The Stanford Microarray Database (SMD) facilitates research performed using microarray technology by storing the resulting data and the biological information associated with many organisms, and by providing interfaces for the retrieval and analysis of that data. The database supports researchers at Stanford University as well as hundreds of their collaborators around the world. As microarray data continue to accumulate, it will become an even more essential type of information for model organism databases to display and help their users understand and exploit. SMD has been making its source code publicly available since June 2001 and aims both to make current software more generic and to create new, innovative software that can be widely used. SMD is committed to creating modular, generic, publicly disseminated software for the analysis and display of microarray data. Not only does this benefit the research community as a whole, it will save redundant efforts by other database projects and make SMD's software easier to maintain and support. Some currently used, popular tools provided by SMD will be re-written to allow other databases to use them easily and to enhance some features. These tools include CaryoScope, which displays microarray data in the context of its position on the genome, XCluster, which performs clustering of microarray data and calculates correlations between profiles, and GeneXplorer, which is a web-based tool for visualization of clustered microarray data. Other tools will be developed to meet obvious needs for any model organism displaying microarray data. SMD proposes to create software to calculate significant Gene Ontology (GO) terms associated with a set of genes and to provide modular software for the manipulation and filtering of microarray data matrices. Lastly, SMD will create and release a generic database table object that will provide a useful and simple architecture for data access that will be database platform-independent.
| Ball, Catherine A; Awad, Ihab A B; Demeter, Janos et al. (2005) The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 33:D580-2 |
| Boyle, Elizabeth I; Weng, Shuai; Gollub, Jeremy et al. (2004) GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20:3710-5 |
| Rees, Christian A; Demeter, Janos; Matese, John C et al. (2004) GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics 5:141 |
| Awad, Ihab A B; Rees, Christian A; Hernandez-Boussard, Tina et al. (2004) Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 5:151 |
