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I am looking for a web library/framework that would allow me to place nodes on a diagram, link them with "tubes" and somehow visualize flow between the nodes. I am only looking for the visualization part. Does such thing exist?

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Essential Diagram for JavaScript supports creating any kind of diagram with nodes and connectors. The library is not open source, but a community license is available (details below)

Example

Diagram JS with animated connectors

The whole product is available for free through the community license if you qualify (less than 1 million USD in revenue).

I work for Syncfusion.

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