Overview The E. coli whole-cell modeling project aims to build a computational model of an E. coli cell that fully captures the dynamics of every known molecule within an E. coli cell. For every EcoCyc release, the WCM collaboration takes a snapshot of curated EcoCyc information and runs computational simulations of the whole cell, under several different growth medium conditions. Such simulations could provide insights in areas that are difficult to access and quantify experimentally.

Slices of the computed data are shown in the "Modeling" tab on the pages for genes/proteins, protein complexes, and reactions. This summary page provides a more global overview of the computed data sets.

The data points in the 'Largest values' row and the 'Cell Properties' table are averages over multiple individual cell simulations.

Version WCM git hash "5b2b412810e4c314ddbbb68880ff096628767829", derived from EcoCyc 29.0

Whole-Cell Model results under the growth medium (aerobic)

 
Genes (RNAs)
Protein Monomers
Protein Complexes
Reactions (Fluxes)
EcoCyc item counts 4,541 4,490 1,195 3,272
WCM data points 4,434 4,309 1,108 2,807
Largest values 21,806.37, 21,758.90, 21,594.02, 4,379.08, 4,227.72 (counts) 245,249.91, 159,238.73, 113,598.78, 112,291.46, 106,789.95 (counts) 79,599.57, 35,587.42, 31,141.44, 22,112.07, 20,336.22 (counts) 107.23, 85.58, 65.56, 63.80, 22.26 (fluxes in mmol/g DCW/h)
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Cell Properties  
Simulation timesteps (1s each) 369,376
Doubling time (min) 48.10
Cell volume (fL) 1.06
Cell mass (fg) 1,162.75
Dry cell mass (fg) 348.99
Protein mass (fg) 151.80
RNA mass (fg) 46.62
DNA mass (fg) 6.17
Membrane mass (fg) 5.93
Small molecule mass (fg) 144.39
mRNA mass to total RNA mass 0.04
rRNA mass to total RNA mass 0.80
tRNA mass to total RNA mass 0.14
Ribosomal protein mass fraction 0.20