Integrated Microarray Database System

The Integrated Microarray Database System is a tool for integrating microarray gene expression results with biological experimental data. The IMDS is designed to store experimental descriptions, protocols, raw microarray data and sets of normalized data. Data generated from both spotted DNA array and Affymetrix GeneChip array experiments are supported by the IMDS. The user interface software for the IMDS is open source and the database itself is written in MySQL, an open source Relational Database Management System (RDBMS). To assist development of additional database features to meet future needs, the IMDS uses a Model-View-Controller application framework, employing the Java Web development core technologies of Java Server Pages (JSP), Java Beans and Struts.

The distinctive feature of the IMDS is the robust search functionality provided through user-friendly menus dynamically populated with current database records. Both the web-accessible user interface and the table structure of the IMDS have been designed to support a variety of detailed queries on the database, allowing the retrieval of microarray experiments based on mutant description, tissue and developmental stage characteristics of source organisms and detailed aspects of growth conditions and sample treatments. Searches are also possible on experimental information such as investigator, laboratory, research institution, date of experiment and experiment and array type. Development is underway to enable complex queries of analyzed experimental results, such as the retrieval of all experiments that show a three or greater fold increase in the expression of a given gene or subset of genes.

A tutorial, which provides training for the use of the database through the web interface, is available in both HTML and PowerPoint formats.

An older presentation describing the design and features of IMDS is available in HTML, PDF, and PowerPoint formats.

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