uptakeFuncDefault function

Uptake Function

Return the value of resource uptake per biomass (i.e. resource quantity per unit time per mass unit of biomass) for given resource

uptakeFuncDefault(
  strainName,
  groupName,
  pathName,
  varName,
  keyResName,
  subst,
  ess,
  boost,
  maxGrowthRate,
  growthLim,
  yield,
  nonBoostFrac,
  stoichiom,
  parms
)

Arguments

• strainName: Name of the strain that is being looped through in the ODE solver
• groupName: Name of microbial group that is being looped through in the ODE solver
• pathName: Name of metabolic path (e.g. path1) that is being looped through in the ODE solver
• varName: (string). Calculate uptake of this variable
• keyResName: (string). Name of the key resource on this pathway
• subst: Vector of strings giving the names of the substitutable resources for given strain, pathway
• ess: Vector of strings giving the names of the essential resources for given strain, pathway
• boost: Vector of strings giving the names of the boosting resources for given strain, pathway
• maxGrowthRate: Vector containing maximum growth rate on each resource (named by resourceNames). If a resource is not on the pathway the value is NA
• growthLim: Vector containing the growth limitation from each resource (named by resourceNames). If a resource is not on the pathway the value is NA
• yield: Named vector (names are resourceNames) giving the mass yield of biomass on each resource (mass microbe/mass resource)
• nonBoostFrac: (scalar) Fraction of max growth achievable if boosting resource is not present but is required on this pathway
• stoichiom: Named vector (names are resourceNames) giving the mass of each resource in the stoichiometry i.e. molar mass of resource multiplied by the number of moles in the stoichiometry
• parms: List containing all system parameters

Returns

(scalar) uptake of resource per mass unit of biomass (units are resource mass/biomass/time)