An Error Occurred:

factory method with defined scope outjected a value: projectInfoItem

+ Stack Trace

java.lang.IllegalArgumentException: factory method with defined scope outjected a value: projectInfoItem
	at org.jboss.seam.Component.handleFactoryMethodResult(Component.java:2070)
	at org.jboss.seam.Component.getInstanceFromFactory(Component.java:2044)
	at org.jboss.seam.Component.getInstance(Component.java:1978)
	at org.jboss.seam.Component.getInstance(Component.java:1950)
	at org.jboss.seam.Component.getInstance(Component.java:1944)
	at org.jboss.seam.Namespace.getComponentInstance(Namespace.java:55)
	at org.jboss.seam.Namespace.getComponentInstance(Namespace.java:50)
	at org.jboss.seam.el.SeamELResolver.resolveBase(SeamELResolver.java:166)
	at org.jboss.seam.el.SeamELResolver.getValue(SeamELResolver.java:53)
	at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:54)
	at com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:64)
	at org.jboss.el.parser.AstIdentifier.getValue(AstIdentifier.java:44)
	at org.jboss.el.parser.AstValue.getValue(AstValue.java:63)
	at org.jboss.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
	at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
	at javax.faces.component.UIOutput.getValue(UIOutput.java:173)
	at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getValue(HtmlBasicInputRenderer.java:189)
	at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.getCurrentValue(HtmlBasicRenderer.java:320)
	at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.encodeEnd(HtmlBasicRenderer.java:200)
	at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:833)
	at javax.faces.component.UIComponent.encodeAll(UIComponent.java:896)
	at javax.faces.component.UIComponent.encodeAll(UIComponent.java:892)
	at com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:578)
	at org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100)
	at org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176)
	at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:106)
	at com.sun.faces.lifecycle.LifecycleImpl.phase(LifecycleImpl.java:251)
	at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:144)
	at javax.faces.webapp.FacesServlet.service(FacesServlet.java:245)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:436)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302)
	at org.tuckey.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:83)
	at org.jboss.seam.web.IdentityFilter.doFilter(IdentityFilter.java:40)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:73)
	at org.jboss.seam.web.ExceptionFilter.doFilter(ExceptionFilter.java:64)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at org.jboss.seam.web.RedirectFilter.doFilter(RedirectFilter.java:45)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:73)
	at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:178)
	at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:290)
	at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:388)
	at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:515)
	at org.jboss.seam.web.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:56)
	at edu.mit.broad.components.Ajax4jsfFilter.doFilter(Ajax4jsfFilter.java:31)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at edu.mit.broad.logging.LoggingFilter.doFilter(LoggingFilter.java:28)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at org.jboss.seam.web.LoggingFilter.doFilter(LoggingFilter.java:58)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at edu.mit.broad.jsf.servlet.DownloadFilter.doFilter(DownloadFilter.java:364)
	at org.jboss.seam.servlet.SeamFilter$FilterChainImpl.doFilter(SeamFilter.java:69)
	at org.jboss.seam.servlet.SeamFilter.doFilter(SeamFilter.java:158)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
	at com.googlecode.psiprobe.Tomcat60AgentValve.invoke(Tomcat60AgentValve.java:30)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:555)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:852)
	at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
	at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:396)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:619)

+ Component Tree

<AjaxViewRoot id="_viewRoot" immediate="false" locale="en_US" renderKitId="HTML_BASIC" renderRegionOnly="false" rendered="true" selfRendered="false" submitted="false" transient="false" viewId="/pages/home.xhtml">
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" >
<html xmlns="http://www.w3.org/1999/xhtml">
<head profile="http://www.w3.org/2005/10/profile"> <meta http-equiv="X-UA-Compatible" content="IE=EmulateIE8"/> <meta name="robots" content="noindex, nofollow, noarchive, nosnippet"/> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <title>
<HtmlOutputText escape="true" id="j_id3" rendered="true" transient="false" value="TCGA Copy Number Portal"/>
</title>
<Stylesheet filtered="false" id="j_id5" inline="false" path="/brandable/css/jquery.dataTables.css" rendered="true" transient="false"/>
<Stylesheet filtered="false" id="j_id6" inline="false" path="/brandable/css/jquery-ui.css" rendered="true" transient="false"/>
<Stylesheet filtered="false" id="j_id7" inline="false" path="/brandable/css/portal_style.css" rendered="true" transient="false"/>
<Stylesheet filtered="false" id="j_id8" inline="false" path="/brandable/css/portal_custom.css" rendered="true" transient="false"/>
<Stylesheet filtered="false" id="j_id9" inline="false" path="/brandable/css/component.css" rendered="true" transient="false"/>
<Stylesheet filtered="false" id="j_id10" inline="false" path="/brandable/css/component_custom.css" rendered="true" transient="false"/>
<link rel="shortcut icon" href="#{facesContext.externalContext.requestContextPath}/brandable/images/favicon.ico" type="image/ico"/> <link rel="icon" href="#{facesContext.externalContext.requestContextPath}/brandable/images/favicon.ico" type="image/png"/> <script src="#{facesContext.externalContext.requestContextPath}/js/prototypeLoader.js" type="text/javascript" charset="utf-8"/> <script type="text/javascript" charset="utf-8">loadPrototype("#{facesContext.externalContext.requestContextPath}/js/prototype.js");</script>
<script src="#{facesContext.externalContext.requestContextPath}/js/utilities.js" type="text/javascript" charset="utf-8"/>
</head>
<body> <div id="BG">
<div id="Header" style="margin-top: 0px;">
<HtmlLink action=" disabled="false" id="HeaderLeft" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" view="/pages/home.xhtml">
<div id="HeaderLeftText"> <b>
<HtmlOutputText escape="false" id="j_id17" rendered="true" transient="false" value="TCGA Copy Number Portal"/>
</b> </div>
</HtmlLink>
<div id="HeaderRight">
<HtmlDiv id="logIn" rendered="true" transient="false">
<HtmlForm enctype="application/x-www-form-urlencoded" id="j_id20" prependId="true" rendered="true" submitted="false" transient="false">
<table cellpadding="3" cellspacing="0" border="0"> <tr> <td align="right" style="white-space:nowrap;">
<HtmlOutputLabel escape="true" id="j_id22" rendered="true" transient="false" value="Username "/>
<HtmlInputText disabled="false" id="j_id23" immediate="false" label="Username" localValueSet="false" maxlength="25" readonly="false" rendered="true" required="true" size="8" style="font-family:Arial;" styleClass="logIn" transient="false" valid="true"/>
<br/>
<HtmlOutputLabel escape="true" id="j_id25" rendered="true" transient="false" value="Password "/>
<HtmlInputSecret disabled="false" id="j_id26" immediate="false" label="Password" localValueSet="false" maxlength="25" readonly="false" redisplay="false" rendered="true" required="true" size="8" style="font-family:Arial;" styleClass="logIn" transient="false" valid="true"/>
</td> <td>
<HtmlCommandButton action="#{identity.login}" actionExpression="#{identity.login}" disabled="false" id="j_id28" image="/brandable/images/sign_in.gif" immediate="false" readonly="false" rendered="true" transient="false" type="submit"/>
<br/>
<HtmlLink action="/pages/forgotPassword.xhtml" actionExpression="/pages/forgotPassword.xhtml" disabled="false" id="forgotButton" immediate="false" includePageParams="true" propagation="none" rendered="true" style="line-height:12px;font-size: 11px;" transient="false">
Forgot<br/>Password?
</HtmlLink>
</td> </tr> <tr> <td colspan="2" class="regInfo">
<HtmlLink action=" disabled="false" id="j_id32" immediate="false" includePageParams="true" propagation="default" rendered="true" style="font-size: 11px;" transient="false" value="Register" view="/pages/register.xhtml"/>
   
<HtmlLink action=" disabled="false" id="j_id34" immediate="false" includePageParams="true" propagation="default" rendered="true" style="font-size: 11px;" transient="false" value="Why Register?" view="/pages/whyregister.xhtml"/>
<a href="#"/></td> </tr> </table>
</HtmlForm>
</HtmlDiv>
<HtmlDiv id="logOut" rendered="false" transient="false">
<div id="userName">
<HtmlOutputText escape="true" id="j_id37" rendered="true" transient="false"/>
</div> <div id="signOut">
<HtmlLink action="#{identity.logout}" actionExpression="#{identity.logout}" disabled="false" id="j_id39" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false"/>
</div>
<HtmlAjaxRegion id="pollingRegion" immediate="false" renderRegionOnly="false" rendered="true" selfRendered="false" submitted="false" transient="false">
<HtmlForm enctype="application/x-www-form-urlencoded" id="j_id41" prependId="true" rendered="true" submitted="false" transient="false">
<AjaxPoll ajaxSingle="false" bypassUpdates="false" enabled="false" eventsQueue="myShelfPoll" id="poll" ignoreDupResponses="true" immediate="true" interval="4000" limitToList="false" rendered="true" requestDelay="-2147483648" submitted="false" timeout="-2147483648" transient="false"/>
</HtmlForm>
</HtmlAjaxRegion>
<HtmlDiv id="myShelfDataWrap" rendered="true" transient="false">
<div id="myShelfData">
<HtmlLink action="/pages/myShelf.xhtml" actionExpression="/pages/myShelf.xhtml" disabled="false" id="myShelfDataLink" immediate="false" includePageParams="true" propagation="begin" rendered="true" styleClass="myShelfData" transient="false"/>
<div id="#{(activeAnalysesForUserOnUserShelf.size()>0) ? 'myShelfStatusRun' : 'myShelfStatusComplete'}"> <div id="myShelfStatus1">#{(activeAnalysesForUserOnUserShelf.size()>0) ? activeAnalysesForUserOnUserShelf.size() : '  '}</div> <div id="myShelfStatus2">#{(analysesForUserOnUserShelf.size()>0) ? analysesForUserOnUserShelf.size() : '  '}</div> </div> </div>
</HtmlDiv>
</HtmlDiv>
</div> </div> <div id="Navigation"> <div id="History"> <div id="HistoryText"> </div> </div> <div id="spacer"> </div>
<div id="SubMenuContainer"> <div id="DataSubMenu" onmouseover="changeText("data","BROWSE▼"); showdiv("DataSubMenu"); hidediv("HelpSubMenu")" onmouseout="changeText("data","BROWSE▲"); hidediv("DataSubMenu")"> <div>
<HtmlLink action=" disabled="false" id="download" immediate="false" includePageParams="true" propagation="begin" rendered="true" styleClass="SubCell" transient="false" value="DATA" view="/pages/data/browseData.xhtml"/>
</div> <div>
<HtmlPanelGroup id="j_id47" rendered="false" transient="false">
<HtmlLink action=" disabled="false" id="projects" immediate="false" includePageParams="true" propagation="none" rendered="true" styleClass="SubCell" transient="false" value="PROJECTS" view="/pages/projects/browseProjects.xhtml"/>
</HtmlPanelGroup>
</div> <div>
<HtmlLink action="#{browseSamplesBean.checkSkipFirstStep()}" actionExpression="#{browseSamplesBean.checkSkipFirstStep()}" disabled="false" id="samples" immediate="false" includePageParams="true" propagation="begin" rendered="true" styleClass="SubCell" transient="false" value="SAMPLES" view="/pages/data/browseSamples.xhtml"/>
</div> <div>
<HtmlLink action=" disabled="false" id="j_id50" immediate="false" includePageParams="true" propagation="default" rendered="false" styleClass="SubCell" transient="false" value="MUTATIONS" view="/pages/data/mutationTagcloud.xhtml"/>
</div> <div>
<HtmlPanelGroup id="j_id52" rendered="false" transient="false">
<HtmlLink action=" disabled="false" id="videos" immediate="false" includePageParams="true" propagation="begin" rendered="true" styleClass="SubCell" transient="false" value="VIDEOS" view="/pages/videos/browseVideos.xhtml"/>
</HtmlPanelGroup>
</div> <div>
<HtmlLink action=" disabled="false" id="tcgaData" immediate="false" includePageParams="true" propagation="begin" rendered="false" styleClass="SubCell" transient="false" value="TCGA DATA" view="/pages/tap/browseTcgaData.xhtml"/>
</div> </div>
<HtmlOutputText escape="true" id="j_id55" rendered="false" transient="false">
<div id="SubMenuSpacer" onmouseover="changeText("help","HELP▼"); showdiv("SubMenuSpacer"); hidediv("DataSubMenu")" onmouseout="changeText("help","HELP▲"); hidediv("SubMenuSpacer")"> <div id="analyses">
<HtmlLink action=" disabled="false" id="j_id57" immediate="false" includePageParams="true" propagation="default" rendered="true" styleClass="SubCell" transient="false" view="/pages/data/browseAnalyses.xhtml">
<UIParameter id="j_id58" name="linkDetail" rendered="true" transient="false" value="index.html"/>
docs
</HtmlLink>
</div> </div>
</HtmlOutputText>
<div id="HelpSubMenu" onmouseover="changeText("help","HELP▼"); showdiv("HelpSubMenu"); hidediv("DataSubMenu")" onmouseout="changeText("help","HELP▲"); hidediv("HelpSubMenu")"> <div id="current">
<HtmlLink action="#{serverBean.resetDocumentationURL}" actionExpression="#{serverBean.resetDocumentationURL}" disabled="false" id="j_id62" immediate="false" includePageParams="true" propagation="default" rendered="true" styleClass="SubCell" transient="false" view="/pages/support/documents.xhtml">
<UIParameter id="j_id63" name="linkDetail" rendered="true" transient="false" value="index.html"/>
DOCUMENTS
</HtmlLink>
</div> <div id="current">
<HtmlLink action=" disabled="false" id="j_id66" immediate="false" includePageParams="true" propagation="default" rendered="true" styleClass="SubCell" transient="false" value="CONTACT US" view="/pages/support/esupport.xhtml"/>
</div> </div> </div> <div id="MainMenuContainer"> <div class="MainMenu">
<HtmlLink action=" disabled="false" id="home" immediate="false" includePageParams="true" propagation="none" rendered="true" styleClass="MainCellOn" transient="false" value="HOME" view="/pages/home.xhtml"/>
</div>
<ComponentRef id="j_id69" rendered="false" transient="false">
<div id="dataDiv" class="MainMenu" onmouseover="changeText("data","BROWSE▼"); showdiv("DataSubMenu"); hidediv("HelpSubMenu")" onmouseout="changeText("data","BROWSE▲"); hidediv("DataSubMenu")"><a href="#" id="data" class="#{(uiBean.tabOn('browseData')) or (uiBean.tabOn('browseSamples')) ?'MainCellOn':'MainCell'}">BROWSE▲</a></div>
</ComponentRef>
<div class="MainMenu">
<HtmlLink action=" disabled="false" id="analyses" immediate="false" includePageParams="true" propagation="none" rendered="false" styleClass="MainCell" transient="false" value="ANALYSIS TOOLS" view="/pages/data/browseAnalyses.xhtml"/>
</div> <div id="helpDiv" class="MainMenu" onmouseover="changeText("help","HELP▼"); showdiv("HelpSubMenu"); hidediv("DataSubMenu")" onmouseout="changeText("help","HELP▲"); hidediv("HelpSubMenu")"><a href="#" id="help" class="#{uiBean.tabOn('support')?'MainCellOn':'MainCell'}">HELP▲</a></div> <div class="MainMenu">
<HtmlLink action=" disabled="false" id="resources" immediate="false" includePageParams="true" propagation="none" rendered="false" styleClass="MainCell" transient="false" value="RESOURCES" view="/pages/resources.xhtml"/>
</div> <div class="MainMenu">
<HtmlLink action=" disabled="false" id="about" immediate="false" includePageParams="true" propagation="none" rendered="true" styleClass="MainCell" transient="false" value="ABOUT" view="/pages/about.xhtml"/>
</div> <div class="MainMenu">
<HtmlPanelGroup id="j_id75" rendered="false" transient="false">
<HtmlLink action=" disabled="false" id="curator" immediate="false" includePageParams="true" propagation="none" rendered="true" styleClass="MainCell" transient="false" value="CURATOR" view="/pages/curator/home.xhtml"/>
</HtmlPanelGroup>
</div> <div class="MainMenu">
<HtmlPanelGroup id="j_id77" rendered="false" transient="false">
<HtmlLink action=" disabled="false" id="admin" immediate="false" includePageParams="true" propagation="none" rendered="true" styleClass="MainCell" transient="false" value="ADMIN" view="/pages/admin/home.xhtml"/>
</HtmlPanelGroup>
</div> </div>
<div id="SimpleSearch">
<HtmlForm enctype="application/x-www-form-urlencoded" id="j_id80" prependId="true" rendered="true" submitted="false" transient="false">
<HtmlOutputText escape="true" id="j_id81" rendered="false" transient="false">
<HtmlCommandButton action="#{searchAction.search}" actionExpression="#{searchAction.search}" disabled="false" id="j_id82" image="/brandable/images/searchBtn.gif" immediate="false" readonly="false" rendered="true" transient="false" type="submit"/>
<HtmlInputText disabled="false" id="searchText" immediate="false" localValueSet="false" maxlength="-2147483648" readonly="false" rendered="true" required="false" size="-2147483648" transient="false" valid="true"/>
</HtmlOutputText>
</HtmlForm>
</div> </div>
<div id="Content"> <div id="HomeTop"> <table width="100%" border="0" cellpadding="0" cellspacing="0"> <tr> <td width="40px" class="HomeTopLeft"/> <td class="HomeTopCenter">
</td> <td width="40px" class="HomeTopRight"/> </tr> </table> </div> <div id="ContentMiddle"> <table width="100%" border="0" cellpadding="0" cellspacing="0"> <tr/> <tr> <td bgcolor="#ffffff" colSpan="3" align="#{identity.loggedIn?'left':'center'}">
<HtmlMessages errorStyle="font-weight:bold; color:red;" globalOnly="true" id="j_id86" layout="table" rendered="true" showDetail="false" showSummary="true" styleClass="Warning" tooltip="false" transient="false"/>
</td> </tr> <tr> <td bgcolor="#eeeeee">
<table class="white" style="padding-top: 20px;" width="100%"> <tr> <td style="padding-left: 20px;" valign="top"> <h2 class="front">
<HtmlOutputText escape="false" id="j_id89" rendered="true" transient="false" value="TCGA Copy Number Portal (TCGA)"/>
</h2> <p>
<HtmlGraphicImage id="j_id91" ismap="false" rendered="true" styleClass="homeSplash" transient="false" url="/brandable/images/HomeSplash.jpg" value="/brandable/images/HomeSplash.jpg"/>
<HtmlOutputText escape="false" id="j_id92" rendered="true" transient="false" value="<p> This portal is designed to facilitate the use and understanding of high resolution copy number data amassed from cancer samples in the <a href='http://cancergenome.nih.gov/'>TCGA</a>. All data in this portal were generated at the <a href='http://www.broadinstitute.org/collaboration/gcc/'>Broad Institute TCGA Genome Characterization Center</a>. This portal is modeled after <a href='http://www.broadinstitute.org/tumorscape/'>Tumorscape</a> which contains copy number data from non-TCGA projects (<a href='http://www.nature.com/nature/journal/v463/n7283/full/nature08822.html'>Beroukhim et al., 2010</a>). </p> "/>
</p> <br/> <p>
<HtmlOutputText escape="false" id="j_id94" rendered="true" transient="false" value=""/>
</p>
<HtmlOutputText escape="true" id="j_id96" rendered="true" transient="false">
<table class="white" width="100%"> <tr> <td> <h2 class="frontSmall">Gene-Centric GISTIC Analyses</h2> </td> </tr> <tr> <td> <p>Genes (including miRNAs) can be individually queried by Gene Symbol here. The available data include:</p> <p> <ol> <li>A summary statement of the significance of copy number alterations affecting that gene or transcript.</li> <li>For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that gene across the entire dataset and within cancer types that are well-represented in the dataset. </li> <li>Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.</li> </ol> </p> <p>
<HtmlLink action=" disabled="false" id="j_id98" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="More details on available analyses" view="/pages/gistic/browseGisticAnalyses.xhtml"/>
    
<HtmlLink action=" disabled="false" id="j_id100" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="More details on gene-centric analyses" view="/pages/gistic/browseGisticData.xhtml#geneCentric"/>
<UIParameter id="j_id101" name="mode" rendered="true" transient="false" value="brandedFeatureSearch"/>
    
<HtmlLink action=" disabled="false" id="j_id103" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="Explore data by gene now" view="/pages/gistic/browseGisticByGene.xhtml"/>
<UIParameter id="j_id104" name="mode" rendered="true" transient="false" value="brandedFeatureSearch"/>
</p> <br/> </td> </tr> <tr> <td> <h2 class="frontSmall">Cancer-Centric GISTIC Analyses</h2> </td> </tr> <tr> <td> <p>Cancer types can be individually queried here. The available data include:</p> <ol> <li>A summary statement of the number of specimens analyzed.</li> <li>For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that cancer type. The significantly aberrant peak regions of the genome are listed. </li> <li>Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.</li> </ol> <p>
<HtmlLink action=" disabled="false" id="j_id106" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="More details on available analyses" view="/pages/gistic/browseGisticAnalyses.xhtml"/>
    
<HtmlLink action=" disabled="false" id="j_id108" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="More details on cancer-centric analyses" view="/pages/gistic/browseGisticData.xhtml#cancerCentric"/>
<UIParameter id="j_id109" name="mode" rendered="true" transient="false" value="brandedFeatureSearch"/>
    
<HtmlLink action=" disabled="false" id="j_id111" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" value="Explore data by cancer type now" view="/pages/gistic/browseGisticByTissue.xhtml"/>
</p> </td> </tr> </table>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id113" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <br/>
<HtmlForm enctype="application/x-www-form-urlencoded" id="j_id115" prependId="true" rendered="true" submitted="false" transient="false">
<div id="Content"> <table width="100%" valign="top"> <tr><td><h2 class="frontSmall">My Studies
<HtmlLink action="#{experimentUploadWizardSelector.startOnePageWizard()}" actionExpression="#{experimentUploadWizardSelector.startOnePageWizard()}" disabled="false" id="createNewStudyButton" immediate="false" includePageParams="true" propagation="default" rendered="false" style="display:block; float :right; font-size: 8pt; padding-right: 5px; padding-top: 3px;" transient="false" type="submit" value="Create new Study"/>
</h2></td></tr> </table> <div style="padding-left: 20px;"> <table width="100%" valign="top" cellspacing="0"> <tr><td/><td> <div class="studies" style="height: 250px;"> <div style="margin-right: 1px;margin-top: 10px; height: 230px; overflow: auto;"> <table width="100%" valign="top" cellspacing="0">
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@13836c80" first="0" id="j_id118" rendered="true" rowIndex="0" rows="0" transient="false" var="anExp">
<tr> <td><p><b>
<HtmlLink action="#{viewExperimentBean.prepareForViewing}" actionExpression="#{viewExperimentBean.prepareForViewing}" disabled="false" id="j_id120" immediate="false" includePageParams="true" propagation="none" rendered="true" title="Project: " transient="false" view="/pages/data/view/exploreExperiment.xhtml">
<UIParameter id="j_id121" name="selectedDatasetId" rendered="true" transient="false"/>
<UIParameter id="j_id122" name="selectedExperimentId" rendered="true" transient="false"/>
</HtmlLink>
</b>
<HtmlOutputText escape="true" id="j_id124" rendered="true" transient="false">
:  
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@53477b21" first="0" id="j_id126" rendered="true" rowIndex="0" rowKeyVar="dsRKkey" rows="0" transient="false" var="ds">
<HtmlOutputText escape="true" id="j_id127" rendered="false" transient="false" value="("/>
#{ds.type.name}
<HtmlOutputText escape="true" id="j_id129" rendered="true" transient="false" value=", "/>
<HtmlOutputText escape="true" id="j_id130" rendered="false" transient="false" value=")."/>
</HtmlAjaxRepeat>
</HtmlOutputText>
<br/>
<HtmlOutputText escape="true" id="j_id132" rendered="true" transient="false">
No experiment description provided.
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id134" rendered="false" transient="false">
#{anExp.description}.
</HtmlOutputText>
</p> </td></tr>
</HtmlAjaxRepeat>
</table> </div> </div> </td> </tr> </table> </div> </div>
</HtmlForm>
</HtmlOutputText>
<br/> <table width="100%"> <tr> <td width="49%" valign="top">
<HtmlOutputText escape="true" id="j_id139" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <h2 class="frontSmall">Tutorials / Manuals</h2> <p>
<HtmlGraphicImage id="j_id141" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/manual.png" value="/brandable/images/manual.png"/>
Tutorials, analysis descriptions and other documentation is available at: <br/>
<HtmlLink action="#{serverBean.resetDocumentationURL}" actionExpression="#{serverBean.resetDocumentationURL}" disabled="false" id="j_id143" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/support/documents.xhtml">
<UIParameter id="j_id144" name="linkDetail" rendered="true" transient="false" value="index.html"/>
HELP > DOCUMENTS
</HtmlLink>
</p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id147" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id149" rendered="true" transient="false">
<h2 class="frontSmall">News / Events</h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@3206ee33" first="0" id="j_id151" rendered="true" rowIndex="0" rowKeyVar="index" rows="7" transient="false" var="aNewsItem">
<HtmlOutputText escape="true" id="j_id152" rendered="false" transient="false">
<p>
<HtmlOutputText escape="false" id="j_id154" rendered="false" transient="false">
<HtmlGraphicImage id="j_id155" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/news.png" value="/brandable/images/news.png"/>
</HtmlOutputText>
<b>
<HtmlOutputText escape="true" id="j_id157" rendered="true" transient="false"/>
</b>: 
<HtmlOutputText escape="false" id="j_id159" rendered="true" transient="false"/>
 
<HtmlOutputText escape="true" id="j_id161" rendered="false" transient="false">
<a href="#{aNewsItem.moreInfoURL}">more...</a>
</HtmlOutputText>
</p>
</HtmlOutputText>
</HtmlAjaxRepeat>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id164" rendered="false" transient="false">
<h2 class="frontSmall">News / Events</h2> <a class="twitter-timeline" data-widget-id="#{serverBean.getTwitterFeedWidgetId()}" data-chrome="nofooter noheader noborders">Tweets by @ICBPDataPortal</a> <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
</HtmlOutputText>
</HtmlOutputText>
</td> <td width="2%"/> <td width="49%" valign="top">
<HtmlOutputText escape="true" id="j_id167" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id169" rendered="true" transient="false">
<h2 class="frontSmall">New User?</h2> <p>
<HtmlGraphicImage id="j_id171" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id172" rendered="false" transient="false">
Please register for full access to the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id174" rendered="true" transient="false">
Only curators need to register and log in when using the portal. They must request curator privileges in order to manage the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<br/>
<HtmlOutputText escape="true" id="j_id177" rendered="false" transient="false">
Once you have successfully registered, you  
<HtmlLink action=" disabled="false" id="j_id179" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" view="/pages/projects/browseProjects.xhtml">
must request access to a laboratory
</HtmlLink>
in order to see non-public data. <br/><br/> If you wish to upload and analyze your own data, you must request Curator privileges
</HtmlOutputText>
<br/>
<HtmlLink action=" disabled="false" id="j_id183" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
  
<HtmlLink action=" disabled="false" id="j_id185" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Register" view="/pages/register.xhtml"/>
</p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id187" rendered="false" transient="false">
<h2 class="frontSmall">Terms of Access</h2> <p>
<HtmlGraphicImage id="j_id189" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id190" rendered="false" transient="false">
Registered users have full access to the data and analyses tools #{msg.title_short} provides. <br/><br/>The  
<HtmlLink action=" disabled="false" id="j_id192" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id194" rendered="true" transient="false">
The  
<HtmlLink action=" disabled="false" id="j_id196" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.<br/>
</HtmlOutputText>
<br/> <br/> </p>
</HtmlOutputText>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id199" rendered="true" transient="false">
<ComponentRef id="j_id200" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id202" rendered="true" transient="false">
<h2 class="frontSmall">New User?</h2> <p>
<HtmlGraphicImage id="j_id204" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id205" rendered="false" transient="false">
Please register for full access to the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id207" rendered="true" transient="false">
Only curators need to register and log in when using the portal. They must request curator privileges in order to manage the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<br/>
<HtmlOutputText escape="true" id="j_id210" rendered="false" transient="false">
Once you have successfully registered, you  
<HtmlLink action=" disabled="false" id="j_id212" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" view="/pages/projects/browseProjects.xhtml">
must request access to a laboratory
</HtmlLink>
in order to see non-public data. <br/><br/> If you wish to upload and analyze your own data, you must request Curator privileges
</HtmlOutputText>
<br/>
<HtmlLink action=" disabled="false" id="j_id216" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
  
<HtmlLink action=" disabled="false" id="j_id218" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Register" view="/pages/register.xhtml"/>
</p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id220" rendered="false" transient="false">
<h2 class="frontSmall">Terms of Access</h2> <p>
<HtmlGraphicImage id="j_id222" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id223" rendered="false" transient="false">
Registered users have full access to the data and analyses tools #{msg.title_short} provides. <br/><br/>The  
<HtmlLink action=" disabled="false" id="j_id225" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id227" rendered="true" transient="false">
The  
<HtmlLink action=" disabled="false" id="j_id229" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.<br/>
</HtmlOutputText>
<br/> <br/> </p>
</HtmlOutputText>
</ComponentRef>
<ComponentRef id="j_id232" rendered="false" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <h2 class="frontSmall">Tutorials / Manuals</h2> <p>
<HtmlGraphicImage id="j_id234" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/manual.png" value="/brandable/images/manual.png"/>
Tutorials, analysis descriptions and other documentation is available at: <br/>
<HtmlLink action="#{serverBean.resetDocumentationURL}" actionExpression="#{serverBean.resetDocumentationURL}" disabled="false" id="j_id236" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/support/documents.xhtml">
<UIParameter id="j_id237" name="linkDetail" rendered="true" transient="false" value="index.html"/>
HELP > DOCUMENTS
</HtmlLink>
</p>
</ComponentRef>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id240" rendered="false" transient="false">
<h2 class="frontSmall">Frequently Altered Genes</h2> <p>
<HtmlGraphicImage id="j_id242" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/manual.png" value="/brandable/images/manual.png"/>
Tag clouds summarizing genes frequently altered in the datasets of this portal are available in the <br/>
<HtmlLink action=" disabled="false" id="j_id244" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/data/mutationTagcloud.xhtml">
Mutation tag cloud
</HtmlLink>
</p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id247" rendered="true" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<ComponentRef id="j_id249" rendered="false" transient="false">
<HtmlDiv id="j_id250" rendered="true" transient="false">
<h2 class="frontSmall">Publications</h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@54820699" first="0" id="j_id252" rendered="true" rowIndex="0" rowKeyVar="index" rows="3" transient="false" var="aPub">
<p>
<HtmlOutputText escape="false" id="j_id254" rendered="false" transient="false">
<HtmlGraphicImage id="j_id255" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/publication.png" value="/brandable/images/publication.png"/>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id256" rendered="true" transient="false"/>
,<small>  
<HtmlOutputText escape="true" id="j_id258" rendered="true" transient="false"/>
<HtmlOutputText escape="true" id="j_id260" rendered="true" transient="false"/>
<HtmlOutputText escape="true" id="j_id262" rendered="true" transient="false"/>
</small></p>
</HtmlAjaxRepeat>
<p>
<HtmlLink action=" disabled="false" id="j_id265" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="All Publications" view="/pages/data/browsePublications.xhtml"/>
</p>
</HtmlDiv>
<HtmlDiv id="j_id267" rendered="false" transient="false">
<h2 class="frontSmall">Recent Publications<a href="#{rssFeedReaderAction.getFeed().getLink()}">
<HtmlGraphicImage id="j_id269" ismap="false" rendered="true" style="float:right; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/rss-feed-icon.gif" value="/brandable/images/rss-feed-icon.gif"/>
</a></h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@6a5c27f0" first="0" id="j_id271" rendered="true" rowIndex="0" rowKeyVar="index_rss" rows="5" transient="false" var="anItem">
<p><b><a href="#{anItem.link}">
<HtmlOutputText escape="true" id="j_id273" rendered="true" transient="false"/>
</a></b>
<HtmlOutputText escape="true" id="j_id275" rendered="true" transient="false"/>
</p> <br/>
</HtmlAjaxRepeat>
<p><a href="#{rssFeedReaderAction.getFeed().getLink()}">More Publications</a></p>
</HtmlDiv>
</ComponentRef>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id278" rendered="false" transient="false">
<h2 class="frontSmall">Complementary Resources</h2> <p> <b><a href="http://www.broadinstitute.org/achilles" target="_blank">Project Achilles</a></b> is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. </p><p> The <b><a href="http://www.broadinstitute.org/CTRP" target="_blank">Cancer Therapeutic Response Portal</a></b> provides profiles of the impact of a small-molecule collection of 185 compounds on a panel of 242 cancer cell lines </p><p> The <b><a href="http://www.broadinstitute.org/gtex" target="_blank">Genotype-Tissue Expression project (GTEx)</a></b> aims to create a comprehensive public atlas of gene expression and regulation across multiple human tissues </p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id280" rendered="false" transient="false">
<h2 class="frontSmall">Complementary Resources</h2>
<HtmlOutputText escape="true" id="j_id282" rendered="false" transient="false">
<p> <b><a href="https://research.themmrf.org" target="_blank">CoMMpass Researcher Gateway</a></b> Longitudinal molecular profiling study following 1000 newly-diagnosed MM patients. The frontline treatments permitted in this clinical study (NCT0145429) include current standard of care therapies containing a proteasome inhibitor, an IMiD or both. Correlating clinical data and endpoints as well as outcomes are also captured. </p>
</HtmlOutputText>
<p> The <b><a href="http://www.broadinstitute.org/CTRP" target="_blank">Cancer Therapeutic Response Portal</a></b> provides profiles of the impact of a small-molecule collection of 185 compounds on a panel of 242 cancer cell lines </p><p> The <b><a href="http://www.broadinstitute.org/ccle" target="_blank">Cancer Cell Line Encyclopedia</a></b> provides public access to genomic data, analysis and visualization for about 1000 cell lines. </p>
</HtmlOutputText>
</td> </tr> </table> </td> <td width="5px"/> <td width="420px" valign="top" style="padding-right: 20px;">
<HtmlOutputText escape="true" id="j_id286" rendered="false" transient="false">
<h2 class="front">What you can do on this portal</h2>
</HtmlOutputText>
<ComponentRef id="j_id288" rendered="false" transient="false">
<center>
<HtmlForm enctype="application/x-www-form-urlencoded" id="searchForm" prependId="true" rendered="true" submitted="false" transient="false">
<HtmlPanelGrid border="-2147483648" columns="1" id="j_id290" rendered="true" transient="false">
<HtmlPanelGroup id="j_id291" rendered="true" style="text-align: center" transient="false">
<div id="SearchBox">
<HtmlPanelGrid border="-2147483648" columns="1" id="j_id293" rendered="true" styleClass="searchBoxWrapper" transient="false" width="100%">
<HtmlPanelGroup id="j_id294" rendered="true" styleClass="searchBoxWrapper" transient="false">
<HtmlPanelGrid border="-2147483648" columns="1" id="j_id295" rendered="true" styleClass="searchBox" transient="false">
<HtmlPanelGroup id="j_id296" rendered="true" style="text-align: center" transient="false">
<HtmlOutputText escape="true" id="j_id297" rendered="true" transient="false" value=""/>
<HtmlInputText disabled="false" id="searchText" immediate="false" localValueSet="false" maxlength="-2147483648" readonly="false" rendered="true" required="false" size="-2147483648" transient="false" valid="true"/>
</HtmlPanelGroup>
<HtmlPanelGroup id="j_id298" rendered="true" style="text-align: center" transient="false">
<HtmlCommandButton action="#{searchAction.search}" actionExpression="#{searchAction.search}" disabled="false" id="searchPortal" immediate="false" readonly="false" rendered="true" styleClass="purpleBtn" transient="false" type="submit" value="Search TCGA"/>
</HtmlPanelGroup>
</HtmlPanelGrid>
</HtmlPanelGroup>
</HtmlPanelGrid>
</div>
</HtmlPanelGroup>
</HtmlPanelGrid>
</HtmlForm>
</center>
</ComponentRef>
<ComponentRef id="j_id301" rendered="true" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id303" rendered="true" transient="false">
<h2 class="frontSmall">New User?</h2> <p>
<HtmlGraphicImage id="j_id305" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id306" rendered="false" transient="false">
Please register for full access to the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id308" rendered="true" transient="false">
Only curators need to register and log in when using the portal. They must request curator privileges in order to manage the data and analyses tools #{msg.title_short} provides.<br/>
</HtmlOutputText>
<br/>
<HtmlOutputText escape="true" id="j_id311" rendered="false" transient="false">
Once you have successfully registered, you  
<HtmlLink action=" disabled="false" id="j_id313" immediate="false" includePageParams="true" propagation="none" rendered="true" transient="false" view="/pages/projects/browseProjects.xhtml">
must request access to a laboratory
</HtmlLink>
in order to see non-public data. <br/><br/> If you wish to upload and analyze your own data, you must request Curator privileges
</HtmlOutputText>
<br/>
<HtmlLink action=" disabled="false" id="j_id317" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
  
<HtmlLink action=" disabled="false" id="j_id319" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Register" view="/pages/register.xhtml"/>
</p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id321" rendered="false" transient="false">
<h2 class="frontSmall">Terms of Access</h2> <p>
<HtmlGraphicImage id="j_id323" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/new.png" value="/brandable/images/new.png"/>
<HtmlOutputText escape="true" id="j_id324" rendered="false" transient="false">
Registered users have full access to the data and analyses tools #{msg.title_short} provides. <br/><br/>The  
<HtmlLink action=" disabled="false" id="j_id326" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id328" rendered="true" transient="false">
The  
<HtmlLink action=" disabled="false" id="j_id330" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="Terms of Access" view="/pages-toa/termsOfAccess.xhtml"/>
are available for review.<br/>
</HtmlOutputText>
<br/> <br/> </p>
</HtmlOutputText>
<br/>
</ComponentRef>
<ComponentRef id="j_id334" rendered="true" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <h2 class="frontSmall">Tutorials / Manuals</h2> <p>
<HtmlGraphicImage id="j_id336" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/manual.png" value="/brandable/images/manual.png"/>
Tutorials, analysis descriptions and other documentation is available at: <br/>
<HtmlLink action="#{serverBean.resetDocumentationURL}" actionExpression="#{serverBean.resetDocumentationURL}" disabled="false" id="j_id338" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/support/documents.xhtml">
<UIParameter id="j_id339" name="linkDetail" rendered="true" transient="false" value="index.html"/>
HELP > DOCUMENTS
</HtmlLink>
</p>
<br/>
</ComponentRef>
<ComponentRef id="j_id343" rendered="true" transient="false">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id345" rendered="true" transient="false">
<h2 class="frontSmall">News / Events</h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@5fc25637" first="0" id="j_id347" rendered="true" rowIndex="0" rowKeyVar="index" rows="7" transient="false" var="aNewsItem">
<HtmlOutputText escape="true" id="j_id348" rendered="false" transient="false">
<p>
<HtmlOutputText escape="false" id="j_id350" rendered="false" transient="false">
<HtmlGraphicImage id="j_id351" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/news.png" value="/brandable/images/news.png"/>
</HtmlOutputText>
<b>
<HtmlOutputText escape="true" id="j_id353" rendered="true" transient="false"/>
</b>: 
<HtmlOutputText escape="false" id="j_id355" rendered="true" transient="false"/>
 
<HtmlOutputText escape="true" id="j_id357" rendered="false" transient="false">
<a href="#{aNewsItem.moreInfoURL}">more...</a>
</HtmlOutputText>
</p>
</HtmlOutputText>
</HtmlAjaxRepeat>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id360" rendered="false" transient="false">
<h2 class="frontSmall">News / Events</h2> <a class="twitter-timeline" data-widget-id="#{serverBean.getTwitterFeedWidgetId()}" data-chrome="nofooter noheader noborders">Tweets by @ICBPDataPortal</a> <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
</HtmlOutputText>
<br/>
</ComponentRef>
<HtmlOutputText escape="true" id="j_id363" rendered="false" transient="false">
<br/>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<HtmlOutputText escape="true" id="j_id366" rendered="true" transient="false">
<h2 class="frontSmall">News / Events</h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@6058c0d7" first="0" id="j_id368" rendered="true" rowIndex="0" rowKeyVar="index" rows="7" transient="false" var="aNewsItem">
<HtmlOutputText escape="true" id="j_id369" rendered="false" transient="false">
<p>
<HtmlOutputText escape="false" id="j_id371" rendered="false" transient="false">
<HtmlGraphicImage id="j_id372" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/news.png" value="/brandable/images/news.png"/>
</HtmlOutputText>
<b>
<HtmlOutputText escape="true" id="j_id374" rendered="true" transient="false"/>
</b>: 
<HtmlOutputText escape="false" id="j_id376" rendered="true" transient="false"/>
 
<HtmlOutputText escape="true" id="j_id378" rendered="false" transient="false">
<a href="#{aNewsItem.moreInfoURL}">more...</a>
</HtmlOutputText>
</p>
</HtmlOutputText>
</HtmlAjaxRepeat>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id381" rendered="false" transient="false">
<h2 class="frontSmall">News / Events</h2> <a class="twitter-timeline" data-widget-id="#{serverBean.getTwitterFeedWidgetId()}" data-chrome="nofooter noheader noborders">Tweets by @ICBPDataPortal</a> <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
</HtmlOutputText>
<br/>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<ComponentRef id="j_id385" rendered="false" transient="false">
<HtmlDiv id="j_id386" rendered="true" transient="false">
<h2 class="frontSmall">Publications</h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@a299ee7" first="0" id="j_id388" rendered="true" rowIndex="0" rowKeyVar="index" rows="3" transient="false" var="aPub">
<p>
<HtmlOutputText escape="false" id="j_id390" rendered="false" transient="false">
<HtmlGraphicImage id="j_id391" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/publication.png" value="/brandable/images/publication.png"/>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id392" rendered="true" transient="false"/>
,<small>  
<HtmlOutputText escape="true" id="j_id394" rendered="true" transient="false"/>
<HtmlOutputText escape="true" id="j_id396" rendered="true" transient="false"/>
<HtmlOutputText escape="true" id="j_id398" rendered="true" transient="false"/>
</small></p>
</HtmlAjaxRepeat>
<p>
<HtmlLink action=" disabled="false" id="j_id401" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" value="All Publications" view="/pages/data/browsePublications.xhtml"/>
</p>
</HtmlDiv>
<HtmlDiv id="j_id403" rendered="false" transient="false">
<h2 class="frontSmall">Recent Publications<a href="#{rssFeedReaderAction.getFeed().getLink()}">
<HtmlGraphicImage id="j_id405" ismap="false" rendered="true" style="float:right; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/rss-feed-icon.gif" value="/brandable/images/rss-feed-icon.gif"/>
</a></h2>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@327f54e7" first="0" id="j_id407" rendered="true" rowIndex="0" rowKeyVar="index_rss" rows="5" transient="false" var="anItem">
<p><b><a href="#{anItem.link}">
<HtmlOutputText escape="true" id="j_id409" rendered="true" transient="false"/>
</a></b>
<HtmlOutputText escape="true" id="j_id411" rendered="true" transient="false"/>
</p> <br/>
</HtmlAjaxRepeat>
<p><a href="#{rssFeedReaderAction.getFeed().getLink()}">More Publications</a></p>
</HtmlDiv>
</ComponentRef>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id414" rendered="false" transient="false">
<h2 class="frontSmall">Search for information</h2> <p>Enter a keyword to search for genes, news items and publications. Search results for a gene include links to annotations and analyses.</p>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<ComponentRef id="j_id417" rendered="false" transient="false">
<h2 class="frontSmall">Data Sets</h2> <p>
<HtmlGraphicImage id="j_id419" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/glass.png" value="/brandable/images/glass.png"/>
Browse, analyze and download studies and data sets. <br/> <p>
<HtmlLink action=" disabled="false" id="j_id421" immediate="false" includePageParams="true" propagation="begin" rendered="true" transient="false" view="/pages/data/browseData.xhtml">
BROWSE   > DATA
</HtmlLink>
</p>
<HtmlOutputText escape="true" id="j_id424" rendered="false" transient="false">
<table width="100%" cellpadding="0px" cellspacing="0px"> <tr> <td align="top">
<HtmlOutputText escape="true" id="j_id426" rendered="true" transient="false">
<h2>Public Data:</h2>
</HtmlOutputText>
<p>
<HtmlOutputText escape="true" id="j_id429" rendered="true" transient="false" value="Studies: 0"/>
<br/>
<HtmlOutputText escape="true" id="j_id431" rendered="true" transient="false" value="Samples: 0"/>
<br/>
<HtmlOutputText escape="true" id="j_id433" rendered="true" transient="false" value="Data Sets: 0"/>
<br/>
<HtmlOutputText escape="true" id="j_id435" rendered="false" transient="false">
<div style="margin-left: 22px;"> <table>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@67323b17" first="0" id="j_id437" rendered="true" rowIndex="0" rows="0" transient="false" var="typeCount">
<tr> <td><font size="-2" color="#333333">  #{typeCount.getType()}:</font></td> <td align="left"><font size="-2">#{typeCount.getCount()}</font></td> </tr>
</HtmlAjaxRepeat>
</table> </div>
</HtmlOutputText>
</p> </td> <td align="top">
<HtmlOutputText escape="true" id="j_id441" rendered="false" transient="false">
<h2>Visible to you:</h2> <p>
<HtmlOutputText escape="true" id="j_id443" rendered="true" transient="false" value="Studies: 22"/>
<br/>
<HtmlOutputText escape="true" id="j_id445" rendered="true" transient="false" value="Samples: 0"/>
<br/>
<HtmlOutputText escape="true" id="j_id447" rendered="true" transient="false" value="Data Sets: 0"/>
<br/>
<HtmlOutputText escape="true" id="j_id449" rendered="true" transient="false">
<div style="margin-left: 22px;"> <table>
<HtmlAjaxRepeat componentState="org.ajax4jsf.component.SequenceDataAdaptor$1@14bea80e" first="0" id="j_id451" rendered="true" rowIndex="0" rows="0" transient="false" var="typeCount">
<tr> <td><font size="-2" color="#333333">  #{typeCount.getType()}:</font></td> <td align="left"><font size="-2">#{typeCount.getCount()}</font></td> </tr>
</HtmlAjaxRepeat>
</table> </div>
</HtmlOutputText>
</p>
</HtmlOutputText>
</td> </tr> </table>
</HtmlOutputText>
</p>
</ComponentRef>
<ComponentRef id="j_id457" rendered="false" transient="false">
<h2 class="frontSmall">Analysis Tools</h2> <p>
<HtmlGraphicImage id="j_id459" ismap="false" rendered="true" style="float:left; margin-right:5px; border-style:none;" transient="false" url="/brandable/images/tools.png" value="/brandable/images/tools.png"/>
The portal provides the following analysis tools:</p>
<HtmlOutputText escape="true" id="j_id461" rendered="true" transient="false">
<p><b>Integrative Genomics Viewer (IGV)</b><br/> Visualize a data set in the Integrative Genomics Viewer (IGV), a high-performance visualization tool for interactive exploration of large integrated data sets. <br/> </p>
</HtmlOutputText>
<HtmlOutputText escape="true" id="j_id463" rendered="true" transient="false">
<p><b>GISTIC Analysis Results Browser</b><br/> Copy number alterations can be explored on a per-gene and per-cancer-subset basis. Significance, frequency, and peak region results are provided, together with links for invoking IGV on the data.</p>
</HtmlOutputText>
<ComponentRef id="j_id465" rendered="false" transient="false">
<p><b>Differential Expression Analysis</b><br/> Find genes that are significantly differentially expressed between two user-defined classes of samples from an expression data set available on this portal.</p>
</ComponentRef>
<ComponentRef id="j_id467" rendered="false" transient="false">
<p><b>Gene co-expression</b><br/> View the top 20 genes in a data set that are co-expressed with a gene of interest.</p>
</ComponentRef>
<ComponentRef id="j_id469" rendered="false" transient="false">
<p><b>Gene Set Enrichment Analysis (GSEA)</b><br/> Find <a href="http://www.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=CP" target="nonportal">pathway gene sets</a> correlated with a gene of interest. Domain experts curate the pathway gene sets based on data from several online pathway databases.</p> <p>
<HtmlLink action=" disabled="false" id="j_id471" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/data/browseAnalyses.xhtml">
ANALYSIS TOOLS
</HtmlLink>
</p>
</ComponentRef>
</ComponentRef>
<ComponentRef id="j_id474" rendered="false" transient="false">
<h2 class="frontSmall">Sample Sets</h2> <p>
<HtmlGraphicImage id="j_id476" ismap="false" rendered="true" style="margin-right:5px; border-style:none;" transient="false" url="/brandable/images/samples.png" value="/brandable/images/samples.png"/>
Create your own sample sets based on a large number of available criteria and use them in differential expression analysis. <br/>
<HtmlLink action=" disabled="false" id="j_id478" immediate="false" includePageParams="true" propagation="default" rendered="true" transient="false" view="/pages/data/browseSamplesets.xhtml">
CREATE SAMPLE SETS
</HtmlLink>
</p>
</ComponentRef>
</HtmlOutputText>
</td> </tr> </table>
</td> </tr> </table> </div> <div id="HomeBottom"> <table width="100%" border="0" cellpadding="0" cellspacing="0"> <tr> <td width="40px" height="62px" class="HomeBottomLeft"/> <td class="HomeBottomCenter" valign="baseline">
</td> <td width="40px" height="62px" class="HomeBottomRight"/> </tr> </table> </div> </div> <div id="Footer"> <center><br/>
<HtmlOutputText escape="false" id="j_id484" rendered="true" transient="false" value="Copyright © 2010, 2019 Broad Institute"/>
</center> </div> </div> </body>
</html>
</AjaxViewRoot>

+ Scoped Variables

Request Parameters
NameValue
None
Request Attributes
NameValue
ajaxContextorg.ajax4jsf.context.AjaxContextImpl@4fc90d2c
announceGisticResultsBeanAnnounceGisticResultsBean@187feca0
browseTcgaDataBeanedu.mit.broad.jsf.tap.BrowseTcgaDataBean@768808f0
documentationManageredu.mit.broad.util.DocumentationManager@5d03015b
emailServiceedu.mit.broad.jsf.service.EmailService@704e2d11
geneAnalysisActionedu.mit.broad.jsf.GeneAnalysisAction@29b5a780
loggingContextEventListeneredu.mit.broad.logging.LoggingContextEventListener@76723358
loginBeanedu.mit.broad.jsf.LoginBean@5c48c9bb
msgcom.sun.facelets.tag.jsf.core.LoadBundleHandler$ResourceBundleMap@2eb44352
pageInfoBeanedu.mit.broad.jsf.PageInfoBean@7f59d713
serverBeanedu.mit.broad.jsf.admin.ServerBean@633761b6
uiBeanedu.mit.broad.jsf.UiBean@e7732d4
Session Attributes
NameValue
breadcrumbsedu.mit.broad.seam.BreadCrumbBean@33aa03b7
dbStatisticsedu.mit.broad.jsf.DBStatistics@5ed9fde0
registeredu.mit.broad.jsf.RegisterBean@39aaadc6
sampleAnnotationEditorBeanedu.mit.broad.jsf.curator.SampleAnnotationEditorBean@7476bfbd
termsOfAccessBeanedu.mit.broad.jsf.TermsOfAccessBean@460f7b18
viewExperimentBeanedu.mit.broad.jsf.ViewExperimentBean@328b170e
Application Attributes
NameValue
aboutedu.mit.broad.datamodel.admin.ProjectInfoItem@44a406e8
brandtcga
dataSetParsingServiceedu.mit.broad.parsing.DataSetParsingService@4483dae0
downloadFilteredu.mit.broad.jsf.servlet.DownloadFilter@2c96cb44
envedu.mit.broad.config.PortalEnvironment@5ffaf43a
filePropertiesManageredu.mit.broad.util.FilePropertiesManager@54b83d10
fileSystemUtiledu.mit.broad.util.FileSystemUtil@bb110e4
footeredu.mit.broad.datamodel.admin.ProjectInfoItem@297b0d9d
fundingedu.mit.broad.datamodel.admin.ProjectInfoItem@197e1a9e
loggingFilteredu.mit.broad.logging.LoggingFilter@15cbeebb
messageProvideredu.mit.broad.jsf.MessageProvider@7fa6422a
portalBuildedu.mit.broad.config.PortalBuildProperties@7c4214de
portalDatabaseorg.jboss.seam.persistence.EntityManagerFactory@54dc2b4c
projectInfoItemedu.mit.broad.datamodel.admin.ProjectInfoItem@7d3a462c
propertiesManageredu.mit.broad.util.PropertiesManager@429eb61a
rssFeedReaderActionedu.mit.broad.jsf.RssFeedReaderAction@f2aa943
uiHelperedu.mit.broad.seam.SeamUIHelper@39ce757c
Jun 13, 2021 9:46:24 AM - Generated by Facelets