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A Model of Problem Solving Environment for Integrated Bioinformatics Solution on Grid by Using Condor [chapter]

Choong-Hyun Sun, Byoung-Jin Kim, Gwan-Su Yi, Hyoungwoo Park
2004 Lecture Notes in Computer Science  
Here we propose a model of simple problem solving environment that enables component based workflow design of integrated bioinformatics applications on Grid environment by using Condor functionalities.  ...  Workflow based problem solving environment on grid can be the efficient solution for this type of software development.  ...  Acknowledgements This research was partially supported by University IT Research Center Project and by national grid project grant 2004-giban-04 through Korea Institute of Science and Technology Information  ... 
doi:10.1007/978-3-540-30208-7_142 fatcat:psj37tvu5bcfvet3gm26nb2dl4

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  
]) BioGrid Application Development Toolkits (section 2.2.3 [78-83]) Grid-based Problem Solving Environments (section 2.2.4 [84-85]) Grid-based Workflow Management Systems (section 2.2.5 [86-87]) Grid-based  ...  A major focus of this technological review is to collate up-to-date information regarding the design and implementation of various bioinformatics Webs, Grids, Web-based grids or Grid-based webs in terms  ...  There are several different grid-based PSEs available for bioinformatics applications e.g. [84] describes the design and architecture of a PSE (Proteus) that provides an integrated environment for a biomedical  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

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.  ...  Knowledge grids should be designed not only from sharing explicit knowledge on computers but also from community formulation for sharing tacit knowledge among a community.  ...  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

ChinaGrid: Making Grid Computing a Reality [chapter]

Hai Jin
2004 Lecture Notes in Computer Science  
Grid computing presents a new trend to distributed computing and Internet applications, which can construct a virtual single image of heterogeneous resources, provide uniform application interface and  ...  The purpose of this paper is to introduce this great grid project to the world completely for the first time.  ...  I also would like to take this opportunity to thank all the experts in ChinaGrid project for their devoting time to this project, and making grid computing a reality in China.  ... 
doi:10.1007/978-3-540-30544-6_2 fatcat:x7wfsimiifeqfoqjjly2ln7uiy

A semantic grid-based data access and integration service for bioinformatics

G. Aloisio, M. Cafaro, I. Epicoco, S. Fiore, M. Mirto
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
Given the heterogeneous nature of biological data and their intensive use in many tools, in this paper we propose a semantic data access and integration (DAI) service, based on the Grid paradigm, for the  ...  The DAI proposed in this work is a fundamental component of the ProGenGrid system, a grid-enabled platform, which aims at the design and implementation of a virtual laboratory where e-scientists could  ...  grid services for bioinformatics applications for data and application integration.  ... 
doi:10.1109/ccgrid.2005.1558554 dblp:conf/ccgrid/AloisioCEFM05 fatcat:ei3cjwgtvfdazpjms2kr2fzk3u

High performance workflow implementation for protein surface characterization using grid technology

Ivan Merelli, Giulia Morra, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2005 BMC Bioinformatics  
Results: Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications.  ...  This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence  ...  Laboratory for Bioinformatics Technologies -LITBIO" and by the European support action for "Bioinformatics in EGEE -BIOINFOGRID".  ... 
doi:10.1186/1471-2105-6-s4-s19 pmid:16351745 pmcid:PMC1866389 fatcat:f67ts34yyvagpbgxkd667a2ajy

GNARE: an environment for grid-based high-throughput genome analysis

D. Sulakhe, A. Rodriguez, M. D'Souza, M. Wilde, V. Nefedova, I. Foster, N. Maltsev
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
It focuses on our approach to Grid resource allocation and to the use of GNARE as a computational framework for the development of bioinformatics applications.  ...  computational backend for datadriven bioinformatics applications.  ...  Department of Energy under Contract W-31-109-ENG-38, and by the National Science Foundation under grants 86044 (GriPhyN), 122557 (iVDGL), and the NCSA Alliance Expedition "A PACI Petascale Data Quest"  ... 
doi:10.1109/ccgrid.2005.1558590 dblp:conf/ccgrid/SulakheRDWNFM05 fatcat:ieavcecyjvcnhpwh5cpztu4n5q

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  
He is the coordinator of the European BIOINFOGRID Bioinformatics Grid Applications for Life Science and the LITBIO Laboratory of Bioinformatics Technologies.  ...  He is leader of Bioinformatics for the University Center for Excellence, Center for Bio-molecular Interdisciplinary Studies and Industrial Applications.  ... 
doi:10.1109/tnb.2007.897434 fatcat:kihmne4uazcivazs5vgh36c6py

Gnare: Automated System For High-Throughput Genome Analysis With Grid Computational Backend

Dinanath Sulakhe, Alex Rodriguez, Mark D'Souza, Michael Wilde, Veronika Nefedova, Ian Foster, Natalia Maltsev
2005 Journal of clinical monitoring and computing  
It focuses on our approach to Grid resource allocation and to the use of GNARE as a computational framework for the development of bioinformatics applications.  ...  computational backend for datadriven bioinformatics applications.  ...  Acknowledgments We extend special thanks to the following individuals who contributed valuable advice and support: Elizabeth Glass, Jens Voeckler, Miron Livny, Zachary Miller, Alain Roy, Susan Coghlan, and the systems  ... 
doi:10.1007/s10877-005-3463-y pmid:16328950 fatcat:224zf24f45gaxon67rpctoadi4

The discovery net system for high throughput bioinformatics

A. Rowe, D. Kalaitzopoulos, M. Osmond, M. Ghanem, Y. Guo
2003 Bioinformatics  
Using the Discovery Net system and a range of different bioinformatics tools, we built a Grid based application for Genome Annotation.  ...  Result: The Discovery Net system is a middleware that allows service developers to integrate tools based on existing and emerging Grid standards such as web services.  ...  We would also like to thank Dr Catherine Rice and Dr Nigel Carter at The Wellcome Trust Sanger Institute for their help and expertise.  ... 
doi:10.1093/bioinformatics/btg1031 pmid:12855463 fatcat:jkbh5rr2u5hx5me5dnec4nxeui

A Study on Applications of Grid Computing in Bioinformatics

K.A Manjula., Dr.G. Raju
2010 International Journal of Computer Applications  
Provided with fundamental mechanisms of access to distributed databases and tools, the grid is an ideal candidate for the integration of bioinformatics applications.  ...  Grid computing is emerging as a key infrastructure for a wide range of disciplines for resource sharing and collaboration over wide and open networks.  ...  Provided with fundamental mechanisms of access to distributed databases and tools, the grid is an ideal candidate for the integration of bioinformatics applications.  ... 
doi:10.5120/1004-39 fatcat:u5yiklrim5gstbus5z4mln4rni

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

Y.-M. Teo, X. Wang, Y.-K. Ng
2004 Bioinformatics  
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.  ...  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,  ...  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

Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences

Sung Lee, Taowei David Wang, Nada Hashmi, Michael P. Cummings
2007 Future generations computer systems  
We also defined an ontology in OWL to model bioinformatics applications.  ...  Our proposed solution is a Semantic Web-enabled computing environment, called Bio-STEER. In Bio-STEER, bioinformatics Grid services are mapped to Semantic Web services, described in OWL-S.  ...  Acknowledgments We thank Adam Bazinet, Matthew Conte, Ryusuke Masuoka, and Zhexuan Song for their help.  ... 
doi:10.1016/j.future.2006.07.011 fatcat:hpqaj35qdnekzjy4b4wykphtte

Agents in bioinformatics, computational and systems biology

E. Merelli, G. Armano, N. Cannata, F. Corradini, M. d'Inverno, A. Doms, P. Lord, A. Martin, L. Milanesi, S. Moller, M. Schroeder, M. Luck
2006 Briefings in Bioinformatics  
The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis  ...  and management in bioinformatics and for systems modelling and simulation in computational and systems biology.  ...  For example, the Grid has become increasingly important to both communities, and suggests a convergence to a serviceoriented vision of bioinformatics underpinned by Grid-based virtual organizations.  ... 
doi:10.1093/bib/bbl014 pmid:16772270 fatcat:7w63k7cfmfgctmrouua24vh74m

Grid computing and bioinformatics development. A case study on the Oryza sativa (rice) genome

Wasinee Rungsarityotin, Noppadon Khiripet, Chularat Tanpraset, Royol Chitradon
2002 Pure and Applied Chemistry  
A preliminary version of our Web-based viewer for the XML data of the Oryza sativa genome is presented to illustrate the idea.  ...  For example, finding a single gene of the Oryza sativa (rice) genome one must spend weeks, if not months, wandering through approximately 40 million base pairs.  ...  division, NECTEC) for information and references about research on the grid data and computing.  ... 
doi:10.1351/pac200274060891 fatcat:mmuaow6dsrfgvbasly3i7w3o6y
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