adapted the names of the observables in the experiments

SFB-ELAINE · Jul 22, 2020 · 1583b35 · 1583b35
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commit 1583b35
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Showing 8 changed files with 36 additions and 36 deletions.
diff --git a/experiments/ExecuteSesslandPlotResults.R b/experiments/ExecuteSesslandPlotResults.R
@@ -2,7 +2,7 @@
 # Script for producing the plots seen in the paper
 # Authors:      Kai Budde, Fiete Haack
 # Created:      2019-07-04
-# Last changed: 2020-01-06
+# Last changed: 2020-07-22
 # Used version of Sessl2R: 0.1.3
 #--------------------------------------------------------------------------#
 

diff --git a/experiments/M1_General_S01_A/M1_General_S01_A.scala b/experiments/M1_General_S01_A/M1_General_S01_A.scala
@@ -16,15 +16,15 @@ execute {
     // Set initial species count as well as experiment specific reaction rate
     // coefficients
     set(
-      "nR"   <~ 4000,
-      "nL"   <~ 2000
+      "nLrp6"  <~ 4000,
+      "nWnt"   <~ 2000
     )
 
     scan("ke" <~ (0.2, 0.3, 0.4))
 
-    observe("LR" ~ count("M/LR"))
-    observe("R" ~ count("M/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"   ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"  ~ count("Membrane/Lrp6(B)"))
+    observe("ELR" ~ count("Endosome/Lrp6(B)"))
 
     observeAt(range(0, 1, stoppingTime))
 

diff --git a/experiments/M1_General_S01_B/M1_General_S01_B.scala b/experiments/M1_General_S01_B/M1_General_S01_B.scala
@@ -16,15 +16,15 @@ execute {
     // Set initial species count as well as experiment specific reaction rate
     // coefficients
     set(
-      "nR"   <~ 4000,
-      "nL"   <~ 2000
+      "nLrp6"  <~ 4000,
+      "nWnt"   <~ 2000
     )
 
     scan("ke" <~ (0.05, 0.075, 0.1))
 
-    observe("LR" ~ count("M/LR"))
-    observe("R" ~ count("M/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"   ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"  ~ count("Membrane/Lrp6(B)"))
+    observe("ELR" ~ count("Endosome/Lrp6(B)"))
 
     observeAt(range(0, 1, stoppingTime))
 

diff --git a/experiments/M2_Microdomains_S02_A/M2_Microdomains_S02_A.scala b/experiments/M2_Microdomains_S02_A/M2_Microdomains_S02_A.scala
@@ -19,11 +19,11 @@ execute {
 
     scan("ke_nonraft" <~ (0.2, 0.3, 0.4))
 
-    observe("R" ~ count("M/R"))
-    observe("LR" ~ count("M/LR"))
-    observe("RaftLR" ~ count("M/Raft/LR"))
-    observe("RaftR" ~ count("M/Raft/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"      ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"     ~ count("Membrane/Lrp6(B)"))
+    observe("RaftR"  ~ count("Membrane/LR/Lrp6(uB)"))
+    observe("RaftLR" ~ count("Membrane/LR/Lrp6(B)"))
+    observe("ELR"    ~ count("Endosome/Lrp6(B)"))
     //observe("DummyNonRaft" ~ count("DummyNonRaft"))
     //observe("DummyRaft" ~ count("DummyRaft"))
 

diff --git a/experiments/M2_Microdomains_S02_B/M2_Microdomains_S02_B.scala b/experiments/M2_Microdomains_S02_B/M2_Microdomains_S02_B.scala
@@ -19,11 +19,11 @@ execute {
     scan("ke_nonraft" <~ (0.2, 0.3, 0.4))
     scan("ke_raft"    <~ (0.05, 0.075, 0.1))
 
-    observe("R" ~ count("M/R"))
-    observe("LR" ~ count("M/LR"))
-    observe("RaftLR" ~ count("M/Raft/LR"))
-    observe("RaftR" ~ count("M/Raft/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"      ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"     ~ count("Membrane/Lrp6(B)"))
+    observe("RaftR"  ~ count("Membrane/LR/Lrp6(uB)"))
+    observe("RaftLR" ~ count("Membrane/LR/Lrp6(B)"))
+    observe("ELR"    ~ count("Endosome/Lrp6(B)"))
     //observe("DummyNonRaft" ~ count("DummyNonRaft"))
     //observe("DummyRaft" ~ count("DummyRaft"))
 

diff --git a/experiments/M2_Microdomains_S02_C/M2_Microdomains_S02_C.scala b/experiments/M2_Microdomains_S02_C/M2_Microdomains_S02_C.scala
@@ -19,11 +19,11 @@ execute {
 
     scan("ke_raft" <~ (0.05, 0.075, 0.1))
 
-    observe("R" ~ count("M/R"))
-    observe("LR" ~ count("M/LR"))
-    observe("RaftLR" ~ count("M/Raft/LR"))
-    observe("RaftR" ~ count("M/Raft/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"      ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"     ~ count("Membrane/Lrp6(B)"))
+    observe("RaftR"  ~ count("Membrane/LR/Lrp6(uB)"))
+    observe("RaftLR" ~ count("Membrane/LR/Lrp6(B)"))
+    observe("ELR"    ~ count("Endosome/Lrp6(B)"))
     //observe("DummyNonRaft" ~ count("DummyNonRaft"))
     //observe("DummyRaft" ~ count("DummyRaft"))
 

diff --git a/experiments/M2_Microdomains_S03_A/M2_Microdomains_S03_A.scala b/experiments/M2_Microdomains_S03_A/M2_Microdomains_S03_A.scala
@@ -19,11 +19,11 @@ execute {
 
     scan("ke_nonraft" <~ (0.05, 0.075, 0.1))
 
-    observe("R" ~ count("M/R"))
-    observe("LR" ~ count("M/LR"))
-    observe("RaftLR" ~ count("M/Raft/LR"))
-    observe("RaftR" ~ count("M/Raft/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"      ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"     ~ count("Membrane/Lrp6(B)"))
+    observe("RaftR"  ~ count("Membrane/LR/Lrp6(uB)"))
+    observe("RaftLR" ~ count("Membrane/LR/Lrp6(B)"))
+    observe("ELR"    ~ count("Endosome/Lrp6(B)"))
     //observe("DummyNonRaft" ~ count("DummyNonRaft"))
     //observe("DummyRaft" ~ count("DummyRaft"))
 

diff --git a/experiments/M2_Microdomains_S03_B/M2_Microdomains_S03_B.scala b/experiments/M2_Microdomains_S03_B/M2_Microdomains_S03_B.scala
@@ -19,11 +19,11 @@ execute {
     scan("ke_raft" <~ (0.05, 0.075, 0.1))
     scan("ke_nonraft" <~ (0.05, 0.075, 0.1))
 
-    observe("R" ~ count("M/R"))
-    observe("LR" ~ count("M/LR"))
-    observe("RaftLR" ~ count("M/Raft/LR"))
-    observe("RaftR" ~ count("M/Raft/R"))
-    observe("ELR" ~ count("E/LR"))
+    observe("R"      ~ count("Membrane/Lrp6(uB)"))
+    observe("LR"     ~ count("Membrane/Lrp6(B)"))
+    observe("RaftR"  ~ count("Membrane/LR/Lrp6(uB)"))
+    observe("RaftLR" ~ count("Membrane/LR/Lrp6(B)"))
+    observe("ELR"    ~ count("Endosome/Lrp6(B)"))
     //observe("DummyNonRaft" ~ count("DummyNonRaft"))
     //observe("DummyRaft" ~ count("DummyRaft"))