This talk will be on using a loose coupling architecture to address integration in bioinformatics. I will give a brief introduction on the necessity for integration in biological research (e.g., using gene expression, sequence, and biochemical pathways data to construct and evaluate hypotheses) and the role of traditional software approaches. I will then describe a software architectural approach that addresses integration at the inter-application level. This approach compartmentalizes bioinformatic tools to within their biological specialty and then addresses interaction and communication amongst the components. This approach is distinct from, and complementary to, those approaches that seek to integrate data under common data models.
The approach has been implemented in a software platform called ISYS. ISYS (an acronym for Integrated SYStem) allows independently developed Java applications to plug-and-play in an integrated visual environment. ISYS also supports non-Java connectivity with data sources, algorithms, and web pages. ISYS's support of inter-application visual synchronization allows users to select data in one application and see associated data highlighted in other applications, even if these applications have been developed by different groups at different times. ISYS employs two patent-pending technologies that allow the DynamicDiscovery(TM) of relevant software programs simply by selecting data, and the moving of data to and from web pages by simple mouse clicks. ISYS comes with an initial set of bioinformatic tools and is free for non-commercial use.