From e3cb9199191bf6674627aec3b884fec94f85d311 Mon Sep 17 00:00:00 2001 From: Silvio Date: Thu, 4 Jul 2024 23:30:28 +0200 Subject: [PATCH] simplified getting started vignette --- vignettes/cobrar.Rmd | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/vignettes/cobrar.Rmd b/vignettes/cobrar.Rmd index 8454eab..eb78226 100644 --- a/vignettes/cobrar.Rmd +++ b/vignettes/cobrar.Rmd @@ -73,16 +73,14 @@ mod <- addReact(mod, id = "ABUTt", Scoef = c(-1,-1,1,1), reactName = "4-aminobutyrate transport in via proton symport", metName = c("4-aminobutyrate",NA, "4-aminobutyrate",NA), metComp = c("e","e","c","c"), metCharge = c(0,NA,0,NA), - metChemicalFormula = c("C4H9NO2",NA,"C4H9NO2",NA), - SBOTerm = "SBO:0000185") + metChemicalFormula = c("C4H9NO2",NA,"C4H9NO2",NA)) ``` Next, we add the exchange reaction for 4-aminobutyrate. ```{r} mod <- addReact(mod, id = "EX_4abut_e", Scoef = c(-1), met = "4abut_e", - lb = -1.5, ub = 1000, reactName = "4-aminobutyrate exchange", - SBOTerm = "SBO:0000627") + lb = -1.5, ub = 1000, reactName = "4-aminobutyrate exchange") ``` The lower bound of this exchange reaction is set to -1.5 mmol/(gDW*hr) to simulate the availability of the metabolite.