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/benchmarks.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>Benchmarks</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>
<li class="#{pagetype=='informatics'?'selected':''}"><a href="/programs/metagenomes/informatics_publications.jsf" class="topmenu" title="Informatics" id="informatics">Informatics</a>
<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>Benchmarks</h1>
<h2>1. Sanger metagenome sequence data processing.</h2><p>Assembly, gene prediction and functional annotation methods developed originally for processing isolate genomes were benchmarked on Sanger metagenome datasets to assess their precision. This benchmark was based on the generation of simulated metagenomic dataset comprised of real sequence reads from finished isolate genomes sequenced at the JGI. As a result, these methods were subsequently adjusted to improve their performance on Sanger metagenome datasets generated at JGI.</p>
<ul>
<li><a href="http://fames.jgi-psf.org/"><b>Results</b></a></li>
<li><a href="http://www.nature.com/nmeth/journal/v4/n6/abs/nmeth1043.html"><b>Reference</b></a></li>
</ul>
<h2>2. 454 metagenome sequence data processing. </h2>
<p>Gene prediction methods used to predict genes on metagenomic reads from 454 technologies (GS-FLX, FLX Titanium) were evaluated on simulated metagenomes which contained real sequence reads from sequenced genomes (these reads contain the inherent errors of this technology) and genomic fragments following the size distribution of this technology (these sequences do not have any errors). On the first set we also evaluated the effect of trimming on the quality of the gene predictions.
</p>
<ul>
<li><b>Results:</b> in order to determine what the best performance we can achieve with ab initio gene calling methods and to further evaluate the effect of sequencing errors on gene calling, we initially used the simulated dataset (SimP) to evaluate Metagene Annotator (MGA), FragGeneScan (FGS), Prodigal (P) and MetaGeneMark (GM) as well as their intersection. The four methods were selected based on our previous observations of their accuracy and speed, both being capable of processing large datasets in minutes. In addition a similarity based method (blastx) was included. A combination of methods that starts initially with similarity search and supplements findings with ab initio predictions was found to perform better at reasonable time. The ab initio predictions come from the weighted consensus of all ab initio gene callers. Trimming had a significant effect on the quality of the predicted genes.
<img width="656" height="351" alt="chart showing performance of gene calling methods on real 454 data" src="/images/metagenome/benchmark_454.png"/>
<div class="caption" style="max-width: 100%">Figure 1: Number of hits identified by each method or long query sequences</div><br/>
</li>
<li><b>Reference:</b> (submitted for publication)</li>
</ul>
<h2>3. Illumina metagenome sequence data processing </h2>
<p>Gene prediction methods used to predict genes on metagenomic reads from Iillumina sequencing technology were evaluated on simulated metagenomes which contained genomic fragments following the size distribution of this technology.</p>
<ul>
<li><b>Results:</b> in order to determine the capabilities of gene calling methods to predict genes on Illumina reads we evaluated the performance and time requirements of four ab initio gene callers, <b>GeneMark, Metagene, Prodigal,</b> and <b>FragGeneScan</b>, and one similarity based method, <b>Uclust</b>. The four ab initio methods were selected based on our previous observations of their accuracy and speed, both being capable of processing large datasets in minutes, while Uclust was selected as an alternative to Blastx. Despite a 50X acceleration compared to Blastx, Uclust was still proved to be quite slow for processing several tenths of millions of sequences. The final prediction is the weighted consensus of all four ab initio methods.<br/>
<img width="656" height="343" alt="chart showing performance of gene calling methods on Illumina 74 bp" src="/images/metagenome/benchmark_illumina.png"/>
<img width="656" height="361" alt="chart showing acceleration in computations achieved by each method" src="/images/metagenome/benchmark_acceleration.png"/>
<div class="caption" style="max-width: 100%">Figure 2: Number of hits identified by each method on short query sequences</div><br/>
</li>
<li><b>Reference</b> (submitted for publication)</li>
</ul>
<h2>4. Computation of sequence similarities. </h2>
<p>Sequence similarity tools are constantly evaluated in order to identify faster yet sensitive methods that can be used instead of Blast.</p>
<ul>
<li><b>Results:</b> We evaluated four different, publicly available methods, <b>Blastp, Blat, Psimscan</b> and <b>Uclust</b>. We compared each method to the results we get from Blast in terms of number of sequences with hits, number of sequences with the same top hit, time in seconds to complete the comparison. All the comparisons were performed on the same computer, with the same datafiles. Two query files were used, one containing full sequences and the other containing fragments of 30-50aa from these sequences. The sequences in the query files were not included in the database. Overall, blat appeared to be the fastest method with significant loss of sensitivity for the detection of the best hit, when the percentage identity between the proteins was falling below 80%. Uclust and Psimscan showed similar performance in terms of sensitivity and Uclust was ~20X faster than Blast while Psimscan ~10X.<br/>
<img width="656" height="254" alt="chart showing sensitivity of uclust and blat compared to blastp" src="/images/metagenome/benchmark_sensitivity.png"/>
<div class="caption" style="max-width: 100%">Figure 3: Sensitivity of uclust and blat compared to blastp</div><br/>
</li>
<li><b>Reference</b></li>
</ul>
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