Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.
Inkscape is a free and open-source vector graphics editor; it can be used to create or edit vector graphics such as illustrations, diagrams, line arts, charts, logos and complex paintings. Inkscape’s primary vector graphics format is Scalable Vector Graphics (SVG), however many other formats can be imported and exported.
Gephi is an open-source software for network visualization and analysis. It helps data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluster, manipulate, export. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps.
GeoGebra is dynamic mathematics software for all levels of education that brings together geometry, algebra, spreadsheets, graphing, statistics and calculus in one easy-to-use package. GeoGebra is a rapidly expanding community of millions of users located in just about every country. GeoGebra has become the leading provider of dynamic mathematics software, supporting science, technology, engineering and mathematics (STEM) education and innovations in teaching and learning worldwide.