From 4f440e6cbc1124d9da0c5621f7949bc340b6379d Mon Sep 17 00:00:00 2001
From: Sajjad Ghaffarinasabsharabiani <ghaffas@hhu.de>
Date: Wed, 15 Nov 2023 11:39:16 +0000
Subject: [PATCH] Upload New File
---
networkComplexityBigg/envirDist/initData.R | 50 ++++++++++++++++++++++
1 file changed, 50 insertions(+)
create mode 100644 networkComplexityBigg/envirDist/initData.R
diff --git a/networkComplexityBigg/envirDist/initData.R b/networkComplexityBigg/envirDist/initData.R
new file mode 100644
index 0000000..dba9188
--- /dev/null
+++ b/networkComplexityBigg/envirDist/initData.R
@@ -0,0 +1,50 @@
+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)
+}
+
--
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