diff --git a/business/src/main/resources/applicationContext-business.xml b/business/src/main/resources/applicationContext-business.xml
index 23c881dea04..8e19f5b364c 100644
--- a/business/src/main/resources/applicationContext-business.xml
+++ b/business/src/main/resources/applicationContext-business.xml
@@ -17,6 +17,7 @@
             <property name="ignoreResourceNotFound" value="true" />
             <property name="locations">
               <list>
+                <value>classpath:/portal.properties</value>
                 <value>file:///${PORTAL_HOME}/src/main/resources/portal.properties</value>
               </list>
             </property>
diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java
index 097780f1e05..1503f3bccc8 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java
@@ -351,7 +351,6 @@ public static void addCancerStudy(CancerStudy cancerStudy, boolean overwrite) th
         }
 
         setImportDate(cancerStudy.getInternalId());
-        reCache();
     }
 
     /**
@@ -362,11 +361,6 @@ public static void addCancerStudy(CancerStudy cancerStudy, boolean overwrite) th
      */
     public static CancerStudy getCancerStudyByInternalId(int internalId) throws DaoException
 	{
-		if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && studyNeedsRecaching(null, internalId)) {
-                    System.out.print("Study with internal ID of "+internalId+" updated.");
-                    reCacheAll(System.currentTimeMillis());
-		}
         return byInternalId.get(internalId);
     }
 
@@ -378,11 +372,6 @@ && studyNeedsRecaching(null, internalId)) {
      */
     public static CancerStudy getCancerStudyByStableId(String stableId) throws DaoException
 	{
-		if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && studyNeedsRecaching(stableId)) {
-                    System.out.print("Study "+stableId+" updated.");
-                    reCacheAll(System.currentTimeMillis());
-		}
         return byStableId.get(stableId);
     }
 
@@ -393,11 +382,6 @@ && studyNeedsRecaching(stableId)) {
      * @return true if the CancerStudy exists, otherwise false
      */
     public static boolean doesCancerStudyExistByStableId(String cancerStudyStableId) {
-        if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && studyNeedsRecaching(cancerStudyStableId)) {
-            System.out.print("Study "+cancerStudyStableId+" updated.");
-            reCacheAll(System.currentTimeMillis());
-        }
         return byStableId.containsKey(cancerStudyStableId);
     }
 
@@ -409,11 +393,6 @@ && studyNeedsRecaching(cancerStudyStableId)) {
      * @return true if the CancerStudy exists, otherwise false
      */
     public static boolean doesCancerStudyExistByInternalId(int internalCancerStudyId) {
-        if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && studyNeedsRecaching(null, internalCancerStudyId)) {
-            System.out.print("Study with internal ID of "+internalCancerStudyId+" updated.");
-            reCacheAll(System.currentTimeMillis());
-        }
         return byInternalId.containsKey(internalCancerStudyId);
     }
 
@@ -423,11 +402,6 @@ && studyNeedsRecaching(null, internalCancerStudyId)) {
      * @return ArrayList of all CancerStudy Objects.
      */
     public static ArrayList<CancerStudy> getAllCancerStudies() {
-        if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && cacheOutOfSyncWithDb()) {
-            System.out.print("cache out of sync updated.");
-            reCacheAll(System.currentTimeMillis());
-        }
         return new ArrayList<CancerStudy>(byStableId.values());
     }
 
@@ -436,11 +410,6 @@ && cacheOutOfSyncWithDb()) {
      * @return number of cancer studies.
      */
     public static int getCount() {
-        if (GlobalProperties.getRecacheStudyAfterUpdate()
-                        && cacheOutOfSyncWithDb()) {
-            System.out.print("cache out of sync updated.");
-            reCacheAll(System.currentTimeMillis());
-        }
         return byStableId.size();
     }
 
@@ -554,7 +523,6 @@ static void deleteCancerStudy(int internalCancerStudyId) throws DaoException {
             JdbcUtil.closeAll(DaoCancerStudy.class, con, pstmt, rs);
         }
         System.out.print("delete a study "+internalCancerStudyId);
-        reCacheAll(System.currentTimeMillis());
     }
 
     /**
diff --git a/core/src/main/java/org/mskcc/cbio/portal/servlet/CancerStudyView.java b/core/src/main/java/org/mskcc/cbio/portal/servlet/CancerStudyView.java
index c777eb53af5..1032dfb0ab7 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/servlet/CancerStudyView.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/servlet/CancerStudyView.java
@@ -103,11 +103,6 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
     
     private boolean validate(HttpServletRequest request) throws DaoException {
         String cancerStudyID = request.getParameter(QueryBuilder.CANCER_STUDY_ID);
-
-		if (DaoCancerStudy.getStatus(cancerStudyID) == DaoCancerStudy.Status.UNAVAILABLE) {
-			request.setAttribute(ERROR, "The selected cancer study is currently being updated, please try back later.");
-			return false;
-		}
         
         CancerStudy cancerStudy = DaoCancerStudy
                 .getCancerStudyByStableId(cancerStudyID);
diff --git a/core/src/main/java/org/mskcc/cbio/portal/servlet/PatientView.java b/core/src/main/java/org/mskcc/cbio/portal/servlet/PatientView.java
index 048a3489a15..2249a3882c4 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/servlet/PatientView.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/servlet/PatientView.java
@@ -213,11 +213,6 @@ private boolean validate(HttpServletRequest request) throws DaoException {
             request.setAttribute(ERROR, "Please specify cancer study ID. ");
             return false;
         }
-
-		if (cancerStudyUpdating(cancerStudyId)) {
-			request.setAttribute(ERROR, "The selected cancer study is currently being updated, please try back later.");
-			return false;
-		}
         
         CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(cancerStudyId);
         if (cancerStudy==null) {
@@ -309,11 +304,6 @@ private boolean validate(HttpServletRequest request) throws DaoException {
         return true;
     }
 
-	private boolean cancerStudyUpdating(String cancerStudyId) throws DaoException
-	{
-		return (DaoCancerStudy.getStatus(cancerStudyId) == DaoCancerStudy.Status.UNAVAILABLE);
-	}
-    
     private void sortSampleIds(int cancerStudyId, int patientId, List<String> sampleIds) {
         if (sampleIds.size()==1) {
             return;
diff --git a/core/src/main/java/org/mskcc/cbio/portal/servlet/QueryBuilder.java b/core/src/main/java/org/mskcc/cbio/portal/servlet/QueryBuilder.java
index 541f49c3c73..0eb2214e6af 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/servlet/QueryBuilder.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/servlet/QueryBuilder.java
@@ -250,8 +250,6 @@ protected void doPost(HttpServletRequest httpServletRequest,
          
             httpServletRequest.setAttribute(XDEBUG_OBJECT, xdebug);
 
-			checkAndRedirectOnStudyStatus(httpServletRequest, httpServletResponse, cancerTypeId);
-
             boolean errorsExist = validateForm(action, profileList, geneticProfileIdSet, geneList,
                                                patientSetId, patientIds, httpServletRequest);
             if (action != null && action.equals(ACTION_SUBMIT) && (!errorsExist)) {
@@ -334,8 +332,6 @@ private void processData(String cancerStudyStableId,
 							 HttpServletResponse response,
 							 XDebug xdebug) throws IOException, ServletException, DaoException {
 
-        checkAndRedirectOnStudyStatus(request, response, cancerStudyStableId);
-
         // parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
         double zScore = ZScoreUtil.getZScore(geneticProfileIdSet, profileList, request);
         double rppaScore = ZScoreUtil.getRPPAScore(request);
@@ -551,13 +547,6 @@ private void outputPlainText(HttpServletResponse response, ProfileData mergedPro
         writer.close();
     }
 
-	private void checkAndRedirectOnStudyStatus(HttpServletRequest request, HttpServletResponse response, String cancerStudyId) throws ServletException, IOException, DaoException
-	{
-		if (DaoCancerStudy.getStatus(cancerStudyId) == DaoCancerStudy.Status.UNAVAILABLE) {
-			redirectStudyUnavailable(request, response);
-		}
-	}
-
 	private void redirectStudyUnavailable(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException
 	{
 		request.setAttribute(QueryBuilder.USER_ERROR_MESSAGE, "The selected cancer study is currently being updated, please try back later.");
@@ -695,4 +684,4 @@ private void forwardToErrorPage(HttpServletRequest request, HttpServletResponse
                 getServletContext().getRequestDispatcher("/WEB-INF/jsp/error.jsp");
         dispatcher.forward(request, response);
     }
-}
\ No newline at end of file
+}
diff --git a/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/clinical_timeline.jsp b/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/clinical_timeline.jsp
index cfd573e56fa..f32d6cc41aa 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/clinical_timeline.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/clinical_timeline.jsp
@@ -73,15 +73,18 @@
         for (var i=0; i<caseIds.length; i++) {
             var caseId = caseIds[i];
             var clinicalData = clinicalDataMap[caseId];
+            var compareAgainstIds = [caseId];
             var OtherSampleId = guessClinicalData(clinicalData,["OTHER_SAMPLE_ID"]);
-            if (!OtherSampleId) OtherSampleId = caseId;
+            if (OtherSampleId) {
+                compareAgainstIds = compareAgainstIds.concat(OtherSampleId);
+            }
             var circle = d3.selectAll(".timelineSeries_0").filter(function (x) {
                 if (x.tooltip_tables.length === 1) {
                     var specRefNum = x.tooltip_tables[0].filter(function(x) {
                         return x[0] === "SpecimenReferenceNumber" || x[0] === "SPECIMEN_REFERENCE_NUMBER";
                     })[0];
                     if (specRefNum) {
-                        return specRefNum[1] === OtherSampleId;
+                        return compareAgainstIds.indexOf(specRefNum[1]) !== -1;
                     }
                 }
                 return undefined;
diff --git a/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp b/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp
index 077067aeb57..70ab21f4298 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp
@@ -457,14 +457,14 @@ function initTabs() {
 
 function fixCytoscapeWebRedraw() {
     // to initially hide the network tab
-    $("#pathways").attr('style', 'display: none !important; height: 0px; width: 0px; visibility: hidden;');
+    $("#tab_pathways").attr('style', 'display: none !important; height: 0px; width: 0px; visibility: hidden;');
 
     // to fix problem of flash repainting
     $("a.patient-tab").click(function(){
-        if($(this).attr("href")==="#pathways") {
-            $("#pathways").removeAttr('style');
+        if($(this).attr("href")==="#tab_pathways") {
+            $("#tab_pathways").removeAttr('style');
         } else {
-            $("#pathways").attr('style', 'display: block !important; height: 0px; width: 0px; visibility: hidden;');
+            $("#tab_pathways").attr('style', 'display: block !important; height: 0px; width: 0px; visibility: hidden;');
         }
     });
 }
@@ -475,7 +475,7 @@ function switchToTab(toTab) {
     $('#patient-tabs').tabs("option",
 		"active",
 		$('#patient-tabs ul a[href="#'+toTab+'"]').parent().index());
-    if (toTab==='images') {
+    if (toTab==='tab_images') {
         loadImages();
     }
 }
diff --git a/portal/src/main/webapp/js/src/study-view/data/StudyViewProxy.js b/portal/src/main/webapp/js/src/study-view/data/StudyViewProxy.js
index d5b01bac962..d3d8b322219 100644
--- a/portal/src/main/webapp/js/src/study-view/data/StudyViewProxy.js
+++ b/portal/src/main/webapp/js/src/study-view/data/StudyViewProxy.js
@@ -153,6 +153,8 @@ var StudyViewProxy = (function() {
                     _dataLength = _data.length,
                     _sampleIds = Object.keys(sampleToPatientMapping),
                     _sequencedSampleIds = [],
+                    _cnaSampleIds = [],
+                    _allSampleIds = [],
                     _locks=0;
 
                 //Keep original data format.
@@ -219,17 +221,26 @@ var StudyViewProxy = (function() {
                 var filteredA3 = removeExtraData(_sampleIds,a3[0]);
 
                 //Find sequenced sample Ids
+                // TODO: this is very hacky, we should switch to the cbioportal-client.js
                 if(a5[0]) {
                     var _lists = a5[0].split('\n');
                     for(var i = 0; i < _lists.length; i++) {
-                        if(_lists[i].indexOf('sequenced samples') !== -1) {
-                            var _info = _lists[i].split('\t');
-                            if(_info.length === 5) {
-                                _sequencedSampleIds = _info[4].split(' ');
-                            }
-                            break;
+                        var _parts = _lists[i].split('\t');
+                        if(_parts.length < 5) continue;
+                        if (_parts[0] === parObject.studyId+"_sequenced") {
+                            _sequencedSampleIds = _parts[4].split(' ');
+                        } else if (_parts[0] === parObject.studyId+"_cna") {
+                            _cnaSampleIds = _parts[4].split(' ');
+                        } else if (_parts[0] === parObject.studyId+"_all") {
+                            _allSampleIds = _parts[4].split(' ');
                         }
                     }
+                    
+                    obtainDataObject.sequencedSampleIds = 
+                            _sequencedSampleIds.length>0 ? _sequencedSampleIds : _allSampleIds;
+                    obtainDataObject.cnaSampleIds = 
+                            _cnaSampleIds.length>0 ? _cnaSampleIds : _allSampleIds;
+                    
                 }
 
                 //Add new attribute MUTATION COUNT for each case if have any
@@ -616,6 +627,8 @@ var StudyViewProxy = (function() {
         getSampleidToPatientidMap: function(){return obtainDataObject.sampleidToPatientidMap;},
         getPatientIdsBySampleIds: getPatientIdsBySampleIds,
         getSampleIdsByPatientIds: getSampleIdsByPatientIds,
+        getSequencedSampleIds: function() {return obtainDataObject.sequencedSampleIds;},
+        getCnaSampleIds: function() {return obtainDataObject.cnaSampleIds;},
         getPatientIds: function () {
             return Object.keys(patientToSampleMapping);
         },
diff --git a/portal/src/main/webapp/js/src/study-view/view/StudyViewInitCharts.js b/portal/src/main/webapp/js/src/study-view/view/StudyViewInitCharts.js
index aa40bde93d5..271b42b2296 100644
--- a/portal/src/main/webapp/js/src/study-view/view/StudyViewInitCharts.js
+++ b/portal/src/main/webapp/js/src/study-view/view/StudyViewInitCharts.js
@@ -303,20 +303,24 @@ var StudyViewInitCharts = (function(){
     }
 
     function initTables() {
-        var initParams = {data: {attr: [], arr: {}}, numOfCases: numOfCases};
+        var initParams = {data: {attr: [], arr: {}}, numberOfSamples: {}};
 
         if(hasMutation) {
+            var numberOfSequencedSamples = StudyViewProxy.getSequencedSampleIds().length;
             initParams.data.attr.push({
                     name: 'mutatedGenes',
-                    displayName: 'Mutated Genes'
+                    displayName: 'Mutated Genes (<span id="number-of-selected-sequenced-samples">'+numberOfSequencedSamples+'</span> profiled samples)'
                 });
+            initParams.numberOfSamples.numberOfSequencedSamples = numberOfSequencedSamples;
         }
 
         if(hasCNA) {
+            var numberOfCnaSamples = StudyViewProxy.getCnaSampleIds().length;
             initParams.data.attr.push({
                     name: 'cna',
-                    displayName: 'Copy Number Altered Genes'
+                    displayName: 'CNA Genes (<span id="number-of-selected-cna-samples">'+numberOfCnaSamples+'</span> profiled samples)'
                 });
+            initParams.numberOfSamples.numberOfCnaSamples = numberOfCnaSamples;
         }
 
         StudyViewInitTables.init(initParams);
diff --git a/portal/src/main/webapp/js/src/study-view/view/StudyViewInitTables.js b/portal/src/main/webapp/js/src/study-view/view/StudyViewInitTables.js
index f4f80351b4d..f849b4b0c50 100644
--- a/portal/src/main/webapp/js/src/study-view/view/StudyViewInitTables.js
+++ b/portal/src/main/webapp/js/src/study-view/view/StudyViewInitTables.js
@@ -85,10 +85,10 @@ var StudyViewInitTables = (function() {
                     _worker.data.getData = function (callback, workerId){
                         StudyViewProxy.getMutatedGenesData().then(
                             function( data ) {
-                                callback(mutatedGenesData(data, numOfCases), workerId);
+                                callback(mutatedGenesData(data, input.numberOfSamples.numberOfSequencedSamples), workerId);
                             },
                             function( status ) {
-                                callback(mutatedGenesData(null, numOfCases), workerId);
+                                callback(mutatedGenesData(null, input.numberOfSamples.numberOfSequencedSamples), workerId);
                                 console.log( status + ", you fail this time" );
                             },
                             function( status ) {
@@ -131,10 +131,10 @@ var StudyViewInitTables = (function() {
                     _worker.data.getData = function (callback, workerId){
                         StudyViewProxy.getCNAData().then(
                             function( data ) {
-                                callback(cnaData(data, numOfCases), workerId);
+                                callback(cnaData(data, input.numberOfSamples.numberOfCnaSamples), workerId);
                             },
                             function( status ) {
-                                callback(cnaData(null, numOfCases), workerId);
+                                callback(cnaData(null, input.numberOfSamples.numberOfCnaSamples), workerId);
                                 console.log( status + ", you fail this time" );
                             },
                             function( status ) {
@@ -356,6 +356,7 @@ var StudyViewInitTables = (function() {
         var genes = [];
 
         if(data) {
+            $('#number-of-selected-sequenced-samples').html(numOfCases);
             for(var i = 0, dataL = data.length; i < dataL; i++){
                 var datum = {},
                     caseIds = data[i].caseIds;
@@ -390,6 +391,7 @@ var StudyViewInitTables = (function() {
         var genes = [];
 
         if(data) {
+            $('#number-of-selected-cna-samples').html(numOfCases);
             for(var i = 0, dataL = data.gene.length; i < dataL; i++){
                 var datum = {},
                     _altType = '';
@@ -444,10 +446,12 @@ var StudyViewInitTables = (function() {
                 if (numSelectedCasesL.length !== 0) {
                     switch (worker.opts.name) {
                         case 'mutatedGenes':
-                            worker.data.arr = mutatedGenesData(StudyViewProxy.getMutatedGeneDataBasedOnSampleIds(data.selectedCases), numSelectedCasesL);
+                            var selectedSequencedSamples = _.intersection(StudyViewProxy.getSequencedSampleIds(), data.selectedCases);
+                            worker.data.arr = mutatedGenesData(StudyViewProxy.getMutatedGeneDataBasedOnSampleIds(data.selectedCases), selectedSequencedSamples.length);
                             break;
                         case 'cna':
-                            worker.data.arr = cnaData(StudyViewProxy.getCNABasedOnSampleIds(data.selectedCases), numSelectedCasesL);
+                            var selectedCnaSamples = _.intersection(StudyViewProxy.getCnaSampleIds(), data.selectedCases);
+                            worker.data.arr = cnaData(StudyViewProxy.getCNABasedOnSampleIds(data.selectedCases), selectedCnaSamples.length);
                             break;
                         default:
                             break;