Network cartography - Netcarto
Given a network, the program identifies modules (densely connected groups of nodes in the network) and classifies nodes according to their roles.
Network C libraries - RGraph
Source code of the C libraries for a variety of network calculations, including community finding using simulated annealing, network cartography, and link and network reliability.
Bipartite modularity - Bipartmod
Module identification in bipartite and directed networks. Given a bipartite (or directed) network, the program returns a partition into groups of the nodes in one of the sets of nodes (the 'actors' or the 'teams').
A network inference method for large-scale unsupervised identification of novel drug-drug interactions.
These are the drug-drug interaction datasets used in our PLOS Computational Biology paper of 2013.
Air transportation networks
Air transportation network datasets, with city identifiers and coordinates
Long-term email network data
Undirected email correspondence between users of a large organization with over 1,000 individuals for four consecutive years (2007-2010)
Network datasets for perturbation reconstruction
A set of networks for studying the reconstruction of perturbation propagation paths.