From 72f607a85764dd253965f973c76ead23cc3d6df1 Mon Sep 17 00:00:00 2001 From: Curtis Madsen Date: Sun, 27 May 2018 22:48:48 -0400 Subject: [PATCH 1/2] Fixed SBML mode in abstraction engine --- .../dataModels/biomodel/network/AbstractionEngine.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/network/AbstractionEngine.java b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/network/AbstractionEngine.java index 9684eb653..31edffaf4 100644 --- a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/network/AbstractionEngine.java +++ b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/network/AbstractionEngine.java @@ -240,9 +240,8 @@ public String abstractOperatorSite(Promoter promoter) { Kao = KaoArray[0]; } if (sbmlMode) { - promRate += "(np__" + promoter.getId() + "*ng__" + promoter.getId() + ")*((kb__" + promoter.getId() + "*Ko__" + promRate += "(ng__" + promoter.getId() + ")*((kb__" + promoter.getId() + "*Ko__" + promoter.getId() + "*RNAP)"; - Utility.Parameter(kl,"np__" + promoter.getId(), np, GeneticNetwork.getMoleParameter(2)); Utility.Parameter(kl,"ng__" + promoter.getId(), ng, GeneticNetwork.getMoleParameter(2)); Utility.Parameter(kl,"kb__" + promoter.getId(), kb, GeneticNetwork.getMoleTimeParameter(1)); Utility.Parameter(kl,"Ko__" + promoter.getId(), Ko, GeneticNetwork.getMoleParameter(2)); @@ -358,10 +357,9 @@ else if (sbmlMode) { Ko = KoArray[0]; } if (sbmlMode) { - promRate += "(np__" + promoter.getId() + "*ko__" + promoter.getId() + "*ng__" + promoter.getId() + promRate += "(ko__" + promoter.getId() + "*ng__" + promoter.getId() + ")*((Ko__" + promoter.getId() + "*RNAP))/((1+(Ko__" + promoter.getId() + "*RNAP))"; - Utility.Parameter(kl,"np__" + promoter.getId(), np, GeneticNetwork.getMoleParameter(2)); Utility.Parameter(kl,"ng__" + promoter.getId(), ng, GeneticNetwork.getMoleParameter(2)); Utility.Parameter(kl,"Ko__" + promoter.getId(), Ko, GeneticNetwork.getMoleParameter(2)); Utility.Parameter(kl,"ko__" + promoter.getId(), ko, GeneticNetwork.getMoleTimeParameter(1)); From 87ccb76c15eb21a2b16ba06a0e688204e3b38b90 Mon Sep 17 00:00:00 2001 From: Curtis Madsen Date: Sun, 27 May 2018 23:44:49 -0400 Subject: [PATCH 2/2] Fixed LPN generation --- .../java/edu/utah/ece/async/lema/verification/lpn/LPN.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/verification/src/main/java/edu/utah/ece/async/lema/verification/lpn/LPN.java b/verification/src/main/java/edu/utah/ece/async/lema/verification/lpn/LPN.java index c762357a1..999abf922 100644 --- a/verification/src/main/java/edu/utah/ece/async/lema/verification/lpn/LPN.java +++ b/verification/src/main/java/edu/utah/ece/async/lema/verification/lpn/LPN.java @@ -345,10 +345,10 @@ public static LPN convertToLHPN(ArrayList specs, ArrayList con } if (!rate.equals("") || !reactionProductions.equals("")) { if (rate.equals("")) { - rate = "(" + reactionProductions + ")"; + rate = "(" + np + "*(" + reactionProductions + "))"; } else if (!reactionProductions.equals("")) { - rate = "(" + rate + "+" + reactionProductions + ")"; + rate = "(" + rate + "+" + np + "*(" + reactionProductions + "))"; } LHPN.addTransition(specs.get(i) + "_trans" + transNum); LHPN.addMovement(previousPlaceName, specs.get(i) + "_trans" + transNum);