Author: Peter Karp

We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope.

Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.

Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.

Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network.

We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP).

We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric.

We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism.

The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases.

The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes.