website/v_2_1_0/index.html

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
   3 <html xmlns="http://www.w3.org/1999/xhtml">
   4
   5 <head>
   6 <meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>
   7 <title>Java Bioinformatics Analyses Web Services (JABAWS) main page</title>
   8 <link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />
   9 <link href="print.css" rel="stylesheet" type="text/css" media="print" />
  10 <link href='http://fonts.googleapis.com/css?family=Yanone+Kaffeesatz:700' rel='stylesheet' type='text/css' />
  11 <script type="text/javascript" src="prototype-1.6.0.3.js"></script>
  12 </head>
  13
  14 <body>
  15 <div id="page">
  16 <div id="banner">
  17 <table>
  18         <tr>
  19                 <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>
  20                 <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>
  21                 <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
  22         </tr>
  23 </table>
  24 </div>
  25 <!-- banner end-->
  26
  27 <div id="panel">
  28         <a class="newpressed" href="index.html">Home</a>
  29         <a class="newa" href="quick_start.html">Getting Started</a>
  30         <a class="newa" href="man_about.html">Manual</a>
  31         <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a>
  32         <a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>
  33         <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>
  34         <a class="newa" href="contacts.html">Contact Us</a>
  35         <a class="newa" href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>
  36         <a class="newa" href="jabaws_funding.html">Funding</a>
  37 </div>
  38 <!-- panel end-->
  39
  40 <div id="wrapper">
  41 <div id="content">
  42 <h2 id="headtitle">JABAWS 2.1</h2>
  43 <p style="color:black; font-weight:normal; text-align:left;">
  44 <span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span>
  45 is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently
  46 packaged to run on your local computer, server, cluster or Amazon EC2 instance.
  47 </p>
  48
  49 <p> Services for multiple sequence alignment include
  50 <a href="http://www.clustal.org/omega">Clustal Omega</a>,
  51 <a href="http://www.clustal.org/clustal2">Clustal W</a>,
  52 <a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>,
  53 <a href="http://www.drive5.com/muscle">MUSCLE</a>,
  54 <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-Coffee</a>,
  55 <a href="http://probcons.stanford.edu/">ProbCons</a>,
  56 <a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and
  57 <a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>.
  58 Analysis services allow prediction of the protein secondary structure with
  59 <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with
  60 <a href="http://dis.embl.de/">DisEMBL</a>,
  61 <a href="http://iupred.enzim.hu">IUPred</a>,
  62 Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and
  63 <a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation
  64 with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>.
  65 The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the
  66 <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
  67 </p>
  68
  69 <p><span style="color:black; font-weight:normal; text-align:left;">
  70 JABAWS 2.1 installation can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop
  71 application</strong> (version 2.8 onwards) and the <a href="man_client.html">JABAWS command-line client</a>. <br/>
  72 JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own
  73 computing resources.<br />
  74 </span></p>
  75
  76 <div id="mainpagefeatures">
  77 <table>
  78 <tr><td>
  79   <div class="brick">
  80   <div class="brick_header"><h2>For Users</h2></div>
  81     <div class="brick_content">
  82         <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download//get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)
  83         or <a href="man_awscloud.html">JABAWS on Amazon Webservices Cloud</a><br/>
  84         <strong>The Main Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)
  85         <p>To use JABAWS web services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a>
  86         the JABAWS Virtual Appliance (VA). <br/>
  87         Or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>
  88      </div>
  89   </div>
  90   </td>
  91   </tr>
  92   <tr>
  93     <td><div class="brick">
  94       <div class="brick_header"><h2>For System Administrators</h2></div>
  95         <div class="brick_content">
  96           <p>
  97           <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web
  98           Application aRchive</a> (55M)
  99           </p>
 100           <p>JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>
 101           to run. Please check the <a href="manual_qs_war.html#qsc">quick start guide</a> for installation instructions.
 102           </p>
 103    </div>
 104   </div></td>
 105   </tr>
 106   <tr>
 107     <td><div class="brick">
 108      <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>
 109      <div class="brick_content">
 110 <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a>  (55M)
 111   <br/>
 112   <strong>The Client: </strong>
 113       Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=
 114 "http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.1.jar">source</a>
 115
 116 <p>
 117 You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.
 118 The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public
 119 server (see below) with the command line client or you own script.
 120 Check out the <a href="manual_qs_client.html#qsc">quick start guide</a> for further details.</p>
 121
 122  </div>
 123 </div></td>
 124  </tr>
 125 </table>
 126 </div>
 127
 128 <h3 style="margin:0;">Public JABAWS Server</h3>
 129 <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>,
 130     <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.
 131     The latest versions of Jalview are configured to use public JABAWS server by default.</p>
 132 <ul>
 133   <li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>
 134   <li>A detailed web services description is available from here: <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"
 135 title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=
 136 "nofollow">WSDL List</a></li>
 137 </ul>
 138 <p>These web services accept submissions of <strong>less than one thousand sequences</strong>.  Should you find this to be insufficient for your needs,
 139    or if you are concerned about privacy or on an unreliable network connection, then you can
 140    <a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>
 141
 142
 143
 144 <h3>Previous versions of JABAWS </h3>
 145 <p>
 146 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
 147 <a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a>
 148 for more information on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p>
 149 <ul>
 150         <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li>
 151         <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>
 152         <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>
 153 </ul>
 154
 155
 156
 157 <h3>Reference</h3>
 158 <p><span class="hightlight">
 159 </span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - &quot;Java Bioinformatics Analysis Web Services for
 160 Multiple Sequence Alignment - JABAWS:MSA&quot; <span class="i">Bioinformatics</span> 2011;
 161 <a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&amp;ijkey=gd0DwuYBzFRhe4T">
 162 doi: 10.1093/bioinformatics/btr304</a>.</p>
 163 </div><!-- content end-->
 164 <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>
 165 </div><!-- wrapper end-->
 166 </div><!-- page end-->
 167
 168
 169 <!-- Google analitics -->
 170 <script type="text/javascript">
 171 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
 172 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
 173 </script>
 174 <script type="text/javascript">
 175 try{
 176 var pageTracker = _gat._getTracker("UA-5356328-1");
 177 pageTracker._trackPageview();
 178 } catch(err) {}
 179 </script>
 180 <!-- page end-->
 181 </body>
 182 </html>