A composable data management architecture for scientific applications

Proceedings - Challenges of Large Applications in Distributed Environments, CLADE 2005

Volumn 2005, Issue , 2005, Pages 35-44

  Ma, Yu ^a   Bramley, Randall ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL POWER; DATA MANAGEMENT SYSTEMS; SCIENTIFIC APPLICATIONS;

DATA PROCESSING; DATABASE SYSTEMS; PHOTOMETRY; RESEARCH AND DEVELOPMENT MANAGEMENT; SOCIETIES AND INSTITUTIONS; X RAY CRYSTALLOGRAPHY;

COMPUTER ARCHITECTURE;

EID: 33748860712     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CLADE.2005.1520897     Document Type: Conference Paper

References (49)

1. Bruker AXS. http://www.bruker-axs.de/. Bruker Instruments.
2. Grid physics network, http://www.griphyn.org/. The GriPhyN Project.
3. The GridFTP protocol and software. http: //www.globus.org/datagrid/ gridftp.html, The Globus Alliance.
4. Maui cluster scheduler. http://www. clusterresources.com/products/maui/, Cluster Resources, Inc.
5. MCAT - a meta information catalog. http://www.npaci.edu/DICE/SRB/mcat. html. San Diego Supercomputer Center, NPACI Data Intensive Computing Environment.
6. MySQL. http://www.mysql.com/. MySQLInc.
7. The NCSA HDF home page, http://hdf.ncsa.uiuc.edu/. The National Center for Supercomputing Applications.
8. NetCDF. http://unidata.ucar.edu/packages/netcdf/. UniData Program Center.
9. The ODBC Solution, Open Database Connectivity in Distributed Environments.
10. PBS Pro. http://www.pbspro.com/. Altair Grid Technologies.
11. PostgreSQL. http://www.postgresql.org/, PostgreSQL Global Development Group.
12. Reciprocal Net. http://www.reciprocalnet.org/. Reciprocal Net.
13. R. Armstrong, D. Gannon, A. Geist, K. Keahey, S. R. Kohn, L. McInnes, S. R. Parker, and B. A. Smolinski. Toward a common component architecture for high-performance scientific computing, In HPDC, 1999.
14. M. Atkinson, A. L. Chervenak, P. Kunszt, I. Narang, N. W. Paton, D. Pearson, A. Shoshani, and P. Watson. Data access, integration, and management, In I. Foster and C. Kesselman, editors, The Grid 2e, 2nd Edition: Blueprint for a New Computing Infrastructure, chapter 22, pages 391-429. Morgan Kaufmann Publishers, Inc., 2003. See also http: //www.ogsadai.org.uk/.
15. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. GenBank: update. Nucleic Acids Research, 32(Database issue):D23-D26, 2004. See also http://www.ncbi.nlm.nih.gov/Genbank/.
16. R. Bramley, K. Chiu, J. C. Huffman, K. Huffman, and D. F. McMullen. Instruments and sensors as network services: Making instrument first class members of the grid. Technical Report TR588, Indiana University, Computer Science Department, December 2003. http://www.cs.indiana.edu/cgibin/ techreportsmiNNN.cgi?trnum=TR588.
17. CCA-Forum. The DOE common component architecture project, http://www.extreme.indiana.edu/~gannon/cca_report.html, 2000.
18. A. Chervenak, E. Deelman, I. Foster, L. Guy, W. Hoschek, A. Iamnitchi, C. Kesselman, P. Kunst, M. Ripeanu, B. Schwartzkopf, H. Stockinger, K. Stockinger, and B. Tierney. Giggle: A framework for constructing scalable replica location services. In Proceedings of Supercomputing 2002 (SC2002), Baltimore, MD, November 2002.
19. A. Chervenak, I. Foster, C. Kesselman, C. Salisbury, and S. Tuecke. The data grid: Towards an architecture for the distributed management and analysis of large scientific datasets. Journal of Network and Computer Applications, 23:187-200, 2001.
20. See also The Globus Data Grid Effort http://www.globus.org/datagrid/.
21. K. Choi, Y. Ma, J.-H. Choi, and S. Kim. PLATCOM: A platform for computational comparative genomics. Bioinformatics, Accepted. See also http://platcom.informatics.indiana.edu/platcom/.
22. E. Deelman, O. Singh, M. P. Atkinson, A. Chervenak, N. P. C. Hong, C. Kesselman, S. Patil, L. Pearlman, and M.-H. Su. Grid-based metadata services. In 16th International Conference on Scientific and Statistical Database Management (SSDBM04), June 2004.
23. I. Foster and C. Kesselman, editors. The Grid: Blueprint for a New Computing Infrastructure. Morgan Kaufmann Publishers, Inc., San Franscisco, CA, 1999.
24. I. Foster, C. Kesselman, J. M. Nick, and S. Tuecke. Grid services for distributed system integration. Computer, 35(6):37-46, June 2002. See also http://www.globus. org/ogsa/.
25. I. Foster, J. Vckler, M. Wilde, and Y. Zhao. Chimera: A virtual data system for representing, querying, and automating data derivation. In 14th International Conference on Scientific and Statistical Database Management (SSDBM), 2002. See also http://www.griphyn.org/chimera/.
26. J. Gray, D. Slutz, A. Szalay, A. Thakar, J. vandenBerg, P. Kunszt, and C. Stoughton. Data mining the SDSS Sky-Server database. Technical Report MSR-TR-2002-01, Microsoft Research, January 2002, 40 pages. See also http://www.sdss.org/.
27. R. K. Honeycutt and G. W. Turner. Architecture of the software for the Indiana ccd automated telescope. In A. V. Filippenko, editor. Robotic Telescopes in the 1990s, volume CS-34. ASP Conference Series, 1992. ISBN 0-937707-53-8.
28. W. Hoschek, F. J. Janez, A. Samar, H. Stockinger, and K. Stockinger. Data management in an international data grid project. In Proceedings of the 1st IEEE/ACM International Workshop on Grid Computing, India, 2000. Springer Verlag Press, Germany. See also The DataGrid Project http://eu-datagrid.web.cern.ch/eu- datagrid/.
29. H. Hulen and O. Graf. Storage area networks and the high performance storage system. In 10th NASA Goddard Conference on Mass Storage Systems, April 2002. See also High Performance Storage System http://www.hpss-collaboration. org/.
30. S. Kohn, G. Kumfert, J. Painter, and C. Ribbens. Divorcing language dependencies from a scientific software library. In 10th SIAM Conference on Parallel Processing, Portsmouth, VA, March 12-14 2001. LLNL document UCRL-JC-140349. See also http://www.llnl.gov/CASC/components/babel.html.
31. J. Lattanzi, S. McNeeley, W. Pinover, E. Horwitz, I. Das, T. E. Schultheiss, and G. E. Hanks. A comparison of daily cc localization to a daily ultrasound-based system in prostate cancer. International Journal of Radiation Oncology*Biology*Physics, 43(4y,719-125, March 1999. See also http://www.nomos.com/page?id=1472.
32. Y. Ma, R. Bramley, and S. Kim. A data management architecture for computational biology. Technical Report TR607, Indiana University, Computer Science Department, January 2005. http://www.cs.indiana.edu/cgibin/techreports/ TRNNN.cgi?trnum=TR607.
33. J. M. May. Parallel I/O for High Performance Computing. Morgan Kaufmann Publishers, Inc, 2001. 366 pages.
34. M. D. McIlroy, E. N. Pinson, and B. A. Tague. Unix time-sharing system forward. The Belt System Technical Journal, 57(6, part 2): 1902, 1978.
35. J. D. Myers, T. C. Allison, S. Bittner, B. Didier, M. Frenklach, J. William H. Green, Y.-L. Ho, J. Hewson, W. Koegler, C. Lansing, D. Leahy, M. Lee, R. McCoy, M. Minkoff, S. Nijsure, G. von Laszewski, D. Montoya, C. Pancerella, R. Pinzon, W. Pitz, L. A. Rahn, B. Ruscic, K. Schuchardt, E. Stephan, A. Wagner, T. Windus, and C. Yang. A collaborative informatics infrastructure for multi-scale science. In 2nd International Workshop on Challenges of Large Applications in Distributed Environments (CLADE), pages 24-33, Honolulu, HI, June 2004.
36. J. D. Myers, A. Chappell, M. Elder, A. Geist, and J. Schwidder. Re-integrating the research record. COMPUTING IN SCIENCE & ENGINEERING, 5(3):44-50, MAY/JUNE 2003. See also http://www.scidac.org/SAM/.
37. W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. In Proceedings of the National Academy of Sciences USA, volume 85, pages 2444-2448, April 1988. See also http://www.ebi.ac.uk/ fasta33/.
38. J. L. Pfaltz, R. F. Haddleton, and J. C. French, Scalable, parallel, scientific databases. In M. Rafanelli and M. Jarke, editors, 10th International Conference on Scientific and Statistical Database Management, Capri, Italy, July 1-3 1998. IEEE Computer Society.
39. L. Pouchard, L. Cinquini, and G. Strand. The earth system grid discovery and semantic web technologies. In Workshop on Semantic Web Technologies for Searching and Retrieving Scientific Data, 2nd International Semantic Web Conference, Sundial Resort, Sanibel Island, Florida, October 20 2003. See also Earth System Grid https://www.earthsystemgrid.org/.
40. A. Rajasekar, M. Wan, R. Moore, W. Schroeder, G. Kremenek, A. Jagatheesan, C. Cowart, B. Zhu, S.-Y. Chen, and R. Olschanowsky. Storage resource broker - managing distributed data in a grid. Computer Society of India Journal, Special Issue on SAN, 33(4):42-54, October 2003. See also http://www.npaci.edu/DICE/SHE/.
41. D. Schissel, K. Keahey, T. Araki, J. Burruss, E. Feibush, S. Flanagan, T. Fredian, M. Greenwald, S. Klasky, T. Leggett, K. Li, D. McCune, P. Lane, M. Papka, Q. Peng, L. Randerson, A. Sanderson, J. Stillerman, M. Thompson, and G. Wallace. The national fusion collaboratory project: Applying grid technology for magnetic fusion research. In Workshop on Case Studies on Grid Applications (GGF 10), Berlin, Germany, March 13 2004. See also The National FusionGrid http://www.fusiongrid.org/.
42. S. Schwarte, W. J. Kent, A. Smit, Z. Zhang, R. Baertsch, R. C. Hardison, D. Haussler, and W. Miller. Human-mouse alignments with BLASTZ, Genome Research, 13(1):103-107, January 2003. See also http://bio.cse.psu.edu/.
43. M. Shaw and D. Garlan, Software Architecture: Perspectives on an Emerging Discipline. Prentice Hall Publishing, 1996. 242 pages.
44. A. Sim, J. Gu, A. Shosham, and V. Natarajan. DataMover: Robust terabyte-scale multi-file replication over wide-area networks. In 16th International Conference on Scientific and Statistical Database Management (SSDBM 2004), Santorini Island, Greece, June 21-23 2004,
45. See also Particle Physics Data Grid http://www.ppdg.net/.
46. G. Singh, S. Bharathi, A. Chervenak, E. Deelman, C. Kesselman, M. Manohar, S. Patil, and L. Pearlman. A metadata catalog service for data intensive applications. In Proceedings of the ACM/IEEE SC2003 Conference, Phoenix, AZ, November 15-21 2003.
47. C. G. Thurston. LIMS/instrument integration computing architecture for improved automation and flexibility. American Laboratory, September 2004. See also http://www.thermo.com/informatics.
48. D. C. Wells, E. Greisen, and R. H. Harten. FITS: A flexible image transport system. Astronomy & Astrophysics Supplement Series, 44:363-370, June 1981.
49. See also FITS: The Astronomical Image and Table Format http://fits.gsfc.nasa.gov/.