diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 2e410265b84814dbc86e0aaee3453d799560d205..7c43df5c05788bbf188fbfdd4927961d4be3d11b 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -700,80 +700,6 @@ CustomMap.prototype.showSelectedLayout = function(layoutId, index, length) {
   return Promise.all(promises);
 };
 
-/**
- * Adds information about reactions visible in the specific layout.
- * 
- * @param layoutId
- *          identifier of the layout
- * 
- * @param jsonAliases
- *          list of reactions in json format
- * 
- */
-CustomMap.prototype.addReactionsForLayout = function(layoutId, jsonReactions) {
-  logger.debug("Adding reactions for layout: " + layoutId);
-  var reactions = JSON.parse(jsonReactions);
-  for (var i = 0; i < reactions.length; i++) {
-    var reaction = reactions[i];
-    var model = this.getSubmodelById(reaction.modelId);
-    if (model !== undefined) {
-      model.getModel().addReactionForLayout(layoutId, reaction);
-    } else {
-      logger.warn("Unknown model: " + reaction.modelId);
-    }
-  }
-  this.retrieveMissingReactions();
-};
-
-/**
- * Adds information about reactions.
- * 
- * @param jsonAliases
- *          list of reactions in json format
- * 
- */
-CustomMap.prototype.addReactions = function(jsonReactions) {
-  var reactions = JSON.parse(jsonReactions);
-  for (var i = 0; i < reactions.length; i++) {
-    var reaction = reactions[i];
-    var model = this.getSubmodelById(reaction.modelId);
-    if (model !== undefined) {
-      model.addReaction(reaction);
-    } else {
-      logger.warn("Unknown model: " + reaction.modelId);
-    }
-  }
-  this.callListeners("onAddReactions");
-};
-
-/**
- * This function will ask server for reactions that should be visualized but the
- * data is still missing on the client side.
- */
-CustomMap.prototype.retrieveMissingReactions = function() {
-  var ids = [];
-  var missing = this.getModel().getMissingReactionIds();
-  for (var k = 0; k < missing.length; k++) {
-    ids.push([ this.getId(), missing[k] ]);
-  }
-  for (var i = 0; i < this.submaps.length; i++) {
-    missing = this.submaps[i].getModel().getMissingReactionIds();
-    for (var j = 0; j < missing.length; j++) {
-      ids.push([ this.submaps[i].getId(), missing[j] ]);
-    }
-  }
-  if (ids.length > 0) {
-    // load data from server about missing reactions
-    ServerConnector.retreiveLightReactions(ids);
-  }
-  if (!ServerConnector.isWaitingForData()) {
-    // if we already have everything then just refresh data to be visualized
-    this.refreshSelectedLayouts();
-    // and close "loading" dialog (if opened)
-    GuiConnector.closeLoadingDialog();
-  }
-};
-
 /**
  * This method checks if the layout contains any overlays (like AliasOverlay or
  * ReactionOverlay) that is currently visible on the map.
@@ -1168,14 +1094,6 @@ CustomMap.prototype.getReferenceGenome = function(type, version) {
   }
 };
 
-CustomMap.prototype.updateReferenceGenome = function(type, version, jsonObj) {
-  if (this._referenceGenome[type] === undefined) {
-    this._referenceGenome[type] = [];
-  }
-  this._referenceGenome[type][version] = new ReferenceGenome(jsonObj);
-  this.refreshInfoWindows();
-};
-
 CustomMap.prototype.getTopMap = function() {
   return this;
 };