Technical Note
Medusa: A tool for exploring and clustering biological networks
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* Corresponding author: Georgios A Pavlopoulos georgios.pavlopoulos@esat.kuleuven.be
1 Katholieke Universiteit Leuven, Faculty of Engineering - ESAT/SCD, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
2 European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Meyerhofstrasse 1, 69117, Heidelberg, Germany
3 Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
4 Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Limpertsberg, 162A, Avenue de la Faïencerie, L-1511, Luxembourg
BMC Research Notes 2011, 4:384 doi:10.1186/1756-0500-4-384
Published: 6 October 2011Abstract
Background
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.
Findings
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.
Conclusions
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: https://sites.google.com/site/medusa3visualization webcite.