BioSilico is a web-based database system that provides integrated access to public metabolic databases available. An integrated data structure and a variety of querying logics are developed to allow easy and efficient retrieval of various data in the metabolic network. The system is installed on the IBM RS/6000 server running the IBM AIX 5.0L operating system, and run on Java Virtual Machine of JDK 1.4.0. The generated codes are written in Java, MySQL (version 3.23.47), and JavaServer Pages (JSP). Two Marvin Java applets (MarvinSketch and MarvinView) and JChem libraries from ChemAxon, Inc are also part of the system. Thus, two databases, the BioSilico and a database of chemical structures (Chem DB) support the system, and its web pages are dynamically generated through JSP scripts.