jotech

#
# Doing a simple simulation using the E. coli model (iJO1366)
#

library(BacArena)

data(bcoli_orth)
bac <- Bac(ecoli)

arena <- Arena()

jotech

#
# In BacArena the activity of each reaction of an organism (flux distribution) is stored in arena@mflux.
# After finishing a simulation, the time series of the reaction activities can be accessed via eval@simlist.
#

library(BacArena)
data("Ec_core")
bac <- Bac(Ec_core)
arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac,amount=20)

jotech

#
# The sihumi example data set consists of a simulation of 8 gut microbes growing on a western diet for 8 hours.
# Here, we use it to study microbial interactions
#


library(BacArena)

data("sihumi_test")

jotech

library(BacArena)
data("Ec_core")

arena <- Arena(n=10,m=10)

# by setting maxweight to infinity, duplication is disabled
# speed=0 indicates no movement
# limit_growth=FALSE removes the limit of biomass increase 
bac <- Bac(Ec_core, speed=0, limit_growth=FALSE, maxweight=Inf)

jotech

library(BacArena)
data("Ec_core")

bac  <- Bac(Ec_core)
arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac,amount=30)
arena <- addSubs(arena, smax=0.05, mediac="EX_glc(e)", unit="mM")
arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_nh4(e)"), unit="mM") 

 # Aenaerobic simulation for 6h

jotech

library("BacArena")
library("R.matlab")

mod <- readMATmod("Actinobacillus_pleuropneumoniae_L20.mat")

arena <- Arena(n=10,m=10)
arena <- addOrg(arena, Bac(mod), 10)
arena <- addDefaultMed(arena, Bac(mod))
sim <- simEnv(arena, time=5)

jotech

library(BacArena)

SYBIL_SETTINGS("SOLVER", "cplexAPI")
set.seed(115)

# C. beijerinckii:
# - publication https://doi.org/10.1007/s00253-008-1654-4 
# - model http://bigg.ucsd.edu/models/iAF692
# M. barkeri:
# - publication: https://doi.org/10.1186/1752-0509-5-130