title: SimArray: a user-friendly and user-configurable microarray design tool.
abstract: BACKGROUND
  Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.
  
  
  RESULTS
  We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.
  
  
  CONCLUSIONS
  SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/.
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, UK. r.auburn@gen.cam.ac.uk
authors.forename: Richard P
authors.initials: RP
authors.lastname: Auburn
authors.forename: Roslin R
authors.initials: RR
authors.lastname: Russell
authors.forename: Bettina
authors.initials: B
authors.lastname: Fischer
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Meadows
authors.forename: Santiago
authors.initials: S
authors.lastname: Sevillano Matilla
authors.forename: Steven
authors.initials: S
authors.lastname: Russell
mesh_terms: D004282:Documentation / Q000379:methods*; D004867:Equipment Design / Q000379:methods; D019544:Equipment Failure Analysis / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D012371:Robotics / Q000295:instrumentation* / Q000379:methods; D012984:Software; D012985:Software Design; D014584:User-Computer Interface