An extensible, scalable architecture for managing Bioinformatics data and analyses

Proceedings - 4th IEEE International Conference on eScience, eScience 2008

Volumn , Issue , 2008, Pages 190-197

  Shah, Anuj R ^a   Singhal, Mudita ^a   Gibson, Tara D ^a   Sivaramakrishnan, Chandrika ^a   Waters, Katrina M ^a   Gorton, Ian ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; INDUSTRIAL RESEARCH;

ANALYSIS OF DATUM; BIOINFORMATICS DATUM; BIOINFORMATICS RESOURCES; COMPLEX ANALYSIS; COMPUTATIONAL CAPABILITIES; DATA MANAGEMENTS; EXPERIMENTAL DATUM; HIGH THROUGHPUTS; HIGH-THROUGHPUT DATUM; INTEGRATION FRAMEWORKS; SCALABLE ARCHITECTURES; SCIENTIFIC ACTIVITIES; SOFTWARE INFRASTRUCTURES; SYSTEMS BIOLOGIES; TOOL INTEGRATIONS; WORK-FLOWS;

SOFTWARE ARCHITECTURE;

EID: 62749127318     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/eScience.2008.69     Document Type: Conference Paper

References (27)

1. Wiley, S.H., Systems Biology. The Scientist, 2006. 20(6): p. 53-57.
2. Kolpakov, F.A., BioUML-A Framework For Visual Modeling And Simulation Biological Systems, in International Conference Bioinformatics of Genome Regulation and Structure. 2002.
3. Marzolf, B., et al., SEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics, 2006. 7: p. 286-291.
4. Bergmann, F.T. and H.M. Sauro. SBW - A Modular Framework For Systems Biology. in Proceedings of the 2006 Winter Simulation Conference. 2006. Monterey, California, USA.
5. Li, P., et al., Taverna: a tool for building and running workflows of services. Nucleic Acid Research, 2006. 34(Web Server Issue): p. W729-732.
6. Shah, A.R., et al., Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager. Bioinformatics, 2007. 23(7): p. 906-909.
7. Wheeler, D.L., et al., Database resources of the National Center for Biotechnology Information. Nucleic Acid Research, 2006. 34(Database issue): p. 173-180.
8. Kersey, P.J., et al., The International Protein Index: An integrated database for proteomics experiments. Proteomics, 2004. 4(7): p. 1985-1988.
9. Bairoch, A., et al., The Universal Protein Resource (UniProt). Nucleic Acid Research, 2005. 33(Database Issue): p. 154-159.
10. Bader, G.D. and C.W. Hogue, BIND: A Data Specification for Storing and Describing Biomolecular Interactions, Molecular Complexes and Pathways. Bioinformatics, 2000. 16(5): p. 465-477.
11. Kanehisa, M. and S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acid Research, 2000. 28(1): p. 27-30.
12. Consortium, T.G.O., Gene Ontology: tool for the unification of biology. Nature Genetics, 2000. 25: p. 25-29.
13. Bowers, P.M., et al., Prolinks: a database of protein functional linkages derived from coevolution. Genome Biology, 2004. 5(5): p. R35.
14. Shannon, P.T., et al., The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics, 2006. 7: p. 176-188.
15. Saeed, A.I., et al., TM4: a free, open-source system for microarray data management and analysis. Biotechniques, 2003. 34: p. 374-378.
16. Shannon, P.T., et al., Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 2003. 13(11): p. 2498-2504.
17. Bare, J.C., et al., The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics, 2007. 8: p. 456-468.
18. Gorton, I., et al., The MeDICI Integration Framework: A Platform for High Performance Data Streaming Applications, in 7th IEEE/IFIP Working Conference on Software Architecture. 2008, IEEE Computer Society: Vancouver, Canada.
19. Buneman, P., S. Khanna, and W.-C. Tan. Data Provenance: Some Basic Issues, in Lecture Notes in Computer Science, Foundations of Software Technology and Theoretical Computer Science 2000: Springer Link.
20. Kiebel, G.R., et al., PRISM: A data management system for high throughput proteomics. Proteomics, 2006. 6(6): p. 1783-1790.
21. Lee, T.J., et al., BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics, 2006. 7: p. 170-175.
22. Michalickova, K., et al., SeqHound: Biological Sequence and Structure Database as a Platform for Bioinformatics Research. BMC Bioinformatics, 2002. 3(1).
23. Goesmann, A., et al., Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. Journal of Biotechnology, 2003. 106: p. 157-167.
24. Oikawa, M.K., et al., GenFlow: Generic flow for integration, management and analysis of molecular biology data. Genetics and Molecular Biology, 2004. 27(4): p. 691-695.
25. Lu, Q., et al., KDE Bioscience: Platform for bioinformatics analysis workflows. Journal of Biomedical Informatics, 2006. 39: p. 440-450.
26. Mewes, H.W., et al., MIPS: a database for genomes and protein sequences. Nucleic Acid Research, 2002. 30(1): p. 31-34.
27. Peri, S., et al., Development of human protein reference database an an initial platform for approaching systems biology in humans. Genome Research, 2003. 13(10): p. 2363-71.