Information management systems for pharmacogenomics

Pharmacogenomics

Volumn 3, Issue 5, 2002, Pages 651-667

  Thallinger, Gerhard G ^a   Trajanoski, Slave ^a   Stocker, Gernot ^a   Trajanoski, Zlatko ^a  

^a GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

Author keywords

Application services; Data warehouse; Information management system; Network technologies; Parallel algorithms

Indexed keywords

ACCURACY; COMPUTER NETWORK; COMPUTER SYSTEM; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; GENE FUNCTION; INFORMATION PROCESSING; INFORMATION PROCESSING DEVICE; INTERNET; MEDICAL RESEARCH; PHARMACOGENOMICS; REVIEW; TECHNOLOGY;

ANIMALS; COMPUTER COMMUNICATION NETWORKS; HUMANS; INFORMATION MANAGEMENT; PHARMACOGENETICS;

EID: 0036737934     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/14622416.3.5.651     Document Type: Review

References (61)

1. Lander ES, Linton LM, Bitten B et al.: Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. Venter JC, Adams MD, Myers EW et al.: The sequence of the human genome. Science 291, 1304-1351 (2001).
3. Shalon D, Smith SJ, Brown PO: A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645 (1996).
4. van't Veer LJ, Dai H, van de Vijver MJ et al: Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
5. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL: GenBank. Nucleic Acids Res. 30, 17-20 (2002).
6. Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48 (2000).
7. Berman HM, Bhat TN, Bourne PE et al.: The Protein Data Bank and the challenge of structural genomics. Nat. Struct. Biol. 7, 957-959 (2000).
8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
9. Pearson WR: Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635-650 (1991).
10. Eddy SR: Profile hidden Markov models. Bioinformatics 14, 755-763 (1998).
11. Kimball R: The Data Warehouse Toolkit: Practical Techniques For Building Dimensional Data Warehouses. John Wiley & Sons, New York, USA 310 (1996).
12. Sheth AP, Larson JA: Federated Database Systems for managing distributed, heterogeneous and autonomous databases. ACM Computing Survey 22, 183-236 (1990).
13. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L: The distributed annotation system. BMC Bioinformatics 20(1), 7 (2001).
14. Trelles O: On the parallelisation of bioinformatics applications. Brief Bioinform. 2(2), 181-194 (2001).
15. Grant JD, Dunbrack RL, Manion FJ, Ochs MF: BeoBLAST. distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics 18(5), 765-766 (2002).
16. Foster I, Kesselman C: The Grid: Blueprint for a New Computing Infrastructure. Morgan Kaufmann Publishers, USA (1999).
17. Graham S, Simeonov S, Boubez T et al.: Building web services with Java: making sense of XML, SOAP, WSDL and UDDI. SAMS (2001).
18. Flynn MJ: Some computer organizations and their effectiveness. IEEE Trans. Computer C-21, 948-960 (1972).
19. Altschul SF, Madden TL, Schaffer AA et al.: Gapped BLAST and PSI-BLAST: a new generation of protein DB search programs. Nucleic Acids Res. 25 (17), 3389-3402 (1997).
20. Foster I: Designing and Building parallel programs: concepts and tools for parallel software engineering. Addison-Wesley Publishing Company, Inc., USA (1994).
21. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
22. Gene expression specification. OMG Final Adopted Specification. http://www.omg.org/cgi-bin/doc?dtc/02-02-05.pdf (2002).
23. Buyya R: High Performance Cluster Computing: Architectures and Systems (Vol. 1 & 2). Prentice Hall, NJ, USA (1999).
24. Brazma A, Hingamp P, Quackenbush J et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 29, 365-371 (2001).
25. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29. (2000).
26. The Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425-1433 (2001).
27. Brazma A, Sarkans U, Robinson A et al.: Microarray data representation, annotation and storage. Adv, Biochem. Eng. Biotechnol. 77(Chip Technology), 113-139 (2002).
28. Gardiner-Garden M, Littlejohn TG: A comparison of microarray databases. Brief Bioinform. 2(2), 143-158 (2001).
29. Stoesser G, Baker W, van den Broek A et al.: The EMBL nucleotide sequence database. Nucleic Acids Res. 30(1), 21-26 (2002).
30. Baxevanis AD: The molecular biology database collection: 2002 update. Nucleic Acids Res. 30(1), 1-12 (2002).
31. Porter J: Disk Trend 1998 Report, Proceedings of the 100th Anniversary conference: Magnetic Recording and Information Storage Technological Milestones and Future Outlook Conference (1998).
32. Hayes B: Terabyte territory. American Scientist 90(3), 212-216 (2002).
33. Buyya R: Economic-based Distributed Resource Management and Scheduling for Grid Computing., PhD Thesis, Monash University; Melbourne, Australia (2002).
34. Allcock B, Bester J, Bresnahan J et al.: Data management and transfer in high-performance computational grid environments. Parallel Computing 28, 749-771 (2002).
35. Buyya R, Branson K, Giddy J, Abramson D: The virtual laboratory: A toolset to enable distributed molecular modeling for drug design on the world-wide grid. J. Concurremy Computations: Practice Experience In press (2002).
36. Richards WG: Virtual screening using grid computing: the screensaver project. Nat. Rev. Drug Discov. 1 (7), 551-555 (2002).
37. Larson S, Snow C, Shirts M, Pande V: FoldingΗome and GenomeΗome: using distributed computing to tackle previously intractable problems in computational biology. To appear in Computational Genomics, Richard Grant, Horizon Press (2002).
38. Rognes T: ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res. 29(7), 1647-1652 (2001).
39. Bjornson RD, Sherman AH, Weston SB, Willard N, Wing J: TurboBLAST©: a parallel implementation of BLAST based on the TurboHub® process integration architecture. Turbogenomics white paper. http://www.turbogenomics.com/products/turboblast.pdf (2002)
40. Camp N, Cofer H, Gomperts R: 1998: high-throughput BLAST. SGI White Paper. http://www.sgi.com/industries/sciences/chembio/resources/papers/ HTBlast/HTitepaper.pdf (1998).
41. Chen R, Taaffe-Hedglin C, Willard N, Sherman A: Benchmark and performance analysis of TurboBLAST on IBM® xSeries™ server cluster. IBM Performance Technical Report. (http://www.redbooks.ibm.com/redpapers/pdfs/redp0443.pdf) (2002).
42. SGI high-throughput computational environment performance sheet, (http://www.sgi.com/industries/sciences/chembio/pdf/htc-perf.pdf) (2001).
43. SGI Bioinformatics Performance Report (http://www.sgi.com/industries/sciences/chembio/pdf/bioperf01.pdf) (2001).
44. Newcomer E: Understanding Web Services: XML, WSDL, SOAP and UDDI. Addison Wesley Professional (2002).
45. IBM Web Services Architecture Team: Web Services architecture overview. ftp://www6.software.ibm.com/software/developer/library/w-ovr.pdf (2000).
46. W3C: Extensible Markup Language (XML) 1.0 (Second Edition). W3C Recommendation. http://www.w3.org/TR/2000/REC-xml-20001006.pdf (2000).
47. W3C: Simple Object Access Protocol (SOAP) 1.1. W3C Note. http://www.w3.org/TR/2000/NOTE-SOAP-20000508 (2000).
48. UDDI.org: UDDI Version 2.01 Operator's Specification. UDDI Published Specification. http://uddi.org/pubs/Operators.pdf (2002).
49. UDDI.org: UDDI Version 2.04 API Specification. UDDI Published Specification. http://uddi.org/pubs/ProgrammersAPI. pdf (2002).
50. W3C: Web Services Description Language (WSDL) 1.1. W3CNote. http://www.w3.org/TR/2001/NOTE-wsdl-20010315 (2001).
51. Anbazhagan M, Nagarajan A: Understanding quality of service for Web services. IBM White Paper ftp://www6.software.ibm.com/software/developer/library/ws-quality.pdf (2002).
52. Macromolecular Structure Specification. OMG Specification. http://cgi.omg.org/cgi-bin/doc?formal/02-05-01.pdf (2002).
53. Etzold T, Ulyanov A, Argos P: SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266, 114-128 (1996).
54. Etzold T, Verde G: Using views for retrieving data from extremely heterogeneous databanks. Pac. Symp. Biocomput. 134-141 (1997).
55. Zdobnov EM, Lopez R, Apweiler R, Etzold T: The EBI SRS server-recent developments. Bioinformatics 18(2), 368-373 (2002).
56. Kerlavage A, Bonazzi V, di Tommaso M et al.: The Celera Discovery System. Nucleic Acids Res. 30, 129-136 (2002).
57. Venter JC: Plenary lecture, RECOMB2002 Conference, Washington DC, April 2002.
58. Sunderam VS: PVM: A framework for parallel distributed computing. J. Concurrency: Practice and Experience 2 (4), 315-339 (1990).
59. Geist GA, Sunderam VS: Network based concurrent computing on the PVM system. J. Concurrency: Practice and Experience 4(4), 293-311 (1992).
60. Dongarra J, Geist AL, Manchek R, Sunderam V: Integrated PVM framework supports heterogeneous network computing. Computers in Physics 7(2), 166-175 (1993).
61. Stankovic N, Zhang KA: A distributed parallel programming framework. IEEE Transactions on Software Engineering 28(5) 478-493 (2002).