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Development of Bioinformatic Tools for Microarray Analysis

We have developed a software platform called BRB ArrayTools for the comprehensive analysis of microarray data. The design objectives are:

  • Front-end friendly to biological scientists
  • Microarray data specific
  • Statistically sophisticated
  • Powerful analytics
  • Powerful data visualization
  • Drill-down linkage to genomic databases
  • Portable to other laboratories
  • Easily extensible in high level language
  • Ease and rapidity of development

The array tools package utilizes an Excel front end. Scientists are familiar with Excel and utilizing Excel as the front end makes the system portable and not tied to any database. The input data is assumed to be in the form of Excel spreadsheets or flat files describing the expression values and a spreadsheet providing user-specified phenotypes for the samples arrayed. The analytic and visualization tools are integrated into Excel as an add-in. The analytic and visualization tools themselves are developed in the powerful R statistical system, in C and Fortran programs and in Java applications. Visual Basic for Applications is the glue that integrates the components and hides the complexity of the analytic methods from the user. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis. A special input format is available for NCI users of the mAdb database to facilitate their use of BRB ArrayTools. The package has been distributed to over 500 institutions internationally.

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Updated on Nov. 2, 2015