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draw.io - Online diagramming application
Cytoscape - Cytoscape Official Web Site
LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
PlantUML - PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.