Abstract
Important issues in bioinformatics are the difficulties for non computer experts to use bioinformatics tools, the transparent access to large biological data sets, and the exploitation of large computing power. Moreover, often such tools and databases are developed by independent groups, so the task of enabling their composition and cooperation is even more difficult. Integrating Computational Grid and Web Services technologies can be a key solution to simplify interaction between bioinformatics tools and biological databases. This paper presents ProGenGrid (Proteomics & Genomics Grid), a distributed and ubiquitous grid environment, accessible through the web, for supporting “in silico” experiments in bioinformatics.
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References
Aloisio, G., Blasi, E., Cafaro, M., and Epicoco, I. (2001). The GRB library: Grid Computing with Globus in C. In Proceedings of HPCN Europe 2001, volume 2110 of Lecture Notes in Computer Science, pages 133–140. Springer-Verlag.
Aloisio, G., Cafaro, M., Epicoco, I., Lezzi, D., Mirto, M., and Mocavero, S. (2003). The Design and Implementation of the GridLab Information Service. In Proceedings of the Second International Workshop on Grid and Cooperative Computing (GCC 2003), volume 3032 of Lecture Notes in Computer Science, pages 131–138. Springer-Verlag.
Aloisio, G., Cafaro, M., Fiore, S., and Mirto, M. (2004a). Bioinformatics Data Access Service in the ProGenGrid System. In OTM Workshops, volume 3292 of Lecture Notes in Computer Science, pages 211–221. Springer-Verlag.
Aloisio, G., Cafaro, M., Fiore, S., and Mirto, M. (2004b). The GRelC Project: Towards GRID-DBMS. In Parallel and Distributed Computing and Networks (PDCN) IASTED.
AutoMS (1996). AutoMS. http://dock.compbio.ucsf.edu/dock4/html/Manual.23.html♯33.
Berman, H.M., Westbrook, J., and G. Gilliland, Z. Feng, Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1):235–242.
Bivens, H.P. (2001). Grid Workflow. Grid Computing Environments Working Group Document. http://dps.uibk.ac.at/uploads/101/draft-bivens-grid-workflow.pdf.
Buyya, R., Branson, K., Giddy, J., and Abramson, D. (2003). The Virtual laboratory: a toolset to enable distributed molecular modelling for drug design on the World-Wide Grid. Concurrency and Computation: Practice and Experience, 15(1):1–25.
Daml (2000). Daml+oil language. http://www.daml.org/2001/03/reference.html.
Eshuis, R. and Wieringa, R. (2002). Verification support for workflow design with UML activity graphs. In Proceedings of the 24th International Conference on Software Engineering (ICSE), pages 166–176. ACM Press.
Ewing, T. J. A. and Kuntz, I.D. (1996). Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening. J. of Computational Chem., 18(9):1175–1189.
Foster, I. and Kesselman, C. (1997). Globus: A Metacomputing Infrastructure Toolkit. Intl J. Supercomputer Applications, 11(2):115–128.
Foster, I. and Kesselman, C. (1998). The Grid: Blueprint for a New Computing Infrastructure. Morgan Kaufmann.
Goodsell, D.S., Morris, G.M., and Olson, A.J. (1996). Automated docking of Flexible Ligands: Applications of AutoDock. J. Mol. Recognition, 9(1):1–5. http://www.scripps.edu/pub/olson-web/doc/autodock/.
LSG-RG (2003). Life Sciences Grid-Research Group. http://www.ggf.org/7_APM/LSG.htm.
MDS (1998). Monitoring Discovery Service. http://www.globus.org/mds/.
myGrid Project (2001). myGrid Project. http://mygrid.man.ac.uk/.
OMG (2003). Uml-unified modeling language: Extensions for workflow process definition. http://www.omg.org/uml/.
Sayle, Roger A. and Milner-White, E. J. (1995). RasMol: Biomolecular graphics for all. Trends in Biochemical Science (TIBS), 20(9):374.
Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S., Windus, T.L., Dupuis, M., and Montgomery, J.A. (1993). General Atomic and Molecular Electronic Structure System. J. of Computational Chem., 14(11):1347–1363. http://www.msg.ameslab.gov/GAMESS/GAMESS.html.
Sphgen (1996). Sphgen. http://dock.compbio.ucsf.edu/dock4/html/Manual.20.html#17338.
Tuecke, S. (2001). Grid Security Infrastructure (GSI) Roadmap. Technical report. www.gridforum.org/security/ggf1_2001-03/drafts/draft-ggf-gsi-roadmap-02.pdf.
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Aloisio, G., Cafaro, M., Fiore, S., Mirto, M. (2005). Progengrid: A Grid Framework for Bioinformatics. In: Apolloni, B., Marinaro, M., Tagliaferri, R. (eds) Biological and Artificial Intelligence Environments. Springer, Dordrecht. https://doi.org/10.1007/1-4020-3432-6_1
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DOI: https://doi.org/10.1007/1-4020-3432-6_1
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