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X3D-Edit is an Extensible 3D (X3D) Graphics authoring tool for simple error-free creation, editing, validation and viewing of X3D scenes for interactive Web-based visualization. X3D-Edit runs as a standalone application or Netbeans plugin. The X3D file format is an advanced XML version of the original VRML97 international standard.
dag-builder-js is a simple-to-use Javascript DAG library with support for N:N vertices/edges. It supports validating that no cycle can be created in real-time, import/export states and it's built on SVG so you can render graphs pretty much anywhere.