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-<p id="headtitle" style="color:black; font-weight:normal; text-align:left;" >\r
-<span class="u">JA</span>va <span class=\r
-"u">B</span>ioinformatics <span class="u">A</span>nalysis <span\r
-class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a collection of SOAP web services for Bioinformatics. <br />\r
-Currently JABAWS provides five web\r
-services for multiple sequence alignment <a href="http://www.clustal.org/">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>. <span style="color:black; font-weight:normal; text-align:left;">Unlike other web services you can run JABAWS services from your own computer. This puts you in control of the web services - they will be where and when you need them, have no restrictions and your data privacy is guaranteed. JABAWS scales well from the single user single computer to the cluster with hundreds of users. Finally, you do not have to be an expert to use JABAWS - the installation is simple and you can use the services from the comfort of your desktop via <a href="http://www.jalview.org">Jalview</a>.</span></p>\r
-<h3>Public JABAWS Server</h3>\r
-<p> You can access our public JABA Web Services with our <a href="download.html">command line client, </a>the <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a>, or write your own program. To guarantee a level service for everyone our public services impose some restrictions on the size and the number of the jobs you can submit. Currently we do not process tasks that exceed 1000 sequences per 1000 letters on average. Should you find this to be insufficient for your needs you can download and run JABAWS Server on your own hardware. This also applies if the privacy is a concern or an Internet connection is a problem. </p>\r
+<h2 id="headtitle">JABAWS 2.1</h2>\r
+<p style="color:black; font-weight:normal; text-align:left;">\r
+<span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> \r
+is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently \r
+packaged to run on your local computer, server, cluster or Amazon EC2 instance.\r
+</p>\r
+\r
+<p> Services for multiple sequence alignment include \r
+<a href="http://www.clustal.org/omega">Clustal Omega</a>, \r
+<a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
+<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, \r
+<a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
+<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-Coffee</a>, \r
+<a href="http://probcons.stanford.edu/">ProbCons</a>,\r
+<a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and\r
+<a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>. \r
+Analysis services allow prediction of the protein secondary structure with \r
+<a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with \r
+<a href="http://dis.embl.de/">DisEMBL</a>, \r
+<a href="http://iupred.enzim.hu">IUPred</a>, \r
+Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and \r
+<a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation \r
+with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. \r
+The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the \r
+<a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
+</p>\r
+\r
+<p><span style="color:black; font-weight:normal; text-align:left;">\r
+JABAWS 2.1 installation can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop \r
+application</strong> (version 2.8 onwards) and the <a href="man_client.html">JABAWS command-line client</a>. <br/>\r
+JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own \r
+computing resources.<br />\r
+</span></p>\r
+\r
+<div id="mainpagefeatures">\r
+<table>\r
+<tr><td>\r
+ <div class="brick">\r
+ <div class="brick_header"><h2>For Users</h2></div>\r
+ <div class="brick_content">\r
+ <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)\r
+ or <a href="man_awscloud.html">JABAWS on Amazon Webservices Cloud</a><br/>\r
+ <strong>The Main Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
+ <p>To use JABAWS web services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
+ the JABAWS Virtual Appliance (VA). <br/>\r
+ Or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
+ </div>\r
+ </div>\r
+ </td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For System Administrators</h2></div>\r
+ <div class="brick_content">\r
+ <p>\r
+ <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web \r
+ Application aRchive</a> (55M)\r
+ </p>\r
+ <p>JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>\r
+ to run. Please check the <a href="manual_qs_war.html#qsc">quick start guide</a> for installation instructions.\r
+ </p>\r
+ </div>\r
+ </div></td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
+ <div class="brick_content">\r
+<strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
+ <br/>\r
+ <strong>The Client: </strong>\r
+ Command Line Client <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
+"http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jaba-client-src-2.1.jar">source</a> \r
+\r
+<p>\r
+You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. \r
+The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public \r
+server (see below) with the command line client or you own script. \r
+Check out the <a href="manual_qs_client.html#qsc">quick start guide</a> for further details.</p>\r
+\r
+ </div>\r
+</div></td>\r
+ </tr>\r
+</table>\r
+</div>\r
+\r
+<h3 style="margin:0;">Public JABAWS Server</h3>\r
+<p> You can access our public JABAWS web services with our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">command line client</a>, \r
+ <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 2.1.\r
+ 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.combio.dundee.ac.uk/jabaws</strong> </li>\r
- <li>Detailed web services description is available from here: <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"\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
-<h3>Contact Us </h3>\r
-<p>Please feel free to post your questions/issues to the <a href="http://www.jalview.org/mailman/listinfo/jabaws-discuss">jabaws-discuss</a> mailing list. </p>\r
-<h3>Authors</h3>\r
-<p>Peter Troshin and Geoff Barton are the authors of the JABA Web\r
-Services. Jim Procter helped with the JABAWS design process and web\r
-pages, and developed the interface and management components in\r
-Jalview to access JABAWS servers.</p>\r
-</div>\r
+<p>These web services accept submissions of <strong>less than one thousand sequences</strong>. Should you find this to be insufficient for your needs, \r
+ or if you are concerned about privacy or on an unreliable network connection, then you can \r
+ <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+\r
+\r
+\r
+<h3>Previous versions of JABAWS </h3>\r
+<p>\r
+We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains \r
+<a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> \r
+for more information on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p>\r
+<ul>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> \r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>\r
+</ul> \r
+\r
+\r
+\r
+<h3>Reference</h3>\r
+<p><span class="hightlight">\r
+</span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for \r
+Multiple Sequence Alignment - JABAWS:MSA" <span class="i">Bioinformatics</span> 2011; \r
+<a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&ijkey=gd0DwuYBzFRhe4T">\r
+doi: 10.1093/bioinformatics/btr304</a>.</p>\r
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