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   7 <title>Java Bioinformatics Analyses Web Services (JABAWS) main\r
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  21 <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
  22 <td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
  23 <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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  31  <a class="selected" href="index.html">Home</a> \r
  32  <a href="quick_start.html">Getting Started</a> \r
  33  <a href="man_about.html">Manual</a> \r
  34  <a href="download.html">Download</a> \r
  35  <a href="contacts.html">Contact Us</a>\r
  36  <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
  37  <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
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  40 <div id="content">\r
  41 <h2 id="headtitle">JABAWS 2</h2>\r
  42 <p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services version 2">JABAWS<sup>2.0</sup>:Disorder</span> is  free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. Disorder prediction services are 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>, conservation is calculated by <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>, multiple sequence alignment services are the <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, <a href=\r
  43 "http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, <a href=\r
  44 "http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. \r
  45 <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> multiple sequence alignment editor and analysis workbench  to allow multiple        alignment calculations limited only by your own local computing        resources.</span></p>\r
  46 \r
  47 <div id="mainpagefeatures">\r
  48 <table>\r
  49 <tr><td>\r
  50   <div class="brick">   \r
  51   <div class="brick_header"><h2>For Users</h2></div>\r
  52     <div class="brick_content">\r
  53         <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip">JABAWS Virtual Appliance:</a> (520M)\r
  54         or <a href="man_awscloud.html" title="Amazon Machine Image">JABAWS AMI</a> for the Amazon EC2 Cloud<br/>\r
  55         <strong>The Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
  56                 <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
  57      </div>\r
  58   </div>\r
  59   </td>\r
  60   </tr>\r
  61   <tr>\r
  62     <td><div class="brick">\r
  63              <div class="brick_header"><h2>For System Administrators</h2></div>\r
  64                  <div class="brick_content">\r
  65                    <p><strong>The Server: </strong><a href=\r
  66 "http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a> (55M)                 </p>\r
  67                    <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
  68                  </div>\r
  69                 </div></td>\r
  70   </tr>\r
  71   <tr>\r
  72     <td><div class="brick">\r
  73              <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
  74                  <div class="brick_content">\r
  75 <strong>The Server: </strong><a href=\r
  76 "http://www.compbio.dundee.ac.uk/jabaws/archive/jaba.war">JABAWS Web Application aRchive</a>  (55M)\r
  77   <br/>\r
  78   <strong>The Client: </strong>\r
  79       Command Line Client <a href="http://www.compbio.dundee.ac.uk/jabaws/archive/min-jaba-client-2.0.jar">binary</a> | <a href=\r
  80 "http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source-2.0.jar">source</a> \r
  81           <!-- <li><a href="http://www.jalview.org/download.html">Jalview</a> (18M)</li> -->\r
  82   \r
  83   \r
  84 <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
  85 Check out the <a href="manual_qs_client.html#qsc">quick start guide</a> for further details.</p>\r
  86 \r
  87                  </div>\r
  88                 </div></td>\r
  89   </tr>\r
  90 </table>\r
  91 </div>\r
  92 \r
  93 <h3 style="margin:0;">Public JABAWS Server</h3>\r
  94 <p> You can access our public JABA Web Services with our <a href="download.html">command line client</a>, <a href="http://www.jalview.org/download.html">Jalview</a>, or with your own program. Jalview is configured to use this public JABAWS server by default.<br/></p>\r
  95 <ul>\r
  96   <li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>\r
  97   <li>A detailed web services description is available from here: <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"\r
  98 title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
  99 "nofollow">WSDL List</a></li>\r
 100 </ul>\r
 101 <p>These web services will reject submissions containing more then 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="download.html">download</a> and run the JABAWS Server on your own hardware.</p>\r
 102 \r
 103 \r
 104 <h3>Reference</h3>\r
 105 <p><span class="hightlight"></span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - &quot;Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA&quot; <span class="i">Bioinformatics</span> 2011; <a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&amp;ijkey=gd0DwuYBzFRhe4T">doi: 10.1093/bioinformatics/btr304</a>.</p>\r
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 109 <div id="copyright">Last update: 2 August 2011<br />\r
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