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.

Keywords: computational genomics; metabolic models; metabolic pathways; systems biology.

Figure 1.

The HumanCyc MAP kinase cascade, a signaling pathway diagram.

Figure 2.

The EcoCyc L-ornithine biosynthesis pathway shown with omics pop-ups containing time-series data from a gene-expression experiment.

Figure 3.

An electron transfer pathway diagram.

Figure 4.

A gene SmartTable. Column 1 shows the gene name, column 2 shows the E. coli genome ‘b-number' accession number for the gene (a property); column 3 shows the gene product name (a property). Column 4 shows the result of a transformation in which the regulator(s) of each gene were computed.

Figure 5.

The Pathway Tools Cellular Overview diagram for EcoCyc, painted with gene-expression data. Omics pop-ups are shown for two genes.

Figure 6.

Pathway Tools supported formats and APIs for data import and export.

Figure 7.

The RouteSearch web interface is shown with the result of one short pathway found. The arrows represent reactions and are tagged with the protein names catalyzing them. All atoms are conserved from the start compound (succinate) to the target compound ((S)-Malate) in this simplified example.