NORMA-The network makeup artist: a web tool for network annotation visualization

Abstract

NORMA is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g. Gene Ontology/Pathway enrichment or clustering results) can be uploaded and visualized in a network either as colored pie-chart nodes or as color-filled convex hulls in a Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are: i) the network, ii) the communities or annotations and iii) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at:

Arena3Dweb: interactive 3D visualization of multilayered networks

“…force-directed, hierarchical, orthogonal and spectral) to generate informative and appealing 2D/3D views thus minimizing any possible node overlaps and connection crossovers ( 3 ). Among a decent variety of applications today ( 4 , 5 ), widely-used interactive 2D visualizers include the Cytoscape ( 6 ), Cytoscape.js ( 7 ), String ( 8 ), NORMA ( 9 ), Gephi ( 10 ), Pajek ( 11 ) and Tulip ( 12 ) whereas successful 3D visualizers include the Graphia (Kajeka) and BioLayout Express ( 13 ).…”

OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

“…All of these resources can be queried manually by the user, or automatically through Application Programming Interfaces (APIs), packages or plugins. Their results can be used to generate, visualize and analyze interaction networks with network viewers such as Cytoscape (18), Gephi (19), NORMA (20) and others (reviewed (21,22)).…”

VICTOR: A visual analytics web application for comparing cluster sets

“…STING [17] and CLIQUE [18] algorithms are typical examples in this category. As far as network clustering is concerned, graph-based clustering analysis can exploit the topology of a network for community detection [19]. Widely used graph-based clustering algorithms include Louvain [20], SPICi [21], Markov clustering (MCL [22]/HipMCL [23]) and Walktrap [24].…”

“…Attribute clustering algorithms include hierarchical, k-means, k-medoid [38] and AutoSOME. NORMA [19], a web server visualization application focusing on the visualization of network annotations, is supported by the igraph library [39], thus allowing the utilization of clustering algorithms such as fast-greedy, Louvain and label-propagation [40].…”