diff --git a/networkComplexityBigg/envirDist/initData.R b/networkComplexityBigg/envirDist/initData.R deleted file mode 100644 index dba91884280fc3d0ffecfd9bac303264654fc453..0000000000000000000000000000000000000000 --- a/networkComplexityBigg/envirDist/initData.R +++ /dev/null @@ -1,50 +0,0 @@ -initData <- function(){ - uptakeLowBnd <- -10 - bioThreshold <- 1e-2 - #bioThreshold <- 10 - - print(load("~/DATA/universalBiGG.ver2.Rdata")) - uni <- uni2 - - print(load("~/DATA/mediaBiGGwithRandom.Rdata")) -modelReactMap[["iIS312"]]=append(modelReactMap[["iIS312"]],c("UMPK_B", "ADKd", "DADNt2_LR", "DGSNt2_LR","NTD8_B", - "TYRabc", "TRPabc", "AMPt6", "CMPt6", "DTMPt6", "DURIK1_1" - ,"DURIt2_B", "MANpts_B" )) -modelReactMap[["iIS312_Amastigote"]]=append(modelReactMap[["iIS312_Amastigote"]],c("DADK_B", "DGSNt","DTTPt","DCTPD2","DADNt2_LR", - "TYRabc","TRPabc", "MAN6Pt6_2", "AMPt6","ADADir_LR", - "CMPt6","DCYTt2_B","DGNSK_1" )) - modelReactMap[["iIS312_Epimastigote"]]=append(modelReactMap[["iIS312_Epimastigote"]],c("UMPK_B", "ADKd","DTTPt","DGSNt2_LR", - "NTD8_B","TYRabc","TRPabc","ADADir_B","AMPt6","CMPt6", "MAN1Pt6","DADNt2_B","DCYTt2_B")) - modelReactMap[["iIS312_Trypomastigote"]]=append(modelReactMap[["iIS312_Trypomastigote"]],c("ADKd","UMPK_copy2_LR", - "DGSNt2_LR","TYRabc","TRPabc","F6Pt6_2","AMPt6","CMPt6","DTMPt6","DADNt2_B","DGNSK_1","DURIK1_1","DURIt2_B")) - modelReactMap[["iLJ478"]]=append(modelReactMap[["iLJ478"]],"ASNt2r_LR") -modelReactMap[["iSM199"]]=append(modelReactMap[["iSM199"]],c("LEUTAi","ILEabc","VALt2r_LR","ILETA2_LR","PHEabc")) - - ex <- findExchReact(uni) - exOnly <- ex[grep("^EX_", react_id(ex))] - exMap <- react_pos(exOnly) - names(exMap) <- gsub("\\[\\w\\]$", "", met_id(exOnly)) - - # setting media constraints - mediaLowBounds <- lapply(mediaBiGG, function(m){ - lb <- lowbnd(uni) - lb[exMap] <- 0 - lb[exMap[names(exMap) %in% m]] <- uptakeLowBnd - return(lb) - }) - - modelReactMapById <- lapply(modelReactMap, function(x){ - union(match(x, react_id(uni)), exMap)# this little fucker... adding all exchange reactions to the models. - }) - - modelBiomassMapSelectionById <- match(modelBiomassMapSelection, react_id(uni)) - names(modelBiomassMapSelectionById) <- names(modelBiomassMapSelection) - - modelRmEnergyCyclesById <- lapply(modelRmEnergyCycles, function(x){ - lapply(x, function(y) match(y, react_id(uni))) - }) - - for(i in ls()) assign(x=i, value=get(i), envir=.GlobalEnv) - return(T) -} -