diff --git a/bootstrap.sh b/bootstrap.sh
index 8a905a9..1b4f326 100644
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -1,24 +1,34 @@
 #!/bin/bash
 
+# Set Timezone (needed for python install)
+ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
 # Updates the package lists for upgrades and new package installations
-sudo apt-get update
+apt-get update
+apt-get install sudo -y
+apt-get install wget -y
+sudo apt install -y software-properties-common cmake git
 
-# Installs the 'sudo' package. The '-y' flag automatically answers yes to prompts.
-apt-get install -y sudo python3.9
+# Installs the  python 3.9 package. The '-y' flag automatically answers yes to prompts.
+sudo add-apt-repository ppa:deadsnakes/ppa -y
+sudo apt update 
+sudo apt install python3.9 -y
+sudo apt install python3.9-distutils -y
 
-# Install the needed packages
-sudo apt install -y software-properties-common cmake python3-pip git
+# Install pip
+wget https://bootstrap.pypa.io/get-pip.py
+python3.9 get-pip.py
 
 # Upgrades pip (Python package installer) to the latest version
-sudo python3 -m pip install -U pip
+sudo python3.9 -m pip install -U pip
 
 # Installs the Conan package manager
-pip3 install conan==1.60.1
-pip3 install nheri-simcenter
+python3.9 -m pip install conan==1.60.1
+python3.9 -m pip install nheri-simcenter
 
-python3 --version
+python3.9 --version
 
-which python3
+which python3.9
 
 which conan
 
diff --git a/build_backend_apps.sh b/build_backend_apps.sh
index 2fe2e68..5efc53c 100644
--- a/build_backend_apps.sh
+++ b/build_backend_apps.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-git clone --branch master --depth 1 https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git
+git clone --branch master https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git
 
 cp ./SimCenterBackendApplications/modules/performUQ/SimCenterUQ/nataf_gsa/CMakeLists.txt.UBUNTU ./SimCenterBackendApplications/modules/performUQ/SimCenterUQ/nataf_gsa/CMakeLists.txt
 
diff --git a/run_examples.sh b/run_examples.sh
index a1c1134..6cc03f6 100644
--- a/run_examples.sh
+++ b/run_examples.sh
@@ -3,29 +3,90 @@
 echo In folder $PWD
    
 # Clone the examples
-git clone --branch master --depth 1 https://github.com/NHERI-SimCenter/quoFEM.git
+git clone --depth 1 https://github.com/NHERI-SimCenter/quoFEM.git
 
-# Create the working directoy
-mkdir tmp.SimCenter
-mkdir tmp.SimCenter/templatedir
-cp -a $PWD/Examples/qfem-0001/src/. $PWD/tmp.SimCenter/templatedir/
+# make sure all packages are installed
+python3 -m pip install --upgrade pip
+python3 -m pip install nheri-simcenter --upgrade
+python3 -m pip install GPy==1.13.2
 
-sudo apt-get install jq
+# Read JSON from file
+json_file="$PWD/quoFEM/Examples/Examples.json"
 
-inputfile=$PWD/Examples/qfem-0001/src/input.json
+# Install jq
+sudo apt-get install -y jq
+rm -rf cache
+mkdir cache
+# Iterate over array elements
+jq -c '.Examples[]' "$json_file" | while read -r example; do
 
-echo "doing jq ================="
-echo $(cat $inputfile | jq '. + { "runDir": "'"$PWD/tmp.SimCenter"'" }') > $inputfile
-echo $(cat $inputfile | jq '. + { "localAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
-echo $(cat $inputfile | jq '. + { "remoteAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
-echo $(cat $inputfile | jq '. + { "runType": "runningLocal" }') > $inputfile
-echo "did jq ==================="
+  name=$(echo "$example" | jq -r '.name')
+  description=$(echo "$example" | jq -r '.description')
+  inputfile=$(echo "$example" | jq -r '.inputFile')
+  
+  inputfile="$PWD/quoFEM/Examples/$inputfile"
+  srcDir="$(dirname $inputfile)"
+  examplenumber="$(dirname $srcDir)"
+  examplenumber="$(basename $examplenumber)"
 
-echo "catting the thing now ==================="
-cat $inputfile
+  echo "==========================================="
+  echo "Example Number: $examplenumber"
+  echo "Example Name: $name"
+  echo "Example Description: $description"
+  echo "Input File: $inputfile"
+  echo "srcDir: $srcDir"
+  echo "---------------------------"
+  echo "Adding json params to input file..."
+  echo $(cat $inputfile | jq '. + { "runDir": "'"$PWD/tmp.SimCenter"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "localAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "remoteAppDir": "'"$PWD/SimCenterBackendApplications"'" }') > $inputfile
+  echo $(cat $inputfile | jq '. + { "runType": "runningLocal" }') > $inputfile
+  
+  echo "copying files"
+  rm -rf tmp.SimCenter
+  mkdir tmp.SimCenter
+  mkdir tmp.SimCenter/templatedir
+  
+  cp -a $srcDir/. $PWD/tmp.SimCenter/templatedir/
 
-ls $PWD/tmp.SimCenter/templatedir
+  if [[ "$examplenumber" == "qfem-0027" ]]; then
+    # do some stuff
+    cp -a $srcDir/model1/. $PWD/tmp.SimCenter/templatedir/
+    cp -a $srcDir/model2/. $PWD/tmp.SimCenter/templatedir/
+  fi
+  if [[ "$examplenumber" == "qfem-0028" ]]; then
+    # do some stuff
+    echo "CAUGHT EXAMPLE 28"
+    echo "$srcDir"
+    cp -a "$srcDir/CouponCyclicTestData_every_20th_point/." "$PWD/tmp.SimCenter/templatedir/"
+  fi
 
-# Run the example in the backend
-python $PWD/SimCenterBackendApplications/applications/Workflow/qWHALE.py "runningLocal" $inputfile $PWD/SimCenterBackendApplications/applications/Workflow/WorkflowApplications.json
+  
+  #echo "Input file contents:"
+  #python3 -m json.tool $inputfile
+    
+  #echo "Template dir contents"
+  #ls $PWD/tmp.SimCenter/templatedir
+  
 
+  # Run the example in the backend
+  echo "Running python:"
+  echo "==============="
+  python3 $PWD/SimCenterBackendApplications/applications/Workflow/qWHALE.py "runningLocal" $inputfile $PWD/SimCenterBackendApplications/applications/Workflow/WorkflowApplications.json
+  mkdir "cache/tmp.SimCenter.$examplenumber/"
+  cp -r tmp.SimCenter/. "cache/tmp.SimCenter.$examplenumber/"
+done
+
+# Check with archives have a dakotaTab.out file
+echo ""
+echo ""
+echo "======================================"
+for dir in $PWD/cache/*; do
+  if [ -f "$dir/dakotaTab.out" ]; then
+    echo "$dir: PASS"
+    # Do something if the file exists
+  else
+    echo "$dir: FAIL"
+    # Do something else if the file does not exist
+  fi
+done
\ No newline at end of file