The Stanford Microarray Database (SMD) is an open source, institutional-scale DNA microarray research database. As a research database system, SMD provides not only data storage and access control, but also current biological annotation and a variety of tools for data retrieval, quality assurance and analysis. SMD supports both two-color data (including the output of the GenePix, ScanAlyze, and Agilent feature extraction software) and single-channel data from Affymetrix GeneChips. SMD serves hundreds of researchers at Stanford and their collaborators at over one hundred institutions worldwide, and provides public access to data from approximately 6000 microarrays. SMD's software has been installed at several other institutions on a variety of operating system and database platforms, serving many researchers at those sites. We propose to improve many aspects of SMD in order to produce a more robust, extensible, installable, upgradeable and useable system that can serve the needs of any university, department or other agency engaged in microarray research. We will develop a comprehensive test suite for SMD, which will both aid in continued development, and allow SMD installers to verify that their installations of SMD are working correctly. We will develop methods for programmatic access to SMD via web services, such that local and remote users can automate data retrieval from SMD installations. We will move to a collaborative, open source system of development in order to take full advantage of the growing community of scientists and developers installing and using SMD around the world. Finally we will adopt flexible and generic schemata for biological annotation and result data storage, such that SMD installers can easily store data from different feature extraction packages and different organisms than the Stanford installation. In sum, completion of these aims will result in a robust, scaleable, open source, institution scale platform for storing and sharing microarray data, that can be easily installed, upgraded and modified at new sites.
| Hubble, Jeremy; Demeter, Janos; Jin, Heng et al. (2009) Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 37:D898-901 |
| Demeter, Janos; Beauheim, Catherine; Gollub, Jeremy et al. (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35:D766-70 |
| Brown, James A; Sherlock, Gavin; Myers, Chad L et al. (2006) Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol 2:2006.0001 |
