add_organism: Add a model/organism to simulation

In Waschina/Eutropia: Agent-based modelling of microbial communities in time and continuous µ-meter-scale space

Add a model/organism to simulation

Description

Adds an organism an its genome-scale metabolic network model to the growth simulation object.

Usage

add_organism(
  object,
  model,
  name,
  ncells,
  coords = NULL,
  distribution.method = "random_centroid",
  distribution.center = NULL,
  distribution.radius = NULL,
  cellDiameter = (3 * 1/(4 * pi))^(1/3) * 2,
  cellMassInit = 0.28,
  cellMassAtDivision = 0.56,
  cellShape = "coccus",
  vmax = 11,
  scavengeDist = cellDiameter * 2.5,
  rm.deadends = T,
  chemotaxisCompound = NULL,
  chemotaxisStrength = 0.01,
  chemotaxisHillKA = 0.1,
  chemotaxisHillCoef = 1.2,
  open.bounds = NULL,
  color = NULL
)

Arguments

object	S4-object of type growthSimulation.
model	The organisms metabolic model of S4-type modelorg
name	Character for the name of the model, that will also be used for plotting.
ncells	integer. Number of initial cells to be added to the growth simulation.
coords	(optional) A two column numerical matrix specifying the coordinates (1st column x, 2nd column y) of the initial cells. If provided, the number of rows should be equal to ncells. Default: NULL
distribution.method	If 'coords' is 'NULL', this parameter specifies the distribution method for initial cells. Default: "random_centroid"
distribution.center	Numeric vector of length 2, which specifies the coordinates of the centre for the 'distribution.method'.
distribution.radius	double. Spcifies the radius (in μm) in which initial cells are distributed.
cellDiameter	double. Diameter in μm of initial cells.
cellMassInit	double. Mass in pg of initial cells. Default is 0.28 pg
cellMassAtDivision	double. Cell mass at which a cell divides into two daughter cells. Default: 0.56 pg
cellShape	character. Shape of cells. Currently only "coccus" is supported.
vmax	double. Maximum velocity of a cell in μm per second.
scavengeDist	double. Distance in μm a cell can scavenge nutrients from its surrounding/microoenvironment.
rm.deadends	If TRUE, dead-end metabolites and reactions are removed from the 'model', which reduces the computation time for FBA, but has otherwise no effect on the flux distribution solutions.
chemotaxisCompound	Character vector of compound IDs, that are signals for directed movement of the organism.
chemotaxisStrength	Numeric vector that indicates the strength of chemotaxis. Positive value for attraction; Negative for repelling effect. A value of 1 indicates that in case of a maximum gradient (concentration-weighted center in cell's scavenge area is at the edge of the area) the cell moves with its maximum speed (vmax) in the direction of the gradient. Default: 0.01
chemotaxisHillKA	Numeric vector for K_A value (unit: mM) in Hill equation in chemotactic metabolite sensing. Default: 0.1 mM
chemotaxisHillCoef	Numeric vector for the Hill coefficient (unitless) in metabolite sensing. Default: 1.2
open.bounds	Numeric value that is used to reset lower bounds of exchange reactions, which have a current lower bound of 0. See Details.
color	Color of organism in visualizations.

Details

Genome-scale metabolic models usually come pre-constraint, which means that lower bounds for exchange reactions (= max. uptake rates) are set to represent, both, (a) a specific growth environment and (b) the physiological limit of nutrient uptake. Yet, lower bounds that have a value of 0 might also be utilizable by the organism if the compound is present in the environment. If the option 'open.bounds' is used, those 0-lower bounds are replaced with a new lower bound to enable the potential uptake in the agent-based simulation. Please note that the value should by convention be negative; however this package changes the value to it's negative counterpart if a positive value is provided.

The default cell diameter ((3 * 1 / (4 * pi))^(1/3) * 2) is that of a sphere with 1 μm^3 volume.

'chemotaxisHillKA' and 'chemotaxisHillCoef' are metabolite sensing sensitivity parameters, which is modeled as a Hill equation. Default values correspond to numbers estimated by Sourjik and Berg (2001, PNAS) for Escherichia coli.

Value

Object of class growthSimulation.

References

https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100008
http://book.bionumbers.org/how-big-is-an-e-coli-cell-and-what-is-its-mass/
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=115616&ver=0&trm=speed+e.+coli&org=
Victor Sourjik and Howard C. Berg. (2001). Receptor sensitivity in bacterial chemotaxis. PNAS 99, 123-127.

Examples

# add two bacterial models (Eubacterium rectale, Bifidobacterium longum)
# to the environment; each with 15 initial cells
models <- list()
models[['eure']] <- readRDS(system.file("extdata", "eure.RDS",
                            package="Eutropia"))
models[['bilo']] <- readRDS(system.file("extdata", "bilo.RDS",
                            package="Eutropia"))

sim <- init_simulation(cbind(c(-100, -100, 100, 100),
                             c(-100, 100, 100, -100)),
                       gridFieldSize = 1.75, gridFieldLayers = 3)

sim <- add_organism(sim, model = models[["eure"]], name = "E. rectale",
                    ncells = 15, distribution.radius = 30)
sim <- add_organism(sim, model = models[["bilo"]], name = "B. longum",
                    ncells = 15, distribution.radius = 30)

plot_cells(sim, xlim = c(-50,50), ylim= c(-50,50))

Waschina/Eutropia documentation built on Jan. 4, 2023, 12:42 p.m.