The LabBase system for data management in large scale biology research laboratories

Bioinformatics

Volumn 14, Issue 7, 1998, Pages 562-574

  Goodman, Nathan ^a   Rozen, Steve ^b   Stein, Lincoln D ^c   Smith, Alex G ^a  

^a JACKSON LABORATORY   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS; ARTICLE; BIOLOGY; COMPUTER PROGRAM; DATA BASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; LABORATORY TEST; MATERIALS; MEDICAL RESEARCH; MODEL; PRIORITY JOURNAL;

EID: 0031706018     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.7.562     Document Type: Article

References (30)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J Molec. Biol., 215, 403-410.
2. Buneman, P., Davidson, S.B., Hillebrand, G. and Suciu, D. (1996) A query language and optimization techniques for unstructured data. Proceedings of the ACM Conference on Management of Data (SIGMOD), Montreal, Quebec, June 1996.
3. Cattell, R. (1994) Object Data Management Revised Edition: Object-Oriented and Extended Relational Database Systems. Addison-Wesley.
4. Chen, I.-M.A. and Markowitz, V.M. (1995) An overview of the Object-Protocol Model (OPM) and OPM data management tools. Inf Sys., 20(5), 393-418.
5. Clark, S.P., Evans, G.A. and Garner, H.R. (1994) Informatics and automation used in physical mapping of the genome. In Smith, D. (ed.), Biocomputing: Informatics and Genome Projects. Academic Press, pp. 13-49.
6. Date, C.J. (1995) An Introduction to Database Systems. Addison-Wesley.
7. Date, C.J. and White, C. (1991) A Guide to Oracle. Addison-Wesley.
8. Dietrich, W.F., Miller, J., Steen, R., Merchant, M.A., Damron-Boles, D., Husain, Z., Dredge, R., Daly, M.J., Ingalls, K.A., O'Connor, T.J., Evans, C.A., DeAngelis, M.M., Levinson, D.M., Kruglyak, L., Goodman, N., Copeland, N.G., Jenkins, N.A., Hawkins, T.L., Stein, L.D., Page, D.C. and Lander, E.S. (1996) A comprehensive genetic map of the mouse genome. Nature, 380, 149-152.
9. Durbin, R. and Mieg, J.T. (1991) A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov.
10. Goodman, N., Rozen, S. and Stein, L.D. (1994) Building a laboratory information system around a C++-based object-oriented DBMS. Proceedings of the 20th International Conference on Very Large Data Bases (VLDB), Santiago de Chile, Chile, The Very Large Data Bases (VLDB) Endowment Inc.
11. Goodman, N., Rozen, S. and Stein, L.D. (1998) The LabFlow system for workflow management in large scale biology research laboratories. Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB), Montreal, Quebec, June 1998.
12. Hudson, T.J., Stein, L.D., Gerety, S.S., Ma, J., Castle, A.B., Silva, J., Slonim, D.K., Baptista, R., Kruglyak, L., Xu, S.-H., Hu, X., Colbert, A.M.E., Rosenberg, C., Reeve-Daly, M.P., Rozen, S., Hui, L., Wu, X., Vestergaard, C., Wilson, K.M., Bae, J.S., Maitra, S., Ganiatsas, S., Evans, C.A., DeAngelis, M.M., Ingalls, K.A., Nahf, R.W., Lloyd, J., Horton, T., Anderson, M.O., Collymore, A.J., Ye, W., Kouyoumjian, V., Zemsteva, I.S., Tam, J., Devine, R., Courtney, D.F., Renaud, M.T., Nguyen, H., O'Connor, T.J., Fizames, C., Faure, S., Gyapay, G., Dib, C., Morissette, J., Orlin, J.B., Birren, B.W., Goodman, N., Weissenbach, J., Hawkins, T.L., Foote, S., Page, D.C. and Lander, E.S. (1995) An STS-based map of the human genome. Science, 270, 1945-1955.
13. Kerlavage, A.R., Adams, M.D., Kelley, J.C., Dubnick, M., Powell, J., Shanmugam, P., Venter, J.C. and Fields, C. (1993). Analysis and management of data from high throughput sequence tag projects. Proceedings of the 26th Annual Hawaii International Conference on System Sciences, IEEE Computer Society Press.
14. Kerlavage, A.R., FitzHugh, W., Glodek, A., Kelley, J.C., Scott, J., Shirley, R., Sutton, G., Wai-Chiu, M., White, O. and Adams, M.D. (1995) Data management and analysis for high-throughput DNA sequencing projects. IEEE Eng. Med. Biol., 14, 710-717.
15. Lamb, C., Landis, G., Orenstein, J. and Weinreb, D. (1991) The Object-Store database system. Commun. ACM, 34(10), 50-63.
16. McGoveran, D. and Date, C.J. (1992) A Guide to Sybase and SQL Server, Addison-Wesley.
17. McHugh, J., Abiteboul, S., Goldman, R., Quass, D. and Widom, J. (1997) Lore: a database management system for semistructured data. SIGMOD Record, 26(3), 54-66.
18. Orfali, R., Harkey, D. and Edwards, J. (1996) The Essential Distributed Objects Survival Guide. John Wiley & Sons.
19. Ramakrishnan, R. and Ullman, J.D. (1995) A survey of research on deductive database systems. J Logic Programm., 23(2), 125-149.
20. Rozen, S., Stein, L.D. and Goodman, N. (1995) LabBase: a database to manage laboratory data in a large-scale genome-mapping project. IEEE Trans. Eng. Med. Biol., 14, 702-709.
21. Sargent, R., Fuhrman, D., Critchlow, T., Sera, T.D., Mecklenburg, R., Lindstrom, G. and Cartwright, P. (1996) The design and implementation of a database for human genome research. Proceedings of the Eighth International Conference on Scientific and Statistical Database Management, Stockholm, Sweden, IEEE Computer Society Press, June 1996.
22. Steen, R. (1997) Genetic maps of the rat genome. http://www.genome.wi.mit.edu/rat/public/. Whitehead Institute/MIT Center for Genome Research.
23. Stein, L.D., Marquis, A., Dredge, E., Reeve, M.P., Daly, M., Rozen, S. and Goodman, N. (1994a) Splicing UNIX into a genome mapping laboratory. Proceedings of the USENIX Summer 1994 Technical Conference, USENIX.
24. Stein, L.D., Rozen, S. and Goodman, N. (1994b) Managing laboratory workflow with LabBase. Proceedings of the 1994 Conference on Computers in Medicine (CompMed94).
25. Stein, L.D. (1996) How Perl saved the human genome project. Perl J., 1(2), 5-9.
26. Ullman, J.D. (1988) Principles of Database and Knowledge-Base Systems. Computer Science Press.
27. Wall, L., Christiansen, T. and Schwartz, R.L. (1996) Programming Perl. O'Reilly & Associates.
28. WfMC (1996) Workflow Management Coalition. http://www.aiim.org/wfmc/. Workflow Management Coalition (WfMC), October 1996.
29. WICGR (1997a) Genetic and physical maps of the mouse genome. http://www.genome.wi.mit.edu/cgi-bin/mouse/index. Whitehead Institute/MIT Center for Genome Research.
30. WICGR (1997b) Welcome to the Whitehead Institute/MIT Genome Sequencing Project. http://www-seq.wi.mit.edu/. Whitehead Institute/MIT Center for Genome Research.