After completion of Human Genome Project, there has been an exponential increase in the available biological data. Although there has been an enormous effort for creating ontologies, standards and tools, current bioinformatics infrastructure is far from coping with this data. The Patika Project aims to provide the community an integrated environment for modeling, analyzing and integrating cellular processes. Patika project develops software tools providing access, visualization and analysis on the data in Patika database. In this thesis, we present analysis, design and implementation of Patikaweb, a Web-service having a user-friendly interface without requiring any registrations, installations. To achieve an enhanced data analysis , Patikaweb provides a multiple-view schema , compartments and compound graphs for visualizing molecular complexes, pathways and black-box reactions. Querying component supports SQL-like queries and an array of graphtheoretic queries for finding feedback loops, common targets and regulators, or interesting subgraphs based on user’s genes of interest. Constructed models can be saved in XML, exported to standard formats such as BioPAX, SBML or converted to static images. A highly interactive and user friendly querying interface is supported with Patikaweb. Visual representation of complex information in pathway research is very important. The information should be presented with high coverage, while providing a user friendly interface. In this thesis we also present a new approach to visualize complex pathway information coping with the limitations introduced by ontology and graphical representation. Patikaweb ’s unique visualization and querying features fill an important gap in the pool of currently available tools and databases.