Organism: Structure of the S4 class "Organism"

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Structure of the S4 class "Organism"

Description

Structure of the S4 class Organism representing the organisms present in the environment.

Slots

lbnd

A numeric vector containing the lower bounds of the model structure.

ubnd

A numeric vector containing the upper bounds of the model structure.

type

A character vector containing the description of the organism.

medium

A character vector containing all exchange reactions of the organism.

lpobj

A sybil optimization object containing the linear programing problem.

fbasol

A list with the solutions of the flux balance analysis.

lyse

A boolean variable indicating if the organism should lyse after death.

feat

A list containing conditional features for the object (contains at the momement only biomass components for lysis).

deathrate

A numeric value giving the factor by which the biomass should be reduced in every iteration if no growth is possible (default (E.coli): 0.21 pg)

minweight

A numeric value giving the growth limit at which the organism dies. (default (E.coli): 0.083 pg)

growtype

A character vector giving the functional type for growth (linear or exponential).

kinetics

A List containing Km and v_max values for each reactions.

speed

A integer vector representing the speed by which bacterium is moving (given by cell per iteration).

cellarea

A numeric value indicating the surface that one organism occupies (default (E.coli): 4.42 mu_m^2)

maxweight

A numeric value giving the maximal dry weight of single organism (default (E.coli): 1.172 pg)

cellweight_mean

A numeric giving the mean of starting biomass (default (E.coli): 0.489 pg)

cellweight_sd

A numeric giving the standard derivation of starting biomass (default (E.coli): 0.132 pg)

model

Object of class sybil::modelorg containging the genome sclae metabolic model

algo

Algorithm to be used during optimization (default fba)

rbiomass

Name of biomass reactions which is used for growth model (set automatically but needs input if objective is not biomass optimization)

limit_growth

If true then a upper bound on growth will be set, see maxweight (default: True).

coupling_constraints

List with coupling parameters.

predator

Name of organism which can kill this one.

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.