Design and implementation of a generalized laboratory data model

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Wendl, Michael C ^a   Smith, Scott ^a   Pohl, Craig S ^a   Dooling, David J ^a   Chinwalla, Asif T ^a   Crouse, Kevin ^a   Hepler, Todd ^a   Leong, Shin ^a   Carmichael, Lynn ^a   Nhan, Mike ^a   Oberkfell, Benjamin J ^a   Mardis, Elaine R ^a   Hillier, LaDeana W ^a   Wilson, Richard K ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTION TECHNIQUES; DESIGN AND IMPLEMENTATIONS; INFORMATION MANAGEMENT SYSTEMS; PROCESSING ENVIRONMENTS; STANDARDIZED INTERFACES; TRADITIONAL APPROACHES; WASHINGTON UNIVERSITY; WORKFLOW MANAGEMENT SYSTEMS;

COMPUTER PROGRAMMING LANGUAGES; INFORMATION MANAGEMENT; LABORATORIES; MODELS; PIPELINES; WORK SIMPLIFICATION;

PIPELINE PROCESSING SYSTEMS;

ARTICLE; COMPUTER INTERFACE; COMPUTER LANGUAGE; GENE MAPPING; GENE SEQUENCE; INFORMATION SYSTEM; LABORATORY AUTOMATION; PROCESS CONTROL; PROCESS DESIGN; BIOLOGY; DATA BASE; FACTUAL DATABASE; INFORMATION RETRIEVAL; LABORATORY; METHODOLOGY; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; INFORMATION STORAGE AND RETRIEVAL; LABORATORIES; MODELS, THEORETICAL; USER-COMPUTER INTERFACE;

EID: 38049134511     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-362     Document Type: Article

References (39)

1. International Human Genome Sequencing Consortium Initial Sequencing and Analysis of the Human Genome Nature 2001, 409(6822):860-921. 11237011
2. Gilbert GN The Transformation of Research Findings into Scientific Knowledge Social Studies of Science 1976, 6(3/4):281-306.
3. Fenyö D Beavis RC Informatics and Data Management in Proteomics Trends in Biotechnology 2002, 20(12):S35-S38. 12570158
4. Pevzner PA Tang H Waterman MS An Eulerian Path Approach to DNA Fragment Assembly Proceedings of the National Academy of Sciences 2001, 98(17):9748-9753.
5. Gordon D Abajian C Green P Consed: A Graphical Tool for Sequence Finishing Genome Research 1998, 8(3):195-202. 9521923
6. Smith TM Abajian C Hood L Hopper: Software for Automating Data Tracking and Flow in DNA Sequencing Computer Applications in the Biosciences 1997, 13(2):175-182. 9146965
7. The Berkeley Database Library: LibDB http://sourceforge.net/projects/ libdb/
8. Dedhia NN McCombie WR Kaleidaseq: A Web-Based Tool to Monitor Data Flow in a High Throughput Sequencing Facility Genome Research 1998, 8(3):313-318. 310700 9521934
9. Haebel PW Arcus VL Baker EN Metcalf P LISA: An Intranet-Based Flexible Database for Protein Crystallography Project Management Acta Crystallographica Section D 2001, 57(9):1341-1343.
10. Sanchez-Villeda H Schroeder S Polacco M McMullen M Havermann S Davis G Vroh-Bi I Cone K Sharopova N Yim Y Schultz L Duru N Musket T Houchins K Fang Z Gardiner J Coe E Development of an Integrated Laboratory Information Management System for the Maize Mapping Project Bioinformatics 2003, 19(16):2022-2030. 14594706
11. Donofrio N Rajagopalon R Brown D Diener S Windham D Nolin S Floyd A Mitchell T Galadima N Tucker S Orbach MJ Patel G Farman M Pampanwar V Soderlund C Lee YH Dean RA PACLIMS:A Component LIM System for High-Throughput Functional Genomic Analysis BMC Bioinformatics 2005, 6. article no. 94 1090558 15826298
12. Conery JS Catchen JM Lynch M Rule-Based Workflow Management for Bioinformatics VLDB Journal 2005, 14(3):318-329.
13. Liang C Sun F Wang H Qu J Freeman RM Pratt LH Cordonnier-Pratt MM MAGIC-SPP: A Database-Driven DNA Sequence Processing Package with Associated Management Tools BMC Bioinformatics 2006 7 article no. 115
14. Kumar CG LeDuc R Gong G Roinishivili L Lewin HA Liu L ESTIMA, A Tool for EST Management in a Multi-Project Environment BMC Bioinformatics 2004 5 article no. 176
15. D'Agostino N Aversano M Chiusano ML ParPEST: A Pipeline for EST Data Analysis Based on Parallel Computing BMC Bioinformatics 2005 6 article no. S9
16. Imbert MC Nguyen VK Granjeaud S Nguyen C Jordan BR LABNOTE: A Laboratory Notebook System Designed for Academic Genomics Groups Nucleic Acids Research 1999, 27(2):601-607. 148221 9862986
17. Prilusky J Oueillet E Ulryck N Pajon A Bernauer J Krimm I Quevillon-Cheruel S Leulliot N Graille M Liger D Trésaugues L Sussman JL Janin J van Tilbeurgh H Poupon A HalX: An Open-Source LIMS (Laboratory Information Management System) for Small- to Large-Scale Laboratories Acta Crystallographica Section D 2005, 61(6):671-678.
18. Pajon A Ionides J Diprose J Fillon J Fogh R Ashton AW Berman H Boucher W Cygler M Deleury E Esnouf R Janin J Kim R Krimm I Lawson CL Oeuillet E Poupon A Raymond S Stevens T van Tilbeurgh H Westbrook J Wood P Ulrich E Vranken W Xueli L Laue E Stuart DI Henrick K Design of a Data Model for Developing Laboratory Information Management and Analysis Systems for Protein Production Proteins 2005, 58(2):278-284. 15562521
19. Goodman N Rozen S Stein LD Smith AG The LabBase System for Data Management in Large Scale Biology Research Laboratories Bioinformatics 1998, 14(7):562-574. 9730921
20. Kokocinski F Wrobel G Hahn M Lichter P QuickLIMS: Facilitating the Data Management for DNA-Microarray Fabrication Bioinformatics 2003, 19(2):283-284. 12538251
21. Stein LD Thierry-Mieg J AceDB: A Genome Database Management System Computing in Science and Engineering 1999, 1(3):44-52.
22. Wilson RK Ley TJ Cole FS Milbrandt JD Clifton S Fulton L Fewell G Minx P Sun H McLellan M Pohl C Mardis ER Mutational Profiling in the Human Genome Cold Spring Harbor Symposia on Quantitative Biology 2003, 68:23-29. 15338599
23. Wall L Christiansen T Orwant J Programming Perl Sebastopol CA: O'Reilly & Associates, Inc 3 2000
24. Wendl MC Dear S Hodgson D Hillier L Automated Sequence Preprocessing in a Large-Scale Sequencing Environment Genome Research 1998, 8(9):975-984. 310779 9750196
25. Palmer RC The Bar Code Book: Comprehensive Guide to Reading, Printing, Specifying, and Applying Bar Code and Other Machine-Readable Symbols Peterborough NH: Helmers Publishing 4, 2001.
26. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank Nucleic Acids Research 2003, 31:23-27. 165504 12519940
27. Hollingsworth D The Workflow Reference Model Tech. Rep. TC00-1003 The Workflow Management Coalition, Hampshire, UK 1995
28. Ewing B Hillier L Wendl MC Green P Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Genome Research 1998, 8(3):175-185. 9521921
29. Ailamaki A Ioannidis YE Livny M Scientific Workflow Management by Database Management Proceedings of the Tenth International Conference on Scientific and Statistical Database Management IEEE Computer Society Rafanelli M, Jarke M 1998, 190-199.
30. Anahory S Murrary D Data Warehousing in the Real World: A Practical Guide for Building Decision Support Systems Boston MA: Addison-Wesley 1997
31. Bonfield JK Staden R Experiment Files and their Application during Large-Scale Sequencing Projects DNA Sequence 1996, 6(2):109-117. 8907307
32. Loney K Oracle Database 10g: The Complete Reference New York NY: McGraw Hill 2004.
33. DuBois P MySQL Cookbook Sebastopol CA: O'Reilly & Associates, Inc 2 2006
34. Worsley JC Drake JD Practical PostgreSQL Sebastopol CA: O'Reilly & Associates, Inc 2002
35. Smith S UR: A Universal Relational Software Framework YAPC North America Conference 2006.
36. Descartes A Bunce T Programming the Perl DBI Sebastopol CA: O'Reilly & Associates, Inc 2000.
37. Quest Software: Toad http://www.quest.com/toad/
38. Duncan A Hull S Oracle and Open Source Sebastopol CA: O'Reilly & Associates, Inc 2001
39. Collins-Snssman B Fitzpatrick BW Pilato CM Version Control With Subversion Sebastopol CA: O'Reilly & Associates, Inc 2004