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 abilityto represent and visualize a wide range ofregulatoryinteractions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation ofatom mappings and estimation ofcompound Gibbs free energies offormation; addition ofeditors for signaling pathways, for genome sequences and for cellular architecture;storage ofgene essentialitydata and phenotype data; displayofmultiple alignments, and ofsignaling and electron-transport pathways;and development ofPython 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.