General Technique
SBEAMS (Systems Biology Experiment Analysis Management System) is a framework for collecting, storing, and accessing data produced by a variety of different experiments which can be managed separately but correlated later. This integrated system is a software framework that combines a relational database management system (RDBMS) back-end; a collection of tools to store, manage, and query experiment information and results in the RDBMS; a web-front end for querying the database and providing integrated access to remote data sources; and an API for further software development. Since all data from each step of the experiment are warehoused in a modular schema in the RDBMS, quality control and data analysis tasks are greatly simplified.
Purpose/use/application of the technique:
The process of data acquisition, from sample preparation, spotting, hybridization, quantitation, and derivation of expression measures for microarray experiments, as well as sample preparation, mass spectrometry, sequence database searches, statistical validation, and annotation for Proteomics experiments, is tracked by the SBEAMS data management package under development at the ISB. This integrated system is a consistent framework that combines a unified RDBMS back-end; a collection of tools to store, manage, and query experiment information and results in the RDBMS; a web-front end for querying the database and providing integrated access to remote data sources; and an interface to existing programs for clustering and other analysis.
Within the SBEAMS framework, each investigator may first store and manage the data unique to his or her experiment. Then, the parameters of the process of executing the microarray, proteomics, or other experiment are captured into the database. The experimental data products are loaded into the database and an automated pipeline processes the raw data into gene expression measures with data quality estimates or protein matches and quality scores. The investigator may then use the SBEAMS built-in tools or custom scripts built on top of the framework to correlate the experimental results and experiment conditions and to further understand the experimental results. Investigator annotations also are captured in the database for later analysis and correlation with other experiments.
Example(s) of projects at ISB that use this technique:
The ISB's Microarray core facility uses SBEAMS for data management. The Halobacterium group manages their microarray, proteomics, genomic information in SBEAMS. The Urologic Epithelial Stem Cell (UESC) project uses SBEAMS for managing microarray, proteomics, immunostains, and cell sorting data. Many Proteomics projects use the SBEAMS — Proteomics module for storage and analysis. The PeptideAtlas project uses SBEAMS — Proteomics as its main experiment repository and is developing an SBEAMS module dedicated for the PeptideAtlas database. The GLUE project uses the SBEAMS — Interaction module to manage its molecular interaction information and integrate it with microarray and proteomic results.
Ongoing area of technology development:
SBEAMS undergoes continual development in order to adapt to the evolving needs of systems biology research projects.
Representative publication(s):
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286.
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http://www.sbeams.org/
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