increasingly sophisticated, the field of medicine is grappling with unprecedented data demands. EGEE, providers of the world's largest multi-disciplinary computing Grid, help scientists from all fields manage their work quickly and efficiently, with medical researchers and doctors increasingly joining their ranks. Grid computing can connect doctors and researchers to both computing power and remote databases of medical information. It has the added benefit of an inbuilt secured system preventing unauthorised access to any sensitive patient information.

The HeMoLab project is interested in the heart as well as the system that it is connected to. They are working on developing models, techniques and tools for simulating the entire cardiovascular system. The first accurate description of how the heart pumps blood around the body was published by the Arabic physician Ibn al-Nafis in 1242. Since then our knowledge of the way our heart works has expanded to fill volumes. The main motivation for this project is the deeper understanding about the complex physiological interactions in the human body and their role in the onset and progress of several cardiovascular diseases. Moreover, with this study it is also possible to provide relevant information so as to use it as complementary data for medical training, diagnosis and eventually surgical planning.

The simulation of a single heart beat can take up to 20 days in a single computer depending on the degree of approximation considered for problem. Using the Grid computing infrastructure offered by the EELA-2 project it is now possible to perform the execution of multiple simulations at the same time. Paulo Ziemer from the HeMoLab team worked on getting the application up and running on the Grid. "Porting the application was a great experience, that certainly helped us a lot to understand how Grid computing could help the simulation of models that demand high computing power. Further tests need to be made yet, but I think the first step was accomplished successfully."

In Europe cancer is responsible for 1 in 4 deaths and is the single greatest killer of people aged 45-64. Again early diagnosis is the best way of helping people with the disease. However doctors frequently face problems in accessing the abundance of data that is constantly generated by labs, hospitals, doctors and health authorities.

Another project, Sentinel, centred in France, brings together many areas of cancer research: screening structures, medical laboratories and both regional and national public health authorities. It aims to enable secured medical data exchanges between cancer screening organisations and cancer analysis laboratories. Grid technology - which easily connects data sources and provides a secure framework - is particularly well suited for this situation, where patient data must only be available to authenticated and authorised users.

Starting in 2009, Sentinel's first objective was to offer access to electronic pathology reports for cancer screening. Since then, Sentinel has been expanded to allow the French national health organisation access to the medical data in order to produce statistics on cancer within the Auvergne region. Recently the team has added a module to allow health professionals to use their smartcards to gain access to the data and are hoping to expand the system nationwide.

Improving the speed of diagnosis and finding areas to focus on in order to treat an illness is essential in tackling cancer and heart disease. All of these projects demonstrate where medical research is going in their use of computers. EGEE has worked for the last 6 years to provide the tools to create a platform for the medical profession and Sentinel, HeMoLab and Gwendia have proven not only its usefulness but also its flexibility.

Since 2007 researchers from Trinity College Dublin (TCD) and the Royal College of Surgeons Ireland (RCSI) have been collaborating on the computing challenge inherent in drug discovery, and so when in the latter half of 2008 Symbiosis Ltd. introduced a PS3 port of their eHITS drug discovery, the TCD team began in early 2009 to look into adapting, or porting EGEE's Grid middleware, gLite, to the PS3 platform. Since then their PS3 cluster has grown to 16 machines, which they can use to investigate the interactions between possible drug candidates and the diseases they are trying to treat. What makes this possible are the seven Synergistic Processing Elements (SPEs) that give the machine its computational power at relatively low cost. These elements are designed especially to support the complex 3D vector calculations that enable graphic intensive gaming - but also happen to be ideally suited to the team's drug discovery work.

Eamonn Kenny who is on the TCD team was delighted with how well received the work has been by EGEE: "EGEE represents a major platform for European science, and its impetus toward multi-platform support is extremely helpful."

While the EGEE computing Grid is known for supplying huge amounts of processing power, it also provides a framework that allows databases and other information sources to be interlinked easily. Teams looking to create global digital repositories can use the Grid to give access to their resources to research communities from all over the world. With both smart phones and high speed 3G networks moving rapidly into the mainstream a group of researchers from INFN Catania and University of Catania in Sicily saw an opportunity for an application to allow people access to digital repositories wherever and whenever they want.

Using gLibrary, which is based on the gLite middleware, an organisation can organise, populate, browse, search and access libraries of digital objects that have been stored on a distributed Grid system. Accessing these resources from a user's home machine is quite straightforward but more problematic if the researcher is travelling. This is where smartphones and multi-media devices such as the iPhone and the upcoming iPad show their strengths. Devices of this type are designed for accessing information while on the move but can also handle different types of data, such as videos, audio files, images, documents, spreadsheets and many more.

Using the Catania team's application, a user can browse the digital libraries stored on the Grid from their iPhone, query and inspect all the objects' metadata and simply tap the screen to download a copy from the closest storage element. They can choose the closest source either by selecting a location from a list or by using the built-in GPS to calculate their current position. During the EGEE User Forum event, the browsing of digital repositories of ancient manuscripts (cultural heritage) and satellite data (earth science) created with gLibrary has been demonstrated.

Both of these projects use commercially available platforms to run or interface with EGEE's software. This demonstrates the flexibility and portability of EGEE's software as well as one of the real world applications for distributed 24/7 access to the digital repositories made possible by EGEE.

The resources currently co-ordinated by EGEE will be managed through the European Grid Infrastructure (EGI) from May 2010. In EGI each country's Grid infrastructure will be run by National Grid Initiatives. The adoption of this model will enable the next leap forward in research infrastructures to support collaborative scientific discoveries. EGI will ensure abundant, high-quality computing support for the European and global research community for many years to come. For more information you can visit the European Grid Infrastructure website.


Source: Enabling Grids for E-sciencE - EGEE

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