Computation Of Microbial Ecosystems in Time and Space (COMETS) is a computational framework which combines stoichiometric modeling of metabolism with the biophysics of molecular and cellular processes, to simulate metabolism in spatially structured environments.
SHEWANELLA MICROARRAY DATA
Data on flux balance predictions of epistatic interactions between yeast metabolic gene deletions, relative to multiple flux phenotypes
SYNTHETIC ECOLOGY PREDICTIONS
Data and software about predictions of symbiotic interactions between different microbial species, using genome-scale stoichiometric models
PORPHYROMONAS GINGIVALIS METABOLIC MODEL
Data and visualization of the genome-scale metabolic network of Porphyromonas gingivalis
YEAST GENE KNOCKOUTS
Visualization of yeast metabolic fluxes for different mutants and growth conditions (using VisANT)
GREAT OXYGENATION EVENT MODELING
Database of reactions and interactive visualization of metabolic pathways associated with the transition form an anoxic to an oxic world
EPISTATIC INTERACTIONS IN YEAST METABOLISM
Monochromatic clustering of epistatic interactions in the metabolic network of S. cerevisiae, computed using flux balance analysis
MINIMIZATION OF METABOLIC ADJUSTMENT (MOMA)
A variety of scripts and links for doing Flux Balance Analysis using open source software.