fix: update tutorial ecYeastGEM.yml

SysBioChalmers · Jul 17, 2024 · 9a0416d · 9a0416d
1 parent bf8cfdc
commit 9a0416d
Showing 1 changed file with 13 additions and 10 deletions.
diff --git a/tutorials/full_ecModel/models/ecYeastGEM.yml b/tutorials/full_ecModel/models/ecYeastGEM.yml
@@ -4,7 +4,7 @@
     id: "yeastGEM_v8.6.2"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
     version: ""
-    date: "2024-06-06"
+    date: "2024-07-17"
     defaultLB: "-1000"
     defaultUB: "1000"
     givenName: "Eduard"
@@ -40877,7 +40877,6 @@
       - id: "prot_pool"
       - name: "prot_pool"
       - compartment: "c"
-      - charge: 0
       - notes: "Enzyme-usage protein pool"
     - !!omap
       - id: "prot_standard"
@@ -197765,7 +197764,8 @@
   - !!omap
     - id: "r_0079"
     - kcat: 5.3357625
-    - source: "from setKcatForReactions"
+    - source: "setKcatForReactions"
+    - notes: "preTuneKcat=0.05 | source:brenda"
     - eccodes: "6.3.5.3"
     - enzymes: !!omap
         - P38972: 1
@@ -198077,7 +198077,8 @@
   - !!omap
     - id: "r_0109"
     - kcat: 12.3
-    - source: "brenda"
+    - source: "sensitivityTuning"
+    - notes: "preTuneKcat=1.23 | source:brenda"
     - eccodes: "6.3.4.14"
     - enzymes: !!omap
         - P48445: 1
@@ -201233,8 +201234,8 @@
   - !!omap
     - id: "r_0450"
     - kcat: 325
-    - source: "custom"
-    - notes: "GECKO v2 manual_data.txt"
+    - source: "sensitivityTuning"
+    - notes: "GECKO v2 manual_data.txt; preTuneKcat=32.5 | source:custom"
     - eccodes: "4.1.2.13"
     - enzymes: !!omap
         - P14540: 1
@@ -201625,8 +201626,8 @@
   - !!omap
     - id: "r_0486_EXP_2"
     - kcat: 290
-    - source: "custom"
-    - notes: "GECKO v2 manualModifications.m growth limiting"
+    - source: "sensitivityTuning"
+    - notes: "GECKO v2 manualModifications.m growth limiting; preTuneKcat=29 | source:custom"
     - eccodes: "1.2.1.12"
     - enzymes: !!omap
         - P00360: 1
@@ -203466,7 +203467,8 @@
   - !!omap
     - id: "r_0698"
     - kcat: 0.193666666666667
-    - source: "brenda"
+    - source: "sensitivityTuning"
+    - notes: "preTuneKcat=0.0019367 | source:brenda"
     - eccodes: "5.4.99.7"
     - enzymes: !!omap
         - P38604: 1
@@ -207794,7 +207796,8 @@
   - !!omap
     - id: "r_1166_EXP_11"
     - kcat: 192.645
-    - source: "DLKcat"
+    - source: "sensitivityTuning"
+    - notes: "preTuneKcat=19.2645 | source:DLKcat"
     - enzymes: !!omap
         - P38695: 1
   - !!omap