From d9a3949569fa23623ac1f048ce3d742909a8b92a Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Fri, 1 Nov 2024 16:00:17 +0700
Subject: [PATCH 1/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index 9ea4672688..0dc71e19fc 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -1,4 +1,4 @@
-function [solICONGEMs, boundEf] = ICONGEMs(model, exp, genetxt, condition, threshold, alpha)
+function [solICONGEMs, boundEf] = ICONGEMs(model, exp, genetxt, condition, threshold, alpha, numericFlag)
 % Algorithm to Integrate a Gene Co-expression Network and Genome-scale Metabolic Model:
 % This algorithm calculates the reaction flux distribution for each condition by applying 
 % quadratic programming.
@@ -14,6 +14,7 @@
 %                     extract from gene expression profile file
 %    genetxt:         list of gene names that extract from gene expression profile
 %                     file
+%    numericFlag:     1 if using Human Recon  (Default = 0).
 %
 % OPTIONAL INPUTS:
 %    threshold:           The value of the correlation coefficient for constructing 
@@ -47,6 +48,9 @@
 if (nargin < 6 || isempty(alpha))
       alpha = 0.99;
 end
+if (nargin < 7 || isempty(numericFlag))
+      numericFlag = 0;
+end
 
 % construct the template model
 
@@ -111,7 +115,7 @@
 
 NameRxn={};
 for i = 1:size(modelIrrev.genes)
-    [z1, NameRxn{i}] = findRxnsFromGenes(modelIrrev, modelIrrev.genes(i, 1), [], 1);
+    [z1, NameRxn{i}] = findRxnsFromGenes(modelIrrev, modelIrrev.genes(i, 1), numericFlag, 1);
 end
 
 % Find reactions that correspond to the gene
@@ -244,7 +248,7 @@
 model2.A = sparse(Aeq);
 model2.sense = [char('=' * ones(size(model2.A,1) - 1, 1)) ; char('>')]; 
 model2.rhs = beq;
-model2.modelsense = 'min'; 
+model2.modelsense = 'max'; 
 numrxn = [1:length(modelIrrev.rxns)]; 
 j = 1;
 for i = 1:length(model.rxns)

From 131f5c9b57a4c6438386cb4a85f72c46ed7c4367 Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Fri, 1 Nov 2024 16:30:40 +0700
Subject: [PATCH 2/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index 0dc71e19fc..a3a93bb284 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -115,7 +115,7 @@
 
 NameRxn={};
 for i = 1:size(modelIrrev.genes)
-    [z1, NameRxn{i}] = findRxnsFromGenes(modelIrrev, modelIrrev.genes(i, 1), numericFlag, 1);
+    [z1, NameRxn{i}] = findRxnsFromGenes(modelIrrev, modelIrrev.genes{i, 1}, numericFlag, 1);
 end
 
 % Find reactions that correspond to the gene

From ac4005cffd8cc56a3bebbdad4e7bb446f308849a Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Sat, 2 Nov 2024 14:30:14 +0700
Subject: [PATCH 3/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index a3a93bb284..228aa09538 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -228,19 +228,25 @@
 Trans0 = zeros(size(modelIrrev.mets, 1),size(modelIrrev.rxns, 1));
 Trans2 = -1 * eye(size(modelIrrev.rxns, 1));
 S2 = zeros(size(modelIrrev.rxns, 1));
+bn = (-1) * ones(size(modelIrrev.rxns, 1), 1);
 for i = 1:length(modelIrrev.rxns)
-    S2(i, i) = 1 / max(nupb(i, :));
+    if  max(nupb(i, :)) ~= 0
+        S2(i, i) = 1 / max(nupb(i, :));
+    end
+    if max(nupb(i, :)) == 0
+        Trans2(i, i) = 0;
+        bn(i, 1) = 0;
+    end
 end
 
+Obj4 = [modelIrrev.c' zeros(1, size(modelIrrev.rxns, 1))];
 
-Obj4 = [modelIrrev.c' zeros(1, size(modelIrrev.rxns, 1))] ;
-
-lob = [model3.lb; (-1) * inf * ones(size(modelIrrev.rxns, 1), 1)];
-upb = [model3.ub; inf * ones(size(modelIrrev.rxns, 1), 1)];
+lob = [model3.lb;  ones(size(modelIrrev.rxns, 1), 1)];
+upb = [model3.ub; 2 * ones(size(modelIrrev.rxns, 1), 1)];
 
 O = [zeros(size(R)) zeros(size(R)); zeros(size(R)) R]; 
 Aeq = [modelIrrev.S Trans0; S2 Trans2; Obj4]; 
-beq = [zeros(size(modelIrrev.mets, 1), 1); (-1) * ones(size(modelIrrev.rxns,1),1); alpha * solution1.f];
+beq = [zeros(size(modelIrrev.mets, 1), 1); bn; alpha * solution1.f];
 
 model2 = struct;
 model2.lb = lob;

From 81dc50a5394e982307c0ef47ec951f91e0e2b6c7 Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Sun, 3 Nov 2024 16:25:46 +0700
Subject: [PATCH 4/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index 228aa09538..08acec93b7 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -54,6 +54,9 @@
 
 % construct the template model
 
+if ~isempty(model.rules)
+    model.grRules = model.rules;
+end
 modelN = model;
 modelN.lb(modelN.lb >= 0) = 0;
 modelN.lb(modelN.lb < 0) = -1000;

From 23ce0afcaa1992238e00dcaf18cbec54877418ff Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Sun, 3 Nov 2024 16:31:42 +0700
Subject: [PATCH 5/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index 08acec93b7..d8978d6a93 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -57,6 +57,7 @@
 if ~isempty(model.rules)
     model.grRules = model.rules;
 end
+
 modelN = model;
 modelN.lb(modelN.lb >= 0) = 0;
 modelN.lb(modelN.lb < 0) = -1000;

From 04a12a64595cad5b512b594ad038ae5d2d291353 Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Mon, 4 Nov 2024 07:25:34 +0700
Subject: [PATCH 6/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index d8978d6a93..c44c32a16d 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -30,7 +30,7 @@
 %
 % EXAMPLES:
 %    % This could be an example that can be copied from the documentation to MATLAB:
-%    solution = ICONGEMs(model, exp, genetxt, condition, threashold, alpha)
+%    solution = ICONGEMs(model, exp, genetxt, condition, threashold, alpha, numericFlag)
 %    % without optional values:
 %    solution = ICONGEMs(model, exp, genetxt)
 %

From a747a6023bae37e5e6f32fbb712ea1598161ba3a Mon Sep 17 00:00:00 2001
From: ThummaratPaklao <81726643+ThummaratPaklao@users.noreply.github.com>
Date: Mon, 4 Nov 2024 07:46:16 +0700
Subject: [PATCH 7/7] Update ICONGEMs.m

---
 src/analysis/ICONGEMs/ICONGEMs.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/analysis/ICONGEMs/ICONGEMs.m b/src/analysis/ICONGEMs/ICONGEMs.m
index c44c32a16d..01f106f563 100644
--- a/src/analysis/ICONGEMs/ICONGEMs.m
+++ b/src/analysis/ICONGEMs/ICONGEMs.m
@@ -5,7 +5,7 @@
 %
 % USAGE:
 %
-%    [solICONGEMs, boundEf] = ICONGEMs(model, exp, genetxt, condition, threashold, alpha)
+%    [solICONGEMs, boundEf] = ICONGEMs(model, exp, genetxt, condition, threashold, alpha, numericFlag)
 %
 % INPUTS:
 %