Graph view thoughts

I would like to publish a post which can be used as source of information about different graphical frameworks.

Let me explain.

Goal: I would like to have a graph view which will allow me to arrange nodes and find them at the same position when I close the program. The reason for that is my learning process. All complicated system consists of less complicated subsystem and so on. It is natural to have a hierarchy and represent the knowledge base as a hierarchical graph.

Requirements: The future plugin has to be able to scan all md-files, collect the links between them, collect tags, present graph in a nice way with colors and link behavior and remember positions of the nodes and links for next session. So it looks like this plugin need some sort of database where every node will keep 2-d coordinates and may be some additional information. Because plugin will be running on workstation the database has to be able to run on small resources (less RAM and CPU than on servers) probably some noSQL databases based on JSON or similar. Another part of plugin has to be able to present the graph saved in database in a nice way.

I am exploring Neo4j but I am not sure if it is the right choice. It has extensive query language but may be we don’t need it.

Anyway I will appreciate if our community will publish here frameworks which are designed for graph presentation and not necessarily include databases. Small noSQL databases also welcomed.

My the only choice now is Neo4j -
Database can be MongoDB -

Please post any other alternatives.

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