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MicroSuite Database System Deployed
at the LSUHSC’s Affymetrix Core Facility

Drs. Urška Cvek and Marjan Trutschl, assistant professors in the Department of Computer Science have been working with their students and Dr. John Sixbey, Dr. Rona Scott and Paula Polk (all LSUHSC) over the past two years to create a comprehensive database system for the Affymetrix Core Facility at LSUHSC-Shreveport. Their current students Brent Nycum, Phillip Kilgore, and former students Cade Cannon, Getachew Gebregziabher and Ashico Wilson were part of the team that designed and implemented the system.

MicroSuite is a MIAME-compliant database system for storage, query, and retrieval of microarray experiment-related data, results, and discoveries. The importance of storage, retrieval, analysis and dissemination of microarray generated data is becoming increasingly prevalent due to the exponential growth of performed experiments, availability of new genome arrays, and the fairly high cost associated with them. Since the GeneChip technology generates massive volumes of information quickly, this demands the implementation of bioinformatics to efficiently handle the data. There was a pressing need for development of tools to expedite data management, and couple it with analysis, and visualization tools. The Affymetrix Core Facility at LSUHSC has already processed more than 1000 chips over the past three years, valued at a total of more than $750,000. Too many researchers kept their data on CDs or DVDs making this data difficult or in some cases impossible to share – e-mailing 75MB worth of data generated based on one Affymetrix microarray was a true “Mission Impossible.”

One of the important features of the database system was handling different levels of access. In many cases the data generated are not immediately released into the public domain because the investigator may want to analyze it and publish the results, first. It was very important for MicroSuite to handle this by implementing several layers of access, including system administrator, data owner, data owner’s group, institution, and general. This not only provides a secure and controlled access to the data but will also encourage the investigators to store all their work (not just the data) into the database for future use or to be shared with various collaborators.

The database is built using the current MIAME (Minimum Information About a Microarray Experiment). In order to collect the information on experimental design, growth conditions, and treatments, just to name a few the standard had to be extended. MicroSuite also provides support for storage of knowledge extracted from the data, including objects such as Spotfire or GeneSpring project files.

These files are important for the research process, although they usually remain on the computer where the analysis took place and their lifespan is as long as the project the data was generated for or till the hard disk crashes and the investigator embarrassingly admits that there are no backup copies available. This not only provides a data management system but it also provides a mechanism for enhancement of current data.

MicroSuite can span multiple platforms; therefore, it has been implemented using a Web browser as its medium, which can present information in a relatively simple, open format. It also has the feature that it is supported by (and often times built into) most recent operating systems, and can be used on PCs, Apple, or some other platform. The system is implemented using Microsoft SQL Server, HTML, and PHP languages. .