I would like to make a simulation of a constrained system indexed by time. This involves a network of agents/nodes that interact based on some logic/relationships. I would like to place the nodes on a grid 2D or 3D does not matter. I would like to have edges drawn between them, and text beside them. I would like to give the logic for the tags on the nodes and give indication of the states. In the style of simjava: simjava
But more based on mathematical simulations than software processes. Graphing tools would be useful etc. Any good recommendations? There is good software for visualizing data sets. Matlab's Simulink has a lot of complexity on non-discretec events, and is not as cartoon-like which is good for testing principle rather than analytics. Unless I am wrong and Simulink provides this
EDIT: A similar question asks about dynamic graphs stack overflow relevant question, it is an issue that does not seems to have any concrete solution except for customized solutions.
hmm. Not sure if I'm on the right track or not, but have you looked at graphviz? It'll render graphs (including auto-layout with various different algorithms). There are bindings from various languages, e.g. pydot for python. If you need graph analysis algorithms (e.g. shortest path) there's also pygraphlib.
There are alternatives to graphviz, e.g. protovis / infovis. Both are javascript based, provide force-directed layout, and render in the browser.
Apologies if I misunderstood question, hope that helps.