ISYS is a dynamic, flexible open source platform for the integration of bioinformatics software tools and databases. ISYS offers a component-based architecture that enables scientists to "plug and play" among tools of interest. These tools may be separately developed and independently evolving, and may include a group's own databases and analytical programs as well as those available publicly or for a fee. In addition, ISYS now allows web-based resources to be integrated with programs running on the scientist's desktop.