The Pathway Tools software provides a suite of capabilities for storing and analyzing collections of genomic and metabolic information .
The EcoCyc Database in 2021
This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression.
The BioCyc Metabolic Network Explorer
The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks.
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains, imposing several quality-control filters to reduce the chances of introducing errors.
Pathway Tools Visualization of Organism-Scale Metabolic Networks
We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.
The MetaCyc Database of Metabolic Pathways and Enzymes – A 2019 Update
This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.
The MultiOmics Explainer: Explaining Omics Results in the Context of a Pathway/Genome Database
We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism’s metabolic and regulatory network to suggest explanations for the results of omics experiments.
A Comparison of Microbial Genome Web Portals
This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.
The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.