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Development of an information platform for new grid users in the biomedical field

Daniela Skrowny, Frank Dickmann, Benjamin Löhnhardt, Tobias A Knoch, Ulrich Sax
2010 Studies in Health Technology and Informatics  
Therefore, the development of an information- and learning platform could support the efforts of grid experts to guide new users.  ...  Bringing new users into grids is a top priority for all grid initiatives and one of the most challenging tasks.  ...  An information-and learning platform for new grid users of the biomedical field supports and follows the movement of improving the grid access and lowering the threshold of using this technology.  ... 
pmid:20543450 fatcat:3eztuc2365drrodyomuohyvw34

Model Driven Engineering for Science Gateways [article]

David Manset, Richard McClatchey, Herve Verjus
2014 arXiv   pre-print
In analysing the requirements from these biomedical applications the authors were able to elaborate on commonly faced Grid development issues, while proposing an adaptable and extensible engineering framework  ...  Suitable access to data and applications resident in SOAs via so-called Science Gateways has thus become a pressing need in various fields of science, in order to realize the benefits of Grid and Cloud  ...  SOAbased Science Gateways are thus emerging in various research fields and biomedical specialties, which operate most of the time for fixed QoS and execution platforms and are deployed over predefined  ... 
arXiv:1402.5768v1 fatcat:sdo7n4ginnbxjf7ahf6d4unuve

A digital repository with an extensible data model for biobanking and genomic analysis management

Massimiliano Izzo, Francesco Mortola, Gabriele Arnulfo, Marco M Fato, Luigi Varesio
2014 BMC Genomics  
Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management.  ...  The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions.  ...  Acknowledgements and funding We thank Luca Corradi and Ivan Porro, who originally conceived the process-event model and first developed the XTENS application.  ... 
doi:10.1186/1471-2164-15-s3-s3 pmid:25077808 pmcid:PMC4083403 fatcat:fqftjr4uezhjhc3xhbdrqbufnq

Building a European biomedical grid on cancer: the ACGT Integrated Project

M Tsiknakis, D Kafetzopoulos, G Potamias, A Analyti, K Marias, A Manganas
2006 Studies in Health Technology and Informatics  
The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable  ...  By doing so, it is expected that the influence of genetic variation in oncogenesis will be revealed, the molecular classification of cancer and the development of individualised therapies will be promoted  ...  Acknowledgements The authors wish to express their gratitude to the whole of the ACGT consortium for their contributions with various ideas on which the ACGT project was developed.  ... 
pmid:16823143 fatcat:y5z67zykjfeydiemgb6emr5oou

Health-e-Child : An Integrated Biomedical Platform for Grid-Based Paediatric Applications [article]

Joerg Freund, Dorin Comaniciu, Yannis Ioannis, Peiya Liu, Richard McClatchey, Edwin Morley-Fletcher, Xavier Pennec, Giacomo Pongiglione, Xiang ZHOU
2006 arXiv   pre-print
This paper outlines the design approach being adopted in Health-e-Child to enable the delivery of an integrated biomedical information platform.  ...  The Health-e-Child project aims at developing an integrated healthcare platform for European Paediatrics, providing seamless integration of traditional and emerging sources of biomedical information.  ...  Acknowledgements The authors thank the European Commission and their institutes for support and particularly acknowledge the contribution to this paper of the following Health-e-Child consortium members  ... 
arXiv:cs/0603036v2 fatcat:2qbhyrzjwbg7xfdzmmynvtjya4

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

Luca Corradi, Ivan Porro, Andrea Schenone, Parastoo Momeni, Raffaele Ferrari, Flavio Nobili, Michela Ferrara, Gabriele Arnulfo, Marco M Fato
2012 BMC Medical Informatics and Decision Making  
There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using  ...  This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of "meta" data model.  ...  experiments in the biomedical field [21] .  ... 
doi:10.1186/1472-6947-12-115 pmid:23043673 pmcid:PMC3560115 fatcat:b2fdeetjpvdinmdmxwo5kdii2e

Real Time Biomedical Data Streaming Platform (RIMES): A Data-Intensive Virtual Environment

Kejun Dong, Kai Nan, Sameer Tilak, Cindy Zheng, Dong Xu, Jurgen Schulze, Peter Arzberger, Wilfred Li
2010 2010 Third International Joint Conference on Computational Science and Optimization  
In this paper we present Real tIme bioMEdical data Streaming platform (RIMES), a data-intensive virtual environment, under joint development by Computer Network Information Center and University of California  ...  RIMES extends scientists' desktops to biomedical grid computation resources and mass storage systems, by means of streaming biomedical data through internet-based Data Turbine cloud.  ...  In conclusion, users can extend user desk to biomedical grid computing and mass storage systems by means of real time biomedical data streaming. Figure 4 gives the architecture of RIMES.  ... 
doi:10.1109/cso.2010.146 fatcat:bydfkyeqfbdehch5gcavq236sa

Online Experimentation for Industrial, Health and Educational Purposes

Alberto Cardoso, Maria Teresa Restivo
2020 International Journal of Online and Biomedical Engineering (iJOE)  
<p>The Special Issue of the International Journal of Online and Biomedical Engineering (iJOE) is publishing extended versions of interesting papers presented at the Experiment@International Conference  ...  An article describes the contribution of a project for the definition of a grid of laboratories, which can be shared and accessed by several users in different contexts of use: • A Federation of Remote  ...  The use of new information and IoT technologies in the context of the Industry 4.0 paradigm opens up several challenges and opportunities to improve industrial production processes, aircraft maintenance  ... 
doi:10.3991/ijoe.v16i04.13883 fatcat:5rkande3kfdp7k6jukjmmhmcb4

Image processing methods and architectures in diagnostic pathology

Gloria Bueno, Oscar DĂŠniz, JesĂşs Salido, Marcial GarcĂ­a Rojo
2010 Folia Histochemica et Cytobiologica  
This methods are focus on the user level middleware. The article describes the distributed programming system developed by the authors for virtual slide analysis in diagnostic pathology.  ...  General grid structures and methodologies for both software and hardware in image analysis for virtual tissue-based diagnosis has been considered in this paper.  ...  Authors want also to thanks the support of COST Action IC0604.  ... 
doi:10.2478/v10042-009-0116-x pmid:20430740 fatcat:yl25ecjpy5ecnopkesumk6paii

Cyberinfrastructure for e-Science

T. Hey
2005 Science  
Users must have the capacity to change all of the above in order to maintain innovation and adjust to changing needs and developing technology. Open source is an oftsuggested solution to this.  ...  All of the above is further confounded by the organization of biomedicine into research fields and disciplines. Such discipline focus generates an insidious challenge to information integration.  ... 
doi:10.1126/science.1110410 pmid:15879209 fatcat:diesixv7pfggpirte5aycfwufi

Advances in the Biomedical Applications of the EELA Project [article]

Vicente Hernández, Ignacio Blanquer, Gabriel Aparicio, Raul Isea, Juan Luis Chavés, Álvaro Hernández, Henry Ricardo Mora, Manuel Fernández, Alicia Acero, Esther Montes, Rafael Mayo
2010 arXiv   pre-print
In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations.  ...  One year ago we presented this e-infrastructure used, among others, by the Biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computation phylogenetics  ...  With this free Open Source software analysis package specially developed for the needs of the molecular biology user community EELA will keep on working in the Biomedical field.  ... 
arXiv:1012.3956v1 fatcat:ucmultt5rnezdewpbuq3lwlr2e

The ACGT project in retrospect: Lessons learned and future outlook

Anca Bucur, Stefan Ruping, Thierry Sengstag, Stelios Sfakianakis, Manolis Tsiknakis, Dennis Wegener
2011 Procedia Computer Science  
Furthermore we provide a number of key "lessons learned" during the process and give directions for further developments in the future.  ...  The objective of the ACGT (Advancing Clinico-Genomic Trials on Cancer: Open Grid Services for improving Medical Knowledge Discovery, www.eu-acgt.org) project that has recently concluded successfully was  ...  Acknowledgements The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996.  ... 
doi:10.1016/j.procs.2011.04.119 fatcat:ls5emmpmrrfwnhnkscbpazorge

Developing a European grid infrastructure for cancer research: vision, architecture, and services

M Tsiknakis
2015 ecancermedicalscience  
Life sciences are currently at the centre of an information revolution. The nature and amount of information now available opens up areas of research that were once in the realm of science fiction.  ...  This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ... 
doi:10.3332/ecancer.2007.56 fatcat:c4imtkihsrh3djksxu6frunesu

Developing a European Grid Infrastructure for Cancer Research: Vision, Architecture, and Services

M Tsiknakis
2007 ecancermedicalscience  
Life sciences are currently at the centre of an information revolution. The nature and amount of information now available opens up areas of research that were once in the realm of science fiction.  ...  This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ... 
doi:10.3332/ecms.2007.56 pmid:22275955 pmcid:PMC3223975 fatcat:w5drhkauzneafiwiuhzaeavtfa

A grid environment consisting of heterogeneous compute resources for high performance computation [article]

Fred Viezens
2010 arXiv   pre-print
ACKNOWLEDGMENT This work was supported from the German Federal Ministry of Education and Research (BMBF) in the project MedInfoGRID, grant 01G07016.  ...  The use of grid resources in the field of biomedical applications opens new ways and strategies for distributed computing; large data sets and a lot of computing time can be engaged for these community  ...  In (3) is an example for running an inter-active job on the particular platform. Note: This is only possible under the middleware user; the root user can't operate in this way.  ... 
arXiv:1005.4018v2 fatcat:sqs5ppuoinf3lcs5vl3bog3hwi
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