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-"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
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<div id="content">\r
-<h4 id="headtitle" style="text-align:left">What is JABAWS?</h4>\r
-\r
-<p><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\r
-collection of <a href=\r
-"http://www.w3schools.com/SOAP/soap_intro.asp">SOAP</a> web\r
-services for bioinformatics.<br />\r
- JABAWS is designed to make it easy to access bioinformatics\r
-analysis programs and databases over the web from anywhere, at\r
-anytime. Unlike other web services, JABAWS can be easily installed on different platforms and work straight out of the box with minimum configuration. JABA Web Services are designed for use by other programs rather\r
-than people.\r
- The current version of JABAWS is compatible with version 2.6 of <a\r
-href="http://www.jalview.org">Jalview</a>, and provides five web\r
-services for multiple sequence alignment:</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=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://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
+ <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://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-2.1.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 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://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><a href="http://www.clustal.org/">Clustal W</a></li>\r
-\r
-<li><a href=\r
-"http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a></li>\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>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
-<li><a href="http://www.drive5.com/muscle">MUSCLE</a></li>\r
\r
-<li><a href=\r
-"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">\r
-TCOFFEE</a></li>\r
\r
-<li><a href="http://probcons.stanford.edu/">PROBCONS</a></li>\r
-</ul>\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
-<h4>Why JABAWS?</h4>\r
\r
-<p> JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to <a href="http://www.drmaa.org/">DRMAA</a> it integrates well with a large variety of cluster job management systems. <a href="http://www.jalview.org">Jalview</a> from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on <a href="howto.html#wjaba">JABAWS benefits</a>. </p>\r
-<h4>Public JABAWS Server</h4>\r
-<p class="attention">Please note that JABAWS computing cluster is going for a maintenance shutdown on the weekend starting from the 8-th of January. Therefore, no services will be available from <span class="style1">6pm Friday the 7th of January</span>, until <span class="style1">12am Monday the 10th of January 2011 GMT</span>. </p>\r
-<table>\r
-<tbody>\r
-<tr>\r
-<th width="22%">Feature</th>\r
-<th width="78%">Description</th>\r
-</tr>\r
-\r
-<tr>\r
-<td><acronym title="Uniform Resource Locator">URL</acronym> </td>\r
-<td><a href="http://www.compbio.dundee.ac.uk/jabaws" title=\r
-"http://www.compbio.dundee.ac.uk/jabaws" rel=\r
-"nofollow">http://www.compbio.dundee.ac.uk/jabaws</a> </td>\r
-</tr>\r
-\r
-<tr>\r
-<td>Execution limits</td>\r
-<td>JABAWS installation is backed up by the College of\r
-Life Sciences HPC cluster. Tasks exceeding 1000×1000\r
-(sequences per letters) will not be accepted for alignment. If you\r
-would like to work with bigger alignments consider installing\r
-JABAWS in your lab.</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>Web Services Description</td>\r
-<td><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> </td>\r
-</tr>\r
-</tbody>\r
-</table>\r
\r
-<p>For programmatic access to JABAWS please refer to the How To section <a href="manual.html#connectto">using JABAWS in your program</a>.</p>\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
-<h4>Authors</h4>\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
+<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
+</div><!-- content end-->\r
+<div id="copyright">Last update: 30 April 2014<br /> This site is best viewed in Firefox 3.6, Google Chrome 10, Internet Explorer 8 or above </div>\r
+</div><!-- wrapper end-->\r
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\r
-<!-- content end-->\r
-<div id="copyright">Last update: 17 November 2010<br />\r
- Peter Troshin and Geoff Barton, The Barton Group, University of\r
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