MODIT (MOtif DIscovery in Temporal Networks) is an algorithm for counting motifs of any size in temporal networks, i.e. networks where edges are associated with timestamps. MODIT is inspired by TemporalRI subgraph matching algorithm in temporal networks.
TemporalRI is an algorithm for subgraph matching in temporal networks, i.e. networks where edges are associated with timestamps. TemporalRI is inspired by RI subgraph matching algorithm.
MultiRI is a software for subgraph matching in multi-relational graphs, i.e. graphs where both nodes and edges can have one or more attributes or labels. MultiRI is an extension of the RI subgraph matching algorithm.
FlashMotif is a tool for finding statistically significant colored motifs with analytically derived p-values. FlashMotif uses the GLabTrie algorithm for counting occurrences of colored motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. FlashMotif works on both directed and undirected networks and can handle induced and non-induced injective and multiset topological colored motifs with color-topology dependency or independency.
GASOLINE (Greedy and Stochastic Algorithm for Optimal Local alignment of Interaction Networks) is an algorithm for multiple local network alignment based on statistical iterative sampling in connection to a greedy strategy. GASOLINE can produce biologically significant alignments in reasonable running time, even for very large input instances.
MultiMotif is a tool for finding statistically significant labeled motifs in multi-relational networks with analytically derived p-values. MultiMotif uses a custom version of RI algorithm for counting occurrences of labeled motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. MultiMotif works on both directed and undirected networks and handle non-induced labeled motifs.
PROPOSAL (PROtein comparison through Probabilistic Optimal Structure local ALignment) is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.
SPECTRA (SPECific Tissue/Tumor Related PPI networks Analyzer) is a framework to build and analyze protein-protein interaction networks specific for a set of tissues or tumors (TS-PPI networks). SPECTRA integrates tissue and tumor specific gene expression data from variuos online repositories with high-quality protein-protein interaction data and provides a web interface for constructing, visualizing and comparing TS-PPI networks, with the aim of identify differential interaction/expression patterns in TS-PPI networks (i.e. distinct tissues, or normal and pathological states of the same tissue). Comparison is performed through an adaptive version of GASOLINE algorithm.