SimArray: a user-friendly and user-configurable microarray design tool

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 userspecified 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 e...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Richard P. Auburn, Roslin R. Russell, Bettina Fischer, Lisa A. Meadows, Santiago Sevillano Matilla, Steven Russell
• Keywords: Array Design, BMCBI 2006, Microtitre Plates, Randomised Spot