The Microarray Data Manager, implemented in Java, facilitates the entry of data into a relational database. MADAM guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials. Although not yet supported, MADAM is being adapted to read and write MAGE-ML, the XML data exchange format being developed by an international consortium of leading public databases and microarray research centers. A MAGE-ML version of MADAM should be available by the end of this year and will facilitate submission of microarray data to public repositories such as Array Express and GEO.
Managing array data effectively requires development and maintenance of a database designed to reflect the experimental process. Central to TM4 is a MySQL database that stores all data related to the microarray process, such as information on experiments, studies, protocols, data normalization, and gene expression. This database supports MIAME (Minimal Information About a Microarray Experiment; (Brazma et al., 2001)) and captures the information deemed essential by this standard. While this may serve as a complete microarray database system for some users, others can use it as a starting point for customized database development. A schema for the database is provided and TM4 can be adapted to work with existing relational databases as the interaction is via JDBC (Sun Microsystem’s Java DataBase Connectivity Application Program Interface).
Copyright © 2005, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA, USA.
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Last modified: 12/06/2005
Download the Latest Full Version: v4.0 for Windows
The v4.0 updater will upgrade a previous installation of MADAM to version 4.0.
The full version plus source code is also available.
New! Madam 4.1 for Linux
The Manual is a detailed description of the workings of MADAM. It contains complete instructions on entering data.
MADAM v3.0 runs on the Windows 2000/NT/XP systems and requires Java v1.4.1 or higher.
Download Java v1.4.2
The powerpoint slides here contain the slides our group uses to teach courses on the program. The MADAM SOP (Standard Operating Procedure) details the TIGR-standard method of entering data into MADAM. This document is only meant to serve as an example of how MADAM can be used.
The frequently asked questions page is very helpful in troubleshooting problems in installation and usage of MADAM.
If the above resources don't answer your questions, please contact email@example.com for more help.