Capabilities of the COMETS platform

COMETS can:

Simulate a range of spatial conditions:

• Microbial growth in 2D and 3D environments
• Diffusive and convective spatial propagation of biomass
• Substrate-dependent nutrient and biomass propagation
• Boundary conditions

Simulate a range of other biologically realistic details:

• Chemostat and batch growth modes
• Parsimonious dFBA
• Cell death
• Neutral population drift
• Evolutionary processes like random mutation (reaction deletions)

The software is implemented in JAVA and can be run via the command-line or in a graphical user interface. In multi-CPU systems, dFBA is parallelized for greater computational performance. Toolboxes in both MATLAB and Python are available to modify the input files for COMETS in a programmatic way.

With the introduction of the signaling class in COMETS, we augment the capabilities of the platform to include:

• Single signal-reaction relationships, where the presence of a metabolite changes the bounds of a metabolic reaction
• Multiple signal-single reaction relationships, where the presence of multiple metabolites additively change the bounds of a metabolic reaction