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http://www.lukelab.com/lab/noder/
http://www.3d-node.com/cmsimple-en/?Home
http://www.soft.com/eValid/Products/Documentation.5/Mapping/3Dsitemap.html
http://www.geom.uiuc.edu/software/weboogl/about.html
http://bioinformatics.icmb.utexas.edu/lgl/
http://www.hpl.hp.com/research/idl/projects/graphs/
http://www.caida.org/tools/visualization/walrus/
http://www.redfish.com/research/graphLayout.htm
http://www.cs.usyd.edu.au/~aquigley/3dfade/
http://www-unix.mcs.anl.gov/~mccrory/bioandgraph.html
there are so many apps that do this… your friend needs to google it.
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He is one of those vague kind of geniuses, so he didn’t specify what he google for. He may not understand precisely what you want to do, but there’s some stuff to look at.
]]>Also sketchup which is a commercial, architecture type program, but I think it might work, esp if you find some models for the nodes.
Has a wonderful interface and the demo works fully for 8 hours and saves and everything from what I remember.
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