Communicability in complex networks

Many topological and dynamical properties of complex networks are defined by assuming that most of the transport on the network flows along the shortest paths. However, there are different scenarios in which non-shortest paths are used to reach the network destination. Thus the consideration of the shortest paths only does not account for the global communicability of a complex network. Here we propose a new measure of the communicability of a complex network, which is a broad generalization of the concept of the shortest path. According to the new measure, most of real-world networks display the largest communicability between the most connected (popular) nodes of the network (assortative communicability). There are also several networks with the disassortative communicability, where the most "popular" nodes communicate very poorly to each other. Using this information we classify a diverse set of real-world complex systems into a small number of universality classes based on their structure-dynamic correlation. In addition, the new communicability measure is able to distinguish finer structures of networks, such as communities into which a network is divided. A community is unambiguously defined here as a set of nodes displaying larger communicability among them than to the rest of nodes in the network.Comment: 20 pages, 5 figure

Snazer: the simulations and networks analyzer

<p>Abstract</p> <p>Background</p> <p>Networks are widely recognized as key determinants of structure and function in systems that span the biological, physical, and social sciences. They are static pictures of the interactions among the components of complex systems. Often, much effort is required to identify networks as part of particular patterns as well as to visualize and interpret them.</p> <p>From a pure dynamical perspective, simulation represents a relevant <it>way</it>-<it>out</it>. Many simulator tools capitalized on the "noisy" behavior of some systems and used formal models to represent cellular activities as temporal trajectories. Statistical methods have been applied to a fairly large number of replicated trajectories in order to infer knowledge.</p> <p>A tool which both graphically manipulates reactive models and deals with sets of simulation time-course data by aggregation, interpretation and statistical analysis is missing and could add value to simulators.</p> <p>Results</p> <p>We designed and implemented <it>Snazer</it>, the simulations and networks analyzer. Its goal is to aid the processes of visualizing and manipulating reactive models, as well as to share and interpret time-course data produced by stochastic simulators or by any other means.</p> <p>Conclusions</p> <p><it>Snazer </it>is a solid prototype that integrates biological network and simulation time-course data analysis techniques.</p

A survey of visualization tools for biological network analysis

The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing

'Dressed in a Little Brief Authority': Authority Before, During, and After Shakespeare's Plays

This essay discusses the concept of authority from Shakespeare’s time to our own, considers examples of Shakespeare’s own explorations of authority, and provides a concise history of the ways in which Shakespeare has been constructed as cultural authority in different historical periods. It summarises the essays contained in the book, and argues that the book illuminates not only how Shakespeare became the archetypal figure of English cultural authority, but, perhaps more interestingly, why

Communicability and multipartite structures in complex networks at negative absolute temperatures

We here present a method of clearly identifying multipartite subgraphs in a network. The method is based on a recently introduced concept of the communicability, which very clearly identifies communities in a complex network. We here show that, while the communicability at a positive temperature is useful in identifying communities, the communicability at a negative temperature is useful in identifying multipartite subgraphs; the latter quantity between two nodes is positive when the two nodes belong to the same subgraph and is negative when they do not. The method is able to discover 'almost' multipartite structures, where intercommunity connections vastly outweigh intracommunity connections. We illustrate the relevance of this work to real-life food web and protein-protein interaction networks

Supplementary methods and results for An anchovy ecosystem indicator of marine predator foraging and reproduction

Forage fishes are key energy conduits that transfer primary and secondary productivity to higher trophic levels. As novel environmental conditions caused by climate change alter ecosystems and predator–prey dynamics, there is a critical need to understand how forage fish control bottom-up forcing of food web dynamics. In the northeast Pacific, northern anchovy (Engraulis mordax) is an important forage species with high interannual variability in population size that subsequently impacts the foraging and reproductive ecology of marine predators. Anchovy habitat suitability from a species distribution model (SDM) was assessed as an indicator of the diet, distribution and reproduction of four predator species. Across 22 years (1998–2019), this anchovy ecosystem indicator (AEI) was significantly positively correlated with diet composition of all species and the distribution of common murres (Uria aalge), Brandt's cormorants (Phalacrocorax penicillatus) and California sea lions (Zalophus californianus), but not rhinoceros auklets (Cerorhinca monocerata). The capacity for the AEI to explain variability in predator reproduction varied by species but was strongest with cormorants and sea lions. The AEI demonstrates the utility of forage SDMs in creating ecosystem indicators to guide ecosystem-based management