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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/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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+ <td style="width:150px;height:80px;"><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/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></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="http://www.compbio.dundee.ac.uk/download">Download</a> \r
- <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
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+ <a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a class="newa" 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
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<h2 id="headtitle">JABAWS 2.1</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> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. \r
-Services for multiple sequence alignment include <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>. Analysis services allow\r
-prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, \r
-<a href="http://iupred.enzim.hu">IUPred</a>, Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), \r
-and <a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The \r
-secondary structure for an RNA aligment can be predicted with the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
-</p><p> \r
-<span style="color:black; font-weight:normal; text-align:left;">\r
-JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) \r
-and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r
-and sequence analysis calculations limited only by your own computing resources.<br />\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>. \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
<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
+ <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) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
</div>\r
</div>\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
</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-2.1.jar">command line client</a>, \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
<p>These web services accept submissions of less than one thousand sequences. 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>We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
- contains <a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
- on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p><ul><li>\r
- <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></ul> \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
git://source.jalview.org / jabaws.git / blobdiff