A single microarray experiment provides thousands of individual pieces of data; it is therefore essential to focus on effective informatics methods in order to draw new biological conclusions efficiently and confidently. We have developed a unified software package that meets several important needs in the area of microarray data analysis. The software achieves several goals: (1) Integrating algorithms developed at the National Human Genome Research Institute into NuTec's GLEAMS software system, creating a single, integrated core platform that is capable of handling the computational aspects of complementary DNA and oligonucleotide array analysis, including imaging, signal processing, data extraction, database management and higher-order data analysis. (2) Developing new bioinformatics strategies to deduce the sequence- and structure-based relationships that are currently hidden within cDNA and oligonucleotide array data, including clustering methods and connections to gene ontologies. (3) Linking microarray data to data being amassed in clinical laboratories, to combine pedigree, phenotypic and genotypic data with gene expression data. (4) Using parallel computing to facilitate the analysis of microarray data. An overriding goal of this project is that the software be as user-friendly as possible, keeping in mind the level of computer training of most of the biologists who will be using it as well as the hardware that is typically available in most laboratories.