introduction to caarray cabig ® molecular analysis tools knowledge center april 3, 2011
TRANSCRIPT
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Introduction to caArray
caBIG® Molecular Analysis Tools
Knowledge Center
April 3, 2011
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caArray Overview
• More than a simple repository for microarray data.• Supports data management throughout the life of
experiment.• Allows collaborative sharing of pre-publication data
with partners.• Provide data to other biomedical/clinical tools to form
a comprehensive solution for array data management, search, and analysis.
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Why use caArray?
• Target Users: • Bench scientists performing microarray data collection and
annotation• Microarray core facility scientists and technicians• Bioinformatics and data management coordinators• Multi-institutional data coordinating center informaticians
• Addressing Critical Needs:• Manage all aspects of array data: raw data, derived data,
sample annotation, experimental design• Ensure data are private (in a local instance) until published• Supports array data sharing using a federated model• Find what you are looking for fast: query annotated data within,
and across, datasets • Facilitate data integration: provide annotated data to other
analytical caBIG® tools
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Key Functions of caArray
• Query annotated data within and across datasets with search and navigate features
• Uploading of array files from industry formats (e.g., Affymetrix, GenePix, Illumina, Agilent)
• Annotation of data to harmonize datasets and reduce time to aggregate data
• MAGE-TAB import and export functionality• GEO-SOFT export functionality• Security and authentication features that include group-
based permissions• Provide annotated data to other caBIG® tools that support
analytical analysis• Rich programmatic APIs that allow analytical tools (on and
off the Grid) to pull data from caArray and visualize/analyze it.
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Web Interface: Find Things Fast
• User-friendly web interface for browse and search
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Platform Support: Grow Towards All Inclusive
• The collection of most available Affymetrix, Illumina, and Agilent array platforms/designs in caArray ensures that most native data files can be stored, parsed, and associated to samples.
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Parsed Data Formats: the More, the Better for Users
• MAGE-TAB format• Agilent raw TXT for aCGH, expression and miRNA assays • Agilent GEML/XML array designs • Nimblegen pair Report TXT (raw and normalized) • Nimblegen NDF array designs • Illumina CSV• Illumina Sample Probe Profile TXT • Illumina genotyping processed data matrix TXT • Illumina BGX/TXT array designs • Affymetrix CEL and CHP in AGCC/Calvin formats in addition to the
GCOS formats • Affymetrix CNCHP copy number data (CN4 and CN5) • Copy Number data in a prescribed MAGE-TAB Data Matrix format.
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MAGE-TAB: Save Time on Sample Annotation
IDF
SDRFExcel-like Format, Controlled Vocabhttp://www.mged.org/mage-tab/
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Data Management: Loading Data
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Data Management: Sample Annotation and Datasets
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Data Export: Zip, MAGE-TAB, or GEO Soft
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Collaboration and Data Sharing
• Investigators define collaboration groups for sharing of pre-publication data with a set of partners.
• Access control at the experiment level or at individual samples.
• Data is private until made public by the Data Owner.
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Data Analysis: Tool Integration
gene expression data gene expression data and SNP data
Cross-query over many caArray instances
gene expression data and copy number data
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A Glance at the Technology
• Tool Platform: • Enterprise-web based system that works within a Firefox or Internet Explorer
browser
• CBIIT-Hosted Installation of caArray: • Limited computer skills are required to use the application; directed at laboratory
researchers
• Local Installation of caArray:• Moderate technical expertise is required to install the tool
• Upgrade Availability:• To make upgrades as seamless as possible, an upgrade installer, both available in
GUI format as well as command line format, upgrades installed caArray instance while maintaining data integrity.
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The Next Step: Accessing Online Resources for caArray
Molecular Analysis Tools Knowledge Center
https://wiki.nci.nih.gov/x/R5GNAg
caArray User Forum https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=6
Tool Landing Page https://cabig.nci.nih.gov/tools/caArray
Access to Demo caArray Instance
https://array-train.nci.nih.gov/caarray/home.action(Register from that site for a training account)
Application Support Email: [email protected]
Phone: 301-451-4384
Toll-free: 888-478-4423