MARS: Microarray analysis, retrieval, and storage system

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MARS Microarray analysis, retrieval, and storage
system

• Albert F. Cervantes

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Overview

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

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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

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Software Architecture

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

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Software Architecture
Maurer, et al. MARS Microarray analysis,
retrieval, and storage system. BMC Bioinformatics
2005, 6101
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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

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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

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Web Services

• MARSExplorer
• Java library distribution
• Software developers
• Data access via SOAP
• Simple Object Access Protocol

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Access Control

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

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Access Control
Maurer, et al. MARS Microarray analysis,
retrieval, and storage system. BMC Bioinformatics
2005, 6101
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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