description information can be edited and uploaded in Microsoft Excel spreadsheet format, and a custom standalone software application, the TIFFreader, is avail- able to be run by the users on their personal computers. The TIFFreader parses both the microarray raw data text and TIFF image ﬁles in order to ﬁrstly read scanning par- ameters and other software information, and secondly to check that the correct data ﬁles (text and TIFF) are being associated. The user then uploads the resulting Zip ﬁle of data to BmG@Sbase. Both these tools ease the process of uploading large amounts of information and reduce the likelihood of errors being made. A submission tool has been developed that will export either a new array design description or a full experimental data set in the Microarray and Gene Expression Markup Language (MAGE-ML) (http://www.mged.org/Workgroups/MAGE/mage-ml. html). Data in this format is submitted to ArrayExpress upon publication of the experiment or pre-publication at the request of the author. Currently 80 published data sets have been submitted to ArrayExpress. The database contains complete array design informa- tion describing all 58 BmG@S microarray designs; these include multi-species/strain pan-genome, species/strain- speciﬁc, capsular typing and whole genome tiling designs representing 16 bacterial species. Information regarding the design and manufacture of BmG@S PCR product custom arrays is stored, including PCR primer sequences, reaction conditions, product size and quality, and array print run dates and glass slide types (manufacturer, coatings etc). In addition, BmG@S designs arrays for the Agilent Inkjet in-situ Synthesized (IJISS) system thus all oligonucleotide and gene mapping information is stored; Nucleic Acids Research, 2012, Vol. 40, Database issue D607 the database is used to automatically generate fully an- notated mapping ﬁles that are available when the arrays are supplied. Presentation of genome context is enabled using an in- tegrated local instance of the genome browser GBrowse (http://gmod.org/wiki/GBrowse). Currently the database contains information for over 260 bacterial genomes and 119 bacterial plasmids in addition to genomic mapping details of all BmG@S array designs and cross-genome gene BLAST similarities. DATA EXPLORER INTERFACE BmG@Sbase uses a web interface to provide maximum ﬂexibility to users without concerns regarding local soft- ware installations or upgrades. The interface has been designed to act as an experiment explorer, guiding the user through the various steps of the experimental process (in BmG@Sbase an experiment is equivalent to a publica- tion). From the overall experiment design, including title, abstract, authorship and experimental factors, the user can link through a schematic summary tree (Figure 1A) to view the sample and treatment descriptions (Figure 1B), the protocols used, an array design graphical explorer (Figure 1C), the raw and analysed data ﬁles associated or a schematic data analysis tree (Figure 1D). Sample treatment steps in the context of biological and technical replication can become complicated, but it is es- sential for the proper understanding of the experimental design that these are presented clearly; thus interactive sample trees are generated (Figure 1B). These are collaps- ible and expandable at all levels of the tree as well as on a Figure 1. BmG@Sbase stores all experimental data and displays an overview schematic on each experiment page (A), sample descriptions are displayed as interactive trees (B), an interactive viewer provides access to array design information (C), raw and analysed data is linked through a network of transformations (D).