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<p>Abstract</p> <p>Background</p> <p>Biological processes such as metabolic pathways, gene regulation or protein-protein interactions are often represented as graphs in systems biology. The understanding of such networks, their analysis, and their visualization are today important challenges in life sciences. While a great variety of visualization tools that try to address most of these challenges already exists, only few of them succeed to bridge the gap between visualization and network analysis.</p> <p>Findings</p> <p>Medusa is a powerful tool for visualization and clustering analysis of large-scale biological networks. It is highly interactive and it supports weighted and unweighted multi-edged directed and undirected graphs. It combines a variety of layouts and clustering methods for comprehensive views and advanced data analysis. Its main purpose is to integrate visualization and analysis of heterogeneous data from different sources into a single network.</p> <p>Conclusions</p> <p>Medusa provides a concise visual tool, which is helpful for network analysis and interpretation. Medusa is offered both as a standalone application and as an applet written in Java. It can be found at: <url>https://sites.google.com/site/medusa3visualization</url>.</p>