BACKGROUND: Public repositories of biological pathways and networks have greatly expanded in recent years. Suchdatabases contain many pathways that facilitate the analysis of high-throughput experimental workand the formulation of new biological hypotheses to be tested, a fundamental principle of the systemsbiology approach. However, large-scale molecular maps are not always easy to mine and interpret. RESULTS: We have developed BiNoM(Biological NetworkManager), a Cytoscape plugin, which provides functionsfor the import-export of some standard systems biology file formats (import from CellDesigner,BioPAX Level 3 and CSML; export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithmsto analyze and reduce the complexity of biological networks. BiNoM can be used to importand analyze files created with the CellDesigner software. BiNoM provides a set of functions allowingto import BioPAX files, but also to search and edit their content. As such, BiNoM is able toefficiently manage large BioPAX files such as whole pathway databases (e.g. Reactome). BiNoMalso implements a collection of powerful graph-based functions and algorithms such as path analysis,decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering anddecomposition of a large network in modules. CONCLUSIONS: Here, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspectssuch as the support of the BioPAX Level 3 format and the implementation of a new algorithm for thequantification of pathways for influence networks. At last, we illustrate some of the BiNoM functionson a detailed biological case study of a network representing the G1/S transition of the cell cycle, acrucial cellular process disturbed in most human tumors.