Detection of community structure has become a fundamental step in the analysis of biological networks with application to protein function annotation, disease gene prediction, and drug discovery. This recent impact creates a need to make these techniques and their accompanying visualization schemes available to a broad range of biologists. Here we present a service-oriented, end-to-end software framework, CDAPS (Community Detection APplication and Service), that integrates the identification, annotation, visualization, and interrogation of multiscale network communities, accessible within the popular Cytoscape network analysis platform. With novel design principles, CDAPS addresses unmet new challenges, such as identifying hierarchical community structures, comparison of outputs generated from diverse network resources, and easy deployment of new algorithms, to facilitate community-sourced science. We demonstrate that the CDAPS framework can be applied to high-throughput protein-protein interaction networks to gain novel insights, such as the identification of putative new members of known protein complexes.

We analyze the traffic-weighted Web host graph obtained from a large sample of real Web users over about seven months. A number of interesting structural properties are revealed by this complex dynamic network, some in line with the well-studied boolean link host graph and others pointing to important differences. We find that while search is directly involved in a surprisingly small fraction of user clicks, it leads to a much larger fraction of all sites visited. The temporal traffic patterns display strong regularities, with a large portion of future requests being statistically predictable by past ones. Given the importance of topological measures such as PageRank in modeling user navigation, as well as their role in ranking sites for Web search, we use the traffic data to validate the PageRank random surfing model. The ranking obtained by the actual frequency with which a site is visited by users differs significantly from that approximated by the uniform surfing/teleportation behavior modeled by PageRank, especially for the most important sites. To interpret this finding, we consider each of the fundamental assumptions underlying PageRank and show how each is violated by actual user behavior

The understanding of the immense and intricate topological structure of the World Wide Web (WWW) is a major scientific and technological challenge. This has been recently tackled by characterizing the properties of its representative graphs, in which vertices and directed edges are identified with Web pages and hyperlinks, respectively. Data gathered in large-scale crawls have been analyzed by several groups resulting in a general picture of the WWW that encompasses many of the complex properties typical of rapidly evolving networks. In this article, we report a detailed statistical analysis of the topological properties of four different WWW graphs obtained with different crawlers. We find that, despite the very large size of the samples, the statistical measures characterizing these graphs differ quantitatively, and in some cases qualitatively, depending on the domain analyzed and the crawl used for gathering the data. This spurs the issue of the presence of sampling biases and structural differences of Web crawls that might induce properties not representative of the actual global underlying graph. In short, the stability of the widely accepted statistical description of the Web is called into question. In order to provide a more accurate characterization of the Web graph, we study statistical measures beyond the degree distribution, such as degree-degree correlation functions or the statistics of reciprocal connections. The latter appears to enclose the relevant correlations of the WWW graph and carry most of the topological information of the Web. The analysis of this quantity is also of major interest in relation to the navigability and searchability of the Web.