diff --git a/app/js/app-menu.js b/app/js/app-menu.js
index 89d5dc01..9c6bf08e 100644
--- a/app/js/app-menu.js
+++ b/app/js/app-menu.js
@@ -648,33 +648,6 @@ module.exports = function() {
       }
     });
 
-    $("#gpml-file-input").change(function () {
-
-      var chiseInstance = appUtilities.getActiveChiseInstance();
-      var cy = appUtilities.getActiveCy();
-      if ($(this).val() != "") {
-        var file = this.files[0];
-        appUtilities.setFileContent(file.name);
-        chiseInstance.loadGpml(file,  success = function(data){
-          if (cy.elements().length !== 0) {
-            promptConfirmationView.render(function () {
-              chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
-            });
-          }
-          else {
-            chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
-          }
-        },
-        error = function(data){
-          promptFileConversionErrorView.render();          
-          document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
-
-        });
-
-        $(this).val("");
-      }
-    });
-
     $("#simple-af-file-input").change(function () {
       var chiseInstance = appUtilities.getActiveChiseInstance();
 
@@ -818,18 +791,6 @@ module.exports = function() {
         // clear urlParams from scratch
         appUtilities.setScratch(cy, 'urlParams', undefined);
 
-
-        // get applyLayout value before map properties are filtered, apply layout
-        // isn't really a map property so its not added to sbgnviz 
-        // validMapProperties
-        const applyLayout = urlParams.applyLayoutOnURL === "true";
-        const fromURL = urlParams.url !== undefined;
-
-        if (urlParams.compoundPadding) {
-          const compoundPadding = urlParams.compoundPadding;
-          chiseInstance.setCompoundPadding(Number(compoundPadding));
-        }
-
         // filter map properties from the url parameters
 
         // get applyLayout value before map properties are filtered, apply layout
@@ -868,24 +829,6 @@ module.exports = function() {
           appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
         }
 
-        if (fromURL && applyLayout) {
-          let currentLayoutProperties = appUtilities.getScratch(cy, 'currentLayoutProperties');
-
-          // Below is copied from sbgnviz.graphUtilities.updateGraph
-          let preferences = {};
-          if(cy.nodes().length > 3000 || cy.edges().length > 3000) {
-            preferences.quality = "draft";
-          }
-          preferences.animate = false;
-          preferences.randomize = true;
-          preferences = $.extend({}, currentLayoutProperties, preferences);
-          layoutPropertiesView.applyLayout(preferences);
-        }
-
-        if (urlParams.mapColorScheme) {
-          appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
-        }
-
         // merge the map properties coming from url into
         // the map properties read from file
         for ( var prop in mapPropsFromUrl ) {