SimArray: a user-friendly and user-configurable microarray design toolReport as inadecuate




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BMC Bioinformatics

, 7:102

First Online: 01 March 2006Received: 11 October 2005Accepted: 01 March 2006

Abstract

BackgroundMicroarrays 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.

ResultsWe 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.

ConclusionSimArray 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-.

List of abbreviations usedcDNA Complementary DNA

gDNA Genomic DNA

Meta-gridThe sub-grids and spots that are printed by one print tool

Sub-gridThe patch of spots that is printed by a single pin

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-102 contains supplementary material, which is available to authorized users.

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Author: Richard P Auburn - Roslin R Russell - Bettina Fischer - Lisa A Meadows - Santiago Sevillano Matilla - Steven Russell

Source: https://link.springer.com/



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