In this paper we describe a system for visualizing and analyzing worldwide research topics, rtopmap . We gather data from google scholar academic research profiles, putting together a weighted topics graph, consisting of over 35,000 nodes and 646,000 edges. The nodes correspond to self-reported research topics, and edges correspond to co-occurring topics in google scholar profiles. The rtopmap system supports zooming panning searching and other google-maps-based interactive features. With the help of map overlays, we also visualize the strengths and weaknesses of different academic institutions in terms of human resources (e.g., number of researchers in different areas), as well as scholarly output (e.g., citation counts in different areas). Finally, we also visualize what parts of the map are associated with different academic departments, or with specific documents (such as research papers, or calls for proposals). The system itself is available at this http URL .
 This is an extensively revised and expanded second edition of the successful textbook on social network analysis integrating theory, applications, and network analysis using Pajek. The main structural concepts and their applications in social research are introduced with exercises. Pajek software and data sets are available so readers can learn network analysis through application and case studies. Readers will have the knowledge, skill, and tools to apply social network analysis across the social sciences, from anthropology and sociology to business administration and history. This second edition has a new chapter on random network models, for example, scale-free and small-world networks and Monte Carlo simulation; discussion of multiple relations, islands, and matrix multiplication; new structural indices such as eigenvector centrality, degree distribution, and clustering coefficients; new visualization options that include circular layout for partitions and drawing a network geographically as a 3D surface; and using Unicode labels. This new edition also includes instructions on exporting data from Pajek to R software. It offers updated descriptions and screen shots for working with Pajek (version 2.03). Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical functional interaction network for Halobacterium, and an interface to detailed stochastic kinetic gene regulatory models. Graph drawing is a basic visualization tool that works well for graphs having up to hundreds of nodes and edges. At greater scale, data density and occlusion problems often negate its effectiveness. Conventional pan-and-zoom, multiscale, and geometric fisheye views are not fully satisfactory solutions to this problem. As an alternative, we propose a topological zooming method. It precomputes a hierarchy of coarsened graphs that are combined on-the-fly into renderings, with the level of detail dependent on distance from one or more foci. A related geometric distortion method yields constant information density displays from these renderings. We describe ASK-GraphView, a node-link-based graph visualization system that allows clustering and interactive navigation of large graphs, ranging in size up to 16 million edges. The system uses a scalable architecture and a series of increasingly sophisticated clustering algorithms to construct a hierarchy on an arbitrary, weighted undirected input graph. By lowering the interactivity requirements we can scale to substantially bigger graphs. The user is allowed to navigate this hierarchy in a top down manner by interactively expanding individual clusters. ASK-GraphView also provides facilities for filtering and coloring, annotation and cluster labeling