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Practical Innovation at BioCon 2003


The TIGR Microarray Data Manager, MADAM
Joseph White, The Institute for Genomic Research

Track: Toolkits
Date: Wednesday, February 05
Time: 2:15pm - 3:00pm
Location: California Ballroom A & B

Microarray experiments produce large amounts of data for even the simplest of experiments. In order to analyze data from many experiments, that data must be stored in an accessible form, such as in a database.

White’s presentation introduces MADAM (MicroArray DAta Manager), a Java-based application designed to store and retrieve microarray data to and from a database (also supplied with the software). MADAM provides data entry forms, data report forms and additional applications necessary to maintain microarray data for further analysis. MADAM is designed to read MAGE-ML to upload data to a database, and to write MAGE-ML in order to exchange microarray data or submit experiments to public repositories. (Although MAGE-ML capability is not available in the currently release of MADAM, it will be available in future versions.)

MADAM maintains information about RNA samples, labeled probes, slide/array printing, hybridizations, array scanning, expression data, PCR amplification data, and clone and microtitre plate information. MADAM requires JRE 1.3.1 and relies on a database schema implemented on a MySQL server, althoug other ANSI-SQL databases can be used. The current MADAM implementation supports the MIAME specification (v.1.1) for microarray data. The MADAM software is freely available in two forms: executable, and executable with source code.

The application working with MySQL and on a laptop to access microarray data will be demonstrated. (Usually, microarray data is stored in large relational databases.) Attendees learn to store and retrieve data for microarray expression experiments and write it out as MAGE-ML.

Download presentation file

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