My Microarray Software Comparison - Accessory/Other Software

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Definition of accessory/other software
Accessory software (in alphabetical order)

[ Array Maker | eXPatGen | GEDS | MatchMiner | MIAME Spice | ProbeMatchDB ]

Definition of accessory/other software

Accessory software (in alphabetical order)

• Array Maker Version 2 - provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface, written by Dr. Joseph Derisi at UCSF; backward compatiable with original Mguide style arrayers.
• eXPatGen - a simulator of gene expression patterns, modeled after the microarray experiments of Pat Brown's group, in order to evaluate different analysis methods, such as clustering, principle component analysis (PCA), and self-organized maps (SOMs). Reference [PubMed]
• Gene Expression Data Simulator (GEDS) - a free, open-source, collaborative online gene expression data simulator that can be used to evaluate any method for the analysis of gene expression data from microarray experiments, with or without array-specific biases, confounding, channel-specific nonlinearity and heteroscedascity, over a wide range of parameter space (effect size, distribution type/shape) using SN, SP, ROC, FDR and a diversity of other evaluation measures.
  
• MatchMiner - a set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene and OMIM data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster ids. Reference [PubMed][pdf]
• MIAME Spice - a standalone program that can package raw and normalized datafiles from a set of related MicroArray experiments, and save everything into one archive file called .mef file. The goal is to save everything for a particular experiment set into the .mef file and facilitates data exchange.
  
• ProbeMatchDB - ProbeMatchDB is a web-based database designed to facilitate the search of EST/cDNA sequences or STS markers that can be used to represent the same gene across different microarray platforms and species.  Reference [PubMed]