The growing dimension and complexity of the available experimental data generating biological networks have increased the need for tools that help in categorizing nodes by their topological relevance. Here we present CentiScaPe, a Cytoscape app specifically designed to calculate centrality indexes used for the identification of the most important nodes in a network. CentiScaPe is a comprehensiv...

UNLABELLED Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a compre...

Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets o...

Networks that represent connections between individuals can be valuable analytic tools. The Social Network Cytoscape app is capable of creating a visual summary of connected individuals automatically. It does this by representing relationships as networks where each node denotes an individual and an edge linking two individuals represents a connection. The app focuses on creating visual summari...

MOTIVATION Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by...

The 7 Amendment to the EU Cosmetics Directive has made developing non-animal approaches to assure the safety of consumer products a key business need to support future innovation. A substantial research programme was initiated by Unilever in 2004, aimed at critically evaluating the feasibility of a proposed new conceptual approach. The key aspects of this approach are: 1. Developing new risk as...

This chapter provides an overview of the computational approaches developed for exploring the modular organization of protein interaction networks. A special emphasis is placed on the module finding tools implemented in three freely available software packages, VisANT, Cytoscape and MATISSE, as well as on their biomedical applications. The selected methods are presented in the broader context o...

SUMMARY The prioritization of candidate disease genes is often based on integrated datasets and their network representation with genes as nodes connected by edges for biological relationships. However, the majority of prioritization methods does not allow for a straightforward integration of the user's own input data. Therefore, we developed the Cytoscape plugin NetworkPrioritizer that particu...

The extensively overlapping structure of network modules is an increasingly recognized feature of biological networks. Here we introduce a user-friendly implementation of our previous network module determination method, ModuLand, as a plug-in of the widely used Cytoscape program. We show the utility of this approach a.) to identify an extensively overlapping modular structure; b.) to define a ...