Software
Software Released at Reed College
Pathway Connectivity. Data and source code for (nearly) all figures and experiments from Hypergraph-based connectivity measures for signaling pathway topologies. Also makes use of halp. 
Localized PathLinker (LocPL). LocPL is a compartment-constrained pathway reconstruction method that refines PathLinker paths by protein localization.
Motility-Related Schizophrenia Gene Predictor. SZ Gene Predictor includes code to identify genes that are functionally associated with a disease (e.g. schizophrenia) and a phenotype (e.g. cell motility).
Software Released at Virginia Tech
PathLinker. Algorithm that computes the k shortest loopless paths in a weighted directed network, originally developed to reconstruct human signaling pathways.
halp: Hypergraph Algorithms Package. Software that provides both directed and undirected hypergraph implementations and algorithms. 
GraphSpace: Sharing and Collaborating through Networks on the Web. Interactive network visualization software designed for interdisciplinary collaborations. View Public Graphs
Software Released at Brown University
MultiBreak-SV. Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
NBC: Neighborhood Breakpoint Conservation. NBC finds recurrent rearrangement breakpoints in DNA copy number data.
Gremlin: Genome Rearrangement Explorer with Multi-Scale, Linked Interactions. Interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.
MoDL: Motif Description Length. MoDL finds mutliple motifs in a set of phosphorylated peptides using an description length, a concept borrowed from information theory.
aritz-at-reed-dot-edu
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