This is only indirectly related to Wandora. Wandora supports layered topic maps that are very close to the multilayer networks, the linked paper discusses:
Mikko Kivelä, Alexandre Arenas, Marc Barthelemy, James P. Gleeson, Yamir Moreno, Mason A. Porter: Multilayer Networks.
http://arxiv.org/abs/1309.7233
http://arxiv.org/pdf/1309.7233v4.pdf