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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><h2><span class="headeru">JA</span>va <span class=\r
-"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
-class="headeru">S</span>ervices</h2></td>\r
+<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" width="265" height="67" title="Java Bioinformatics Analysis Web Services version 2.0"/></td>\r
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-<div id="panel"><a class="selected" href="index.html">Home</a> <a\r
-href="manual.html">Manual</a> <a href="howto.html">How To</a> <a\r
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<div id="content">\r
-<h4>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 over the web, by providing web services, which\r
-make it easy to access programs and databases from anywhere, at\r
-anytime. The flavour of web services that JABAWS provides are SOAP\r
-web services, which are designed for use by other programs, rather\r
-than people.<br />\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
-\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
-\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
-\r
-<h4>Why JABAWS?</h4>\r
-\r
-<p>JABA Web Services has a number of distinct features that are not\r
-found in other bioinformatics web services systems. In particular,\r
-JABAWS:</p>\r
-\r
-<ol>\r
-<li>Provides uniform remote access to a number of command line\r
-tools <span class="box">This allows you to access a number of\r
-programs anywhere, at any time. For instance, all multiple sequence\r
-alignment services can be accessed with a single command line\r
-interface, simplifying their invocation. However, most of the\r
-command line options for each program are supported, so you have\r
-nearly the same level of control as if you were running them on the\r
-command line yourself.</span></li>\r
-\r
-<li>Enables web based or stand-alone applications, like Jalview, to\r
-access a variety of bioinformatics analysis methods <span class=\r
-"box">The java web service client library makes it very easy to\r
-connect to one or more instances of JABAWS, so if one server is off\r
-line, all you need to know is the URL of another server that will\r
-do the job for you.<br />\r
-JABAWS provides <a href="http://www.ws-i.org/">WS-I basic\r
-profile</a> v. 1.1 compatible services, which means that clients\r
-can be created for them in almost any programming\r
-language.</span></li>\r
-\r
-<li>Can be easily deployed as a server on a variety of platforms,\r
-with command line tools run on the same machine or on a\r
-cluster.<span class="box"><a href="howto.html#clustsubsys">JABAWS\r
-integrates with a number of cluster job management systems (e.g.\r
-GridEngine, PBS, LSF, Condor).</a> It also intelligently manages\r
-task scheduling depending on their size, eliminatng the scalability\r
-issues and let you focus on your research.</span></li>\r
-</ol>\r
-\r
-<p>Here are just some of the problems that JABAWS can solve:</p>\r
-\r
-<ul>\r
-<li>\r
-<p><strong>The default settings for a program don't work for my\r
-data!</strong><br />\r
- JABAWS includes a comprehensive parameter model and validation\r
-mechanism, allowing you to specify additional options and\r
-arguments. Want to use PAM200 substitution matrix, set the number\r
-of iterations, or sequence clustering method? No problem - JABAWS\r
-lets you do that. You are no longer limited to defaults!</p>\r
-</li>\r
-\r
-<!--<li>\r
- <p><strong>JABAWS in Dundee is not available?</strong> No problem,\r
- choose a different service provider and off you go. We hope that\r
- other major service providers like EBI will soon be housing\r
- JABAWS.</p>\r
- </li> -->\r
-<li>\r
-<p><strong>I don't want to send my data to the\r
-internet!</strong><br />\r
- Simply <a href="download.html">download</a> and <a href=\r
-"howto.html#hdjaba">install</a> JABAWS on a trusted machine in your\r
-lab or institute, and use its web address instead of the public\r
-JABAWS services. No data will leave your lab any longer.</p>\r
-</li>\r
-\r
-<li>\r
-<p><strong>Running programs using the public services is slower\r
-than using my own computer!</strong><br />\r
- The JABAWS server can run programs on a single machine or on a\r
-cluster, and are <a href="howto.html#hdjaba">easy to install</a>.\r
-If your server is going to be heavily used, then it is better to <a\r
-href="howto.html#clustsubsys">configure JABAWS to access your\r
-cluster</a>, which is straightforward.</p>\r
-</li>\r
-</ul>\r
-\r
-<h3>Public JABAWS Server</h3>\r
-\r
+<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">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> 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
+<div id="mainpagefeatures">\r
<table>\r
-<tbody>\r
-<tr>\r
-<th>Feature</th>\r
-<th>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>Local execution limit is 40 sequnces with no more than 500\r
-letters average length. Larger tasks are send to 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
+<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.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) 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><strong>The Server: </strong><a href=\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
+ </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=\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/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
+ \r
+ \r
+<p>You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public 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
-<h4>Authors</h4>\r
-\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
+<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.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>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
</div>\r
\r
<!-- content end-->\r
-<div id="copyright">Last update: 19 August 2010<br />\r
- Peter Troshin and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
+<div id="copyright">Last update: 10 December 2011<br />\r
+ This site is best viewed in Firefox 3.6, Google Chrome 10, Internet Explorer 8 or above </div>\r
</div>\r
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