Pathway Tools includes two integrated computational modules, MetaFlux and RouteSearch, to perform metabolic modeling and engineering of organisms. These tools use atom-mapping and taxonomic-range information from Pathway Tool's multi-organism MetaCyc database.
MetaFlux is a Flux Balance Analysis (FBA) tool that solves FBA models and that uses gap filling to help develop new models. MetaFlux solves FBA models for either a single organism or a community of organisms. Its user interface targets biologists who have no programming experience. The resulting fluxes can be displayed on metabolic maps showing compounds, reactions, pathways, and more. MetaFlux's gap-filling capability helps users develop FBA models and engineer new metabolic pathways. MetaFlux has been used to develop a high-quality E. coli metabolic model.
RouteSearch is a tool for finding optimal metabolic routes (that is, a series of biochemical reactions that connects starting and goal compounds, given various cost parameters to control the optimality of the routes found). In computing optimality, RouteSearch considers the conservation of non-hydrogen atoms from the starting compound to the goal compound, based on the atom-mapping data available in MetaCyc. Users can solve pathway metabolic-engineering problems by having RouteSearch add reactions from MetaCyc to the computed metabolic routes. RouteSearch is available as a web application from BioCyc.org or from your locally running web server using Pathway Tools.