SOFTWARE Microarray Design/Management Software Array Genetics (µArrayDB) BioDiscovery (CloneTracker) Silicon Genetics (GeNet) MADAM (TIGR) TM4 (Comprehensive suite ­ TIGR) BioConductor (Whitehead Institute) Genowiz™ (Ocimumbio)   Annotation/Data Standards Minimal Information About a Microarray Experiment (MIAMI) MAGE-ML (European Bioinformatics Institute) GeneX-Lite (National Center for Genome Resources) Manatee (TIGR) GenMapp (University of California at San Francisco)   Imaging Software (Academia/Commercial) BioDiscovery (ImaGene) Axon Instruments (GenePix Pro 6.0) EisenLab ­ Stanford University (ScanAlyze) Spotfinder (TIGR) Imaxia (ArrayFox) F-Scan (Analytical Biostatistics Section - NIH) MicroDiscovery (GeneSpotter) CLONDIAG(IconoClust) Koada Technology (Koadarray) Vigene Tech (MicroVigene) Nonlinear Dynamics (Phoretix) CSIRO Mathematical and Information Sciences (SPOT) Niles Scientific (SpotReader)   Data Analysis Software (Academia/Non-Profit) BRB Array Tools (Biometric Research Branch - NCI) caGEDA (University of Pittsburgh) Cleaver 1.0 (Stanford Biomedical Informatics) ChipSC2C (Peterson Lab - Baylor College of Medicine) Cluster (Eisen Lab ­ Stanford/UC Berkeley) DNA-Chip Analyzer (dChip) (Wong Laboratory - Harvard University) Expression Profiler (European Bioinformatics Institute) FuzzyK (Eisen Lab ­ Stanford/UC Berkeley) GeneCluster 2.0 (Broad Institute) GenePattern (Broad Institute) GeneXPress (Stanford University) Genesis (Alexander Sturn - Graz University of Technology) GEPAS (Spanish National Cancer Center) GLR (University of Utah) GQL (Max Planck Institute for Molecular Genetics) INCLUSive (Katholieke Universiteit Leuven) Maple Tree (Eisen Lab ­ Stanford/UC Berkeley) MeV (TIGR) MIDAS (TIGR) Onto-Tools (Sorin Draghici - Wayne State University) Short Time-series Expression Miner (Carnegie Mellon University) Significance Analysis of Microarrays (Rob Tibshirani ­ Stanford University) SNOMAD (Johns Hopkins Schools of Medicine and Public Health) SparseLOGREG (Shevade & Keerthi - National University of Singapore) SuperPC Microarrays (Rob Tibshirani ­ Stanford University) TableView (University of Minnesota) TreeView (Eisen Lab ­ Stanford/UC Berkeley) Venn Mapper (Universitais Medisch Centrum Rotterdam)   Data Analysis Software (Commercial) Applied Maths (GeneMaths XT) Array Genetics (AffyMate) Axon Instruments (Acuity 4.0) BioDiscovery (GeneSight) BioSieve (ExpressionSieve) CytoGenomics (SilicoCyte)  Microarray Data Analysis (GeneSifter) MediaCybernetics (ArrayPro Analyzer) Microarray Fuzzy Clustering (BioRainbow) Molmine (J-Express Pro) Optimal Design (ArrayMiner) Partek (Partek Pro) Predictive Patterns Software (GeneLinker) Promoter Extractor (BioRainbow) SAS Microarray Silicon Genetics (GeneSpring) Spotfire (Spotfire) Strand Genomics (Avadis) Vialogy Corp.   Data Analysis Services (Commercial) CyberArrayAnalysis