ArrayAssist is a single-user desktop application
designed for fast and efficient microarray data
mining. It consists of an intuitive user interface
relational database storing microarray data and
intermediate analysis results, and an application
logic layer performing operations requested by the
user on the data stored in the database. It is also
capable of retrieving microarray data directly from an
Affymetrix. GCOS. (or LIMS) server.

The interface allows users to import Affymetrix.
GeneChip. files or spotted microarray files into the
database , to specify parameters for a range of data
processing operations, and to visualize the results of
data analysis.

The database, fully compliant with the Affymetrix AADM
database schema, ensures data integrity, consistency
and security, while allowing very fast data access
manipulation.

The application logic layer lets the user choose from
a variety of options and actions aimed at obtaining
meaningful information from raw experiment data. Data
filtering, building data sets based on ad hoc queries,
mean and median centering, merging data, deleting
data, aggregation, statistical significance analys
principal component analysis, hierarchical and k-means
clustering (partitioning) are all included.

Each installed copy of ArrayAssist runs on one
processor, a single desktop workstation. Multiple
users can easily access the functionality of the
program and no provision is made to store separate
user profiles or data access permissions to enforc
data security. (Stratagene's advanced server-based
GeneTraffic package is an enterprise-level software
solution designed with these requirements in mind.)

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