The AMAD FAQ

What is AMAD?
Another MicroArray Database. AMAD is a flat file, web driven database system written entirely in PERL and javascript, and intended for use with microarray generated data. AMAD is also an evolving software project. Future releases of AMAD will include a MySQL backend combined with new analysis tools.

What is the goal of AMAD?
To provide a means for storage, retrieval, and extraction of microarray data by means of a centralized web based server. Many investigators pursuing array based experiments are ill-prepared to handle the overwhelming flood of data. The use of stop-gap measures, such as Excel and FileMaker Pro, become rapidly inadequate and cumbersome. With AMAD, a researcher with no prior UNIX or database skills may rapidly and cheaply set up a database system capable of storing thousands of gene expression experiments.

Who wrote AMAD?
AMAD was written by Mike Eisen, Max Diehn, Paul Spellman, and Joseph DeRisi.

What are the main features of AMAD?
A simple submission function for uploading array data into the data base via browser upload, with some annotation capability, including the ability to randomly access experiments by user or category of experiment. A view script which allows the user to easily sort, filter, and find specific data within a given experiment. An extract script which provides the ability to extract data from multiple experiments. Data can be filtered and extracted in a form that is seamlessly compatible with Mike Eisen's popular Cluster and TreeView. Additional forms allow administration capabilities, modification of database keys, and definitions of custom gene lists.

How much does AMAD cost?
AMAD is completely free.

What kind of computer do I need to run AMAD?
AMAD will run on any web server that supports PERL. This includes Windows, Macintosh, and any flavor of UNIX. The install guide was written for those who wish to install it on Linux based machines.

What kind of microarray data does AMAD support?
Any kind of microarray data. The keys (the type of information the database stores) can be completely customized. The version available for download was written with cDNA or oligo spotted microarrays in mind.

What kind of image analysis software does AMAD support?
ScanAlyze, the free image analysis program written by Mike Eisen, and GenePix, the analysis program that ships with the GenePix 4000 Scanner, by Axon Inc.

I've just written a cool tool for AMAD that I would like to share with the community. Will you post it on www.microarrays.org?
YES! Please send e-mail to joe@derisilab.ucsf.edu. We are actively seeking people to write tools, updates, and enhancements for AMAD.