The Pathway Tools Software for Metabolic Reconstruction and Modeling

Pathway Tools [1] provides an array of capabilities for storing and analyzing integrated collections of genomic, metabolic, and regulatory information, and for deriving metabolic models from sequenced genomes.  It supports development of organism-specific Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes.  It supports querying, analysis, scientific visualization, and web publishing of those organism-specific DBs. It provides tools for analysis of omics datasets, comparative analysis, and metabolic engineering.

 The MetaFlux module of Pathway Tools generates steady-state metabolic flux models from sequenced genomes using flux-balance analysis (FBA).  MetaFlux contains a number of tools for accelerating model development for individual organisms and for organism communities, including a gap filler tool.  Models can be executed using both FBA and Dynamic FBA, with gene knockouts. MetaFlux has been used to generate a very accurate E. coli metabolic flux model from EcoCyc.

 Pathway Tools now includes the ability to integrate gene-knockout data and Phenotype Microarray data within a PGDB. A new RouteSearch capability enables users to search for optimal routes through the metabolic network that connect two metabolites, with the option of adding additional reactions from MetaCyc to support metabolic engineering.  New web services allow metabolomics data to be painted onto pathway diagrams.  A new pathway collage tool allows users to create diagrams of interconnected pathways painted with omics data.

[1] P.D. Karp et al, Pathway Tools version 19.0 update: Software for Pathway/Genome Informatics and Systems Biology, Briefings in Bioinformatics 2015 doi:10.1093/bib/bbv079.