title: Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
abstract: Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Paley
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Quang D
authors.initials: QD
authors.lastname: Ong
authors.forename: Richard
authors.initials: R
authors.lastname: Billington
authors.forename: Anamika
authors.initials: A
authors.lastname: Kothari
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.forename: Thomas
authors.initials: T
authors.lastname: Lee
authors.forename: Pallavi
authors.initials: P
authors.lastname: Subhraveti
authors.forename: Aaron
authors.initials: A
authors.lastname: Spaulding
authors.forename: Carol
authors.initials: C
authors.lastname: Fulcher
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
mesh_terms: D019295:Computational Biology; D016678:Genome; D023281:Genomics; D020407:Internet; D053858:Metabolic Networks and Pathways; D012985:Software Design; D049490:Systems Biology
keywords: computational genomics; metabolic models; metabolic pathways; systems biology