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Title: Process Management for the Chip Fabrication
P82
Kokocinski,Felix; Wrobel,Gunnar; Lichter,Peter

f.kokocinski@dkfz.de
Deutsches Krebsforschungszentrum

The rather laborious production of DNA-microarrays as well as the high price of commercially available slides has lead to a number of "core facilities" being established in non-commercial environments. These sites provide the centralized service of spotting arrays at fairly low costs and thus make the arrays available to researchers associated to the facility. The production process of microarrays leads to the generation of large amounts of data even before any data analysis of the hybridized arrays is accomplished.
This initial part of the experiment is not covered by most database applications. Existing Laboratory information management system (LIMS) are either realized as small additions to other database projects or are expensive commercial products. For the core facility we run, the QuickLIMS database system was created to collect all data of interest and to control the process of array production. It has a user-friendly interface for manual data entries and simple queries and it is able to guide even inexperienced users safely through the protocol. It acts as the informational backbone for the laboratory robot performing most of the steps in the array production.
The main benefits of the application are
- storage and retrieval of information about all individual processes in a convenient way
- data consistency and completeness as well as a guidance of the user
- seamless interaction with the laboratory robot using bar-code identification of the microtiter plates
- tracking of all arrays, plates and clones currently in use
- flexible definition of the workflow as a series of successive and interdependent steps stored in a meta-table

QuickLIMS is therefore an software example for the data and process management in facilities involved in the production of microarrays and it can serve as the central unit to control the entire process.
[1] Fellenberg K., Hauser N.C., Brors B., Hoheisel J.D., Vingron M. (2002) Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics 18(3):423-33.
[2] Brazma A., Robinson A., Vilo J., Vingron M., Hoheisel J.D., Fellenberg K., Muilu J. (in press) ArrayExpress, establishing a public repository for DNA array-based gene expression data. In DNA-Chip Technology; Advances in Biochemical Engineering/Biotechnology.