Author: Peter Karp

The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).

We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network.

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.

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.

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

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.