MARS: Advanced Microarray Analysis, Retrieval, and Storage System Overview
MARS is a robust software system designed for microarray data analysis, retrieval, and storage. It facilitates the cataloging of vast amounts of genomic data generated during microarray experiments, enabling researchers to study gene expression patterns effectively. Built on a J2EE platform, MARS employs a three-tier architecture, ensuring efficient data management and web services integration. It supports various data formats and adheres to MIAME standards, making it a comprehensive solution for laboratory information management and experiment annotation. Developed by Albert F. Cervantes and colleagues, MARS meets the evolving needs of bioinformatics research.
MARS: Advanced Microarray Analysis, Retrieval, and Storage System Overview
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Presentation Transcript
MARS: Microarray analysis, retrieval, and storage system Albert F. Cervantes
Overview • Microarray Background • Mars Implementation • Software Architecture • Systems • Data Interfaces • Web Services • Access Control • Remarks
Microarray Background • Popular technique • Study gene expression patterns on genomic scale • Produces wealth of data • Tens of thousands of elements • Annotated by dozens of parameters. • Need for a fast, robust cataloging method • Solution: Mars • MIAME software suite • Minimum Information about a Microarray Experiment • Microarray Gene Expression Data society initiative
Software Architecture • J2EE platform • 3 tier architecture • Enterprise Information System • Data in relational database • Application • Manage DB interaction & data access • Presentation • Web-server
Software Architecture Maurer, et al. MARS: Microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6:101
Systems – 5 major sub-groups • DB schema, Business Model, & Web Interface • Microarray production • LIMS – laboratory information management sys • Sample preparation • Hybridization and raw data management • Experiment annotation • Quality Management
Data Interfaces • MAGE-ML • MicroArray Gene Expression Markup Language • Initiative by MGED • Microarray Gene Expression Data Society • Import Interface • Define file parsers • Use generic files • Tab-delimited files • Allows for storage of previous data
Web Services • MARSExplorer • Java library distribution • Software developers • Data access via SOAP • Simple Object Access Protocol
Access Control • AAS • Authentication and authorization system • Fine grained user access levels • Prevention • Unauthorized access • Data modification • Legacy code integration
Access Control Maurer, et al. MARS: Microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6:101
Remarks • Novel solution • Catalog & archive experimental data in microarray production • Obsolescence Resistant • Awareness of data annotation standards • Scalable and distributable • Offers a complete laboratory solution
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