The Synechococcus WH8102 knowledge base (http://www.csbl.bmb.uga.edu/WH8J02) is a Web based relational database developed to facilitate computational effort to reconstruct regulatory pathways and serve as a gateway for biologist to access the data. It is the repertoire that integrates a variety of knowledge derived both from literature and computational prediction. Those data are organized in hierarchical fashion. The basic building blocks are functional annotation and structure prediction of individual molecule. Those data are then organized into clusters based on computationally predicted operon, regulon and molecular complexes. Finally all data are complied into pathways derived from combined efforts of literature mining and computational prediction. A number of tools have been developed to facilitate the data retrieval including a SQL query engineer and several viewers to browse genome, molecular complexes and pathways.