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.GeneratedMethodAccessor5260.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/cow_rumen_analysis.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>Cow Rumen Metagenome Data Analysis</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>
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<li><a href="/programs/metagenomes/poplar_biomass.jsf">Poplar Biomass</a></li>
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</ul>
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<ul>
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</ul>
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<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>
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<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>Cow Rumen Metagenome Data Analysis</h1>
<h3>Motivation</h3>
<p>Cow rumen harbors a complex microbial community with thousands of species that efficiently degrade biomass into fermentable sugar, a bottleneck step in biofuel production. Discovering genes coding for cellulolytic enzymes and genomes harboring these enzymes are the scientific goals of the cow rumen metagenome analysis project. Initial cow rumen metagenome sequence datasets totaled 279 Gb of sequences consisting of 3 billion short reads with lengths from 75-125bp. Challenges to analyze these sequences include not only the size of the data and their suboptimal quality, but also the paucity of existing tools that can process data of this scale. To address these challenges a novel metagenome data processing has been developed.</p>
<h3>Results</h3>
<p>The metagenome data analysis pipeline consists of three components:
<ol>
<li>The <b>data preprocessing</b> component aims at improving the quality of metagenome sequence data. In the first step reads that are originated from spike-in controls, sequencing adaptors, sequencing artifacts, low complexity and tandem repetitive regions of the genome are removed. In the second step reads containing sequencing errors are trimmed using a k-mer based approach. Finally near identical reads originated from PCR amplification are grouped and collapsed into a consensus sequence by using Nary-tree and suffix tree data structures.
</li>
<li>The <b>genome-based cellulase gene prediction</b> component. The pipeline begins with selecting reads from abundant species by an empirical k-mer based approach, followed by assembling contig using Velvet and predicting gene using the IMG pipeline, and ends with predicting genes for cellulase signatures.
</li>
<li>The <b>gene-based cellulase gene prediction</b>. This part of the pipeline begins with selecting reads that are homologous to known enzyme coding genes, followed by assembling genes using Velvet and extending the resulted contigs, and ends with assigning novel candidates to known enzyme categories using BLAST.
</li>
</ol>
</p>
<p>The pipeline outlined above is limited to identifying enzymes that share significant similarity to the domains of existing known enzymes, and largely exclude novel enzymes that do not show homology but may possess novel enzymatic dynamics or novel substrate.
</p>
<p>
The pipeline has been used successfully to predict novel enzyme candidates , with a significant portion of them expected to be true cellulases.
</p>
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