sipper

SIPPER is a tool that compute k-SIPs (and more): First, SIPPER integrates bacteria metabolic network and genome from Metacyc tabular files into a directed graph called integrated model. Each arc of the integrated model is weighted with an omic distance (usually a genomic one). Then, given two sets of reactions R and R", SIPPER computes in this model, the set of k shortest paths from R to R". Given a reaction r, each path of a k-SIP uses r at most one time (this constraint can be removed). Finally, it is possible to group some k-SIP by modules. Two k-SIPs are a part of the same group if they have at least a common vertex. PS : some features are experimental and are in development.

sipper
.DS_Store
bin
biological_data
compute_kSIPs.sh
compute_SGS.sh
ecoli.profil
experiments
generate_integrated_model.sh
libs
readme.html
readme.md