-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"\r
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<?xml version="1.0" encoding="UTF-8"?>\r
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
+\r
<head>\r
-<meta name="generator" content="HTML Tidy, see www.w3.org" />\r
-<meta http-equiv="Content-Type" content=\r
-"text/html; charset=iso-8859-1" />\r
-<title>Java Bioinformatics Analyses Web Services (JABAWS) main\r
-page</title>\r
-<link href="ws.css" rel="stylesheet" type="text/css" media=\r
-"screen, projection, handheld, tv" />\r
-<link rel="stylesheet" type="text/css" media="print" href=\r
-"print.css" />\r
-<script type="text/javascript" src="prototype-1.6.0.3.js">\r
- \r
-</script>\r
+<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS) main page</title>\r
+<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
+<link href="print.css" rel="stylesheet" type="text/css" media="print" />\r
+<link href='http://fonts.googleapis.com/css?family=Yanone+Kaffeesatz:700' rel='stylesheet' type='text/css' />\r
+<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
</head>\r
+\r
<body>\r
<div id="page">\r
<div id="banner">\r
-<table> \r
-<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>\r
+<table>\r
+ <tr>\r
+ <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
+ </tr>\r
</table>\r
-<!-- \r
-Future use?\r
-<div class="uniicon"><a href="http://www.compbio.dundee.ac.uk"><img src="images/uod.gif" alt="University of Dundee, The Barton Group" title="University of Dundee, The Barton Group" longdesc="http://www.compbio.dundee.ac.uk"/></a></div>\r
--->\r
</div>\r
-\r
<!-- banner end-->\r
-<div id="wrapper">\r
-<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
-href="download.html">Download</a> <a href=\r
-"http://www.jalview.org">Jalview</a>\r
-<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a> \r
-</div>\r
\r
+<div id="panel">\r
+ <a class="newpressed" href="index.html">Home</a> \r
+ <a class="newa" href="quick_start.html">Getting Started</a> \r
+ <a class="newa" href="man_about.html">Manual</a> \r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+ <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
+ <a class="newa" href="contacts.html">Contact Us</a>\r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a class="newa" href="jabaws_funding.html">Funding</a>\r
+</div>\r
<!-- panel end-->\r
+\r
+<div id="wrapper">\r
<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
+<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
-\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
+ <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
-<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
+<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
-<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
-</table>\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
-</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
+</div><!-- page end-->\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>\r
\r
-<!-- wrapper end-->\r
-</div>\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
<!-- page end-->\r
</body>\r
</html>\r
-\r
git://source.jalview.org / jabaws.git / blobdiff