Laboratory Information Management System (LIMS)
The laboratory information management system (LIMS) for the pilot Genomic Science Center is the central data repository for all information related to processing and analysis of Center samples. It maintains a detailed history for each sample by capturing processing parameters, protocols, stocks, tests and analytical results for the complete life cycle of the sample. Project and study data are also maintained to define each sample in the context of the research tasks it supports.
LIMS systems were implemented at both ORNL and PNNL using the Nautilus™ software from Thermo Electron Corporation (http://www.thermo.com). This software provides a comprehensive yet extensible framework for a LIMS that can be customized to meet the requirements of the Genomic Science project. Nautilus™ uses client/server architecture to access data maintained in a central Oracle database and presents an interface based on the Microsoft Windows Explorer paradigm.
The LIMS maintains the history of all stock items. An expression construct can be traced back through all the processing steps to the original entry clone primers.
The LIMS is configured by establishing workflows that parallel the processing steps completed in the laboratory. When samples are logged into the LIMS using the predefined workflows the required data records are automatically generated and ready for data entry. The LIMS maintains complete sample pedigrees by tracking all items contributing to a sample as well as all the items derived from the sample. The LIMS interface also provides links to external records such as such as lab protocols, gel images, and data analysis results such as SEQUEST DTA Select HTML files.
The rigorous LIMS configuration enforces project standards and provides data security necessary to ensure high quality defensible data for the Center’s scientific mission.
Related Publications
2008
- Article: J.M. Gilmore, D.L. Auberry, J.L. Sharp, A.M. White, K.K. Anderson, D.S. Daly, "A Bayesian Estimator of Protein-Protein Association Probabilities," Bioinformatics, 24 (13): 1554–1555, 2008. [PDF]
- Article: W. R. Cannon, B.-J. Webb-Robertson, A. R. Willse, M. Singhal, L. A. McCue, J. E. McDermott, R. C. Taylor, K. M. Waters, C. S. Oehmen, "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics, in Computational and Systems Biology: Applications and Methods," Computational Systems Biology, 2008 (in press).
- Article: R.C. Taylor, M. Singhal, D.S. Daly, K.O. Domico, A.M. White, D.L. Auberry, K.J. Auberry, B.S. Hooker, G.B. Hurst, J.E. McDermott, W.H. McDonald, D.A. Pelletier, D.D. Schmoyer, W.R. Cannon, "SEBINI-CABIN: an analysis pipeline for biological network inference, with a case study in protein-protein interaction network reconstruction," Int. J. Data Mining Bioinform. 2008 (accepted).
- Abstract: Kevin K. Anderson, et al., Advanced Data Analysis Pipeline for Determination of Protein Complexes and Interaction Networks at the Genomics:GTL Center for Molecular and Cellular Systems, 2008 Genomics:GTL Awardee Workshop VI, Bethesda, Maryland.
- Abstract: William R. Cannon, et al., Analysis of the Dynamical Modular Structure of Rhodopseudomonas palustris Based on Global Analysis of Protein-Protein Interactions, 2008 Genomics:GTL Awardee Workshop VI, Bethesda, Maryland.
- Article: J.L. Sharp, J.J. Borkowski, D.D. Schmoyer, D.S. Daly, S. Purvine, W.R. Cannon, G.B. Hurst, "Statistically Appraising Process Quality of Affinity Isolation Experiments," Comp. Stat. Data Analysis 2008. [PDF]
2007
- Abstract: Denise D. Schmoyer, et al., The Microbial Protein-Protein Interaction Database (MiPPI), 2007 Genomics:GTL Awardee Workshop V, Bethesda, Maryland
2006
- Abstract: William R. Cannon, et al., Computational Approaches for Aggregating and Scoring Protein-Protein Interaction Data, 2006 Contractor-Grantee Workshop, North Bethesda, MD (PDF)
- Abstract: G.B. Hurst, et al., The Microbial Interactome Database: An Online System for Identifying Interactions Between Proteins of Microbial Species, 2006 Contractor-Grantee Workshop, North Bethesda, MD (PDF)
- Article: Chongle Pan, et al., "ProRata: A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation," Analytical Chemistry, 78, 7121-31, 2006. [PDF]
- Article: Chongle Pan, et al.,"Robust Estimation of Peptide Abundance Ratios and Rigorous Scoring of Their Variability and Bias in Quantitative Shotgun Proteomics," Analytical Chemistry, 78, 7110-20, 2006. [PDF]
2005
- Presentation: D.L. Auberry, et al., "Using Nautilus to Capture Metadata for Identification of Protein Interactions," Thermo Informatics World, Bonita Springs, FL, September 20, 2005. PNNL-SA-46394.
- Abstract: Frank W. Larimer, et al., Center for Molecular and Cellular Systems: Statistical Screens for Datasets from High- Throughput Protein Pull-Down Assays, 2005 Contractor-Grantee Workshop, Washington, DC
- Article: David L. Tabb, C. Narasimhan, M. B. Strader, and R. L. Hettich, "DBDigger: Reorganized Proteomic Database Identification That Improves Flexibility and Speed," Analytical Chemistry 77, 2464-74, 2005 [PDF]
2004
- Abstract: Gordon Anderson, et al., Advanced Computational Methodologies for Protein Mass Spectral Data Analysis, 2004 Genomics:GTL Contractor-Grantee Workshop, Washington, DC
- Abstract: F. W. Larimer, et al., Bioinformatics and Computing in the Genomics:GTL Center for Molecular and Cellular Systems - LIMS and Mass Spectrometric Analysis of Proteome Data, 2004 Genomics:GTL Contractor-Grantee Workshop, Washington, DC
2003
- Article: Frank W. Larimer, et al, "Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris," Nature Biotechnology, December 14, 2003. See also Website Rhodopseudomonas palustris complete genome sequence and annotation [PDF (opens new window)]
- Poster and Abstract: Deborah Payne, et al., "Bioinformatics and Computing in the Genomes to Life Center for Molecular and Cellular Systems," 2003 Genomes to Life Contractor-Grantee Workshop, Arlington, Virginia [Poster PDF shorter download or higher quality]
