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Auxotrophic example in Introduction doc #175

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spburillo opened this issue Mar 8, 2022 · 0 comments
Open

Auxotrophic example in Introduction doc #175

spburillo opened this issue Mar 8, 2022 · 0 comments

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@spburillo
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Hi,

First very nice tool.
The example with auxotrophic E coli in the Introduction doc does not work, at least is not working for me. I am using the same code as specified

ecore_aux <- changeBounds(Ec_core, "EX_o2(e)",lb=0)
bac2 <- Bac(ecore_aux,type="ecoli_aux", setExInf=FALSE)
bac1 <- Bac(Ec_core,type="ecoli_wt")
arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac1,amount=5)
arena <- addOrg(arena,bac2,amount=5)
arena <- addSubs(arena, smax=0.5, mediac="EX_glc(e)", unit="mM")arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_o2(e)", "EX_nh4(e)"), unit="mM")
eval <- simEnv(arena,time=10)
``
![Rplot](https://user-images.githubusercontent.com/101190433/157244650-b888c132-8a36-4dab-9b33-78cb230e7e69.jpeg)
`
Thanks!
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