An Error Occurred:
javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy
javax.faces.FacesException: javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_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:284)
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.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:235)
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:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.view.common.StaticContentFilter.doFilter(StaticContentFilter.java:167)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.framework.data.EntityManagerFilter.doFilter(EntityManagerFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
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: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 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at gov.doe.jgi.portal.tomcat.SessionInvalidateValve.invoke(SessionInvalidateValve.java:74)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:774)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703)
at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:896)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
at java.lang.Thread.run(Thread.java:722)
Caused by: javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:76)
at javax.faces.component.UIOutput.getValue(UIOutput.java:173)
... 48 more
Caused by: java.lang.NullPointerException
at java.util.regex.Matcher.getTextLength(Matcher.java:1233)
at java.util.regex.Matcher.reset(Matcher.java:308)
at java.util.regex.Matcher.<init>(Matcher.java:228)
at java.util.regex.Pattern.matcher(Pattern.java:1088)
at gov.doe.jgi.portal.framework.config.PortalConfig.getOrganismsMatching(PortalConfig.java:1012)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.init(ProgramHome.java:124)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.check(ProgramHome.java:114)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.getLatestReleases(ProgramHome.java:74)
at gov.doe.jgi.portal.view.pages.ProgramHome.getLatestReleases(ProgramHome.java:224)
at gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy.getLatestReleases(MetagenomesHome$Proxy$_$$_WeldClientProxy.java)
at sun.reflect.GeneratedMethodAccessor2367.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at javax.el.BeanELResolver.getValue(BeanELResolver.java:62)
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:54)
at com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:64)
at org.apache.el.parser.AstValue.getValue(AstValue.java:123)
at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
at org.jboss.weld.el.WeldValueExpression.getValue(WeldValueExpression.java:50)
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
... 49 more
- <AjaxViewRoot id="_viewRoot" immediate="false" locale="en_US" renderKitId="HTML_BASIC" renderRegionOnly="false" rendered="true" selfRendered="false" submitted="false" transient="false" viewId="/programs/metagenomes/poplar_biomass.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" xmlns:t="http://myfaces.apache.org/tomahawk">
<head>
- <HtmlOutputText escape="false" id="j_id2" rendered="true" transient="false" value="<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
<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">var _gaq = _gaq || [];_gaq.push(['_setAccount', 'UA-23422913-1']);_gaq.push(['_trackPageview']);_gaq.push(['_setCustomVar',3,'Looged-In','No',2]);(function() {var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);})();</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.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/metagenome-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.get(url, function(data) {
treeOfLife[nodeName] = 1;
eval(data);
multitool( x, y, nodeName, nodeLabel );
});
} 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/metagenome.css" rel="stylesheet" type="text/css"/>
<link rel="stylesheet" media="screen" href="/css/superfish.css"/>
<link rel="stylesheet" media="screen" href="/css/superfish_metagenome.css"/>
- <title>Poplar Biomass</title>
</head>
<body onload="init();">
- <HtmlOutputText escape="false" id="j_id5" rendered="true" transient="false" value="<div class="header_wrap">
<div class="header_top"><div id="subnavleft"><a class="skipnav" href="#skipnav" accesskey="S"><img src="/images/clear.gif" alt="skip navigation" width="1" height="1" border="0" /></a><ul id="subnavicons"><li><a target="_parent" href="http://www.jgi.doe.gov" alt=""> <img class="header_image" alt="DOE Joint Genome Institute logo" style="padding-right: 2em" src="/images/jgiLogo_icon.gif"/></a></li><li><a target="_parent" href="/"><img border="0" alt="Genome Portal icon" src="/images/tree_icon.gif"/></a></li>
<li><a class="textlink" target="_parent" href="/">Home</a></li>
<li><a target="_parent" href="/genome-projects/"><img border="0" alt="Genome Projects icon" src="/images/genomeProjects_icon.gif"/></a></li>
<li><a class="textlink" target="_parent" href="/genome-projects/">Project List</a></li>
<li><a href="javascript: if(top.window.location.href.search('accessDenied')==-1) { document.cookie='jgi_return=' + escape(top.window.location.href) + '; domain=.jgi-psf.org; path=/;'; } top.window.location.href='https://signon2.jgi-psf.org/signon';"><img border="0" alt="Login icon" src="/images/login_icon.gif"/></a></li><li><a class="textlink" target="_parent" href="javascript: if(top.window.location.href.search('accessDenied')==-1) { document.cookie='jgi_return=' + escape(top.window.location.href) + '; domain=.jgi-psf.org; path=/;'; } top.window.location.href='https://signon2.jgi-psf.org/signon';">Login</a></li></ul></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 id="nav">
<ul class="sf-menu">
<li class="#{pagetype=='home'?'selected':''}"><a href="/programs/metagenomes/index.jsf" title="Back to home page" class="topmenu" id="home">Home</a></li>
<li class="#{pagetype=='project_list'?'selected':''}"><a href="/programs/metagenomes/metagenomic-projects.jsf" class="topmenu" title="Projects sequenced at JGI" id="project_list">Project List</a>
</li>
<li class="#{pagetype=='user_programs'?'selected':''}"><a href="http://www.jgi.doe.gov/CSP/index.html" title="Community Sequencing Program" class="topmenu" id="user_programs">User Programs</a></li>
<li class="#{pagetype=='science'?'selected':''}"><a href="/programs/metagenomes/publications_genomes.jsf" class="topmenu" title="Metagenome Projects and Publications" id="science">Science</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/poplar_biomass.jsf">Projects<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://genomebiology.jgi-psf.org/Content/Metagenomic_analysis.htm">Metagenome Analysis</a></li>
<li><a href="/programs/metagenomes/poplar_biomass.jsf">Poplar Biomass</a></li>
<li><a href="/programs/metagenomes/CowRumenMetagenome.pdf">Cow Rumen Metagenome</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/publications_genomes.jsf">Publications</a>
</li>
</ul>
</li>
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<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/systems.jsf">Systems<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://img.jgi.doe.gov/">IMG/M</a></li>
<li><a href="http://www.genomesonline.org/">GOLD</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/methods.jsf">Methods<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="/programs/metagenomes/assembly.jsf">Assembly</a></li>
<li><a href="http://journals.sfu.ca/sigen/index.php/sigen/article/viewFile/sigs.632/sigs632.pdf">Annotation Pipeline</a></li>
<li><a href="http://clams.jgi-psf.org/">CLaMS</a></li>
<li><a href="http://coal.jgi-psf.org/CoverageServer/">GammaCov</a></li>
<li><a href="http://pyrotagger.jgi-psf.org/cgi-bin/index.pl">PyroTagger</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/benchmarks.jsf">Benchmarks</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/data_reduction.jsf">Projects<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://fames.jgi-psf.org/">FAMeS</a></li>
<li><a href="/programs/metagenomes/data_reduction.jsf">Data Reduction</a></li>
<li><a href="/programs/metagenomes/binning.jsf">Binning</a></li>
<li><a href="/programs/metagenomes/cow_rumen_analysis.jsf">Cow Rumen Metagenome Data Analysis</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/informatics_publications.jsf">Publications</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/credits.jsf">Credits</a></li>
</ul>
</li>
<li class="#{pagetype=='outreach'?'selected':''}"><a href="/programs/metagenomes/workshops.jsf" class="topmenu" title="Metagenomics workshops and Meetings" id="outreach">Outreach</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/workshops.jsf">Workshops</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/meetings.jsf">Meetings</a></li>
</ul>
</li>
<li class="#{pagetype=='about_program'?'selected':''}"><a href="/programs/metagenomes/mission.jsf" title="about program, mission, organization, advisory_committee" class="topmenu" id="about_program">About Program</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/mission.jsf">Mission</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/organization.jsf">Organization</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/advisory_committee.jsf">Advisory Committee</a></li>
</ul>
</li>
</ul>
</div>
<img src="/images/metagenome/metagenome_banner.png" width="" height="" border="0" usemap="#logomap" class="banner" alt="banner with logo of Metagenomics program"/>
<map name="logomap" id="logomap">
<area shape="rect" coords="10,0,350,72" href="/programs/metagenomes/index.jsf" alt="Metagenomics Program at JGI, Home"/>
</map>
<a name="skipnav" id="skipnav"/>
- <!--end of navigation and top banner-->
<!-- content section-->
<div id="content">
<!--left side panel -->
- <div id="leftside"><!--section navigation --> <!-- <div id="sectionnav">
<a href="/pages/fungi/about_program.jsf"><h2 class="list_title" >Genomic Encyclopedia of Fungi</h2></a>
<ul>
<li><a class="list_header_feedstock" href="/pages/fungi/about_program.jsf#feedstock">Plant Feedstock Health</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#symbiosis">Mycorrhizal Symbiosis</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#pathogenicity">Plant Pathogenicity</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biocontrol">Biocontrol</a></li>
<li><a class="list_header_biorefinery" href="/pages/fungi/about_program.jsf#biorefinery">Biorefinery</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Lignocellulose Degradation</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Sugar Fermentation</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Industrial Organisms</a></li>
<li><a class="list_header_diversity" href="/pages/fungi/about_program.jsf#diversity">Fungal Diversity</a></li>
</ul>
</div>--> <!--end of section navigation -->
<div class="clear"/>
<!--Announcements -->
<div id="announcements">
<h2 class="red">Announcements</h2>
<ul>
<li><span class="date">January 23-24, 2012 <br/>
</span><a href="http://www.jgi.doe.gov/meetings/csp-pi-workshop/">CSP 2012 PI Workshop</a>, Walnut Creek, CA
</li>
</ul>
</div>
<a class="link_arrow" href="/programs/metagenomes/workshops.jsf">more</a>
<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_id10" rendered="true" transient="false"/>
- <a class="link_arrow" href="/programs/metagenomes/genome-releases.jsf">more</a>
<!--end of New Releases -->
<div class="grey_divider"/>
</div>
</div>
- <!--end of left side panel -->
<!--right side panel -->
<div id="rightside">
<h1>Poplar Biomass</h1>
<h2>Microbial community actively degrading poplar biomass</h2>
<p>The successful production of carbon-neutral biofuels requires efficient deconstruction of lignocellulosic biomass into fermentable sugars. Current industrial processes rely on harsh and energy intensive pretreatments in combination with enzymes which are expensive to produce, and yet fail to extract much of the useful energy from the biomass. This project is aimed at identifying and characterizing free-living organisms which colonize and degrade poplar woodchips without pretreatment, and determine whether they or their enzymes could be exploited for enzymatic deconstruction of biofuel feedstocks.</p>
<div class="picture" style="float:right"><img border="0" title="TEM micrographs of control (A) and composted (B) poplar cell walls." alt="TEM micrographs of control (A) and composted (B) poplar cell walls." src="/images/metagenome/Poplar_biomass_TEMs.png"/><div class="caption">TEM micrographs of control (A) and composted (B) poplar cell walls.<br/><b>Photo</b>: Safiyh Taghavi and Bryon Donohoe</div></div>
<p>Samples were taken from the anaerobic core of a large poplar woodchip pile at the National Renewable Energy Laboratory (NREL) in Golden, CO. Some of this material was used for small-scale sequencing, and some used to seed a semi-closed bioreactor incubated at 30C at Brookhaven National Lab for more than a year. Some material was then removed from the anaerobic zone at the bottom of the bucket and used for microscopic imaging as well as DNA extraction and large-scale sequencing.</p>
<p>In total we have generated more than 950 Mb shotgun metagenome sequence data from this sample, using a combination of Sanger and 454 pyrosequencing technologies, which assembled into contigs totaling <b>51 Mb</b> and singlets totaling <b>331 Mb</b>. Much of the assembled sequence could be partitioned into 6 genome-sized phylogenetic bins including both known biomass-degrading lineages (e.g. Bacteroidetes and Clostridiales) and organisms not typically associated with biomass degradation (e.g. Magnetospirillum and deeply rooted Cyanobacteria). Within these sequences we have identified thousands of sequences with homology to carbohydrate-active enzymes, particularly glycosyl hydrolase families 2, 3, 38 and 78, most with relatively low identity to previously sequenced genes. Comparison with other biomass-degrading communities reveals a unique enzyme profile, including some enzymes not commonly found in other metagenome datasets. Where only partial genes were observed, we are using complete fosmid sequencing and inverse PCR / primer walking to obtain full-length clones for further investigation. These full-length genes are being examined for novel domain structures and tested for cellulolytic activity.</p>
<p><b><a href="http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&taxon_oid=2010388001">Data for this project in IMG/M</a></b></p>
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