Data Visualization

Cytospace is a free network visualization tool available on web browsers and Windows systems. Users can upload molecular, genetic, or tabular data across numerous formats (including CX2, JSON, SIF, GML, XGMML, SBML, BioPAX, Graph ML, delimited text, XLS, and XLSX0, or connect directly to public databases like Pathway Commons, IntAct, BioMart, NCBI, and Entrez Gene. Cytoscape enables users to search, filter, annotate, and visualize their data. Users can choose from network layouts like acyclic, tree, force-directed, and edge-width to display biological pathways, gene expressions, or interpersonal relationships. The thickness, colors, and labels of nodes and borders can be customized on visualizations. Visualization can be exported as PDF, DS, SVG, PNG, JPEG, and DMP files. 

Gephi is a fee network visualization tool designed to map biological, technological, natural, informational, and social networks. It is accessible through web browsers or can downloaded on Mac, Windows, and Linux systems. Users can upload data in various file formats, including GEXF, GDF, GML, Graph ML, Graphviz Dot, CSV, UCINET, Tulip TPL, Pajek NET, VNA, XLSX, XLS, XLSM, and ODS. Gephi allows users to uncover structural patterns using community detection, clustering, and central measuring. Users can interact with their visualization zooming in and out, panning, and selecting individual nodes, and more using Gephi plugins. Projects can be saved or exported as SVG, PNG, or PDF files.