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The BioJAKE program has been created for the visualization, creation and manipulation of metabolic pathways. It has been designed to provide a familiar and easy-to-use interface while still allowing for the input and manipulation of complex and detailed metabolic data. In recognition of the detailed and diverse sources of data available across the Internet, it also provides a mechanism by which remote database queries can be stored and performed with respect to individual molecules within a pathway. This remote database access functionality is offered in addition to comprehensive local database creation, management and querying capability. The program has been developed in Java so as to provide for platform independence and maximum extendibility.