diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 2228ada0bcd49f9e6e61e25be52e6ff3d6985183..95eb552d432196f8dac5af239e82b6a270349c46 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -4,6 +4,7 @@
 
 var Promise = require("bluebird");
 
+// noinspection JSUnusedLocalSymbols
 var logger = require('./logger');
 
 var request = require('request');
@@ -17,7 +18,6 @@ var Comment = require('./map/data/Comment');
 var Configuration = require('./Configuration');
 var Drug = require('./map/data/Drug');
 var ConfigurationType = require('./ConfigurationType');
-var Functions = require('./Functions');
 var IdentifiedElement = require('./map/data/IdentifiedElement');
 var InvalidCredentialsError = require('./InvalidCredentialsError');
 var LayoutAlias = require('./map/data/LayoutAlias');
@@ -1671,6 +1671,7 @@ ServerConnector.updateOverlay = function (overlay) {
   var filterParams = {
     overlay: {
       name: overlay.getName(),
+      order: overlay.getOrder(),
       description: overlay.getDescription(),
       creator: overlay.getCreator(),
       publicOverlay: overlay.getPublicOverlay(),
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index c762b574ab51261e04c6dba43d6385558bee3338..ad37c125c195eb7df8100f049686d28253205a14 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -234,15 +234,14 @@ OverlayPanel.prototype.createOverlayRow = function (overlay, checked) {
   return result;
 };
 
-OverlayPanel.prototype.overlayToDataRow = function (overlay, checked, index) {
-  var self = this;
+OverlayPanel.prototype.overlayToDataRow = function (overlay, checked) {
   // if (checked && !overlay.getInputDataAvailable()) {
   //   result.className = "active";
   // }
   // result.title = overlay.getDescription();
 
   var result = [];
-  result[0] = index + 1;
+  result[0] = overlay.getOrder();
   result[1] = overlay.getName();
 
   if (overlay.getInputDataAvailable()) {
@@ -403,7 +402,7 @@ OverlayPanel.prototype.refresh = function (showDefault) {
         if (showDefault && overlay.isDefaultOverlay()) {
           selectedOverlay[overlay.getId()] = true;
         }
-        data.push(self.overlayToDataRow(overlay, selectedOverlay[overlay.getId()], i));
+        data.push(self.overlayToDataRow(overlay, selectedOverlay[overlay.getId()]));
       }
       table.clear().rows.add(data).draw();
 
@@ -415,7 +414,6 @@ OverlayPanel.prototype.refresh = function (showDefault) {
     if (showDefault) {
       for (var key in selectedOverlay) {
         if (selectedOverlay.hasOwnProperty(key) && selectedOverlay[key]) {
-          logger.debug(key);
           promises.push(self.getMap().openDataOverlay(key));
         }
       }
@@ -453,9 +451,10 @@ OverlayPanel.prototype.openAddOverlayDialog = function () {
 };
 
 OverlayPanel.prototype.init = function () {
+  var self = this;
   var backgroundOverlay = ServerConnector.getSessionData().getSelectedBackgroundOverlay();
   var showDefault = (backgroundOverlay === undefined || backgroundOverlay === "undefined");
-  $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable({
+  var table = $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable({
     columns: [{
       title: 'No',
       className: "no_padding"
@@ -479,10 +478,27 @@ OverlayPanel.prototype.init = function () {
     info: false,
     rowReorder: true
   });
+  table.on('row-reorder', function (e, diff, edit) {
+    var promises = [];
+
+    for (var i = 0, ien = diff.length; i < ien; i++) {
+      var rowData = table.row(diff[i].node).data();
+      var overlayId = $(rowData[2]).attr("data");
+      promises.push(self.updateOverlayOrder(overlayId, diff[i].newData));
+    }
+    promises.push(self.getMap().redrawSelectedDataOverlays());
+    return Promise.all(promises);
+  });
 
   return this.refresh(showDefault);
 };
-
+OverlayPanel.prototype.updateOverlayOrder = function (overlayId, order) {
+  var self = this;
+  return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
+    overlay.setOrder(order);
+    return ServerConnector.updateOverlay(overlay);
+  });
+};
 OverlayPanel.prototype.removeOverlay = function (overlay) {
   self = this;
   return self.getMap().hideDataOverlay(overlay.getId()).then(function () {
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 4e37ed47406857b5a21deb8a243ff783b7fbda7c..36497cd2e704329f9a7f1f4a78951c0b92f8d6be 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -546,22 +546,22 @@ CustomMap.prototype.hideDataOverlay = function (identifier) {
  * Refresh visualization of selected layouts.
  */
 CustomMap.prototype.redrawSelectedDataOverlays = function () {
-  logger.debug("Refreshing layouts");
+  logger.debug("Redrawing overlays");
   var self = this;
   return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
-    // show layouts that should be visualized (resize or show them)
+    // show overlays that should be visualized (resize or show them)
     var promises = [];
     for (var i = 0; i < visibleDataOverlays.length; i++) {
-      var layoutId = visibleDataOverlays[i].getId();
-      if (self.layoutContainsOverlays(layoutId)) {
+      var overlayId = visibleDataOverlays[i].getId();
+      if (self.layoutContainsOverlays(overlayId)) {
         // resize element on the map
-        promises.push(self.resizeSelectedDataOverlay(layoutId, i, visibleDataOverlays.length));
+        promises.push(self.resizeSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
       } else {
-        promises.push(self.showSelectedDataOverlay(layoutId, i, visibleDataOverlays.length));
+        promises.push(self.showSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
       }
     }
     return Promise.all(promises).then(function () {
-      // remove layouts that were
+      // hide overlays that were visible
       for (var key in self.selectedLayoutOverlays) {
         if (!self._selectedOverlays.hasOwnProperty(key) || self._selectedOverlays[key] === false) {
           if (self.layoutContainsOverlays(key)) {
@@ -1135,14 +1135,23 @@ CustomMap.prototype.destroy = function () {
 CustomMap.prototype.getVisibleDataOverlays = function () {
   var dataOverlayPromises = [];
 
-  // get list of layouts
   for (var key in this._selectedOverlays) {
     if (this._selectedOverlays.hasOwnProperty(key) && this._selectedOverlays[key] === true) {
       dataOverlayPromises.push(this.getProject().getDataOverlayById(key));
     }
   }
 
-  return Promise.all(dataOverlayPromises);
+  return Promise.all(dataOverlayPromises).then(function (overlays) {
+    overlays.sort(function (dataOverlay1, dataOverlay2) {
+      if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
+        return -1;
+      if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
+        return 1;
+      return 0;
+    });
+
+    return overlays;
+  });
 };
 
 
diff --git a/frontend-js/src/main/js/map/data/DataOverlay.js b/frontend-js/src/main/js/map/data/DataOverlay.js
index c2e5812ca02e2ea5e2d35029acfc0c3629c107ad..3231fc430dbb0c520ef019ff3108a5a0c4d2c7fb 100644
--- a/frontend-js/src/main/js/map/data/DataOverlay.js
+++ b/frontend-js/src/main/js/map/data/DataOverlay.js
@@ -17,6 +17,7 @@ function DataOverlay(layoutId, name) {
     // from json structure
     var object = layoutId;
     this.setId(object.idObject);
+    this.setOrder(object.order);
     this.setName(object.name);
     this.setImagesDirectory(object.images);
     this.setDescription(object.description);
@@ -216,6 +217,14 @@ DataOverlay.prototype.setContent = function (content) {
   this._content = content;
 };
 
+DataOverlay.prototype.getOrder = function () {
+  return this._order;
+};
+
+DataOverlay.prototype.setOrder = function (order) {
+  this._order = order;
+};
+
 DataOverlay.prototype.getFilename = function () {
   return this._filename;
 };
@@ -232,7 +241,7 @@ DataOverlay.prototype.setType = function (type) {
   this._type = type;
 };
 
-DataOverlay.prototype.update= function (overlay) {
+DataOverlay.prototype.update = function (overlay) {
   this.setName(overlay.getName());
   this.setDescription(overlay.getDescription());
 };
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index 720ce27f9e28be5d3240a3423b5ee805c118eb9a..799145f3751c645a40ab9265ad65b39896a8b160 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -244,6 +244,13 @@ Project.prototype.getDataOverlays = function () {
       result.push(this._dataOverlays[id]);
     }
   }
+  result.sort(function (dataOverlay1, dataOverlay2) {
+    if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
+      return -1;
+    if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
+      return 1;
+    return 0;
+  });
   return result;
 };
 
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 7778866df4a9458068fca68dcc576597f7a14538..0604023f5d225347a0c7403f3a49e5cb59d6dbff 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"annotators":[{"className":"lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"BRENDA","parametersDefinitions":[],"url":"http://www.brenda-enzymes.org"},{"className":"lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"Biocompendium","parametersDefinitions":[],"url":"http://biocompendium.embl.de/"},{"className":"lcsb.mapviewer.annotation.services.annotators.CazyAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"CAZy","parametersDefinitions":[],"url":"http://commonchemistry.org"},{"className":"lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Chemical"],"name":"Chebi","parametersDefinitions":[],"url":"http://www.ebi.ac.uk/chebi/"},{"className":"lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"Uniprot","parametersDefinitions":[],"url":"http://www.uniprot.org/"},{"className":"lcsb.mapviewer.annotation.services.annotators.GoAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Phenotype","lcsb.mapviewer.model.map.compartment.Compartment","lcsb.mapviewer.model.map.species.Complex"],"name":"Gene Ontology","parametersDefinitions":[],"url":"http://amigo.geneontology.org/amigo"},{"className":"lcsb.mapviewer.annotation.services.annotators.HgncAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"name":"HGNC","parametersDefinitions":[],"url":"http://www.genenames.org"},{"className":"lcsb.mapviewer.annotation.services.annotators.KeggAnnotator","description":"Annotations extracted from KEGG ENZYME Database based on species EC numbers. Annotation include relevant publications and homologous genes for given EC numbers.","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"KEGG","parametersDefinitions":[{"name":"KEGG organism identifier","description":"Space-delimited list of organisms codes for which homologous genes (GENE section in the KEGG enzyme record) should be imported. Currently only ATH (Arabidopsis Thaliana) is supported.","type":"java.lang.String"}],"url":"http://www.genome.jp/kegg/"},{"className":"lcsb.mapviewer.annotation.services.annotators.PdbAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"name":"Protein Data Bank","parametersDefinitions":[],"url":"http://www.pdbe.org/"},{"className":"lcsb.mapviewer.annotation.services.annotators.ReconAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Chemical","lcsb.mapviewer.model.map.reaction.Reaction"],"name":"Recon annotator","parametersDefinitions":[],"url":"http://humanmetabolism.org/"},{"className":"lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"name":"Entrez Gene","parametersDefinitions":[],"url":"http://www.ncbi.nlm.nih.gov/gene"},{"className":"lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"name":"Ensembl","parametersDefinitions":[],"url":"www.ensembl.org"},{"className":"lcsb.mapviewer.annotation.services.annotators.StitchAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.SimpleMolecule"],"name":"STITCH","parametersDefinitions":[],"url":"http://stitch.embl.de/"},{"className":"lcsb.mapviewer.annotation.services.annotators.StringAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"STRING","parametersDefinitions":[],"url":"http://string-db.org/"},{"className":"lcsb.mapviewer.annotation.services.annotators.TairAnnotator","description":"","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"name":"TAIR","parametersDefinitions":[],"url":"http://arabidopsis.org/index.jsp"}],"buildDate":"12/03/2018 13:24","elementTypes":[{"className":"lcsb.mapviewer.model.map.species.Degraded","name":"Degraded","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.species.IonChannelProtein","name":"Protein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"className":"lcsb.mapviewer.model.map.compartment.TopSquareCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.species.Ion","name":"Ion","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"className":"lcsb.mapviewer.model.map.species.Species","name":"Species","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"className":"lcsb.mapviewer.model.map.compartment.RightSquareCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.species.Drug","name":"Drug","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.Protein","name":"Protein","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.TruncatedProtein","name":"Protein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"className":"lcsb.mapviewer.model.map.compartment.PathwayCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.species.Rna","name":"RNA","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.Chemical","name":"Chemical","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.compartment.Compartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"className":"lcsb.mapviewer.model.map.compartment.OvalCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.compartment.SquareCompartment","name":"Compartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"className":"lcsb.mapviewer.model.map.species.Unknown","name":"Unknown","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.Element","name":"Element","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"className":"lcsb.mapviewer.model.map.species.Phenotype","name":"Phenotype","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.Complex","name":"Complex","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.AntisenseRna","name":"Antisense RNA","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"className":"lcsb.mapviewer.model.map.species.ReceptorProtein","name":"Protein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"className":"lcsb.mapviewer.model.map.species.SimpleMolecule","name":"Simple molecule","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"className":"lcsb.mapviewer.model.map.species.GenericProtein","name":"Protein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"className":"lcsb.mapviewer.model.map.species.Gene","name":"Gene","parentClass":"lcsb.mapviewer.model.map.species.Species"}],"gitHash":"28785dc808e25a7b8717e82fffe3906892972bd2","imageFormats":[{"extension":"png","handler":"lcsb.mapviewer.converter.graphics.PngImageGenerator","name":"PNG image"},{"extension":"pdf","handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","name":"PDF"},{"extension":"svg","handler":"lcsb.mapviewer.converter.graphics.SvgImageGenerator","name":"SVG image"}],"mapTypes":[{"id":"DOWNSTREAM_TARGETS","name":"Downstream targets"},{"id":"PATHWAY","name":"Pathway"},{"id":"UNKNOWN","name":"Unknown"}],"miriamTypes":{"BRENDA":{"commonName":"BRENDA","homepage":"http://www.brenda-enzymes.org","registryIdentifier":"MIR:00100101","uris":["urn:miriam:brenda"]},"CAS":{"commonName":"Chemical Abstracts Service","homepage":"http://commonchemistry.org","registryIdentifier":"MIR:00000237","uris":["urn:miriam:cas"]},"CAZY":{"commonName":"CAZy","homepage":"http://commonchemistry.org","registryIdentifier":"MIR:00000195","uris":["urn:miriam:cazy"]},"CCDS":{"commonName":"Consensus CDS","homepage":"http://www.ncbi.nlm.nih.gov/CCDS/","registryIdentifier":"MIR:00000375","uris":["urn:miriam:ccds"]},"CHEBI":{"commonName":"Chebi","homepage":"http://www.ebi.ac.uk/chebi/","registryIdentifier":"MIR:00000002","uris":["urn:miriam:obo.chebi","urn:miriam:chebi"]},"CHEMBL_COMPOUND":{"commonName":"ChEMBL","homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000084","uris":["urn:miriam:chembl.compound"]},"CHEMBL_TARGET":{"commonName":"ChEMBL target","homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000085","uris":["urn:miriam:chembl.target"]},"CHEMSPIDER":{"commonName":"ChemSpider","homepage":"http://www.chemspider.com//","registryIdentifier":"MIR:00000138","uris":["urn:miriam:chemspider"]},"COG":{"commonName":"Clusters of Orthologous Groups","homepage":"https://www.ncbi.nlm.nih.gov/COG/","registryIdentifier":"MIR:00000296","uris":["urn:miriam:cogs"]},"DOI":{"commonName":"Digital Object Identifier","homepage":"http://www.doi.org/","registryIdentifier":"MIR:00000019","uris":["urn:miriam:doi"]},"DRUGBANK":{"commonName":"DrugBank","homepage":"http://www.drugbank.ca/","registryIdentifier":"MIR:00000102","uris":["urn:miriam:drugbank"]},"DRUGBANK_TARGET_V4":{"commonName":"DrugBank Target v4","homepage":"http://www.drugbank.ca/targets","registryIdentifier":"MIR:00000528","uris":["urn:miriam:drugbankv4.target"]},"EC":{"commonName":"Enzyme Nomenclature","homepage":"http://www.enzyme-database.org/","registryIdentifier":"MIR:00000004","uris":["urn:miriam:ec-code"]},"ENSEMBL":{"commonName":"Ensembl","homepage":"www.ensembl.org","registryIdentifier":"MIR:00000003","uris":["urn:miriam:ensembl"]},"ENSEMBL_PLANTS":{"commonName":"Ensembl Plants","homepage":"http://plants.ensembl.org/","registryIdentifier":"MIR:00000205","uris":["urn:miriam:ensembl.plant"]},"ENTREZ":{"commonName":"Entrez Gene","homepage":"http://www.ncbi.nlm.nih.gov/gene","registryIdentifier":"MIR:00000069","uris":["urn:miriam:ncbigene","urn:miriam:entrez.gene"]},"GO":{"commonName":"Gene Ontology","homepage":"http://amigo.geneontology.org/amigo","registryIdentifier":"MIR:00000022","uris":["urn:miriam:obo.go","urn:miriam:go"]},"HGNC":{"commonName":"HGNC","homepage":"http://www.genenames.org","registryIdentifier":"MIR:00000080","uris":["urn:miriam:hgnc"]},"HGNC_SYMBOL":{"commonName":"HGNC Symbol","homepage":"http://www.genenames.org","registryIdentifier":"MIR:00000362","uris":["urn:miriam:hgnc.symbol"]},"HMDB":{"commonName":"HMDB","homepage":"http://www.hmdb.ca/","registryIdentifier":"MIR:00000051","uris":["urn:miriam:hmdb"]},"INTERPRO":{"commonName":"InterPro","homepage":"http://www.ebi.ac.uk/interpro/","registryIdentifier":"MIR:00000011","uris":["urn:miriam:interpro"]},"KEGG_COMPOUND":{"commonName":"Kegg 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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
index 490c516171610f577c6740077dc67b7a4d8eacce..43b7a1ea9bc3ec911de7726ada4d3f3c5ac557f2 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/publicOverlay=true&token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true}]
\ No newline at end of file
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","order":1,"publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","order":1,"publicOverlay":true}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
index f96087ce1072fe79770ae5f18f024a35169c526c..147f4ea24c3d4d6992bb40614e0901073bcab0fe 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=ADMIN_TOKEN_ID&
@@ -1 +1 @@
-[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26107,"images":[{"modelId":15781,"path":".26107"}],"inputDataAvailable":true,"name":"s1","publicOverlay":false},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26108,"images":[{"modelId":15781,"path":".26108"}],"inputDataAvailable":true,"name":"s2","publicOverlay":false}]
\ No newline at end of file
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","order":1,"publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","order":1,"publicOverlay":true},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26107,"images":[{"modelId":15781,"path":".26107"}],"inputDataAvailable":true,"name":"s1","order":1,"publicOverlay":false},{"creator":"admin","defaultOverlay":false,"description":"","idObject":26108,"images":[{"modelId":15781,"path":".26108"}],"inputDataAvailable":true,"name":"s2","order":2,"publicOverlay":false}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
index 490c516171610f577c6740077dc67b7a4d8eacce..43b7a1ea9bc3ec911de7726ada4d3f3c5ac557f2 100644
--- a/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/projects/sample/overlays/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","publicOverlay":true}]
\ No newline at end of file
+[{"defaultOverlay":false,"description":"","idObject":14081,"images":[{"modelId":15781,"path":"_nested0"}],"inputDataAvailable":false,"name":"Pathways and compartments","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":14082,"images":[{"modelId":15781,"path":"_normal0"}],"inputDataAvailable":false,"name":"Network","order":1,"publicOverlay":true},{"defaultOverlay":true,"description":"","idObject":14083,"images":[{"modelId":15781,"path":"_empty0"}],"inputDataAvailable":false,"name":"Empty","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"xxx","idObject":18076,"images":[{"modelId":15781,"path":".18076"}],"inputDataAvailable":true,"name":"C:\\fakepath\\test.txt","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"yyy","idObject":18077,"images":[{"modelId":15781,"path":".18077"}],"inputDataAvailable":true,"name":"xxx","order":1,"publicOverlay":true},{"defaultOverlay":false,"description":"","idObject":22750,"images":[{"modelId":15781,"path":".22750"}],"inputDataAvailable":true,"name":"new-global","order":1,"publicOverlay":true}]
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
index 0597502175abd4208f8decefe26979c94f534e6c..382550c682f8ac8336cd240da853db01ce160ce0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/Layout.java
@@ -47,6 +47,14 @@ public class Layout implements Serializable {
     }
   };
 
+  public static final Comparator<? super Layout> ORDER_COMPARATOR = new Comparator<Layout>() {
+
+    @Override
+    public int compare(Layout o1, Layout o2) {
+      return o1.getOrderIndex() - o2.getOrderIndex();
+    }
+  };
+
   /**
    * Default class logger.
    */
@@ -115,6 +123,9 @@ public class Layout implements Serializable {
    */
   private double progress = 0.0;
 
+  @Column(name = "order_index")
+  private int orderIndex = 0;
+
   /**
    * List of layouts for submodels.
    */
@@ -468,4 +479,12 @@ public class Layout implements Serializable {
     this.defaultOverlay = defaultOverlay;
   }
 
+  public int getOrderIndex() {
+    return orderIndex;
+  }
+
+  public void setOrderIndex(int orderIndex) {
+    this.orderIndex = orderIndex;
+  }
+
 }
diff --git a/persist/src/db/12.0.0~alpha.1/fix_db_20180206.sql b/persist/src/db/12.0.0~alpha.1/fix_db_20180206.sql
new file mode 100644
index 0000000000000000000000000000000000000000..56c66ff5814b21306bcaeeecb1c1bf8a46289048
--- /dev/null
+++ b/persist/src/db/12.0.0~alpha.1/fix_db_20180206.sql
@@ -0,0 +1,2 @@
+alter table layout add order_index integer default 0;
+update layout l set order_index = (select count(*) from layout where iddb<l.iddb and creator_iddb=l.creator_iddb and l.model_iddb=model_iddb) +1;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 6e1fe9f0eed7f9369ee93aafd7453ffd71197273..ae0568257d0e2ad77737f8a9a61c54d984f63bcb 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -17,6 +17,7 @@ import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.ObjectNotFoundException;
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.FileEntry;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
@@ -88,6 +89,7 @@ public class OverlayRestImpl extends BaseRestImpl {
     Map<String, Object> result = new TreeMap<>();
     result.put("idObject", overlay.getId());
     result.put("name", overlay.getTitle());
+    result.put("order", overlay.getOrderIndex());
     result.put("description", overlay.getDescription());
     result.put("publicOverlay", overlay.isPublicLayout());
     result.put("defaultOverlay", overlay.isDefaultOverlay());
@@ -206,6 +208,8 @@ public class OverlayRestImpl extends BaseRestImpl {
           layout.setDescription((String) value);
         } else if (key.equalsIgnoreCase("name")) {
           layout.setTitle((String) value);
+        } else if (key.equalsIgnoreCase("order")) {
+          layout.setOrderIndex(parseInteger(value));
         } else if (key.equalsIgnoreCase("publicOverlay")) {
           layout.setPublicLayout(parseBoolean(value));
         } else if (key.equalsIgnoreCase("defaultOverlay")) {
@@ -235,6 +239,16 @@ public class OverlayRestImpl extends BaseRestImpl {
     }
   }
 
+  private int parseInteger(Object value) {
+    if (value instanceof Integer) {
+      return (int) value;
+    } else if (value instanceof String) {
+      return Integer.parseInt((String) value);
+    } else {
+      throw new InvalidArgumentException("Invalid class of object: " + value);
+    }
+  }
+
   public Map<String, Object> removeOverlay(String token, String projectId, String overlayId)
       throws QueryException, SecurityException, IOException {
     Model model = getModelService().getLastModelByProjectId(projectId, token);
@@ -249,6 +263,16 @@ public class OverlayRestImpl extends BaseRestImpl {
       }
       if (layoutService.userCanRemoveLayout(layout, token)) {
         layoutService.removeLayout(layout, null);
+        List<Layout> overlays = layoutService.getCustomLayouts(model, token, false,
+            getUserService().getUserByToken(token));
+        overlays.sort(Layout.ORDER_COMPARATOR);
+        for (int i = 0; i < overlays.size(); i++) {
+          Layout overlay = overlays.get(i);
+          if (overlay.getOrderIndex() != i + 1) {
+            overlay.setOrderIndex(i + 1);
+            layoutService.updateLayout(overlay);
+          }
+        }
         return okStatus();
       } else {
         throw new SecurityException("You cannot remove given overlay");
@@ -320,6 +344,11 @@ public class OverlayRestImpl extends BaseRestImpl {
       Layout layout = layoutService.createLayout(new CreateLayoutParams().async(false).colorInputStream(stream)
           .description(description).layoutFileName(filename).model(model).name(name).user(user)
           .colorSchemaType(colorSchemaType).directory("."));
+
+      int count = layoutService.getCustomLayouts(model, token, false, user).size();
+      layout.setOrderIndex(count);
+      layoutService.updateLayout(layout);
+
       return getOverlayById(token, projectId, layout.getId() + "");
     } catch (InvalidColorSchemaException e) {
       throw new QueryException(e.getMessage(), e);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 5a82534e0bf7a9de829ed722d98195d3edf879ad..089665f647990ff95cf34e597a5b77259091846a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -188,10 +188,12 @@ public class LayoutService implements ILayoutService {
     }
 
     String projectId = layout.getModel().getProject().getProjectId();
-    String email = null;
+    final String email;
     User user = layout.getCreator();
     if (user != null) {
       email = user.getEmail();
+    } else {
+      email = null;
     }
 
     layout.getModel().removeLayout(layout);
@@ -201,13 +203,19 @@ public class LayoutService implements ILayoutService {
     logService.log(params);
 
     if (email != null) {
-      try {
-        sendSuccesfullRemoveEmail(projectId, layout.getTitle(), email);
-      } catch (MessagingException e) {
-        logger.error(e);
-      }
+      Thread sendEmailThread = new Thread(new Runnable() {
+        @Override
+        public void run() {
+          try {
+            sendSuccesfullRemoveEmail(projectId, layout.getTitle(), email);
+          } catch (MessagingException e) {
+            logger.error(e);
+          }
+        }
+      });
+      sendEmailThread.start();
     }
-    Thread computations = new Thread(new Runnable() {
+    Thread removeFilesThread = new Thread(new Runnable() {
       @Override
       public void run() {
         MapGenerator generator = new MapGenerator();
@@ -219,7 +227,7 @@ public class LayoutService implements ILayoutService {
 
       }
     });
-    computations.start();
+    removeFilesThread.start();
   }
 
   @Override
@@ -424,15 +432,6 @@ public class LayoutService implements ILayoutService {
 
     layoutDao.flush();
 
-    boolean customSession = false;
-
-    if (params.isAsync()) {
-      customSession = !dbUtils.isCustomSessionForCurrentThread();
-      if (customSession) {
-        dbUtils.createSessionForCurrentThread();
-      }
-    }
-
     Layout topLayout = new Layout(params.getName(), simpleDir, false);
     if (params.getUser() == null) {
       topLayout.setPublicLayout(true);
@@ -469,29 +468,16 @@ public class LayoutService implements ILayoutService {
       layoutDao.update(layout);
     }
 
-    if (params.isAsync()) {
-      if (customSession) {
-        dbUtils.closeSessionForCurrentThread();
-      } else {
-        layoutDao.commit();
-      }
-    }
     Thread computations = new Thread(new Runnable() {
       @Override
       public void run() {
-        if (params.isAsync()) {
+        try {
           // open transaction for this thread
           dbUtils.createSessionForCurrentThread();
-        }
-
-        try {
           sendSuccessfullGenerationEmail(params, schemas);
         } catch (MessagingException e) {
           logger.error("Problem with sending email", e);
-        }
-
-        if (params.isAsync()) {
-          // close the transaction for this thread
+        } finally {
           dbUtils.closeSessionForCurrentThread();
         }
       }
@@ -564,7 +550,7 @@ public class LayoutService implements ILayoutService {
    * @param layoutName
    *          name of the layout
    * @param email
-   *          otification email
+   *          notification email
    * @throws MessagingException
    *           thrown when there is a problem with sending email
    */
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 8dc37c8a7c57e7defae75f518845ffa12ca8b0bf..6289c3bc819a80cd78a919784bbf5984fe44c592 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -49,548 +49,554 @@ import lcsb.mapviewer.services.search.data.SearchElementResult;
 import lcsb.mapviewer.services.utils.SearchIndexer;
 
 public class SearchServiceTest extends ServiceTestFunctions {
-	static Logger					logger										 = Logger.getLogger(SearchServiceTest.class);
-
-	SearchIndexer					indexer										 = new SearchIndexer();
-
-	Map<Class<?>, String>	speciesSearchPrefix				 = new HashMap<Class<?>, String>();
-	Map<String, Class<?>>	speciesSearchReversePrefix = new HashMap<String, Class<?>>();
-
-	@Before
-	public void setUp() throws Exception {
-		addSearchPrefix("complex", Complex.class);
-		addSearchPrefix("degrded", Degraded.class);
-		addSearchPrefix("drug", Drug.class);
-		addSearchPrefix("gene", Gene.class);
-		addSearchPrefix("ion", Ion.class);
-		addSearchPrefix("phenotype", Phenotype.class);
-		addSearchPrefix("protein", Protein.class);
-		addSearchPrefix("rna", Rna.class);
-		addSearchPrefix("molecule", SimpleMolecule.class);
-		addSearchPrefix("unknown", Unknown.class);
-	}
-
-	private void addSearchPrefix(String prefix, Class<?> clazz) {
-		speciesSearchPrefix.put(clazz, prefix);
-		speciesSearchReversePrefix.put(prefix, clazz);
-	}
-
-	protected Model createFullModel() throws Exception {
-		Model model = getModelForFile("testFiles/searchModel.xml", false);
-		model.setProject(new Project("unknown project"));
-		return model;
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testSearchByName() throws Exception {
-		try {
-			Model model = createFullModel();
-			long count = searchHistoryDao.getCount();
-			SearchElementResult result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertEquals(4, result.getElements().size());
-			FullReactionView reaction = (FullReactionView) result.getElements().get(0);
-			assertTrue(reaction.getName().contains("re21"));
-
-			long count2 = searchHistoryDao.getCount();
-
-			assertEquals(count + 1, count2);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchByName2() throws Exception {
-		try {
-			Model model = createFullModel();
-			SearchElementResult result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertTrue(result.getElements().size() > 0);
-			FullAliasView alias = (FullAliasView) result.getElements().get(0);
-			assertEquals("BAD:BCL-2", alias.getName());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchById() throws Exception {
-		try {
-			Model model = createFullModel();
-			MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
-			model.getElements().iterator().next().addMiriamData(md);
-			SearchElementResult global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
-			assertNotNull(global);
-			assertEquals(1, global.size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchByElementId() throws Exception {
-		try {
-			Model model = createFullModel();
-			Element element =model.getElements().iterator().next(); 
-			element.setId(907);
-			SearchElementResult global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
-			assertNotNull(global);
-			assertEquals(1, global.size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchByName4() throws Exception {
-		try {
-			Model model = createFullModel();
-			SearchElementResult result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
-
-			assertNotNull(result);
-			assertEquals(0, result.size());
-
-			result = searchService.searchByQuery(model, "BC", 50, false, "127.0.0.1");
-			assertNotNull(result);
-			assertTrue(result.size() > 0);
-
-			result = searchService.searchByQuery(model, "BAD:BCL-2", 50, true, "127.0.0.1");
-			assertNotNull(result);
-			assertEquals(1, result.size());
-			FullAliasView alias = (FullAliasView) result.get(0);
-			assertEquals("BAD:BCL-2", alias.getName());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryName() throws Exception {
-		try {
-			Model model = createFullModel();
-			SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertEquals(4, result.size());
-			FullReactionView reaction = (FullReactionView) result.get(0);
-			assertTrue(reaction.getName().contains("re21"));
-			assertTrue(result.get(1) instanceof FullAliasView);
-			assertTrue(result.get(2) instanceof FullAliasView);
-			assertTrue(result.get(3) instanceof FullAliasView);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryReactionId() throws Exception {
-		try {
-			Model model = createFullModel();
-			model.getReactions().iterator().next().setIdReaction("R_x1");
-			SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertTrue(result.size() > 0);
-			FullReactionView reaction = (FullReactionView) result.get(0);
-			assertTrue(reaction.getName().contains("R_x1"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryReactionId2() throws Exception {
-		try {
-			Model model = createFullModel();
-			Reaction reaction = model.getReactions().iterator().next();
-			reaction.setId(154);
-			reaction.setIdReaction("test-name");
-			SearchElementResult result = searchService.searchByQuery(model, indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertTrue(result.size() > 0);
-			FullReactionView resultReaction = (FullReactionView) result.get(0);
-			logger.debug(resultReaction.getName());
-			assertTrue(resultReaction.getName().contains("test-name"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryName2() throws Exception {
-		try {
-			Model model = createFullModel();
-			model.getModelData().setId(-13);
-			SearchElementResult result = searchService
-					.searchByQuery(model, indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
-			assertNotNull(result);
-			assertTrue(result.size() > 0);
-			FullAliasView alias = (FullAliasView) result.get(0);
-			assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryName3() throws Exception {
-		try {
-			Model model = createFullModel();
-			SearchElementResult result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
-
-			assertNotNull(result);
-			assertEquals(0, result.size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testQueryName4() throws Exception {
-		try {
-			Model model = createFullModel();
-			SearchElementResult result = searchService
-					.searchByQuery(model, indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
-			assertNotNull(result);
-			assertTrue(result.size() > 0);
-			FullAliasView alias = (FullAliasView) result.get(0);
-			assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchClosest() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-			List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
-			assertNotNull(elements);
-			assertEquals(5, elements.size());
-			assertTrue(elements.get(0) instanceof Species);
-			Species sAlias = (Species) elements.get(0);
-			assertEquals("s1", sAlias.getName());
-			assertTrue(elements.get(1) instanceof Reaction);
-			Reaction reaction = (Reaction) elements.get(1);
-			assertEquals("re1", reaction.getIdReaction());
-			assertTrue(elements.get(2) instanceof Species);
-			sAlias = (Species) elements.get(2);
-			assertEquals("s3", sAlias.getName());
-			assertTrue(elements.get(3) instanceof Reaction);
-			reaction = (Reaction) elements.get(3);
-			assertEquals("re2", reaction.getIdReaction());
-			assertTrue(elements.get(4) instanceof Species);
-			sAlias = (Species) elements.get(4);
-			assertEquals("s2", sAlias.getName());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchClosest2() throws Exception {
-		try {
-			Model model = new ModelFullIndexed(null);
-			GenericProtein protein1 = new GenericProtein("s1");
-			protein1.setWidth(20);
-			protein1.setHeight(20);
-			protein1.setX(5);
-			protein1.setY(5);
-			model.addElement(protein1);
-			GenericProtein protein2 = new GenericProtein("s2");
-			protein2.setWidth(10);
-			protein2.setHeight(10);
-			protein2.setX(5);
-			protein2.setY(5);
-			model.addElement(protein2);
-			GenericProtein protein3 = new GenericProtein("s3");
-			protein3.setWidth(30);
-			protein3.setHeight(30);
-			protein3.setX(0);
-			protein3.setY(0);
-			model.addElement(protein3);
-
-			List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
-			assertNotNull(elements);
-			assertEquals(3, elements.size());
-			BioEntity sAlias = elements.get(0);
-			assertEquals("s2", sAlias.getName());
-			BioEntity reaction = elements.get(1);
-			assertEquals("s1", reaction.getName());
-			sAlias = elements.get(2);
-			assertEquals("s3", sAlias.getName());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testSearchClosestWithEmptyModel() throws Exception {
-		try {
-			Model model = new ModelFullIndexed(null);
-			List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
-			assertNotNull(elements);
-			assertEquals(0, elements.size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetAutocompleList() {
-		try {
-			Model model = new ModelFullIndexed(null);
-			Species proteinAlias = new GenericProtein("a");
-			proteinAlias.setName("PROT identifier");
-			proteinAlias.getSynonyms().add("PROT synonym");
-			proteinAlias.getSynonyms().add("another synonym");
-			proteinAlias.setFullName("Protein common name");
-			model.addElement(proteinAlias);
-
-			SimpleMolecule alias = new SimpleMolecule("a2");
-			alias.setName("Molecule2");
-			model.addElement(alias);
-
-			int oldVal = Configuration.getAutocompleteSize();
-			Configuration.setAutocompleteSize(5);
-
-			List<String> list = searchService.getAutocompleteList(model, "P");
-			assertNotNull(list);
-			assertEquals(4, list.size());
-			assertTrue(list.contains("PROT identifier".toLowerCase()));
-			assertTrue(list.contains("PROT synonym".toLowerCase()));
-			assertTrue(list.contains("Protein common name".toLowerCase()));
-
-			list = searchService.getAutocompleteList(model, "PROTEIN");
-			assertNotNull(list);
-			assertEquals(2, list.size());
-			assertTrue(list.contains("Protein common name".toLowerCase()));
-
-			list = searchService.getAutocompleteList(model, "m");
-			assertNotNull(list);
-			assertEquals(2, list.size());
-			assertTrue(list.contains("Molecule2".toLowerCase()));
-
-			list = searchService.getAutocompleteList(model, "blablabla");
-			assertNotNull(list);
-			assertEquals(0, list.size());
-
-			Configuration.setAutocompleteSize(oldVal);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetAutocompleList2() {
-		try {
-			Model model = new ModelFullIndexed(null);
-			GenericProtein proteinAlias = new GenericProtein("a1");
-			proteinAlias.setName("PROT identifier");
-			proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
-			model.addElement(proteinAlias);
-
-			SimpleMolecule alias = new SimpleMolecule("a2");
-			alias.setName("Molecule2");
-			model.addElement(alias);
-
-			List<String> list = searchService.getAutocompleteList(model, "PROT identifier");
-			assertNotNull(list);
-			assertEquals(1, list.size());
-			assertTrue(list.get(0).equalsIgnoreCase("PROT identifier"));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchGenericProtein() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/generic.xml", true);
-
-			List<String> list = searchService.getAutocompleteList(model, "generic");
-			assertNotNull(list);
-			assertEquals(2, list.size());
-			assertTrue(list.contains("generic"));
-			assertTrue(list.contains("generic protein"));
-
-			SearchElementResult result = searchService.searchByQuery(model, "generic protein", 10, false, null);
-			assertNotNull(result);
-
-			assertTrue(result.size() > 0);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchByCoordCompartment() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
-			// we search in non-nested model
-			SearchElementResult res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50));
-			assertNotNull(res);
-			assertEquals(0, res.size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchByCoordCompartment2() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
-			Layout layout = new Layout();
-			layout.setHierarchicalView(true);
-			model.addLayout(layout);
-			// we search in nested model
-			SearchElementResult res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50).layoutIdentifier(0));
-			assertNotNull(res);
-
-			assertTrue(res.get(0) instanceof FullAliasView);
-			FullAliasView view = (FullAliasView) res.get(0);
-			assertEquals("Compartment", view.getType());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchByCoordReaction() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
-			// find compartment
-			SearchElementResult res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model));
-			// reaction is too far
-			assertEquals(0, res.size());
-
-			res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).distance(1000));
-			assertEquals(3, res.size());
-
-			assertTrue(res.get(0) instanceof FullReactionView);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchByCoordAlias() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
-			SearchElementResult res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(60).y(60));
-			assertNotNull(res);
-			assertTrue(res.size() > 0);
-
-			assertTrue(res.get(0) instanceof FullAliasView);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetMiriamTypeForQuery() throws Exception {
-		try {
-			MiriamData md = new SearchService().getMiriamTypeForQuery("hgnc:SNCA");
-			assertNotNull(md);
-			assertEquals(MiriamType.HGNC, md.getDataType());
-			assertEquals("SNCA", md.getResource());
-
-			md = new SearchService().getMiriamTypeForQuery("reactome:REACT_15128");
-			assertNotNull(md);
-			assertEquals(MiriamType.REACTOME, md.getDataType());
-			assertEquals("REACT_15128", md.getResource());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testSearchByMiriamInSubmap() throws Exception {
-		try {
-			String query = "HGNC_SYMBOL:SNCA";
-			Model model = new ModelFullIndexed(null);
-			Model submodel = new ModelFullIndexed(null);
-			GenericProtein protein = new GenericProtein("s1");
-			protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-			submodel.addElement(protein);
-			model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
-
-			SearchElementResult result = searchService.searchByQuery(model, query, 50, null, "127.0.0.1");
-
-			assertEquals(1, result.getElements().size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetMiriamTypeForQuery2() throws Exception {
-		try {
-			MiriamData md = new SearchService().getMiriamTypeForQuery("UNKNOWN_HGNC:SNCA");
-			assertNull(md);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
+  static Logger logger = Logger.getLogger(SearchServiceTest.class);
+
+  SearchIndexer indexer = new SearchIndexer();
+
+  Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
+  Map<String, Class<?>> speciesSearchReversePrefix = new HashMap<String, Class<?>>();
+
+  @Before
+  public void setUp() throws Exception {
+    addSearchPrefix("complex", Complex.class);
+    addSearchPrefix("degrded", Degraded.class);
+    addSearchPrefix("drug", Drug.class);
+    addSearchPrefix("gene", Gene.class);
+    addSearchPrefix("ion", Ion.class);
+    addSearchPrefix("phenotype", Phenotype.class);
+    addSearchPrefix("protein", Protein.class);
+    addSearchPrefix("rna", Rna.class);
+    addSearchPrefix("molecule", SimpleMolecule.class);
+    addSearchPrefix("unknown", Unknown.class);
+  }
+
+  private void addSearchPrefix(String prefix, Class<?> clazz) {
+    speciesSearchPrefix.put(clazz, prefix);
+    speciesSearchReversePrefix.put(prefix, clazz);
+  }
+
+  protected Model createFullModel() throws Exception {
+    Model model = getModelForFile("testFiles/searchModel.xml", false);
+    model.setProject(new Project("unknown project"));
+    return model;
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testSearchByName() throws Exception {
+    try {
+      Model model = createFullModel();
+      long count = searchHistoryDao.getCount();
+      SearchElementResult result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertEquals(4, result.getElements().size());
+      FullReactionView reaction = (FullReactionView) result.getElements().get(0);
+      assertTrue(reaction.getName().contains("re21"));
+
+      long count2 = searchHistoryDao.getCount();
+
+      assertEquals(count + 1, count2);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchByName2() throws Exception {
+    try {
+      Model model = createFullModel();
+      SearchElementResult result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertTrue(result.getElements().size() > 0);
+      FullAliasView alias = (FullAliasView) result.getElements().get(0);
+      assertEquals("BAD:BCL-2", alias.getName());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchById() throws Exception {
+    try {
+      Model model = createFullModel();
+      MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
+      model.getElements().iterator().next().addMiriamData(md);
+      SearchElementResult global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
+      assertNotNull(global);
+      assertEquals(1, global.size());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchByElementId() throws Exception {
+    try {
+      Model model = createFullModel();
+      Element element = model.getElements().iterator().next();
+      element.setId(907);
+      SearchElementResult global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
+      assertNotNull(global);
+      assertEquals(1, global.size());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchByName4() throws Exception {
+    try {
+      Model model = createFullModel();
+      SearchElementResult result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
+
+      assertNotNull(result);
+      assertEquals(0, result.size());
+
+      result = searchService.searchByQuery(model, "BC", 50, false, "127.0.0.1");
+      assertNotNull(result);
+      assertTrue(result.size() > 0);
+
+      result = searchService.searchByQuery(model, "BAD:BCL-2", 50, true, "127.0.0.1");
+      assertNotNull(result);
+      assertEquals(1, result.size());
+      FullAliasView alias = (FullAliasView) result.get(0);
+      assertEquals("BAD:BCL-2", alias.getName());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryName() throws Exception {
+    try {
+      Model model = createFullModel();
+      SearchElementResult result = searchService.searchByQuery(model,
+          indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertEquals(4, result.size());
+      Reaction reaction = (Reaction) result.get(0);
+      assertEquals("re21",reaction.getIdReaction());
+      assertTrue(result.get(1) instanceof Species);
+      assertTrue(result.get(2) instanceof Species);
+      assertTrue(result.get(3) instanceof Species);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryReactionId() throws Exception {
+    try {
+      Model model = createFullModel();
+      model.getReactions().iterator().next().setIdReaction("R_x1");
+      SearchElementResult result = searchService.searchByQuery(model,
+          indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertTrue(result.size() > 0);
+      Reaction reaction = (Reaction) result.get(0);
+      assertTrue(reaction.getIdReaction().contains("R_x1"));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryReactionId2() throws Exception {
+    try {
+      Model model = createFullModel();
+      Reaction reaction = model.getReactions().iterator().next();
+      reaction.setId(154);
+      reaction.setIdReaction("test-name");
+      SearchElementResult result = searchService.searchByQuery(model,
+          indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertTrue(result.size() > 0);
+      FullReactionView resultReaction = (FullReactionView) result.get(0);
+      logger.debug(resultReaction.getName());
+      assertTrue(resultReaction.getName().contains("test-name"));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryName2() throws Exception {
+    try {
+      Model model = createFullModel();
+      model.getModelData().setId(-13);
+      SearchElementResult result = searchService.searchByQuery(model,
+          indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
+      assertNotNull(result);
+      assertTrue(result.size() > 0);
+      FullAliasView alias = (FullAliasView) result.get(0);
+      assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryName3() throws Exception {
+    try {
+      Model model = createFullModel();
+      SearchElementResult result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
+
+      assertNotNull(result);
+      assertEquals(0, result.size());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testQueryName4() throws Exception {
+    try {
+      Model model = createFullModel();
+      SearchElementResult result = searchService.searchByQuery(model,
+          indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
+      assertNotNull(result);
+      assertTrue(result.size() > 0);
+      FullAliasView alias = (FullAliasView) result.get(0);
+      assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchClosest() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+      List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+      assertNotNull(elements);
+      assertEquals(5, elements.size());
+      assertTrue(elements.get(0) instanceof Species);
+      Species sAlias = (Species) elements.get(0);
+      assertEquals("s1", sAlias.getName());
+      assertTrue(elements.get(1) instanceof Reaction);
+      Reaction reaction = (Reaction) elements.get(1);
+      assertEquals("re1", reaction.getIdReaction());
+      assertTrue(elements.get(2) instanceof Species);
+      sAlias = (Species) elements.get(2);
+      assertEquals("s3", sAlias.getName());
+      assertTrue(elements.get(3) instanceof Reaction);
+      reaction = (Reaction) elements.get(3);
+      assertEquals("re2", reaction.getIdReaction());
+      assertTrue(elements.get(4) instanceof Species);
+      sAlias = (Species) elements.get(4);
+      assertEquals("s2", sAlias.getName());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchClosest2() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      GenericProtein protein1 = new GenericProtein("s1");
+      protein1.setWidth(20);
+      protein1.setHeight(20);
+      protein1.setX(5);
+      protein1.setY(5);
+      model.addElement(protein1);
+      GenericProtein protein2 = new GenericProtein("s2");
+      protein2.setWidth(10);
+      protein2.setHeight(10);
+      protein2.setX(5);
+      protein2.setY(5);
+      model.addElement(protein2);
+      GenericProtein protein3 = new GenericProtein("s3");
+      protein3.setWidth(30);
+      protein3.setHeight(30);
+      protein3.setX(0);
+      protein3.setY(0);
+      model.addElement(protein3);
+
+      List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
+      assertNotNull(elements);
+      assertEquals(3, elements.size());
+      BioEntity sAlias = elements.get(0);
+      assertEquals("s2", sAlias.getName());
+      BioEntity reaction = elements.get(1);
+      assertEquals("s1", reaction.getName());
+      sAlias = elements.get(2);
+      assertEquals("s3", sAlias.getName());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testSearchClosestWithEmptyModel() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+      assertNotNull(elements);
+      assertEquals(0, elements.size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testGetAutocompleList() {
+    try {
+      Model model = new ModelFullIndexed(null);
+      Species proteinAlias = new GenericProtein("a");
+      proteinAlias.setName("PROT identifier");
+      proteinAlias.getSynonyms().add("PROT synonym");
+      proteinAlias.getSynonyms().add("another synonym");
+      proteinAlias.setFullName("Protein common name");
+      model.addElement(proteinAlias);
+
+      SimpleMolecule alias = new SimpleMolecule("a2");
+      alias.setName("Molecule2");
+      model.addElement(alias);
+
+      int oldVal = Configuration.getAutocompleteSize();
+      Configuration.setAutocompleteSize(5);
+
+      List<String> list = searchService.getAutocompleteList(model, "P");
+      assertNotNull(list);
+      assertEquals(4, list.size());
+      assertTrue(list.contains("PROT identifier".toLowerCase()));
+      assertTrue(list.contains("PROT synonym".toLowerCase()));
+      assertTrue(list.contains("Protein common name".toLowerCase()));
+
+      list = searchService.getAutocompleteList(model, "PROTEIN");
+      assertNotNull(list);
+      assertEquals(2, list.size());
+      assertTrue(list.contains("Protein common name".toLowerCase()));
+
+      list = searchService.getAutocompleteList(model, "m");
+      assertNotNull(list);
+      assertEquals(2, list.size());
+      assertTrue(list.contains("Molecule2".toLowerCase()));
+
+      list = searchService.getAutocompleteList(model, "blablabla");
+      assertNotNull(list);
+      assertEquals(0, list.size());
+
+      Configuration.setAutocompleteSize(oldVal);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testGetAutocompleList2() {
+    try {
+      Model model = new ModelFullIndexed(null);
+      GenericProtein proteinAlias = new GenericProtein("a1");
+      proteinAlias.setName("PROT identifier");
+      proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
+      model.addElement(proteinAlias);
+
+      SimpleMolecule alias = new SimpleMolecule("a2");
+      alias.setName("Molecule2");
+      model.addElement(alias);
+
+      List<String> list = searchService.getAutocompleteList(model, "PROT identifier");
+      assertNotNull(list);
+      assertEquals(1, list.size());
+      assertTrue(list.get(0).equalsIgnoreCase("PROT identifier"));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchGenericProtein() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/generic.xml", true);
+
+      List<String> list = searchService.getAutocompleteList(model, "generic");
+      assertNotNull(list);
+      assertEquals(2, list.size());
+      assertTrue(list.contains("generic"));
+      assertTrue(list.contains("generic protein"));
+
+      SearchElementResult result = searchService.searchByQuery(model, "generic protein", 10, false, null);
+      assertNotNull(result);
+
+      assertTrue(result.size() > 0);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchByCoordCompartment() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+      // we search in non-nested model
+      SearchElementResult res = searchService
+          .searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50));
+      assertNotNull(res);
+      assertEquals(0, res.size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchByCoordCompartment2() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+      Layout layout = new Layout();
+      layout.setHierarchicalView(true);
+      model.addLayout(layout);
+      // we search in nested model
+      SearchElementResult res = searchService
+          .searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50).layoutIdentifier(0));
+      assertNotNull(res);
+
+      assertTrue(res.get(0) instanceof FullAliasView);
+      FullAliasView view = (FullAliasView) res.get(0);
+      assertEquals("Compartment", view.getType());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchByCoordReaction() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+      // find compartment
+      SearchElementResult res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model));
+      // reaction is too far
+      assertEquals(0, res.size());
+
+      res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).distance(1000));
+      assertEquals(3, res.size());
+
+      assertTrue(res.get(0) instanceof FullReactionView);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchByCoordAlias() throws Exception {
+    try {
+      Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+      SearchElementResult res = searchService
+          .searchByCoordinates(new CoordinatesSearchParams().model(model).x(60).y(60));
+      assertNotNull(res);
+      assertTrue(res.size() > 0);
+
+      assertTrue(res.get(0) instanceof FullAliasView);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testGetMiriamTypeForQuery() throws Exception {
+    try {
+      MiriamData md = new SearchService().getMiriamTypeForQuery("hgnc:SNCA");
+      assertNotNull(md);
+      assertEquals(MiriamType.HGNC, md.getDataType());
+      assertEquals("SNCA", md.getResource());
+
+      md = new SearchService().getMiriamTypeForQuery("reactome:REACT_15128");
+      assertNotNull(md);
+      assertEquals(MiriamType.REACTOME, md.getDataType());
+      assertEquals("REACT_15128", md.getResource());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSearchByMiriamInSubmap() throws Exception {
+    try {
+      String query = "HGNC_SYMBOL:SNCA";
+      Model model = new ModelFullIndexed(null);
+      Model submodel = new ModelFullIndexed(null);
+      GenericProtein protein = new GenericProtein("s1");
+      protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+      submodel.addElement(protein);
+      model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
+
+      SearchElementResult result = searchService.searchByQuery(model, query, 50, null, "127.0.0.1");
+
+      assertEquals(1, result.getElements().size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testGetMiriamTypeForQuery2() throws Exception {
+    try {
+      MiriamData md = new SearchService().getMiriamTypeForQuery("UNKNOWN_HGNC:SNCA");
+      assertNull(md);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
 
 }