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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  
, computational biology and systems biology.  ...  In this paper we present a trace of these technological changes in Web and Grid technology, including details of emerging infrastructures, standards, languages and tools, as they apply to bioinformatics  ...  technologies as applied to bioinformatics, computational biology and systems biology.  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

SAMasGC: Sequencing Analysis with a Multiagent System and Grid Computing [chapter]

Roberto González, Carolina Zato, Rocío Benito, María Hernández, Jesús M. Hernández, Juan F. De Paz
2012 Advances in Intelligent and Soft Computing  
Advances in bioinformatics have contributed towards a significant increase in available information.  ...  Information analysis requires the use of distributed computing systems to best engage the process of data analysis.  ...  such as grid computing [6] .  ... 
doi:10.1007/978-3-642-28839-5_24 dblp:conf/pacbb/GonzalezZBHHP12 fatcat:idy4p5futffylipzjtdpircfve

Grid-Based Interactive Decision Support in Biomedicine [chapter]

Alfredo Tirado-Ramos, Peter M. A. Sloot, Marian Bubak
Grid Computing for Bioinformatics and Computational Biology  
A huge gap exists between what we know is possible with today's machines and what we have so far been able to finish. -Donald Knuth i ii GRID-BASED INTERACTIVE DECISION SUPPORT IN BIOMEDICINE  ...  This research is partly funded by the EU IST CrossGrid (IST200132243) and ViroLab (IST027446), and the Bsik Virtual Laboratory for eScience (VL-e) projects.  ...  Acknowledgments The authors wish to thank the members of the CrossGrid and ViroLab consortia.  ... 
doi:10.1002/9780470191637.ch10 fatcat:pcj63lmbgbdifhugjiwe2xgvo4

Recent Advances in Solving the Protein Threading Problem [chapter]

Rumen Andonov, Guillaume Collet, J.-F. Gibrat, A. Marin, Vincent Poirriez, N. Yanev
Grid Computing for Bioinformatics and Computational Biology  
In this paper, we present the diverse components of FROST, emphasizing on the recent advances in formulating and solving new versions of the PTP and on the way of solving on a computer cluster a million  ...  between the SYMBIOSE group in IRISA and MIG in Jouy-en-Josas.  ...  Grids are emerging as a powerful tool to improve bioinformatic applications effectiveness, particularly for protein threading.  ... 
doi:10.1002/9780470191637.ch14 fatcat:mhcinyfefzhaxfkbmevx6tovey

A Study on Applications of Grid Computing in Bioinformatics

K.A Manjula., Dr.G. Raju
2010 International Journal of Computer 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.  ...  Integration of these biological data and tools is becoming one of the major topics in the bioinformatics community.  ...  The integration of a platform dedicated to biology into GRID opens up new avenues in terms of computing resources and data storage.  ... 
doi:10.5120/1004-39 fatcat:u5yiklrim5gstbus5z4mln4rni

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region

Asif M. Khan, Tin Wee Tan, Christian Schönbach, Shoba Ranganathan
2013 PLoS Computational Biology  
In response to an increasing demand for high-performance and highthroughput computational biology, in 2001 APBioNet partnered with the NUS Bioinformatics Centre to promote the concept of grid computing  ...  Computational Biology (ISCB).  ... 
doi:10.1371/journal.pcbi.1003317 pmid:24204244 pmcid:PMC3814852 fatcat:xtrunnc4r5gtbdcljvc5oxsv3i

An Agent-Based Multilayer Architecture for Bioinformatics Grids

E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, E. Merelli, L. Milanesi, P. Romano
2007 IEEE Transactions on Nanobioscience  
Bioinformatics BMC Bioinformatics Journal of Computational Biology Computational Biology and Chemistry Briefings in Bioinformatics IEEE Trans. Comp. Biol.  ...  And Bioinformatics Applied Bioinformatics PLoS Computational Biology Int.J.of Bioinf. Res.& Appl. (IJBRA)It has become really hard to find resources!  ...  A computer system capable of flexible, autonomous (problem-solving) actions, situated in dynamic, unpredictable and typically multi-agent environment.  ... 
doi:10.1109/tnb.2007.897492 pmid:17695749 fatcat:32ogekykr5aspfkavite3oufc4

Establishing bioinformatics research in the Asia Pacific

Shoba Ranganathan, Martti Tammi, Michael Gribskov, Tin Wee Tan
2006 BMC Bioinformatics  
We also thank the BMC Bioinformatics Editorial Office for their support and encouragement in making this issue possible.  ...  Acknowledgements We thank the referees for their dedication and effort in reviewing the manuscripts submitted for this supplement.  ...  Grid computing As computational problems in biology evolve in size, resource requirements and complexity, grid computing has emerged as a viable solution in many instances.  ... 
doi:10.1186/1471-2105-7-s5-s1 fatcat:tum4rfre35exhp4i3jzn4hkwlq

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  
R ECENT progress in the application of bioinformatics, computational biology, and systems biology to biomedicine has made it essential to devise technological platforms able to ensure appropriate support  ...  He has published several refereed publications in journals, books and conference proceedings relating to the areas of bioinformatics, system biology, and medical informatics.  ... 
doi:10.1109/tnb.2007.897434 fatcat:kihmne4uazcivazs5vgh36c6py

The Finnish EMBnet node: AGM 2010 report

Kimmo Mattila
2010 EMBnet journal  
CSC is also participating in several European Grid projects: these range from technology-oriented Grid projects, like EGEE2 and DEISA, to collaborative projects, like ELIXIR and EMBRACE.  ...  In addition to the instruction pages, CSC provides on-line support by e-mail and phone, and arranges bioinformatics related training courses and events.  ...  CSC is also participating in several European Grid projects: these range from technology-oriented Grid projects, like EGEE2 and DEISA, to collaborative projects, like ELIXIR and EMBRACE.  ... 
doi:10.14806/ej.16.1.187 fatcat:ibmwqtqtcbhrnhxllxyorsyeva

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar, Erik Bongcam-Rudloff
2009 BMC Bioinformatics  
such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies.  ...  The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20 th anniversary.  ...  Leading applications and technologies in bioinformatics. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/10?issue=S6.  ... 
doi:10.1186/1471-2105-10-s6-s1 pmid:19534734 pmcid:PMC2697632 fatcat:rmmdm6bjazhqfdvbv77egcgmnu

OBIYagns: a grid-based biochemical simulator with a parameter estimator

S. Kimura, T. Kawasaki, M. Hatakeyama, T. Naka, F. Konishi, A. Konagaya
2004 Bioinformatics  
estimators distributed over an OBIGrid (Open BioInformatics Grid).  ...  This grid-based biochemical simulation system can achieve high performance and provide a secure simulation environment for estimating kinetic parameters in a proper time period.  ...  The grid is equipped with functions that are indispensable in the life sciences fields, such as database systems, computation systems, and access control systems, as well as various bioinformatics application  ... 
doi:10.1093/bioinformatics/bth122 pmid:14962919 fatcat:dqlc2oliw5dstdnuzizuwaebca

ABCGrid: Application for Bioinformatics Computing Grid

Y. Sun, S. Zhao, H. Yu, G. Gao, J. Luo
2007 Bioinformatics  
We have developed a package named Application for Bioinformatics Computing Grid (ABCGrid).  ...  ABCGrid was designed for biology laboratories to use heterogeneous computing resources and access bioinformatics applications from one master node.  ...  ACKNOWLEDGEMENTS We thank X Wu, L Kong and WZ Zhang for helpful discussions. This study was supported by grants of the  ... 
doi:10.1093/bioinformatics/btm086 pmid:17344235 fatcat:zxoybuasyncyhd5luvisxozsty

BIOINFOGRID: BIOINFORMATICS SIMULATION AND MODELING BASED ON GRID

LUCIANO MILANESI
2007 Modelling and Simulation in Science  
Gene to Protein wireless networks 15-22 April 2007, EMFCSC, Erice, Italy Proteomics Applications in GRID Aim : use of computational GRIDs to analysis molecular biological data in proteomics Description  ...  • Perform functional protein analysis in GRID by using the functional protein domain annotations on large protein families using GRID and related databases.  ...  Description • GRID Bioinformatics User Tools: unification of larger groups of bioinformatics tools into single analytical steps and their optimization for GRIDGRID analysis of cDNA data: computer-aided  ... 
doi:10.1142/9789812779458_0022 fatcat:vcoyibrv2nduve7mjp44xcbrc4

Grid Computing in Drug Discovery

M.C. Peitsch
2006 Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)  
This presentation will outline how in silico approaches and High Performance Computing can impact Drug Discovery through specific examples.  ...  These methods range from data mining, modeling and simulation of molecular interactions, biological networks and processes and the large scale computer-aided analysis of scientific literature and patents  ...  In this position, he directs a department spanning experimental sciences (Proteomics), Computational Systems Biology, Computational Knowledge Management and Text Mining as well as Information Sciences.  ... 
doi:10.1109/ccgrid.2006.50 dblp:conf/ccgrid/Peitsch06 fatcat:xnfe2mlf75dsfjw7qqpc3jrcka
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