Author: Suzanne Paley

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.

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.

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.

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators.

The BioCyc update notifications service is a new mechanism to keep researchers informed of the latest developments in their areas of interest.

New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.

We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.

We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.

The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.

BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.

The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations.