COMETS
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.
Lab GitHub
On our GitHub you can find repositories associated with tools developed in the lab and with manuscript published or posted on BioRxiv.
Other resources
SHEWANELLA MICROARRAY DATA
S. oneidensis Affymetrix Microarray platform (GPL8434)
S. oneidensis time series microarray data from Beg et al. 2012 Nucleic Acids Research
S. oneidensis-L. lactis microarray data from Rosenbaum et al. 2012 PloS One
S. oneidensis-L. lactis microarray data from Rosenbaum et al. 2011 Bioresource Technology
MULTI-PHENOTYPE EPISTASIS
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
Oxygen metabolism and the evolution of complex life
EPISTATIC INTERACTIONS IN YEAST METABOLISM
Monochromatic clustering of epistatic interactions in the metabolic network of S. cerevisiae, computed using flux balance analysis
Monochromatic clustering of epistatic networks
MINIMIZATION OF METABOLIC ADJUSTMENT (MOMA)
A variety of scripts and links for doing Flux Balance Analysis using open source software.
Flux Balance Analysis and Minimization of Metabolic Adjustment (MOMA)