Greetings to bioconductor users, The purpose of this letter is to introduce you to ArrayQuest. ArrayQuest? is a web-based program for the analysis of DNA microarray data. ArrayQuest? is designed to apply various types of analysis scripts (i.e., Bioconductor statistical and graphical methods) to microarray data stored in the MUSC DNA Microarray Database and the Gene Expression Omnibus (GEO). We have developed a software suite that includes four modules that work in conjunction to mediate the archiving and analysis of DNA microarray data. The four modules of this suite are as follows: 1. ?ArrayDB? module: ?ArrayDB? is a program for archiving DNA microarray data derived from experimentation performed through our DNA Microarray Facility. The data for ?ArrayDB? is stored on our Internet front-end server, a Dell PoweEdge 440. ?ArrayDB? and ArrayQuest? (see next) both utilize MySQL server to store meta data such as project information (scanned and analysis project information), cRNA target information and process controlling information. 2. ArrayQuest? analysis module: this module allows a client to select microarray information from the ?ArrayDB? database for analysis. The ArrayQuest? analysis paradigm can be thought of as an analysis process controller in which a user specifies an analysis process that includes a selectable analysis method (i.e., a particular R script such as RMA) and related input for that method (i.e., Affymetrix .CEL files). ArrayQuest? has been designed to automatically distribute loads across a computing cluster. Before assigning a clients job, ArrayQuest? will query a load control program that will indicate which CPU in the cluster is best suited to analyzing the job at the time. ArrayQuest presently uses Linux operating systems RedHat and Fedora Core2. ArrayQuest? is operated through web browsing portals such as (i.e., Internet Explorer, Safari, Mozilla). The R package that is used to run many ArrayQuest methods can be compiled to utilize the increased performance that a 64 bit architecture offers. 3. Analysis job-distribution module: ArrayQuest? communicates with a job-distribution module to send an analysis job to a CPU within the backend analysis cluster, that is ready to accomplish the job. A key application used in the analysis system is a statistics package entitled R. Most analysis jobs that are launched by clients will take a considerable amount of time for the results to be returned. ArrayQuest? will notify the client by email as well through flagging status within the process database, the current state of any process being executed. 4. Upload module: This module will allow off site clients to import data into ?ArrayDB? or to a private database. This will allow the ?ArrayDB? database to grow. When the database grows then our client base will grow and in turn our analysis requirements will grow. For this reason we need the CPU Analysis Custers. ?ArrayDB? is designed to protect user data and not allow it to be released into the public domain without authorization, as data security is a major issue in the field. The ?ArrayDB? module has been describe in a published article (Argraves et al., 2003). URL: http://proteogenomics.musc.edu/quickSite/arrayQuest.php?page=home&act= manage Please direct your interest in this system to: W. Scott Argraves, Ph.D., Professor Medical University of South Carolina Dept of Cell Biology and Anatomy 173 Ashley Avenue Charleston, SC 29425 Email: argraves at musc.edu or to garyArgraves at sbcglobal.net Sincerely, Gary Argraves