After a long day in the microarray lab, some researchers may leave seeing nothing but those fluorescent spots and dots on the chips. Playing upon this possibility, Ellen Graves, a researcher at the University of California, San Francisco, Ernest Gallo Clinic and Research Center, has named her new microarray laboratory information management system “UC Spots.”
UC Spots, which is free to academics with a standard license, and will soon be available to commercial micorarray users for an as-yet-undetermined price, is designed to allow researchers to manage their data flow from plate preparation stages to image analysis results, Graves said.
“We collect information, such as quality control information, on gels. You can put in the precipitate in PCR gels and can mark down which elements aren’t great, and provide a database on where the quality control issues are,” said Graves.
The system offers an interface that prompts the user to input information about the microarray process at all stages. When information is input on the plate preparation stages, each element has an individual quality control value, and transfers to and from different-sized plates are recorded. At the array fabrication stage, the data includes configuration of the robot, grid locations of the elements in the arrayed plates, and slide usage. At the experimental level, the LIMS collects data on hybridization, probe, and wash parameters, and data results from image and analysis software.
The LIMS software also allows users to group elements in different tables in the database, and to import different elements from other institutions, as well as image analysis tools into the system. “You can have a different table for each of the analysis tools and can compare across tools to see where they are differing in their results,” Graves explained.
This feature allows groups who are doing research on which image analysis tools to use to input their database and write a query that enables them to analyze the results and compare the results among different tools.
The system, which Graves has been working on for two years, runs on Oracle, as well as IBM’s DB2, and the data entry application is written in Java. This insures data integrity, Graves said, beyond that provided by a relational DBMS.
To find out more, interested researchers can visit the UC Spots website at www.egcrc.org/bio/ucspots or e-mail Graves at [email protected]