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Grid Enabled Data Integration Framework for Bioinformatics Research

Jia Liu, Yongwei Wu, Weimin Zheng
2006 2006 Fifth International Conference on Grid and Cooperative Computing Workshops  
A framework is proposed to manage the distributed and heterogeneous databases in grid environment for understanding protein-protein interaction.  ...  TAMBIS [15] and BioMediator [16] consider data integration in biomedical domain. In this paper, we are going to discuss data integration in grid environment for bioinformatics research.  ...  We propose the grid-enabled data integration framework that based on OGSA-DAI middleware, then the heterogeneous databases can be accessed by the uniform interface transparently, data integration could  ... 
doi:10.1109/gccw.2006.48 dblp:conf/gcc/LiuWZ06 fatcat:ljdm5qxqrfgjdl7ekwkptz7gve

Trends in life science grid: from computing grid to knowledge grid

Akihiko Konagaya
2006 BMC Bioinformatics  
Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics.  ...  Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity  ...  Acknowledgements The authors express special thanks for the member of the Open Bioinformatics Grid project and anonymous reviewers for their valuable discussion and useful comments for this manuscript.  ... 
doi:10.1186/1471-2105-7-s5-s10 pmid:17254294 pmcid:PMC1764466 fatcat:tlemqfzeljfdbaxa6gw5mid7f4

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
//www.gmod.org/home An integrated organism database PSI-MI [56] Proteomics Standards Initiative: Molecular Interactions http://psidev.sourceforge.net/ Data standard for proteomics  ...  Frameworks (section 2.2.6 [88-92]) BioGrid Data Management Approaches (section 2.2.7 [4, 5, 96]) Computing & Service Grid Middleware (section 2.2.8 [10, 11, 37, 39, 107]) Local Resource Manager Systems  ...  Similarly, some specific grid-based frameworks for life sciences have also been proposed and demonstrated such as Grid Enabled Bioinformatics Application Framework (GEBAF) [90] , that proposes an integrated  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Adoption and Adaptation of caGrid for CTSA

Shannon Hastings, Scott Oster, Stephen Langella, Calixto Melean, Tara Borlawsky, Rakesh Dhavel, Philip Payne
2009 Summit on translational bioinformatics  
environment such as caBIG™[6-8] (Cancer Bioinformatics Grid), BIRN[9] (Bioinformatics Research Network), and CTSA(Clinical and Translational Science Awards) have lead to new ways to bring together information  ...  The TRIAD (Translational Informatics and Data Management Grid) System, which will be used as the middleware system enabling the OSU CTSA to create a scalable, secure, and knowledge anchored data sharing  ...  . • Complex federal and local data integrity and privacy constraints. • Semantic and syntactic differences in data within and across research groups and institutions.  ... 
pmid:21347169 pmcid:PMC3041578 fatcat:2caqzb3bknd2bkzorg7as4wsr4

Article Withdrawn: GNARE: A Grid-based Server for the Analysis of User Submitted Genomes

E. Glass, A. Rodriguez, M. Romine, Y. Zhang, M. D'Souza, D. Sulakhe, M. Syed, N. Maltsev
2007 Nucleic Acids Research  
GNARE (GeNome Analysis Research Environment) is a bioinformatics server that supports both automated and expert-driven (interactive) analysis of user-submitted genomes and metagenomes.  ...  GNARE also provides a framework for comparative and evolutionary analysis as well as annotation of genomes and metabolic networks in the context of phenotypic and taxonomic information.  ...  GADU is an automated, scalable, high-throughput computational workflow engine that enables the Grid execution of bioinformatics tools.  ... 
doi:10.1093/nar/gkm366 pmid:17526513 pmcid:PMC3526309 fatcat:fueqtvjswvhkjct4ovcfd7ztdm

Managing The Data Ecosystem In Life Sciences Through Bioinformatics

Fotis Psomopoulos
2016 Zenodo  
In essence, they can a form a framework for Bioinformatics analysis that (a) enables the re-analysis of old data with new methods, (b) facilitates data remixing and data integration for increased resolution  ...  it addresses, and by providing novel opportunities for systematic integration of different data, thus facilitating horizontal studies.  ...  (2015), Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis. Front.  ... 
doi:10.5281/zenodo.154409 fatcat:s2tidnmvhbgftlj77yutyjk6xe

Bioinformatics' Challenges to Computer Science [chapter]

Mario Cannataro, Mathilde Romberg, Joakim Sundnes, Rodrigo Weber dos Santos
2008 Lecture Notes in Computer Science  
The workshop Bioinformatics' Challenges to Computer Science covers the topics of data management and integration, modelling and simulation of biological systems and data visualization and image processing  ...  This short paper describes the requirements Bioinformatics has towards computer science, summarizes the papers accepted for the workshop and gives a brief outlook on future developments.  ...  We would like to thank the members of the program committee for the invaluable assistance on reviewing the papers and the organizers of ICCS for promoting this workshop.  ... 
doi:10.1007/978-3-540-69389-5_9 fatcat:kf5zfpmkmzflboixxh6cx6jhne

Grid-Enabled High-Throughput In Silico Screening Against Influenza A Neuraminidase

Hurng-Chun Lee, Jean Salzemann, Nicolas Jacq, Hsin-Yen Chen, Li-Yung Ho, Ivan Merelli, Luciano Milanesi, Vincent Breton, Simon C. Lin, Ying-Ta Wu
2006 IEEE Transactions on Nanobioscience  
Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM) [1], the second data challenge battling avian flu kicked off in April 2006 to identify new drugs for the potential  ...  for further biological analysis and testing.  ...  The following institutes contributed computing resources to the data challenge:  ... 
doi:10.1109/tnb.2006.887943 pmid:17181029 fatcat:6abw4jzwarhkhbexridjdgbigu

BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks

L.-A. Qiao
2004 Nucleic Acids Research  
We herein established the BOD (Bioinformatics on demand) system to use Grid computing technology to set up a virtual workbench via a web-based platform, to assist researchers performing customized comprehensive  ...  The integration of bioinformatics resources worldwide is one of the major concerns of the biological community.  ...  ACKNOWLEDGEMENTS The authors are very grateful to Dr Jinghui Zhang (NCI of NIH) for discussions of BOD idea at early stage, to Professor Zihe Rao (Tsinghua University) for generous sharing of the Threader  ... 
doi:10.1093/nar/gkh756 pmid:15302917 pmcid:PMC514377 fatcat:bn4jelxhtnbirgm2efpnxqiqou

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

F. Pappalardo, M. D. Halling-Brown, N. Rapin, P. Zhang, D. Alemani, A. Emerson, P. Paci, P. Duroux, M. Pennisi, A. Palladini, O. Miotto, D. Churchill (+11 others)
2008 Briefings in Bioinformatics  
Halling-Brown has research interests in the areas of Bioinformatics, Computational Immunology, Chemogenomics and Grid Computing.  ...  His research interests focus on merging computational modeling and machine learning methods to explain experimental data in Biology.  ...  INTEGRATED SYSTEM AND GRID COMPUTING Integrated systems for data management and laboratory automation are emerging as cyber infrastructure that is the new research environment that enables research using  ... 
doi:10.1093/bib/bbp014 pmid:19383844 fatcat:b6jsotye35g2tcpxwqftgsj7vm

Virtual health care infrastructures: Markets and hierarchies

Ann Seror
2011 2011 24th International Symposium on Computer-Based Medical Systems (CBMS)  
The objective of this review is to develop a conceptual framework for analyzing the evolution of large scale virtual infrastructures in ideologically diverse health care systems.  ...  Large scale grid and cloud computing systems are considered as well as the emerging influence of global social networks.  ...  National and regional grid infrastructures emerging in the European Union facilitate integration of research, access to federated data grids, education and health care service delivery, while fragmented  ... 
doi:10.1109/cbms.2011.5999036 dblp:conf/cbms/Seror11 fatcat:kglh7eqh4ja63kukq4bjeg4pri

Guest Editorial: Special Section on Grid, Web Services, Software Agents, and Ontology Applications for Life Sciences

Luciano Milanesi, Giuliano Armano, Vincent Breton, Paolo Romano
2007 IEEE Transactions on Nanobioscience  
His research interests include data modeling, ontologies, Web Services, and data integration.  ...  data sources through semantic integration.  ... 
doi:10.1109/tnb.2007.897434 fatcat:kihmne4uazcivazs5vgh36c6py

GLAD: a system for developing and deploying large-scale bioinformatics grid

Y.-M. Teo, X. Wang, Y.-K. Ng
2004 Bioinformatics  
But up to now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems,  ...  Herein, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), to facilitate the development and deployment of bioinformatics applications on a grid.  ...  Acknowledgement The authors would like to thank Dr Li Kuo-Bin from the Bioinformatics Institute of Singapore for the many useful discussions and helpful suggestions.  ... 
doi:10.1093/bioinformatics/bti034 pmid:15388517 fatcat:rqsuhyckbrfibjansaddkbz3c4

myGrid: personalised bioinformatics on the information grid

R. D. Stevens, A. J. Robinson, C. A. Goble
2003 Bioinformatics  
is building high level services for data and application integration such as resource discovery, workflow enactment and distributed query processing.  ...  Motivation: The my Grid project aims to exploit Grid technology, with an emphasis on the Information Grid, and provide middleware layers that make it appropriate for the needs of bioinformatics. my Grid  ...  However, much bioinformatics requires support for a scientific process that has more modest computational needs, but has significant semantic complexity. my Grid is building services for integration such  ... 
doi:10.1093/bioinformatics/btg1041 pmid:12855473 fatcat:q7rys4q5bbh43aq66t6rdnnxzi

A Distributed Information Services Architecture to Support Biomarker Discovery in Early Detection of Cancer

Daniel Crichton, Sean Kelly, Chris Mattmann, Qing Xiao, J. Hughes, Jane Oh, Mark Thornquist, Donald Johnsey, Sudhir Srivastava, Laura Essermann, William Bigbee
2006 2006 Second IEEE International Conference on e-Science and Grid Computing (e-Science'06)  
Partnering with NASA, the Early Detection Research Network (EDRN), a program managed by the National Cancer Institute, has been defining and building an informatics architecture to support the discovery  ...  The architecture established by EDRN serves as a blueprint for constructing a set of services focused on the capture, processing, management and distribution of information through the phases of biomarker  ...  The work more or less falls into three fundamental principalities: grid computing, large-scale, data-intensive systems, and bioinformatics.  ... 
doi:10.1109/e-science.2006.261128 dblp:conf/eScience/CrichtonKMXHOTJSEB06 fatcat:hmiz4j7cu5c3ln2yan2wiuomy4
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