Closed fairquestion closed 5 years ago
Hi,
The analysis details are in the method section of the paper in "Syntrophic two-species community model". Here is the the script to perform the simulations:
library(BacArena)
library(sybil)
library(sybilSBML)
library(ggplot2)
barkeri <- readSBMLmod("barkeri_mod.xml")
beijerinckii <- readSBMLmod("beijerinckii_mod.xml")
sybil::SYBIL_SETTINGS("SOLVER","cplexAPI") #set solver to CPLEX
arena <- Arena(100, 100, stir=F, Lx=0.025, Ly=0.025, tstep=0.3)
bac1 <- Bac(model=barkeri)
bac2 <- Bac(model=beijerinckii)
arena <- addOrg(arena, bac1, amount=1,x=60,y=50,biomass=1)
arena <- addOrg(arena, bac2, amount=1,x=40,y=50,biomass=1)
minmed = c("EX_4abz(e)","EX_cobalt2(e)","EX_nac(e)","EX_h2o(e)","EX_h(e)","EX_nh4(e)","EX_ni2(e)","EX_pi(e)","EX_so3(e)","EX_cys_L(e)","EX_so4(e)")
arena <- addSubs(arena, smax=0, unit="mmol/cell")
arena <- addSubs(arena, mediac=minmed, smax=1, unit="mmol/cell")
arena <- addSubs(arena, mediac="EX_glc_D(e)", smax=1, unit="mmol/cell")
arena <- addSubs(arena, mediac="EX_co2(e)", smax=1, unit="mmol/cell")
arena <- addSubs(arena, mediac="EX_h2(e)", smax=1e-10, unit="mmol/cell")
sim=simEnv(arena, time=24)
Here are also the sbml model files: beijerinckii_barkeri_mod.zip
Best, Eugen
Hi Eugen,
Thanks a lot. Are these attached models already modified like the paper states?, otherwise I can modify it myself.
Hi,
No problem. Yes, they should already have all the modifications.
Best, Eugen
Super :D , it is working properly. Excellent material for my research. Maybe you can add it to the examples, It is an easy to follow and understandable 2 organism interaction arena, SIHUMI is way much more complex to decipher what is going on there.
Great! Thanks for the suggestion, we will consider including it in the next version of the vignette.
Dear all,
In your paper is written: Syntrophic two-species community model Manual curated genome-scale metabolic models were retrieved for the hydrogen producing bacterium Clostridium beijerinckii [35] and the methanogenic archaeon Methanosarcina barkeri [36].
But the simulation was not uploaded. Is it possible to get the simulation, the models and the nutrients .csv file like with SIHUMI? I would really apreciate it.
Best and thanks, Fair