Neugrid
neuGRID is a project that is financed by the European Union in the 7th Framework Program. Its purpose is to develop a digital infrastructure for scientific research. This infrastructure is based on grid computing , has a user-friendly interface and is intended to enable European neuroscientists to advance research in the field of neurodegenerative diseases. The neuGRID project allows the collection and archiving of a considerable amount of data from imaging processes and also allows sophisticated computer analyzes through distributed computing .
description
The aim of the project is to share two existing digital infrastructures that have previously been developed to allow European scientists to advance in their studies of neurodegenerative diseases such as Alzheimer's disease .
Computer analysis of three-dimensional magnetic resonance spectroscopy and a series of distributed services will make it possible to identify markers of neurodegenerative diseases. Thanks to the flexibility of the technological infrastructure, the functionality of neuGRID can also be expanded for other medical applications in the future.
- At the highest level, the user interface services strive to meet the requirements of the application domains (calculation of the cortical thickness). These services are generally kept to be used in the future.
- At the lowest level, the grid interface services consist of software components that are already available. They can be recognized through the grid and supply the interface with the assigned grid computing software ( EGEE / gLite). These interface services map the files that are present and available in the system in a common hierarchy to which other centers can have access, and thus supply the virtual access system to files.
- Between these two levels there is a series of general services; among them the database language or the storage and movement of images.
Network activities ( Networking Activities )
The so-called network activities include various aspects of distributed resource coordination . An external supervisory body (Advisory Board) checks the timely compliance of the scientific core of the project. This area also includes the following activities: the development of ethical standards and data protection protocols (in accordance with the emerging standards for health care networks), the establishment of a database of medical images which form the basis for tests for the validation, performance and availability of the System and the organization for the purpose of providing training for users. An intensive activity in the announcement to users, politicians and responsible persons, combined with harmonization and coordination actions with technically and clinically coupled projects, guarantee an essential communication with the outside world.
Data protection and security in the neuGRID
Data protection and security play a very important role in the neuGRID project in the following contexts:
- Context A .: Images and clinical data are only collected by specially authorized subjects who have authorized access to the neuGRID network.
- Context B.1: Images and clinical data that were previously collected in various other projects are stored in the neuGRIID.
- Context B.2: Images and clinical data that were previously collected in various other projects are analyzed in neuGRID but not saved.
International cooperation
neuGRID works together with:
- CBRAIN - CBRAIN is a Canadian network and consists of five research centers that are pioneers in cerebral images. These research centers are connected to each other with a service-oriented architecture for the systematization of the distributed processes and the cataloging of the information of cerebral images. As with neuGRID, CBRAIN LORIS is used for archiving and data communication together with CIVET (pipeline for extracting the cortical thickness) as a test of the user software. LORIS was developed in the neuroImaging Laboratory (ACE) of the McConnel Brain Imaging Center at the Montreal Neurological Institute (MNI), thanks to support from the National Health Institute (NIH). CBRAIN uses the high effectiveness of the national Canadian digital network. A consortium of seven regional centers representing 61 institutions is linked by CANARIE to support HPC distributed applications (computecanada.org) The researcher in charge is Alan Evans from the Montreal Neurological Institute at McGill University.
- LONI - Laboratory of neuroImaging. LONI is an extensive research infrastructure of UCLA (University of California, Los Angeles) with the world's largest database for neuroimaging studies in the field of neurodegenerative diseases (ADNI initiative for the study and research of Alzheimer's disease in the USA, Japan and Australia (ADNis) with 12,000 studies on the brain). With LONI's workflow management application, neuroscientists can easily create new pipelines and have access to a wide range of algorithms that calculate the morphological and functional analysis of the brain. The scientist in charge is Arthur Toga.
- AddNeuroMed - AddNeuroMed consists of a perspective and multicenter study of Alzheimer's disease. The study involved examining 900 people as role models and collected 2500 cerebral images. This study is fully compatible with the ADNI images. The scientist in charge is Simon Lovestone from the Psychiatric Institute at King's College London, UK.
Service activities ( Service Activities )
The distributed services are based on the experience and professionalism acquired during the development of existing digital infrastructures. These structures were individually developed for the research of neurodegenerative diseases and can offer intensive calculations as well as the administration of data performance to the respective communities. These infrastructures also offer "general" services which facilitate and optimize the use of the infrastructure. Neugrid emerges from the union of these structures as a network platform that offers users a wide variety of services. The activities in the center of this area include the development and maintenance of medical services and of specific services for the images and for the network.
The infrastructure
- Level 0 - provides the basic infrastructure services, from the management of the Grid information system to the management of the database neuGRID.
- Level 1 - encompasses one's own and true computer science resources and grants neuroscientists access during data acquisition, pipeline specification and experimentation with new possible markers for neurodegenerative diseases.
Joint research activities ( Joint Research Activities )
In the area of joint research activities , the project foresees:
- The determination of the user's requirements for creating a space for collaborative activities.
- The planning and implementation of their integration on a technical level.
- Conducting extensive validation tests.
neuGRID must function transparently for the user at the interface in order to achieve identical results in comparison to the systems of the "demonstration" centers, but without their computer speed or potential restrictions on storage capacity. The work plan provides:
- Identification of requirements, technical assessment, planning and implementation;
- Evaluation of performance;
- Validation.
The activities are divided into the analysis of the requirements of the user and the system, network capability of the algorithms and the pipeline, integration of the prototype and validation.
User example
A researcher interacts with neuGRID to analyze a group of images with the selected algorithm. As soon as the calculations have been processed in the network, the data output is compared with the data input in order to determine the process result.
User
neuGRID addresses the following user communities:
- Neuroscientists working in the field of Alzheimer's disease. These will have an extensive database with clinical variables and neuro-images combined with an interface for managing the algorithms.
- Algorithmic researchers can rely on a powerful test database with the possibility of reaching a large community of neuroscientists who are potential users of their products.
- Pharmaceutical industry can test disease markers as a surrogate indicator in clinical trials for drugs for neurodegenerative diseases.
Awards and recognitions
The presentation by neuGRID was recognized as “Best Live Demonstration” at the EGEE'09 (Enabling Grid for E-science) conference in Barcelona (Spain). This success was repeated at the EGEE'10 conference in Uppsala (Sweden).
Individual evidence
- ↑ glite.web.cern.ch
- ↑ cbrain.mcgill.ca
- ↑ LONI. ( Memento from April 3, 2013 in the web archive archive.today )
- ↑ EGEE'09 Conference in Barcelona. ( Memento of July 8, 2012 in the web archive archive.today ) at: egee09.eu-egee.org
- ↑ 5th EGEE User Forum. ( Memento from July 11, 2012 in the web archive archive.today ) at: egee-uf5.eu-egee.org