Table 3 Overview of the parameters used for each of the methods
From: Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
Method | ID | Name | Description | Value in experiment | |
|---|---|---|---|---|---|
MMT | c | Coupling factor | Define how the reaction fluxes are coupled to the biomass reaction flux and defined as: flux span = − (c * flux(biomass)) to + (c * flux(biomass)) | 400 | |
SigD | Significant difference | Value that counts as a significant difference between monoculture and coculture growth rate | 0.1 | ||
u | Threshold u | Flux allowed in reactions if biomass flux = 0 | 0 | ||
mergeGenes | Gene merging variable | Boolean, wether the gene are added and merge in the community mode (Time consuming) | FALSE | ||
MICOM | cooperative_tradeoff | cooperative_tradeoff(= fraction) | Minimum proportion of the maximal community growth to allocate to species growth rate | Min value where both species are growing between 0.1 and 1 with 0.1 step | |
pfba | Parsimonious FBA | Define if a parsimonious FBA is performed | TRUE | ||
min_growth | Minimum growth rate | Minimum growth rate required for each species | 0 | ||
Abundance | Relative abundance of each species in the community. By default each species has the same abundance | 0.5 and 0.5 | |||
OptCom | Strategy | Strategy used to solve the optimization problem | MOMA | ||
lMOMA | |||||
Original | |||||
min_growth | Minimal growth | Minimal growth required for each species | 0 | ||
pfba | Parsimonious FBA | Define if a parsimonious FBA is performed | TRUE | ||
COMETS | H/10 | initial_pop | Gram of biomass in the environment | 0.002 | |
time_step | Time step of a FBA problem in hour | 0.1 | |||
maxCycles | Number of steps max | 20 | |||
H | initial_pop | Gram of biomass in the environment | 1 | ||
time_step | Time step of a FBA problem in hour | 1 | |||
maxCycles | Number of steps max | 10 | |||
BOTH | defaultVmax | V max value per default in mmol/g. CDW/h | 18.5 | ||
defaultKm | KM value per default in M (molar conc.) | 0.000015 | |||
SpaceWidth | size of the cell in cm3 | 1 | |||
maxSpaceBiomass | Capacity maximum in gr. cell dry weight | 100 | |||
minspaceBiomass | Capacity minimum in gr. cell dry weight | 1.00E−11 | |||
obj_stype | Objective type | Define if the strategy used to solve the optimization problem | MAX_OBJ_MIN_TOTAL = > Pfba AND MAXIMIZE_OBJECTIVE_FLUX = > pFBA | ||
Grid | Grid size | Number of boxes in the x and y axis to define the grid size | [1,1] | ||
Static | Related to metabolites in media definition, define if the metabolites are in limited amount | TRUE | |||