A human grid initiative.
ACGT Advancing Clinico Genomic Trials on cancer
HealthGrid is participating to a European Project called ACGT, taking in charge all the dissemination part.
The Vision
The vision of ACGT is to fight cancer in a defined way. We know already techniques not preventing but curing these diseases like biopsies. Researchers have been inspired by these techniques and have thought of using them in a different way for better results.
All begins with patients who have developed cancers like breast cancer or nephroblastoma (mainly detected on children). The technique of biopsies, which is very used nowadays would be taken before, during and after treatment. The result would be made also anonymously and the analysis stored promptly in an accessible fashion.
In one another perspective, the patient?s data could readily be compared with those from other trials. Therapies could be possible thanks to studies of clinical and personal databases reducing the search in an intelligent way from months to hours. Cancer profiles could then be rapidly identified and the corresponding therapy would be concluded as the best.
- The ACGT project is designed to realise this vision and will focus on this achievement by
- defining common standards of data storage;
- developing new ontologies for cross-referencing terms and their biological contexts;
- implementing a bio-medical Grid infrastructures offering seamless medication services for sharing data and data-processing tools.
Project Description
- Three core activities are organising ACGT workplan:
- INTEGRATION with the creation of advanced databases that combine clinical history; symptoms and signs; laboratory and hispathology; medical imaging; procedural and surgery results; and genetic data, taking into account standard clinical and genomic ontologies.
- KNOWLEDGE GRID with the development of Knowledge Grid infrastructures for the distributed mining and extraction of knowledge from data repositories offering information services in the domain of biomedical informatics and creating a high-performing computational environment: (a) cope with the huge-amount of both clinical and genomic data; and (b) meet the computationally costly data processing needs.
- CLINICAL TRIALS with the design and implementation of specific clinico-genomic trials based on: (a) clear-cut research objectives for cancer-related clinical and genomic inquiries; (b) incorporation of the clinical trials in an integrated GRID environment enriched with knowledge-discovery capabilities; and (c) interpretation of results into standardised clinical guidelines and protocols.
Purposes
As said before, the ACGT project is designed to deliver a new weapon in the fight against cancer. Its main goal is to give a faster diagnosis and sharper information of the optimal treatment for every patient.
ACGT hopes to trigger the emergence of latent clinico-genomic synergies to ensure faster diagnosis and more efficient therapy.
- To that end, ACGT has laid down some goals, which are mainly:
- to present the "next step" in cancer research;
- to target two major diseases (breast cancer and pediatric nephroblastoma);
- to develop a Grid-enabled European infrastructure;
- and for reaching those aims, it is necessary for the project to:
- deliver a month-saving technology in cancer diagnosis, while prescribing early and appropriate therapy to every patient.
- provide the advanced tools needed by biomedical scientific researchers in their daily lab- or clinical work;
- facilitate exchanges and interactions among clinical and genetic researchers to pool their expertise towards identifying the best treatment tailored to every patient;
- allow discoveries in laboratories to be quickly transferred to clinical management and treatment of patients. New technologies such as in silico experimentation, Grid or data and text mining are contributing to reducing periods of time;
- contribute to the scientific development of new biomedical informatics approaches, where Europe is already leading the initiatives in the field, but strengthening the competitive efforts of industry to reach economic success.
Links
For more and complete information, please click on http://eu-acgt.org
EGEE-II Enabling Grids for E-sciencE
The Description
The organisation
- Here are also the main topics that healthgrid's has been working on:
- EGEE brings together experts (such as scientists, researchers or engineers) who bring resources for advances in Grid technology and developing a service of available Grid infrastructure.
- EGEE gathers 90 partners from 32 countries around the world grouped in 13 federations.
- EGEE Grid consists of over 30,000 CPU available to users 24 hours a day, 7 days a week, in addition to about 5 Petabytes (5 million gigabytes) of storage, and maintains 30,000 concurrent jobs on average.
- EGEE is the biggest multi-science infrastructure world-wide with more than 200 sites in 45 countries.
- 100 000 jobs per day are observed as peak usage.
EGEE Community
The Community gathers all the people interested in the project and participating to its evolvement. Tools and means have been put available for the participants to enrich and inform the project.
- For instance, the EGEE portal for Registered Community Members allows the Community Members to have free access to a series of online tools like:
- personalise and update the member profile including the current work or its own organisation;
- showcase the user organisation's experience and expertise in Grid;
- view other member profiles and maybe contact them;
- contribute to the EGEE discussion boards;
- be in relation with the Industry area.
The Vision
Global vision of the project
According to the Project Director, Bob Jones, said:
EGEE is providing a production quality Grid infrastructure spanning more than 30 countries with over 150 sites to a myriad of applications from various scientific domains, including Earth Sciences, High Energy Physics, Bioinformatics and Astrophysics. The first phase of EGEE was conceived during the first two years of the four-year programme. The end use of the EGEE infrastructure depends on the user's needs like large storage capacity, the bandwidth that the infrastructure provides, or the sheer computing power available.
- The EGEE project concentrates on some core areas:
- to continuously improve and maintain the middleware in order to deliver a reliable service to users;
- to attract new users from industry as well as science and ensure they receive the high standard of training and support they need;
- to combine national, regional and thematic Grid efforts, for as seamless Grid infrastructure for scientific research and to build a sustainable Grid for business research and industry.
EGEE-II
The second phase of the project (EGEE-II) started on the 1st April 2006 and has been submitted for underlying the work of the EGEE project.
- Thus, the project:
- will significantly extend and consolidate this infrastructure by linking national, regional and thematic Grid efforts;
- will interoperate with other Grids around the Globe;
- will expand the portfolio of supported applications to include Fusion as well as other disciples, because communities use the EGEE infrastructure as an every-day tool for their work.
Purposes
EGEE-II will be able to further develop its infrastructure into a truly pervasive global platform for e-Science.
- The EGEE-II Project is organised into ten "activities", which come under three main areas:
- Networking Activities (NA) are the management and coordination of all the communication aspects of the project;(Overall management, Dissemination, Training and Induction, Application Identification, Policy and International Cooperation)
- Service Activities (SA) are the support, operation and management of the Grid as well as the provision of network resources; (European Grid Support, Networking suppport, Integration, testing and certification);
- Research Activities (JRA) concentrate on Grid research and development; (Middleware Re-engineering, Quality Assurance).
These three main areas have been responding to the advanced stage of Grid technologies. Moreover, the project is increasing the proportion of funding going to Service and Networking activities. Thus the project may facilitate new countries and applications as well as applications and sites to join the infrastructure. This will also ease the expansion of the dissemination, the training and finally the application support.
Grid foundation components have been concentrating efforts in software development and have been integrating the third party components coming from other projects and sources.
Links
For more and complete information, please click on http://eu-egee.org
fGATE
Purposes and vision
High-quality services within the medical sector are more and more in demand by patients wishing always better healthcare treatments and thereby always higher medical imaging quality. Improving the quality, speed and availability of new imaging toolset dedicated to the simulation of emission tomography will lead to better and more accurate analysis and allows the definition of better treatments for the patient.
To this end, GATE (Geant4 Application for Emission Tomography) has been developed since 2001 by a open community of researchers. It offers accurate simulations packages and include well-validated physics models, geometry modeling tools, and efficient visualization utilities. It allows not only the design of performed and realistic simulations of data acquisitions in time but also the accurate description of time-dependent phenomena such as source or detector movement and sourced decay kinetics. Now, and since it has been publicly released in 2004, more than 1000 users have been already using it.
The goals of the fGATE project are to enhance the development and the use of the GATE software.
The role of the Grid
The use of the Grid is seen here as an advantage as it allows faster and better analysis and visualisations. Data provided by medical imaging simulations can be added and crossed with data already available on the grid. Therefore is considered the use of healthgrid in this context as a useful tool offering the means to make a faster analysis and diagnosis for a higher treatment quality.
Links
For more information visit the fGATE project website on http://www.fgate.fr
DREAMS Asia