title: MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France. honore@ipsogen.com
authors.forename: Paul
authors.initials: P
authors.lastname: Honoré
authors.forename: Samuel
authors.initials: S
authors.lastname: Granjeaud
authors.forename: Rebecca
authors.initials: R
authors.lastname: Tagett
authors.forename: Stéphane
authors.initials: S
authors.lastname: Deraco
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Beaudoing
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Stéphane
authors.initials: S
authors.lastname: Debono
authors.forename: Pascal
authors.initials: P
authors.lastname: Hingamp
mesh_terms: D003001:Cloning, Molecular; D003628:Database Management Systems; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D020407:Internet; D009757:Nylons / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D014584:User-Computer Interface
chemical_list: D009757:Nylons