COMETS (Computation of Microbial Ecosystems in Time and Space) Download software, organisms, and environments for 3D flux balance simulations of microbial communities 2014


Shewanella Microarray S. oneidensis Affymetrix Microarray platform (GPL8434)

S. oneidensis time series microarray data from Beg et al. 2012 Nucleic Acids Research

S. oneidensisL. lactis microarray data from Rosenbaum et al. 2012 PloS One

S. oneidensisL. 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 2011
Synthetic ecology predictions Data and software about predictions of symbiotic interactions between different microbial species, using genome-scale stoichiometric models 2010
P. gingivalis metabolism Data and visualization of the genome-scale metabolic network of
Porphyromonas gingivalis
Yeast gene knockout fluxes Visualization of yeast metabolic fluxes for different mutants and

growth conditions (using VisANT)

Oxygen metabolism
and the evolution of complex life
Database of reactions and interactive visualization of metabolic pathways associated with the transition form an anoxic to an oxic world 2006
Monochromatic clustering of epistatic networks Data and scripts related to epistatic interactions  in the metabolic network of S. cerevisiae, computed using flux balance analysis 2006
Flux Balance Analysis and Minimization of Metabolic Adjustment (MOMA) A variety of scripts and links for doing Flux Balance Analysis using open source software. The page is no longer maintained. Please contact us for latest versions. 2002
Lipid World simulations Scripts and outputs of simulations of growth and division cycles of collectively autocatalytic assemblies of self-aggregating molecules (primordial compositional inheritance) 2000