The Genomics and Bioinformatics Facilities Core was created in September 2001 to provide Center members with integrated facilities for microarray fabrication, microarray analysis, database storage, large-scale database management, data mining and data modeling. The Core is comprised of the CEHS Bioinformatics Computing Facility tightly integrated with the MIT BioMicro Center. The latter is a joint endeavor of the Center for Environmental Health Sciences, the Department of Biology, the Center for Cancer Research, and Biological Engineering Division that was founded in 2000 as the central bio-fabrication and bio-information technology resource at MIT.
The specific aims of the Genomies and Bioinformatics Facilities Core are: (1) To provide integrated support for both commercial and custom microarrays. The Core will support the fabrication of spotted oligo arrays and spotted cDNA arrays when commercially available arrays are not available. The Core will also support the use of Affymetrix GeneChips and Agilent microarrays providing flexibility with enabled comparisons and are immensely valuable for studies where whole-genome coverage is needed. Though the current focus of most Center members is on mRNA analysis, the capabilities of the Core can be extended to the fabrication and analysis of other types of arrays including protein arrays. (2) To provide strong three-tier architecture for data storage, management and processing. The Core has installed several three-tier client-server systems based on open-source and commercial database management systems (DBMS). These systems will be strengthened and extended to achieve integrated support for GeneChips and spotted microarrays. (3) To provide networks of managed desktop computers for data analysis and mining. The Core has licensed commercial software such as the Affymetrix MicroArray Suite-DataMiningTools suite and Spotfire Decision Site for microarray data analysis. The number of licenses will be increased and open-source tools integrated into the 3-tier Core IT system. Client software will be deployed on a network of managed desktop computers based on the MIT Win-Athena, Windows 2000 and Linux-Athena environments. (4) To provide training and educational programs in commercial and open-source bioinformatics software. A program of professional training seminars for commercial software will be strengthened and supplemented with seminars taught in-house for open-source software. Center investigators will have free access to training sessions that are usually fee-based. (5) To provide Center members with technical assistance with programming, database administration and data analysis. Bioinformatics applications that currently operate separately from each other will be integrated. (6) To work with Center members in applying their results to the development of data models and quality control procedures, error modeling as well as the development of new technologies. The introduction of new devices and computational methods will be accelerated through close collaborations between Center members and other researchers at MIT. The Center maintains a strong commitment to new technology development and deployment. A focus on new technology also helps to ensure that the Genomics and Bioinformatics Facilities Core remains at the cutting edge of high throughput analytical methods.
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