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Open Access Software

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

Paul Honoré1, Samuel Granjeaud2, Rebecca Tagett1, Stéphane Deraco15, Emmanuel Beaudoing23, Jacques Rougemont23, Stéphane Debono1 and Pascal Hingamp24*

Author Affiliations

1 IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France

2 TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France

3 Now at Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland

4 Now at IGS, CNRS UPR 2589, 163 Avenue de Luminy Case 934, 13288 Marseille Cedex 09, France

5 Now at CNRS – DSI, Tour Gaïa, rue Pierre-Gilles de Gennes, BP 21902, 31319 LABEGE CEDEX, France

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BMC Genomics 2006, 7:240  doi:10.1186/1471-2164-7-240

Published: 20 September 2006

Abstract

Background

High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option.

GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported.

Results

MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF.

Conclusion

MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.