Grid-Based Computing Project Devised to Fight Neurologic Disease

Grid computing, long utilized by astronomers and physicists to gather masses of data rapidly and effectively, is moving into the world of biomedicine. Supported by European Union (EU)-funding, researchers have networked hundreds of computers to help find treatments for neurologic diseases such as Alzheimer’s disease (AD).

The scientists have named their system the “Google” for brain imaging. Through the Neugrid project, the pan-European grid-computing infrastructure has created up new avenues of research into degenerative neurologic disorders and other illnesses, while also having the potential for quicker and more effective clinical diagnoses of individual patients.

The infrastructure, initiated with the support of EUR 2.8 million in funding from the European Commission, was developed over three years by researchers in seven countries. Their objective, principally, was to give neuroscientists the ability to analyze quickly and efficiently magnetic resonance imaging (MRI) scans of the brains of patients suffering from Alzheimer’s disease. However, their work has also helped open the door to the use of grid computing for research into other neurological disorders, and many other areas of medicine.

“Neugrid was launched to address a very real need. Neurology departments in most hospitals do not have quick and easy access to advanced MRI analysis resources. They would have to send researchers to other labs every time they needed to process a scan. So we thought, why not bring the resources to the researchers, rather than sending the researchers to the resources,” explained Dr. Giovanni Frisoni, a neurologist and the deputy scientific director of IRCCS Fatebenefratelli (Brescia), the Italian National Center for Alzheimer's and Mental Diseases, in Brescia.

Five years’ research in two weeks, the Neugrid team, led by Dr. David Manset from MaatG (Archamps, France) and Dr. Richard McClatchey, from the University of the West of England (Bristol, UK), provided the foundations for the grid infrastructure, starting with five distributed nodes of 100 core central processing units (CPUs) each, interconnected with grid middleware and accessible via the internet with an easy-to-use web browser interface. To assess the infrastructure, the team used datasets of images from the Alzheimer’s Disease Neuroimaging Initiative in the United States, the largest public database of MRI scans of patients with AD and a lesser condition termed mild cognitive impairment.

“In Neugrid we have been able to complete the largest computational challenge ever attempted in neuroscience: we extracted 6,500 MRI scans of patients with different degrees of cognitive impairment and analyzed them in two weeks,” Dr. Frisoni, the lead researcher on the project, said, “on an ordinary computer it would have taken five years.”

The analysis of MRI scans conducted as part of the Neugrid project should help researchers gain significant clues into some of the big mysteries surrounding the disease such as which areas of the brain deteriorate first, what changes occur in the brain that can be identified as biomarkers for the disease and what sort of drugs might work to suppress or prevent progression.

Neugrid built on research conducted by two earlier EU-funded projects: Mammogrid, which set up a grid infrastructure to analyze mammography data, and AddNeuroMed, which sought biomarkers for Alzheimer's. The investigators are now continuing their work in a series of follow-up projects. An expanded grid and a new paradigm Neugrid for You (N4U), a direct continuation of Neugrid, will build upon the grid infrastructure, integrating it with high performance computing (HPC) and cloud computing resources. Using EUR 3.5 million in European Commission funding, it will also expand the user services, algorithm pipelines, and datasets to establish a virtual laboratory for neuroscientists.

“In Neugrid we built the grid infrastructure, addressing technical challenges such as the interoperability of core computing resources, and ensuring the scalability of the architecture. In N4U we will focus on the user-facing side of the infrastructure, particularly the services and tools available to researchers,” Dr. Frisoni noted. “We want to try to make using the infrastructure for research as simple and easy as possible, learning curve should not be much more difficult than learning to use an iPhone.”

N4U will also expand the grid infrastructure from the initial five computing clusters through connections with CPU nodes at new sites, including 2,500 CPUs recently added in Paris in collaboration with the French Alternative Energies and Atomic Energy Commission (CEA) and in partnership with Enabling Grids for E-science (EGEE) Biomed VO, a biomedical virtual organization.

The project’s findings were published in April 2012, in CORDIS Features, formerly called ICT Results.

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IRCCS Fatebenefratelli
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University of the West of England