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- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.1" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
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+ <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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<div id="content">\r
-<h2 id="headtitle">JABAWS 2.0.1</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">JABAWS</span> \r
-is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> for multiple sequence alignment \r
-(programs available: <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
-<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
-<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">, TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>), \r
-prediction of protein disorder (programs available: <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, \r
-<a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a>), \r
-and amino acid conservation (program available: <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>) \r
-conveniently packaged to run on your local computer, server or cluster. \r
-<span style="color:black; font-weight:normal; text-align:left;">\r
-JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> desktop application and provide multiple alignment \r
-and sequence analysis calculations limited only by your own local computing resources.<br />\r
-<br />\r
-</span>Please note that JABAWS 2.0.1 is supported by Jalview 2.8 onwards. You can also access all JABAWS 2.0.1 services through the JABAWS command-line client.</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://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm-201.tar.gz">JABAWS Virtual Appliance:</a> (440M)\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download//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 JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
- the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\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
<td><div class="brick">\r
<div class="brick_header"><h2>For System Administrators</h2></div>\r
<div class="brick_content">\r
- <p><strong>The Server: </strong><a href="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. \r
- Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
+ <p>\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/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
<strong>The Server: </strong><a href="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/download/get?id=min-jaba-client-2.0.1.jar">binary</a> | <a href=\r
-"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.0.1.jar">source</a> \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/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 just script against our public \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
\r
<h3 style="margin:0;">Public JABAWS Server</h3>\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-2.0.1.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 2.0.1.\r
+<p> You can access our public JABAWS web services with our <a href="http://www.compbio.dundee.ac.uk/download/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.compbio.dundee.ac.uk/jabaws</strong> </li>\r
title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
"nofollow">WSDL List</a></li>\r
</ul>\r
-<p>These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, \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://www.compbio.dundee.ac.uk/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>Old JABAWS versions are available here:\r
- <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a> and \r
- <a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong>. \r
- We advise you to update to the JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
- contain numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
- on compatibility between versions.\r
-</p>\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
<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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