Software Tools

Microarray Analysis Tools

Open Source Software

• TIGR MicroArray Data Manager MADAM
  A java-based application designed to load and retrieve microarray data to and from a database (also supplied with the software). MADAM provides data entry forms, data report forms and additional applications necessary to maintain microarray data for further analysis.
  
• TIGR SpotFinder
  A software tool designed for Microarray image processing using the TIFF image files generated by most microarray scanners.
  
• TIGR Microarray Data Analysis System MIDAS
  a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline.
  
• TIGR MultiExperiment Viewer MEV
  A Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes.
  
• The Deutsche Krebsforschungszentrum (DKFZ)
  Microarray Data Warehouse and Analysis Tools
  
• SourceForge BASE
  A database server to manage (locally) the massive amounts of data generated by microarray analysis.

Commercial Software

• Silicon Genetics GeneSpring
  A widely used java-based application designed to do expression data analysis.
  
• Rosetta Resolver
  An enterprise gene expression data analysis system.

Links

• The Arabidopsis Information Resource (TAIR)
  Arabidopsis resource for the scientific community working with Arabidopsis thaliana.
  
• The Institute for Genomic Research(TIGR)
  Resource for structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms.
  
• National Center for Biotechnolory Information(NCBI)
  A national resource for molecular biology information.
  
• Arabidopsis Biological Resource Center (ABRC)
  Arabidopsis resource for collection, preservation and distribution of seeds, and DNA clone and library storage and DNA clone distribution services
  
• Arabidopsis Genome Resource(AGR)
  A database developed at NASC using the ACEDB database system. Sequences, maps, and other information has been combined to form a large and powerful information resource.