diff --git a/js/lattice/Lattice.js b/js/lattice/Lattice.js
index 03dfa973b3d499104f682e1494973bd41f6df200..92ee61096dd0773a2f21c3af40eaa63f8ca966a3 100644
--- a/js/lattice/Lattice.js
+++ b/js/lattice/Lattice.js
@@ -119,6 +119,7 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'materialsPlis
                 myConsole.warn("no cell type " + cellType + ", lattice.setCellType operation cancelled");
                 return;
             }
+            myConsole.clear();
             myConsole.write("lattice.setCellType('" + cellType + "')");
             return this.setProperty("cellType", cellType, silent);
         },
@@ -131,6 +132,8 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'materialsPlis
                     ", lattice.setConnectionType operation cancelled");
                 return;
             }
+            myConsole.clear();
+            myConsole.write("lattice.setCellType('" + cellType + "')");
             myConsole.write("lattice.setConnectionType('" + connectionType + "')");
             return this.setProperty("connectionType", connectionType, silent);
         },
@@ -192,6 +195,8 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'materialsPlis
                 console.warn("no cells given to setSparseCells");
                 return;
             }
+            myConsole.clear();
+            myConsole.write("lattice.setCells(" + JSON.stringify(cells) + ")");
             this._setSparseCells(cells, this._getSubclassForLatticeType());
         },
 
@@ -208,7 +213,8 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'materialsPlis
 
         _setSparseCells: function(cells, subclass){
 
-            if ((this.get("numCells") > 0 && (this.get("connectionType") == "gik" || this.previous("connectionType") == "gik"))) this.clearCells();
+            if ((this.get("connectionType") == "gik" || this.previous("connectionType") == "gik") &&
+                this.get("applicationType") != this.previous("applicationType")) this.clearCells();
 
             this._setDefaultCellMode();//cell mode
 
diff --git a/js/lattice/LatticeBase.js b/js/lattice/LatticeBase.js
index 0ce171b815d8dcd78d1fe60c6fbb49030739c948..1f226c4ba0bc074885b4ddedb96d38d16c934444 100644
--- a/js/lattice/LatticeBase.js
+++ b/js/lattice/LatticeBase.js
@@ -235,7 +235,9 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
                 myConsole.warn("no cell, lattice.removeCell operation cancelled");
                 return;
             }
-            myConsole.write("lattice.removeCell(" + cell + ")");
+            var json = cell.toJSON();
+            json.index = cell.getIndex();
+            myConsole.write("lattice.removeCell(" + JSON.stringify(json) + ")");
             this._removeCell(cell);
             three.render();
         },
@@ -256,6 +258,7 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
         },
 
         clearCells: function(silent){
+            myConsole.clear();
             myConsole.write("lattice.clearCells()");
             this._clearCells(silent);
         },
diff --git a/js/menus/otherUI/Console.js b/js/menus/otherUI/Console.js
index 3e09e5f2316a94e86701cc9abe10bf44e59ea066..625095bc5b74f9c50b462298d0235518fe6c2fdf 100644
--- a/js/menus/otherUI/Console.js
+++ b/js/menus/otherUI/Console.js
@@ -54,6 +54,10 @@ define(['jquery', 'underscore', 'backbone', 'appState'], function($, _, Backbone
 
         },
 
+        clear: function(){
+            $("#consoleOutput").html("");
+        },
+
         _writeOutput: function(html){
             var $output = $("#consoleOutput");
             var height = $output.height();