SUMMARY: The increasing availability of large network datasets along with the progresses in experimental high-throughput technologies have prompted the need for tools allowing easy integration of experimental data with data derived form network computational analysis. In order to enrich experimental data with network topological parameters, we have developed the Cytoscape plug-in CentiScaPe. The plug-in computes several network centrality parameters and allows the user to analyze existing relationships between experimental data provided by the users and node centrality values computed by the plug-in. CentiScaPe allows identifying network nodes that are relevant from both experimental and topological viewpoints. CentiScaPe also provides a Boolean logic-based tool that allows easy characterization of nodes whose topological relevance depends on more than one centrality. Finally, different graphic outputs and the included description of biological significance for each computed centrality facilitate the analysis by the end users not expert in graph theory, thus allowing easy node categorization and experimental prioritization. AVAILABILITY: CentiScaPe can be downloaded via the Cytoscape web site: http://chianti.ucsd.edu/cyto_web/plugins/index.php. Tutorial, centrality descriptions and example data are available at: http://profs.sci.univr.it/ approximately scardoni/centiscape/centiscapepage.php CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Metabolic P systems, shortly MP systems, are a special class of P systems, introduced for expressing biological metabolism. Their dynamics is computed by metabolic algorithms which transform populations of objects according to a mass partition principle, based on suitable generalizations of chemical laws. The basic principles of MP systems are discussed and Psim, a simulation tool we developed in this context to discretely compute systems dynamics, is highlighted in its basic features. A concrete example is reported as well including a real simulation experiment by means of Psim.