title: MIMAS 3.0 is a Multiomics Information Management and Annotation System.
abstract: BACKGROUND
  DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types.
  
  
  METHODS
  MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure.
  
  
  CONCLUSIONS
  We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.
authors.affiliation: Inserm, U625, GERHM; IFR-140; Université de Rennes 1, Rennes F-35042, France. alexandre.gattiker@epfl.ch
authors.forename: Alexandre
authors.initials: A
authors.lastname: Gattiker
authors.forename: Leandro
authors.initials: L
authors.lastname: Hermida
authors.forename: Robin
authors.initials: R
authors.lastname: Liechti
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Olivier
authors.initials: O
authors.lastname: Collin
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software