Three canonical COMETS-literature benchmarks wrapped as
process-bigraph Processes: the virtual test tube
(mixed-acid fermentation with acetate reuptake), the virtual petri
dish (Fisher-Kolmogorov colony expansion), and a Harcombe-style
cross-feeding mutualism. Built on cobra FBA plus an
explicit 5-point Laplacian diffusion step; see Dukovski et al.,
Nature Protocols 16, 5030–5082 (2021).
The classic COMETS well-mixed batch experiment: a single E. coli inoculum is grown in a test tube of defined media containing glucose under oxygen-limited conditions. The simulation reproduces three sequential physiological phases that COMETS highlights in the literature: (1) rapid exponential growth on glucose with overflow metabolism — acetate is secreted as a fermentation byproduct; (2) glucose depletion and an inflection in the growth curve; (3) acetate reuptake once glucose runs out and a final slow-respiration phase. All three are visible in the biomass and media panels below.
E_coli
Species1
Snapshots121
Biomass gain2668.7×3.00e-04 → 8.01e-01 gDW
Glucose0.0010.0 → 0.00 mmol
Acetate (final)0.00mmol
Max μ0.621/hr
Runtime0.48s
Community Dynamics
Bigraph Architecture
Composite Document
Spatial Dynamics — 2D Grid with Local FBA + Diffusion
The next configurations run on a spatial lattice using
SpatialDynamicFBAProcess, which mirrors the per-cell-FBA +
Fickian-diffusion model used by COMETS. Each cell solves its own FBA
against local media concentrations; biomass and metabolites spread via
an explicit Laplacian stencil between cells.
S1
Virtual Petri Dish — Fisher-Kolmogorov Colony Expansion
Radial growth wave on a uniform glucose field (Dukovski 2021, Box 1)
The canonical COMETS spatial benchmark: a single E. coli inoculum is placed at the center of a 30×30 agar-plate lattice seeded with a uniform glucose background. With very slow biomass diffusion and faster metabolite diffusion, the colony forms a Fisher-Kolmogorov travelling wave — a sharp, radially-symmetric growth front that advances outward at constant speed. At the wavefront local glucose drops while interior cells reach carrying capacity. This is the figure that opens the COMETS Nature Protocols tutorial.
Inspired by Harcombe et al. (2014, Cell Reports) and the multi-species COMETS examples in Dukovski 2021, this simulation seeds two E. coli variants with complementary metabolic capabilities:
E_glc — placed as a line inoculum down the left edge — consumes glucose and ferments it to acetate under oxygen-limited conditions. It cannot grow on acetate.
E_ac — placed as a line inoculum down the right edge — has its glucose uptake blocked and its acetate uptake opened. It has its own abundant oxygen supply and therefore grows whenever acetate reaches it.
As the glucose line invades the plate rightward, acetate diffuses ahead of the colony front and lights up the E_ac line. The stoichiometric coupling between the two strains is visible as layered growth bands — a signature pattern of cross-feeding mutualisms in COMETS.
