Architectures for Java‐based bioinformatics applications

Bioinformatics projects are currently under way at numerous universities and in industry. These projects typically involve processing large amounts of biological data and comparison of biological signals or sequences. Much of the existing work in bioinformatics software is based on such languages and platforms as Perl and Unix. This paper, proposes software architectures in Java to support biological applications allowing access of biological data using server‐side Java programs on the Internet. The architecture follows the standards of unified modeling language (UML). UML architecture diagrams are presented for the Java‐based bioinformatics applications. In addition, an overview of the Bio‐Soft project under way at The Biomedical Research Institute (BRI) of the University of Wisconsin‐Parkside is provided, which includes research and instructional software for bioinformatics applications.