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<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0" width="265" height="67" title="Java Bioinformatics Analysis Web Services version 2.0"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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<a class="selected" href="index.html">Home</a> \r
<a href="quick_start.html">Getting Started</a> \r
<a href="man_about.html">Manual</a> \r
- <a href="download.html">Download</a> \r
- <a href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
+ <a href="contacts.html">Contact Us</a>\r
<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
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<h2 id="headtitle">JABAWS 2</h2>\r
-<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services version 2">JABAWS<sup>2.0</sup>:Disorder</span> is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are based on <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a>, conservation is calculated by <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>, multiple sequence alignment services are the <a href="http://www.clustal.org/">Clustal W</a>, <a href=\r
+<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> is free software which provides web services for multiple sequence alignment, prediction of protein disorder, and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.0 introduces protein disorder prediction services based on <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a> and protein sequence alignment conservation measures calculated by <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. A new multiple sequence alignment service for <a href="http://www.clustal.org/omega">Clustal Omega</a> is also provided, in addition to standard JABAWS:MSA services for <a href="http://www.clustal.org/clustal2">Clustal W</a>, <a href=\r
"http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, <a href=\r
"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. \r
-<span style="color:black; font-weight:normal; text-align:left;">JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> multiple sequence alignment editor and analysis workbench to allow multiple alignment calculations limited only by your own local computing resources.</span></p>\r
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+<span style="color:black; font-weight:normal; text-align:left;">JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.<br />\r
+<br />\r
+</span>Please note that JABAWS 2 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012). In the meantime you can access all JABAWS2 services through the JABAWS command-line client.</p>\r
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<div class="brick_header"><h2>For Users</h2></div>\r
<div class="brick_content">\r
- <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip">JABAWS Virtual Appliance:</a> (520M)\r
- <br/>\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance:</a> (520M)\r
+ or <a href="man_awscloud.html">use JABAWS on Amazon Webservices Cloud</a><br/>\r
<strong>The Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
- <p>To use JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> the JABAWS Virtual Appliance (VA) and point Jalview at it.</p>\r
+ <p>To use JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
</div>\r
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</td>\r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
<p><strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M) </p>\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M) </p>\r
<p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
</div>\r
</div></td>\r
<div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
<div class="brick_content">\r
<strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (51M)\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
<br/>\r
<strong>The Client: </strong>\r
- Command Line Client <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">binary</a> | <a href=\r
-"http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">source</a> \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.0.jar">source</a> \r
<!-- <li><a href="http://www.jalview.org/download.html">Jalview</a> (18M)</li> -->\r
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<h3 style="margin:0;">Public JABAWS Server</h3>\r
-<p> You can access our public JABA Web Services with our <a href="download.html">command line client</a>, <a href="http://www.jalview.org/download.html">Jalview</a>, or with your own program. Jalview is configured to use this public JABAWS server by default.<br/></p>\r
+<p> You can access our public JABA Web Services with our <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">command line client</a>, <a href="http://www.jalview.org/download.html">Jalview</a>, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2. The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
<ul>\r
<li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>\r
<li>A detailed web services description is available from here: <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"\r
title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
"nofollow">WSDL List</a></li>\r
</ul>\r
-<p>The maximum number of sequences you can align with this public web service is 1000 with up to 1000 letters average length. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can <a href="quick_start.html">download</a> and run the JABAWS Server on your own hardware.</p>\r
-\r
-\r
-<h3>Publication</h3>\r
+<p>These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can <a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+<h3>Previous versions of JABAWS </h3>\r
+<p>JABAWS 1 is available from here <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong>. We advise you to update to the JABAWS 2 as this version is fully backward compatible with JABAWS 1 and contain numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information on versions compatibility. </p>\r
+<h3>Reference</h3>\r
<p><span class="hightlight"></span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" <span class="i">Bioinformatics</span> 2011; <a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&ijkey=gd0DwuYBzFRhe4T">doi: 10.1093/bioinformatics/btr304</a>.</p>\r
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+<div id="copyright">Last update: 10 December 2011<br />\r
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