Stanford Microarray Database (SMD)

Stanford Microarray Database (SMD) stores, annotates, analyzes, and shares microarray data to support MIAME-compliant data management, exchange, and downstream analysis.

Key Features:

• Data storage: Stores raw and normalized microarray data and associated image files from experiments.
• Platform support: Supports GenePix (Axon Instruments), Affymetrix GeneChips, Agilent arrays, and other major microarray platforms.
• Standards and formats: Is MIAME-supportive and supports import and export in MAGE-ML format.
• Analysis integration: Integrates the GenePattern software package to design, execute, and share analysis pipelines.
• Quality and analysis tools: Provides tools to assess data quality and perform detailed microarray analyses.
• Data sharing: Enables sharing of datasets among users at any stage of analysis to support collaboration.
• Open source: Source code is available under an Open Source license for local deployment.
• Repository submission: Can submit MIAME-compliant data in MAGE-ML format to ArrayExpress and GEO.

Scientific Applications:

• Microarray data management: Centralizes storage, annotation, and retrieval of microarray experiments for downstream analysis.
• Data quality assessment: Supports evaluation and normalization workflows to assess microarray data quality.
• Computational analysis pipelines: Enables design and execution of pipeline-based analyses through GenePattern integration.
• Data dissemination and deposition: Facilitates MIAME-compliant data sharing and submission to public repositories such as ArrayExpress and GEO.

Methodology:

Stores raw and normalized data and image files; imports and exports MAGE-ML; integrates GenePattern for pipeline execution; submits MIAME-compliant MAGE-ML to ArrayExpress and GEO.