An Error Occurred:

javax.el.ELException: /programs/fungi/left-side.xhtml @73,70 value="#{fungi_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.FungiHome$Proxy$_$$_WeldClientProxy

+ Stack Trace

javax.faces.FacesException: javax.el.ELException: /programs/fungi/left-side.xhtml @73,70 value="#{fungi_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.FungiHome$Proxy$_$$_WeldClientProxy
	at javax.faces.component.UIOutput.getValue(UIOutput.java:176)
	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:836)
	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:592)
	at gov.doe.jgi.portal.view.common.DefaultViewHandler.renderView(DefaultViewHandler.java:281)
	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:291)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206)
	at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:295)
	at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:393)
	at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:520)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at gov.doe.jgi.portal.view.log.LogFilter.doFilter(LogFilter.java:82)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at gov.doe.jgi.portal.view.common.StaticContentFilter.doFilter(StaticContentFilter.java:281)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at gov.doe.jgi.portal.framework.view.RequestLifecicleAwareFilter.doFilter(RequestLifecicleAwareFilter.java:39)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at gov.doe.jgi.portal.framework.config.ConfigFilter.doFilter(ConfigFilter.java:27)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
	at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:676)
	at gov.doe.jgi.portal.tomcat.SessionInvalidateValve.invoke(SessionInvalidateValve.java:88)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:518)
	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:844)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1527)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1484)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:745)
Caused by: javax.el.ELException: /programs/fungi/left-side.xhtml @73,70 value="#{fungi_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.FungiHome$Proxy$_$$_WeldClientProxy
	at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:76)
	at javax.faces.component.UIOutput.getValue(UIOutput.java:173)
	... 54 more
Caused by: java.lang.NullPointerException

+ Component Tree

<AjaxViewRoot id="_viewRoot" immediate="false" locale="en_US" renderKitId="HTML_BASIC" renderRegionOnly="false" rendered="true" selfRendered="false" submitted="false" transient="false" viewId="/programs/fungi/index.xhtml">
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" >
<html ng-app="SearchGenomeApp" xmlns="http://www.w3.org/1999/xhtml" xmlns:t="http://myfaces.apache.org/tomahawk"> <head> <title>JGI Fungi Portal - Home</title>
<HtmlOutputText escape="false" id="j_id2" rendered="true" transient="false" value="<link href="/css/genome2.css" rel="stylesheet" type="text/css"/> <!--[if lt IE 8]><script src="/js/IE8.js" type="text/javascript"></script><![endif]--><script type="text/javascript" src="/js/ie_workarounds.js"></script><!--[if IE 6]><link type="text/css" rel="stylesheet" href="/css/ie6.css"><![endif]--><script type="text/javascript">(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-54904231-1', 'auto'); ga('send', 'pageview'); var _gaq = _gaq || [];</script>"/>
<script type="text/javascript" src="/js/jquery.js"/> <script type="text/javascript" src="/js/treeUtils.js"/> <script type="text/javascript" src="/js/preload.js"/> <script type="text/javascript" src="/js/superfish.js"/> <script type="text/javascript" src="/js/supersubs.js"/> <script type="text/javascript"> <!-- jQuery.noConflict(); var g_selectOrg = null; var g_wasInitialized = false; function gotoOrganism() { if( !g_wasInitialized ) initOrgSelectionBoxes(); var selectLocation = document.getElementById('selectLocation'); var encodedString = g_selectOrg.options[g_selectOrg.selectedIndex].value; var loc = selectLocation.options[selectLocation.selectedIndex].value; var url = "error"; if( loc == "home" ) url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2'); else if( loc == "browse" ) url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/cgi-bin/browserLoad?db=$2&position=$3'); else if( loc == "blast" ) url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/pages/blast-query.jsf?db=$2'); else if( loc == "download" ) url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2/$2.download.html'); else if( loc == "annotation" ) url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2/$2.annotation.html'); //alert('redirecting to ' + url); top.location.href = url; } function emailCollaborator() { var selectEmail = document.getElementById("selectEmail"); var emailObj = selectEmail.options[ selectEmail.selectedIndex ]; location.href = "mailto:" + emailObj.value.replace(/\+/g, "%20") + "?subject=" + escape(emailObj.text); } function filterOrganisms() { if( !g_wasInitialized ) initOrgSelectionBoxes(); var category = jQuery("#selectCategory").val(); var selectOrg; if( category == "all" ) selectOrg = jQuery( "#selectOrg" ); else if( category == "Bacteria" ) selectOrg = jQuery( "#selectOrgBacteria" ); else if( category == "Eukaryota" ) selectOrg = jQuery( "#selectOrgEukaryota" ); else if( category == "Archaea" ) selectOrg = jQuery( "#selectOrgArchaea" ); else if( category == "Microbiome" ) selectOrg = jQuery( "#selectOrgMicrobiomes" ); g_selectOrg = selectOrg[0]; selectOrg[0].selectedIndex = 0; jQuery(".orgSelectBox").hide(); selectOrg.show(); filterLocations(selectOrg[0]); } function filterLocations(selectOrg) { if( !g_wasInitialized ) initOrgSelectionBoxes(); var sel = selectOrg.options[selectOrg.selectedIndex]; var isEuk = sel.value.indexOf("Eukaryota") == 0; var selectedLocation = jQuery( "#selectLocation" )[0]; if( !isEuk ) { var showAnnotation = sel.value[sel.value.length - 1] == '1'; if( showAnnotation ) { selectedLocation.options[1].text = "Annotation"; selectedLocation.options[1].value = "annotation"; selectedLocation.options[1].disabled = false; } else { if( selectedLocation.selectedIndex == 1 ) // Browse selectedLocation.selectedIndex = 0; // Home var browseLoc = selectedLocation.options[1]; browseLoc.disabled = true; } } else { selectedLocation.options[1].text = "Browse"; selectedLocation.options[1].value = "browse"; selectedLocation.options[1].disabled = false; } } function initOrgSelectionBoxes() { var selectCategory = jQuery( "#selectCategory" ); if( selectCategory.length == 0 ) // if the page is rendered without the organism drop-downs, then selectOrg.length will be 0 return; g_wasInitialized = true; jQuery("#selectCategory").change( function () { filterOrganisms(); }); jQuery(".orgSelectBox").change( function () { filterLocations(this); }); filterOrganisms(); // initialize } jQuery(document).ready(function(){ jQuery("ul.sf-menu").supersubs({ minWidth: 12, // minimum width of sub-menus in em units maxWidth: 20, // maximum width of sub-menus in em units extraWidth: 1 // extra width can ensure lines don't sometimes turn over // due to slight rounding differences and font-family }).superfish(); // call supersubs first, then superfish, so that subs are // not display:none when measuring. Call before initialising // containing tabs for same reason. }); var treeOfLife = new Object; function showTreeOfLifeNodeMenu(nodeName, nodeLabel) { var url = '/ext-api/tree-of-life/fungi-node/' + nodeName; // The 'menu' array will be filled in with data during the eval(data) call below. if( typeof menu[nodeName + ".menuindex"] != 'number' || typeof menu[nodeName + ".Name"] != 'string' || menu[nodeName + ".menuindex"] < 1) { jQuery("#pleaseWait").show(); jQuery.get(url, function(data) { treeOfLife[nodeName] = 1; eval(data); multitool( x, y, nodeName, nodeLabel ); jQuery("#pleaseWait").hide(); }); } else { multitool( x, y, nodeName, nodeLabel ); } } --> </script> <script type="text/javascript"> function init() { MM_preloadImages('/images/closeBtn_over.gif','/images/questionBtn_over.gif'); initOrgSelectionBoxes(); } </script> <link href="/css/tree.css" rel="stylesheet" type="text/css"/> <link href="/css/search.css" rel="stylesheet" type="text/css"/> <link href="/css/fungi.css" rel="stylesheet" type="text/css"/> <link rel="stylesheet" media="screen" href="/css/superfish.css"/> <link rel="stylesheet" media="screen" href="/css/superfish_fungi.css"/>
<script src="/pages/angular/js/libs/jquery-1.9.1.js"/> <script src="/pages/angular/js/libs/jquery-ui-1.10.3.js"/> <script src="/pages/angular/js/libs/angular-1.2.5.js"/> <script src="/pages/angular/js/libs/angular-sanitize-1.1.5.min.js"/> <script src="/pages/angular/js/libs/ui-bootstrap-tpls-0.9.0.js"/> <script src="/pages/angular/js/libs/ng-table.js"/> <link rel="stylesheet" type="text/css" href="/pages/angular/css/ng-table.css"/> <link rel="stylesheet" href="/pages/angular/css/bootstrap-3.0.0.min.css"/> <script src="/pages/angular/js/libs/ui-bootstrap-tpls-0.10.0.js"/> <script src="/pages/angular/js/services/searchGenomeApp.js"/> <script src="/pages/angular/js/controllers/tableController.js"/> <script src="/pages/angular/js/libs/bindonce.js"/> <script src="/pages/angular/js/libs/spin.js"/> <script src="/pages/angular/js/libs/hashmap.js"/> <script src="/pages/angular/js/libs/angular-spinner.js"/> <script src="/pages/angular/js/libs/ng-infinite-scroll.js"/> <script src="/pages/angular/js/libs/ng-csv.js"/> <script src="/pages/angular/js/libs/angular-cookies-1.0.0rc10.js"/> <link rel="stylesheet" type="text/css" href="/pages/angular/css/jquery-ui-1.9.2.css"/> <link rel="stylesheet" type="text/css" href="/pages/angular/css/ng-table.css"/> <link rel="stylesheet" type="text/css" href="/pages/angular/css/style.css"/> <link href="/pages/angular/css/search.css" rel="stylesheet" type="text/css"/> <link href="/css/tree.css" rel="stylesheet" type="text/css"/> <link href="/css/search.css" rel="stylesheet" type="text/css"/> <script src="/pages/angular/js/libs/jquery-1.9.0.min.js"/> <script src="/pages/angular/js/libs/jquery-ui-1.10.3.min.js"/> <script type="text/javascript" src="/pages/angular/js/treeUtils.js"/> <script type="text/javascript" src="/pages/angular/js/preload.js"/> <script type="text/javascript" src="/pages/angular/js/directives/dataSubmission.js"/> <script type="text/javascript" src="/pages/angular/js/directives/autocomplete.js"/> <script type="text/javascript" src="/pages/angular/js/directives/dynamicHtml.js"/> <script type="text/javascript" src="/pages/angular/js/overlay-bubbles.js"/> <script type="text/javascript"> <!-- jQuery.noConflict(); var documentLoaded = false; var autocompleteLoaded = false; function autocompleteLoad() { if( documentLoaded && !autocompleteLoaded ) { autocompleteLoaded = true; loadAutocomplete(); } if( !autocompleteLoaded ) setTimeout("autocompleteLoad()", 1000); } jQuery(document).ready(function() { documentLoaded = true; autocompleteLoad(); }); --> </script> <style> [ng\:cloak], [ng-cloak], .ng-cloak { display: none; } </style> </head> <body ng-cloak="true" data-ng-init="init()" ng-controller="TableController" class="ng-cloak"> <span us-spinner="{radius:10, width:8, length: 16,top:150, left:150, speed: 2,color:'#C0C0C0'}" spinner-key="spinner1"/> <a name="top"/>
<HtmlOutputText escape="false" id="j_id5" rendered="true" transient="false" value="<div class="header_wrap"> <header id="jgi-header"><div id="jgi-logo"><a href="/programs/fungi/index.jsf" title="DOE Joint Genome Institute - JGI MycoCosm" target="_parent"><img width="480" height="70" src="/images/fungi/logo-JGI-MycoCosm.png" alt="DOE Joint Genome Institute's MycoCosm logo" /></a></div><nav class="jgi-nav"><ul><li id="skipto"><a href="#skipnav" accesskey="S">Skip To Main Content</a></li> <li><a href="http://jgi.doe.gov" target="_parent">JGI Home</a></li> <li><a href="/" target="_parent">Genome Portal</a></li> <li><a class="textlink" id="mycocosm" target="_parent" href="/programs/fungi/index.jsf">MycoCosm</a></li> <li><a class="textlink" id="login" target="_parent" href="javascript: if(top.window.location.href.search('accessDenied')==-1) { document.cookie='jgi_return=' + escape(top.window.location.href) + '; domain=.jgi.doe.gov; path=/;'; } top.window.location.href='https://signon.jgi.doe.gov/signon';">Login</a></li></ul></nav></header><div class="header_top"><div class="float_right"></div></div></div> <a name="skipnav"></a> "/>
<!--ui:define name="body"--> <!-- div id="toolmenudiv" style="position: absolute; left: 100px; top: 100px; visibility: visible; overflow: auto;" / --> <div id="toolmenudiv" style="position: absolute; padding:0;margin:0; left: 100px; top: 100px; visibility: visible; overflow: auto;" onmouseover="window.clearTimeout(timeoutId);" onmouseout="timeoutId = window.setTimeout('divoff(\'toolmenudiv\')', APP_TIMEOUT);"/> <!--Main content section--> <div id="container"> <!--navigation and top banner--> <div ng-if="isThisPageType('project_list');">
<div id="nav"> <ul class="sf-menu"> <li class="#{pagetype=='home'?'selected':''}"><a target="_self" href="/programs/fungi/index.jsf" title="Back to home page" class="topmenu" id="home">Home</a></li> <li class="#{pagetype=='outreach'?'selected':''}"><a target="_self" href="/programs/fungi/video_tutorials.jsf" class="topmenu" title="Fungal Tutorials, Workshops, Publications" id="outreach">Outreach</a> <ul class="submenu"> <li><a target="_self" class="sf-with-ul" href="/programs/fungi/video_tutorials.jsf">Tutorials</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/events/program-meetings-and-workshops/">Workshops</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/fungal-publications/">Publications</a></li> </ul> </li> <li class="#{pagetype=='about_program'?'selected':''}"><a href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/" title="about program, mission, organization" class="topmenu" id="about_program">About</a> <ul class="submenu"> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/">JGI Fungal Program</a></li> <li><a target="_self" class="sf-with-ul" href="/programs/fungi/FungalGenomeAnnotationSOP.pdf">Annotation</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/mycocosm-jgi-fungal-portal/">MycoCosm</a></li> </ul> </li> </ul> </div> <a name="skipnav" id="skipnav"/> <!--start of global message-->
<HtmlOutputText escape="false" id="j_id8" rendered="true" transient="false" value=""/>
<!--end of global message-->
</div> <div ng-if="isThisPageType('fungalHome');">
<div id="nav"> <ul class="sf-menu"> <li class="#{pagetype=='home'?'selected':''}"><a target="_self" href="/programs/fungi/index.jsf" title="Back to home page" class="topmenu" id="home">Home</a></li> <li class="#{pagetype=='outreach'?'selected':''}"><a target="_self" href="/programs/fungi/video_tutorials.jsf" class="topmenu" title="Fungal Tutorials, Workshops, Publications" id="outreach">Outreach</a> <ul class="submenu"> <li><a target="_self" class="sf-with-ul" href="/programs/fungi/video_tutorials.jsf">Tutorials</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/events/program-meetings-and-workshops/">Workshops</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/fungal-publications/">Publications</a></li> </ul> </li> <li class="#{pagetype=='about_program'?'selected':''}"><a href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/" title="about program, mission, organization" class="topmenu" id="about_program">About</a> <ul class="submenu"> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/">JGI Fungal Program</a></li> <li><a target="_self" class="sf-with-ul" href="/programs/fungi/FungalGenomeAnnotationSOP.pdf">Annotation</a></li> <li><a target="_self" class="sf-with-ul" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/mycocosm-jgi-fungal-portal/">MycoCosm</a></li> </ul> </li> </ul> </div> <a name="skipnav" id="skipnav"/> <!--start of global message-->
<HtmlOutputText escape="false" id="j_id12" rendered="true" transient="false" value=""/>
<!--end of global message-->
</div> <!--end of navigation and top banner-->
<HtmlPanel id="pleaseWait" rendered="true" style="display: none;" styleClass="network-status" transient="false">
<HtmlOutputText escape="true" id="j_id15" rendered="true" transient="false" value="Communicating. Please wait ..."/>
<br/>
<HtmlGraphicImage alt="Please wait." id="j_id17" ismap="false" rendered="true" transient="false" url="/images/wait_spinner.gif" value="/images/wait_spinner.gif"/>
</HtmlPanel>
<!-- content section--> <div class="content_portal"> <!--left side panel -->
<div id="leftside"><!--section navigation --> <div id="sectionnav"> <h2 id="thousand_title"><a target="_self" href="/programs/fungi/1000fungalgenomes.jsf">1000 Fungal Genomes project</a>.<br/> <a target="_self" href="/pages/fungi-1000-projects.jsf"><b><span style="color:#F30">Nominate New Species!</span></b></a></h2> <br/> <h2 id="list_title"><a target="_self" href="/programs/fungi/GE_Fungi.jsf">Genomic Encyclopedia of Fungi</a></h2> <ul> <li><a target="_self" class="list_header_feedstock" href="/programs/fungi/GE_Fungi.jsf#feedstock">Plant Feedstock Health</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#symbiosis">Mycorrhizal Symbiosis</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#pathogenicity">Plant Pathogenicity</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#biocontrol">Biocontrol</a></li> <li><a target="_self" class="list_header_biorefinery" href="/programs/fungi/GE_Fungi.jsf#biorefinery">Biorefinery</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#biorefinery">Lignocellulose Degradation</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#biorefinery">Sugar Fermentation</a></li> <li><a target="_self" class="list_subheader" href="/programs/fungi/GE_Fungi.jsf#biorefinery">Industrial Organisms</a></li> <li><a target="_self" class="list_header_diversity" href="/programs/fungi/GE_Fungi.jsf#diversity">Fungal Diversity</a></li> </ul> </div> <h2> <a target="_self" href="http://www.jgi.doe.gov/CSP/user_guide/index.html"> <span style="color:#F30; font-size: 0.9em; padding:0 5px 0 20px;">Submit CSP proposal</span> </a> </h2> <div class="grey_divider"/> <!--end of section navigation --> <div class="clear"/> <!--Announcements --> <div id="announcements"> <h2 class="red">Announcements</h2> <ul style="list-style-type: none;"> <li><span class="date">March 21-24, 2016<br/> </span><a target="_self" href="http://jgi.doe.gov/events/">Fungal genomics workshop @ JGI User Meeting</a>, Walnut Creek, CA, U.S.A. </li> <li><span class="date">April 3-6, 2016<br/> </span><a target="_self" href="http://www.ecfg13.org/events.php?IDManif=896&IDModule=71&IDRub=1858">European Conference on Fungal Genetics</a>, Paris, France </li> <li><span class="date">August 7-11, 2016<br/> </span><a target="_self" href="http://msafungi.org/meetings/">MSA Annnual Meeting</a>, Berkeley,CA, U.S.A. </li> </ul> </div> <div class="grey_divider"/> <!--end of Announcements --> <div class="clear"/> <!--New Releases --> <div id="new_releases"> <h2 class="red">Releases</h2>
<HtmlOutputText escape="false" id="j_id20" rendered="true" transient="false" value="<div class="release_section"> <ul class="releases_list" style="list-style-type:none;"> <li><span class="date">July 14, 2016<br /></span><a target="_self" href="/Xenvag1">Xenasmatella vaga CBS212.54 v1.0</a></li> <li><span class="date">July 14, 2016<br /></span><a target="_self" href="/Oudmuc1">Oudemansiella mucida CBS 558.79 v1.0</a></li> <li><span class="date">July 14, 2016<br /></span><a target="_self" href="/Tubbor1">Tuber borchii Tbo3840 v1.0</a></li> <li><span class="date">July 11, 2016<br /></span><a target="_self" href="/Zyghet1">Mucor heterogamus NRRL 1489 v1.0</a></li> <li><span class="date">July 11, 2016<br /></span><a target="_self" href="/Mycafr1">Mycotypha africana NRRL 2978 v1.0</a></li> </ul> </div> "/>
<a target="_self" class="link_arrow" href="http://jgi.doe.gov/our-science/science-programs/fungal-genomics/recent-fungal-genome-releases/">more</a> <!--end of New Releases --> <div class="grey_divider"/> </div> </div>
<!--end of left side panel --> <!--right side panel --> <div id="rightside">
<div class="section_container genome_search"> <div class="sub_section" style="position:relative;padding-right: 0.5em"> <div class="float_right"> <span><a class="textlink" href="/help/frontPage.jsf#Search" target="_blank"><span class="button_styled_blue">Help?</span></a></span> <span><a ng-click="isCollapsed = !isCollapsed">Advanced Search<i class="glyphicon" ng-class="{'dropdown-toggle-down': isCollapsed,'dropdown-toggle-right': !isCollapsed }"/></a></span> </div> <div class="together"> <label class="label">Within:</label> <select ng-model="selectedSearchIn" ng-selected="searchType[0]" ng-options="currOption for currOption in searchIn"/> </div> <div class="together"> <label class="label">By:</label> <select ng-model="selectedSearchType" ng-selected="searchType[0]" ng-options="currOption for currOption in searchType" id="search_criteria" class="select_query search_criteria" name="search_criteria" onchange="checkQueryForNumeric()"/> </div> <div class="together"> <label class="label">Search for:</label> <input type="text" ng-model="query" class="field query_field" id="query" autocomplete="onEnter"/> </div> <div class=""> <input title="'Search for' should contain query" type="submit" id="submit" ng-click="onSubmit()" value="Search" class="search_button button_styled_blue"/> <input type="submit" id="showAll" ng-click="onShowAll()" value="Show All" class="search_button button_styled_blue"/> <span class="red_message" id="query_error" style="display:none;"><b>Numeric only, please.</b></span> </div> </div> <div class="clear"/> </div> <div class="section_container procedure-details" collapse="!isCollapsed"> <div style="margin-top:0; border: none;"> <div class="float_left sub_section" ng-show="renderFilters()"> <div ng-hide="disableFundingProgram()" class="together"> <label class="label">Funding Program</label><br/> <select ng-model="programName" ng-options="opt for opt in programNames" ng-change="updateProgramYearsP = updateProgramYears(); onChange()"/> </div> <div ng-hide="disableFundingProgram()" class="together"> <label class="label">Program Year</label><br/> <select ng-model="programYear" ng-options="opt for opt in programYears" ng-change="updateProgramNamesP = updateProgramNames(); onChange()" style="min-width:90px"/> </div> <div ng-hide="disableTaxonomy()" class="together"> <label class="label">Taxonomy</label><br/> <select ng-model="superkingdom" ng-options="opt for opt in superkingdoms" ng-change="onChange()"/> </div> <div ng-hide="disableScientificProgram()" class="together"> <label class="label">Scientific Program</label><br/> <select ng-model="scientificProgram" ng-options="opt for opt in scientificPrograms" ng-change="onChange()"/> </div> <div ng-hide="disableProductName()" class="together"> <label class="label">Product Name</label><br/> <select ng-model="productCategory" ng-options="opt for opt in productCategories" ng-change="onChange()"/> </div> <div class="together"> <label><br/></label><br/> <img onmouseover="MM_swapImage('questionBtn_search_filters','','/images/questionBtn_over.gif',1)" onmouseout="MM_swapImgRestore()" onclick="window.open('/help/projectSearch.jsf#search_filters', 'small', 'height=600,width=980,status=0,titlebar=0,toolbar=1,location=0,menubar=0,scrollbars=1,resizable=1');" target="_parent" id="questionBtn_search_filters" style="float:left" class="float_right" alt="question toolbar" src="/images/questionBtn.gif"/> </div> <div class="together"> <br/> For additional search capabilities please use <strong><a target="_self" href="https://gold.jgi-psf.org/">GOLD</a></strong> </div> <div class="clear"/> </div> </div> <!-- end of renderFilters() --> <div ng-show="renderPublishedPanel()" style="margin-top:0;"> <div class="sub_section" style="vertical-align: bottom"> <div class="genomeTableOrganizer"> <div ng-show="renderCheckboxes()" class="together"> <label class="label">Show: </label> <input type="checkbox" name="showOnlyPublished" ng-true-value="true" ng-false-value="false" ng-change="onChange()" ng-model="showOnlyPublished" id="showOnlyPublished"/><label for="showOnlyPublished">Published Organisms Only</label> <input type="checkbox" name="showSuperseded" ng-true-value="true" ng-false-value="false" ng-change="onChange()" ng-model="showSuperseded" id="showSuperseded"/><label for="showSuperseded">Superseded</label> </div> </div> <div class="clear"/> </div> </div> <div class="clear"/> </div> <!-- end of renderFilters() --> <!-- end of renderGenomeTable() -->
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<html ng-app="SearchGenomeApp" xmlns="http://www.w3.org/1999/xhtml" xmlns:t="http://myfaces.apache.org/tomahawk"> <script type="text/ng-template" id="hiddenList.html"> <div bo-show="result.aliases != ''"> <div class="modal-header"> <h3>Aliases</h3> </div> <ul bindonce="alias" ng-repeat="alias in result.aliases track by $index"> <li><a target="_self" bo-href="'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name='+alias" bo-text="alias"/></li> </ul> <div class="modal-footer"> <button class="btn btn-primary" ng-click="ok()">OK</button> </div> </div> </script> <body data-ng-init="init()" ng-controller="TableController"> <div ng-show="searchGenomeExecuted()" class="regular_margins" style="position:relative;"> <div class="together"> <!-- <input type="checkbox" name="externallySequenced" ng-true-value="true" ng-false-value="false" ng-change="onChange()" ng-model="externallySequenced" id="externallySequenced"/><label for="externallySequenced">Non-JGI projects</label> --> <input type="checkbox" name="showRestricted" ng-true-value="true" ng-false-value="false" ng-change="onChange()" ng-model="showRestricted" id="showRestricted"/><label for="showRestricted" class="label">Non-Public</label> </div> <div class="together"> <span ng-show="superUser()"> <input type="checkbox" name="withoutrestrictions" ng-true-value="true" ng-false-value="false" ng-change="onChange()" ng-model="showAll" id="withoutrestrictions"/><label for="withoutrestrictions" class="label">Without restrictions (superusers only)</label> </span> </div> <div class="clear"/> <div class="ng-cloak" ng-show="searchResults.total > 0"> <div class="highlight together small_paddings"><strong>{{searchResults.total}}</strong> results found</div>
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<a ng-show="searchResults.total > 0" ng-click="onClear()" class="closeBtn" title="close table"> <span class="button_label">Close Table</span> </a>
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<span ng-show="renderExport(#{empty callingPage })">
<HtmlPanelGroup id="excel" rendered="true" styleClass="float_right" transient="false">
<a target="_self" ng-href="{{exportToExcelFunction()}}"><button class="search_button button_styled_blue">Export Projects to Excel</button></a>
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</span> <ul class="highlight one_row_list small_area pointer" id="showLegend_faq" title="Legend" onclick="showLegend();return false"> <li>Legend: </li> <!-- <li ng-hide="isThisPageType('fungalHome')"><img title="Legend: JGI sequenced project" src="/images/portal_icon.gif"/></li> --> <li><img title="Legend: Mycocosm genome" alt="Mycocosm genome" src="/images/mycocosm_icon.gif"/></li> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="Legend: IMG genome" alt="IMG portal icon" src="/images/IMG_16X16.png"/></li> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="Legend: Phytozome genome" alt="Phytozome portal icon" src="/images/phytozome_16X16.png"/></li> <!-- <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="Legend: IMG externally sequenced project" alt="IMG externally sequenced project icon" src="/images/externalImg_icon.gif"/></li> <li><img title="Legend: Fungal externally sequenced project" alt="Fungal externally sequenced project icon" src="/images/externalFungal_icon.gif"/></li>--> <li class="pink"><img title="Legend: None-public" src="/images/private_locked.png" alt="Restricted to view icon"/></li> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="Legend: Proposal/Group of projects" src="/images/groupGenomes_icon.gif" alt="Group Genomes icon"/></li> <li><img title="Legend: Group of fungal genomes" src="/images/groupFungiGenomes_icon.gif" alt="Group Fungi Genomes icon"/></li> </ul> <div class="overlay_bubble" id="showLegend" style="overflow: visible; z-index: 200"> <div class="bubble_header"><strong>Legend</strong> <img src="/images/closeBtn.gif" alt="Close" id="closeBtn_message_help" onclick="hideOverlayHelp(); return false" class="closeBtn float_right" onmouseout="MM_swapImgRestore()" onmouseover="MM_swapImage('closeBtn_message_help','','/images/closeBtn_over.gif',1)"/> </div> <div class="inner_bubble"> <div class="content_bubble"> <div id="jgiSequenced" class=""> <p class="sub_header"><strong>JGI sequenced data</strong></p> <ul class="regular_margins"> <!-- <li ng-hide="isThisPageType('fungalHome')"><img title="JGI sequenced project" src="/images/portal_icon.gif"/> - Download files and metadata are available at genome.jgi.doe.gov</li> --> <li><img title="MycoCosm Genome Portal" alt="MycoCosm Genome Portal" src="/images/mycocosm_icon.gif"/> - Related genome resource and analysis tools are at <a href="http://jgi.doe.gov/fungi">http://jgi.doe.gov/fungi</a></li> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="IMG genome" alt="IMG icon" src="/images/IMG_16X16.png"/> - Related genome resource and analysis tools are at <a href="img.jgi.doe.gov">img.jgi.doe.gov</a></li> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="Phytozome Genome Portal" alt="Phytozome Genome Portal" src="/images/phytozome_16X16.png"/> - Related genome resource and analysis tools are at <a href="http://phytozome.jgi.doe.gov">http://phytozome.jgi.doe.gov</a></li> </ul> </div> <!-- <div id="externallySequenced" class=""> <p class="sub_header"><strong>Externally sequenced</strong></p> <ul class="regular_margins"> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img title="IMG externally sequenced project" alt="IMG externally sequenced project icon" src="/images/externalImg_icon.gif"/> - IMG externally sequenced project</li> <li><img title="Fungal externally sequenced project" alt="Fungal externally sequenced project icon" src="/images/externalFungal_icon.gif"/> - Fungal externally sequenced project</li> </ul> </div> --> <div id="restricted" class=""> <p class="sub_header"><strong>Non-public resource</strong></p> <ul class="regular_margins"> <li class="pink"><img src="/images/private_locked.png" alt="Restricted to view icon" title="Non-public"/> - Non-public resource. Access can be restricted. For access information please email to Principal investigator</li> </ul> </div> <div id="group" class=""> <p class="sub_header"><strong>Group</strong></p> <ul class="regular_margins"> <li ng-hide="isThisPageType('project_list') || isThisPageType('fungalHome')"><img src="/images/groupGenomes_icon.gif" alt="Group Genomes icon" title="Group Genomes"/> - Proposal/Group of Projects</li> <li><img src="/images/groupFungiGenomes_icon.gif" alt="Group Fungi Genomes icon" title="Legend: Group of Genomes"/> - Group of Fungal Genomes</li> </ul> </div> </div> </div> </div> </div> </div> <div class="ng-cloak" ng-show="renderGenomeTable();"> <div class="search_table"> <div infinite-scroll="addMoreSearchResults()" infinite-scroll-distance="0"> <table id="genome-table" ng-table="genomeTableParams" class="sortable"> <thead> <tr> <th class="sortable" ng-class="{ 'sort-asc': isSortBy('displayNameStr', 'asc'),'sort-desc': isSortBy('displayNameStr', 'desc')}" ng-click="setColumnSort('displayNameStr')"> <div>Name</div> </th> <th class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('name', 'asc'),'sort-desc': isSortBy('name', 'desc')}" ng-click="setColumnSort('name')"> <div>Resources</div> </th> <th class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('jgiProjectIdNum', 'asc'),'sort-desc': isSortBy('jgiProjectIdNum', 'desc')}" ng-click="setColumnSort('jgiProjectIdNum')"> <div>JGI Info</div> </th> <th ng-hide="hideProduct()" class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('productName', 'asc'),'sort-desc': isSortBy('productName', 'desc')}" ng-click="setColumnSort('productName')"> <div>Product</div> </th> <th ng-hide="hideStatus()" class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('projectStatus', 'asc'),'sort-desc': isSortBy('projectStatus', 'desc')}" ng-click="setColumnSort('projectStatus')"> <div>Status</div> </th> <th class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('piStr', 'asc'),'sort-desc': isSortBy('piStr', 'desc')}" ng-click="setColumnSort('piStr')"> <div>Principal Investigator</div> </th> <th ng-hide="hideTaxonomyInfo" class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('taxonomyIdNum', 'asc'),'sort-desc': isSortBy('taxonomyIdNum', 'desc')}" ng-click="setColumnSort('taxonomyIdNum')"> <div>Taxonomy</div> </th> <th ng-hide="isThisPageType('fungalHome')" class="text-center sortable" ng-class="{ 'sort-asc': isSortBy('sampleSiteStr', 'asc'),'sort-desc': isSortBy('sampleSiteStr', 'desc')}" ng-click="setColumnSort('sampleSiteStr')"> <div>Other</div> </th> </tr> </thead> <tbody> <tr ng-repeat="result in $data | limitTo:limit" ng-class="getClass(result.isPrivateOrganism)"> <td data-title="'Name'" sortable="'homelink'" style="min-width: 300px"> <div bindonce="result"> <div bo-show="result.homelink != ''"> <!-- <span ng-html-compile="result.homelink"/>--> <div dynamic="result.homelink"/> </div> <div ng-hide="isDeletedRecord($index)"> <div bo-show="result.supersededBy != ''"> <span bo-show="result.supersededBy != ''" style="font-weight: bold">Superseded by: </span> <span bo-text="result.supersededBy"/> </div> </div> </div> </td> <td data-title="'Resources'" sortable="'name'" class="nowrap"> <div bindonce="result"> <div ng-hide="isDeletedRecord($index)"> <div bo-show="result.name != ''"> <!-- <a ng-hide="disablePrivateLink(result.isPrivateOrganism)" target="_self" ng-click="onClick($event,$index)" bo-href="'/'+result.name+'/'+result.name+'.info.html'">Info</a><br/> --> <a ng-hide="disablePrivateLink(result.isPrivateOrganism)" target="_self" ng-click="onClick($event,$index)" bo-href="'/'+result.name+'/'+result.name+'.download.html'">Download</a><br/> <div bo-show="displayMetaviz($index)"> <a target="_self" class="elviz" ng-click="onClick($event,$index)" bo-href="'/viz/plot?jgiProjectId='+result.elvizProjectId">elviz</a> </div> <div bo-show="isSuperUser == 'true'"> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/ext-api/genome-admin/'+result.name+'/parameters'">Properties</a><br/> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/organism-admin/organism-access-admin.jsf?organism='+result.name">Access Control</a><br/> </div> </div> <div bo-show="showGenomePortals($index)"> <span style="font-weight: bold">Genome Portals: </span> <div bindonce="genomePortal" ng-repeat="genomePortal in result.genomePortals track by $index"> <ul class="other_names"> <div dynamic="genomePortal"/> </ul> </div> </div> </div> </div> </td> <td data-title="'JGI Info'" sortable="'jgiProjectId'" class="nowrap"> <div bindonce="result"> <div ng-hide="isDeletedRecord($index)"> <div bo-show="isGreaterThan10000($index)"> <span style="font-weight: bold">JGI Project Id: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/pages/projectStatus.jsf?db='+result.name" bo-text="result.jgiProjectId"/> <br/> </div> <div ng-show="result.proposalShortName != ''"> <div ng-show="result.gptsProposalId != ''"> <span style="font-weight: bold">JGI Proposal Id: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/'+result.proposalShortName+'/'+result.proposalShortName+'.info.html'" bo-text="result.proposalId"/><span bo-text="' / '+result.gptsProposalId"/> </div> <div ng-show="result.gptsProposalId == ''"> <span style="font-weight: bold">JGI Proposal Id: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/'+result.proposalShortName+'/'+result.proposalShortName+'.info.html'" bo-text="result.proposalId"/> </div> </div> <div bo-show="result.directoryNumber != ''"> <span style="font-weight: bold">Directory Number: </span> <span bo-text="result.directoryNumber"/> <br/> </div> <div> <span style="font-weight: bold" bo-show="result.releaseDate != ''">Release Date: </span> <!-- <span bo-hide="result.releaseDate != ''"><Private></span> --> <span bo-show="result.releaseDate != ''" bo-text="result.releaseDate"/> </div> <div bo-show="showFdList($index)"> <span style="font-weight: bold">Related Projects: </span></div> <div bindonce="fd" ng-repeat="fd in result.fdList track by $index"> <ul class="other_names"> <li><a target="_self" ng-click="onClick($event,$index)" bo-href="'/'+fd.name+'/'+fd.name+'.info.html'" bo-text="fd.jgiProjectId"/></li> </ul> </div> </div> <div bo-show="showProjects($index)"> <span style="font-weight: bold">Related Projects: </span> <div bindonce="project" ng-repeat="project in result.projects track by $index"> <ul class="other_names"> <li><a target="_self" ng-click="onClick($event,$index)" bo-href="'/'+project.name+'/'+project.name+'.info.html'" bo-text="project.jgiProjectId"/></li> </ul> </div> </div> </div> </td> <td ng-hide="hideProduct()" data-title="'Product'" sortable="'productName'"> <div bindonce="result"> <div bo-show="result.productName != ''"> <span bo-text="result.productName"/> </div> </div> </td> <td ng-hide="hideStatus()" data-title="'Status'" sortable="'projectStatus'" class=""> <div bindonce="result"> <div bo-show="displayStatus($index)"> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/pages/projectStatus.jsf?db='+result.name"> <span bo-text="result.projectStatus"/> </a> </div> <div bo-show="!displayStatus($index)"> <span bo-text="result.projectStatus"/> </div> </div> </td> <td data-title="'Principal Investigator'" sortable="'allPis'" class="nowrap"> <div bindonce="result"> <div bo-show="showPiInfo($index)"> <span style="font-weight: bold">Principal Investigator: </span></div> <div bindonce="pi" ng-repeat="pi in result.allPis track by $index"> <ul class="other_names"> <div bo-show="pi.email != ''"> <li><a target="_self" ng-click="onClick($event,$index)" bo-href="'mailto:'+ pi.email" bo-text="pi.name != '' ? pi.name : pi.email"/></li> </div> </ul> </div> <div bo-show="showSampleContact($index)"> <span style="font-weight: bold">Sample Contact: </span></div> <div bindonce="sampleContact" ng-repeat="sampleContact in result.sampleContact track by $index"> <ul class="other_names"> <div bo-show="sampleContact.email != ''"> <li><a target="_self" ng-click="onClick($event,$index)" bo-href="'mailto:'+ sampleContact.email" bo-text="sampleContact.name != '' ? sampleContact.name : sampleContact.email"/></li> </div> </ul> </div> </div> </td> <td ng-hide="hideTaxonomyInfo" data-title="'Taxonomy'" sortable="'taxonomyId'" class="nowrap"> <div bindonce="result"> <div ng-hide="isDeletedRecord($index)"> <div bo-show="result.taxonomyId != ''"> <span style="font-weight: bold">Taxonomy: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+result.taxonomyId" bo-text="result.taxonomyId"/> </div> <div bo-show="result.ncbiProjectId != ''"> <span style="font-weight: bold">NCBI Project Id: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids='+result.ncbiProjectId" bo-text="result.ncbiProjectId"/> </div> <div bo-show="result.ecosystem != ''"> <span style="font-weight: bold">Ecosystem: </span> <span bo-text="result.ecosystem"/> </div> <div bo-show="result.genbankAccessionId != ''"> <span style="font-weight: bold">Genbank</span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/nuccore/'+result.genbankAccessionId" bo-text="result.genbankAccessionId"/> <br/> </div> <div bo-show="result.aliases != ''"> <span class="dropdown" on-toggle="toggled(open)"> <a href="" ng-click="onClick($event,$index)" class="dropdown-toggle" style="font-weight: bold">Aliases List</a> <ul class="dropdown-menu"> <li ng-repeat="alias in result.aliases track by $index"> <a target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name='+alias" bo-text="alias"/> </li> </ul> </span> </div> <div bo-show="result.all_aliases != ''"> <span class="dropdown" on-toggle="toggled(open)"> <a href="" ng-click="onClick($event,$index)" class="dropdown-toggle" style="font-weight: bold">Lineage hits</a> <ul class="dropdown-menu"> <li ng-repeat="alias in result.all_aliases track by $index"> <a target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name='+alias" bo-text="alias"/> </li> </ul> </span> </div> <div bo-show="result.lineageTaxonomyIds != ''"> <span class="dropdown" on-toggle="toggled(open)"> <a href="" ng-click="onClick($event,$index)" class="dropdown-toggle" style="font-weight: bold">Lineage Taxonomy Ids: </a> <ul class="dropdown-menu"> <li bindonce="taxonomyId" ng-repeat="taxonomyId in result.lineageTaxonomyIds"> <a bindonce="taxonomyId" target="_self" ng-click="onClick($event,$index)" bo-href="'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+getTaxonId(taxonomyId)" bo-text="taxonomyId"/> </li> </ul> </span> </div> <div bo-show="result.genus != ''"> <span style="font-weight: bold">Genus: </span> <span bo-text="result.genus"/> <br/> </div> <div bo-show="result.species != ''"> <span style="font-weight: bold">Species: </span> <span bo-text="result.species"/> <br/> </div> <div bo-show="result.strain != ''"> <span style="font-weight: bold">Strain: </span> <span bo-text="result.strain"/> <br/> </div> </div> </div> </td> <td ng-hide="isThisPageType('fungalHome')" data-title="'Other'" sortable="'sampleSite'" style="min-width: 200px"> <div bindonce="result"> <div ng-hide="isDeletedRecord($index)"> <div bo-show="result.sampleSite != ''"> <span style="font-weight: bold">Sample site: </span> <span bo-text="result.sampleSite"/><br/> </div> <div bo-show="result.habitat != ''"> <span style="font-weight: bold">Habitat: </span> <span bo-text="result.habitat"/> <br/> </div> <div bo-show="result.imgSubmissionId != ''"> <span style="font-weight: bold">Img submission id: </span> <span bo-text="result.imgSubmissionId"/> <br/> </div> <div bo-show="result.taxon_oids != ''"> <span class="dropdown" on-toggle="toggled(open)"> <a href="" ng-click="onClick($event,$index)" class="dropdown-toggle" style="font-weight: bold">Img taxon oids: </a> <ul class="dropdown-menu"> <li bindonce="taxon_oid" ng-repeat="taxon_oid in result.taxon_oids"> <a bindonce="taxon_oid" target="_self" ng-click="onClick($event,$index)" bo-href="'http://img.jgi.doe.gov/genome.php?id='+taxon_oid" bo-text="taxon_oid"/> </li> </ul> </span> </div> <div bo-show="result.groups != ''"> <div ng-hide="isSingleGroup($index)"> <span class="dropdown" on-toggle="toggled(open)"> <a href="" ng-click="onClick($event,$index)" class="dropdown-toggle" style="font-weight: bold">Groups</a> <ul class="dropdown-menu"> <li bindonce="group" ng-repeat="group in result.groups"> <a bindonce="group" target="_self" ng-click="onClick($event,$index)" bo-href="'/'+group+'/'+group+'.info.html'" bo-text="group"/> </li> </ul> </span> </div> <div bo-show="isSingleGroup($index)"> <span style="font-weight: bold">Group: </span> <a target="_self" ng-click="onClick($event,$index)" bo-href="'/'+result.groups[0]+'/'+result.groups[0]+'.info.html'" bo-text="result.groups[0]"/> </div> </div> </div> </div> </td> </tr> </tbody> </table> </div> </div> </div> </body> </html>
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<!-- tree of life section --> <img src="/images/fungi/fungi_tree_of_life.gif" width="" height="" usemap="#Map3" alt="MycoCosm -the fungal genomic resource"/> <map id="Map3" name="Map3"> <area alt="Video Tutorials" target="_top" href="/programs/fungi/video_tutorials.jsf" coords="0,67,101,90" shape="rect"/> <area alt="Pucciniomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('pucciniomycotina', 'Pucciniomycotina'); return false;" coords="489,1,667,30" shape="rect" href="/"/> <area alt="Ustilaginomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('ustilaginomycotina', 'Ustilaginomycotina'); return false;" coords="489,30,667,54" shape="rect" href="/"/> <area alt="Agaricomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('agaricomycotina', 'Agaricomycotina'); return false;" coords="489,54,667,78" shape="rect" href="/"/> <area alt="Pezizomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('pezizomycetes', 'Pezizomycetes'); return false;" coords="489,78,667,101" shape="rect" href="/"/> <area alt="Orbiliomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('orbiliomycetes', 'Orbiliomycetes'); return false;" coords="489,101,667,126" shape="rect" href="/"/> <area alt="Eurotiomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('eurotiomycetes', 'Eurotiomycetes'); return false;" coords="489,126,667,149" shape="rect" href="/"/> <area alt="Dothideomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('dothideomycetes', 'Dothideomycetes'); return false;" coords="489,149,667,175" shape="rect" href="/"/> <area alt="Lecanoromycetes" target="_top" onclick="showTreeOfLifeNodeMenu('lecanoromycetes', 'Lecanoromycetes'); return false;" coords="489,175,667,200" shape="rect" href="/"/> <area alt="Leotiomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('leotiomycetes', 'Leotiomycetes'); return false;" coords="489,200,667,222" shape="rect" href="/"/> <area alt="Sordariomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('sordariomycetes', 'Sordariomycetes'); return false;" coords="489,222,667,245" shape="rect" href="/"/> <area alt="Xylonomycetes" target="_top" onclick="showTreeOfLifeNodeMenu('xylonomycetes', 'Xylonomycetes'); return false;" coords="489,245,667,271" shape="rect" href="/"/> <area alt="Saccharomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('saccharomycotina', 'Saccharomycotina'); return false;" coords="489,271,667,296" shape="rect" href="/"/> <area alt="Taphrinomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('taphrinomycotina', 'Taphrinomycotina'); return false;" coords="489,296,667,318" shape="rect" href="/"/> <area alt="Glomeromycota" target="_top" onclick="showTreeOfLifeNodeMenu('glomeromycota', 'Glomeromycota'); return false;" coords="489,318,667,343" shape="rect" href="/"/> <area alt="Mortierellomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('mortierellomycotina', 'Mortierellomycotina'); return false;" coords="489,343,667,367" shape="rect" href="/"/> <area alt="Mucoromycotina" target="_top" onclick="showTreeOfLifeNodeMenu('mucoromycotina', 'Mucoromycotina'); return false;" coords="489,367,667,390" shape="rect" href="/"/> <area alt="Zoopagomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('zoopagomycotina', 'Zoopagomycotina'); return false;" coords="489,390,667,413" shape="rect" href="/"/> <area alt="Entomophthoromycotina" target="_top" onclick="showTreeOfLifeNodeMenu('entomophthoromycotina', 'Entomophthoromycotina'); return false;" coords="489,413,667,439" shape="rect" href="/"/> <area alt="Kickxellomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('kickxellomycotina', 'Kickxellomycotina'); return false;" coords="489,439,667,463" shape="rect" href="/"/> <area alt="Blastocladiomycota" target="_top" onclick="showTreeOfLifeNodeMenu('blastocladiomycota', 'Blastocladiomycota'); return false;" coords="489,463,667,487" shape="rect" href="/"/> <area alt="Chytridiomycota" target="_top" onclick="showTreeOfLifeNodeMenu('chytridiomycota', 'Chytridiomycota'); return false;" coords="489,487,667,511" shape="rect" href="/"/> <area alt="Neocallimastigomycota" target="_top" onclick="showTreeOfLifeNodeMenu('neocallimastigomycota', 'Neocallimastigomycota'); return false;" coords="489,511,667,533" shape="rect" href="/"/> <area alt="Microsporidia" target="_top" onclick="showTreeOfLifeNodeMenu('microsporidia', 'Microsporidia'); return false;" coords="489,533,667,557" shape="rect" href="/"/> <area alt="Cryptomycota" target="_top" onclick="showTreeOfLifeNodeMenu('cryptomycota', 'Cryptomycota'); return false;" coords="489,557,667,579" shape="rect" href="/"/> <area alt="Pezizomycotina" target="_top" onclick="showTreeOfLifeNodeMenu('pezizomycotina', 'Pezizomycotina'); return false;" coords="311,140,420,176" shape="rect" href="/"/> <area alt="Ascomycota" target="_top" onclick="showTreeOfLifeNodeMenu('ascomycota', 'Ascomycota'); return false;" coords="195,214,288,251" shape="rect" href="/"/> <area alt="Basidiomycota" target="_top" onclick="showTreeOfLifeNodeMenu('basidiomycota', 'Basidiomycota'); return false;" coords="192,96,291,126" shape="rect" href="/"/> <area alt="Dikarya" target="_top" onclick="showTreeOfLifeNodeMenu('dikarya', 'Dikarya'); return false;" coords="181,171,240,205" shape="rect" href="/"/> <area alt="Fungi" target="_top" onclick="showTreeOfLifeNodeMenu('fungi', 'Fungi'); return false;" coords="54,441,115,474" shape="rect" href="/"/> </map> <p>To use the tree navigation click a branch name and select an organism from the list.</p> <p> <b>For MycoCosm, please cite:</b> Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I. (2014) <a href="http://www.ncbi.nlm.nih.gov/pubmed/24297253">MycoCosm portal: gearing up for 1000 fungal genomes</a>. Nucleic Acids Res. 42(1):D699-704. </p> <p> <b>For JGI Fungal Program, please cite:</b> <a href="http://www.tandfonline.com/doi/abs/10.1080/21501203.2011.584577">Fueling the future with fungal genomics.</a> Grigoriev IV, Cullen D, Goodwin SB, Hibbett D, Jeffries TW, Kubicek CP, Kuske C, Magnuson JK, Martin F, Spatafora JW, Tsang A, Baker SE.(2011) , Mycology. 2(3):192-209.</p> <!-- end of tree of life section -->
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