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MARS: Microarray analysis, retrieval, and storage system

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

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MARS: Microarray analysis, retrieval, and storage system

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  1. MARS: Microarray analysis, retrieval, and storage system Albert F. Cervantes

  2. Overview • Microarray Background • Mars Implementation • Software Architecture • Systems • Data Interfaces • Web Services • Access Control • Remarks

  3. 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

  4. Software Architecture • J2EE platform • 3 tier architecture • Enterprise Information System • Data in relational database • Application • Manage DB interaction & data access • Presentation • Web-server

  5. Software Architecture Maurer, et al. MARS: Microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6:101

  6. 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

  7. 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

  8. Web Services • MARSExplorer • Java library distribution • Software developers • Data access via SOAP • Simple Object Access Protocol

  9. Access Control • AAS • Authentication and authorization system • Fine grained user access levels • Prevention • Unauthorized access • Data modification • Legacy code integration

  10. Access Control Maurer, et al. MARS: Microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005, 6:101

  11. 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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