"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\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
+<meta name="Last-modified" content="Mon, 19 Dec 2010 01:03:33 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) main\r
page</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media=\r
"print.css" />\r
<script type="text/javascript" src="prototype-1.6.0.3.js">\r
\r
-</script>\r
-</head>\r
+</script></head>\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
+<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><h1><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
+class="headeru">S</span>ervices</h1></td>\r
</tr>\r
</table>\r
<!-- \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
+<div id="panel"><a class="selected" href="index.html">Home</a> \r
+ <a href="manual.html">Manual</a> \r
+<a href="download.html">Download</a> \r
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
\r
<!-- panel end-->\r
<div id="content">\r
-<h4>What is JABAWS?</h4>\r
-\r
-<p><span class="u">JA</span>va <span class=\r
+<p id="headtitle" style="color:black; font-weight:normal; text-align:left;" >\r
+<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
+class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a collection of SOAP web services for Bioinformatics. <br />\r
+Currently JABAWS provides five web\r
+services for multiple sequence alignment <a href="http://www.clustal.org/">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>. <span style="color:black; font-weight:normal; text-align:left;">Unlike other web services you can run JABAWS services from your own computer. This puts you in control of the web services - they will be where and when you need them, have no restrictions and your data privacy is guaranteed. JABAWS scales well from the single user single computer to the cluster with hundreds of users. Finally, you do not have to be an expert to use JABAWS - the installation is simple and you can use the services from the comfort of your desktop via <a href="http://www.jalview.org">Jalview</a>.</span></p>\r
<h3>Public JABAWS Server</h3>\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
+<p> You can access our public JABA Web Services with our <a href="download.html">command line client, </a>the <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a>, or write your own program. To guarantee a level service for everyone our public services impose some restrictions on the size and the number of the jobs you can submit. Currently we do not process tasks that exceed 1000 sequences per 1000 letters on average. Should you find this to be insufficient for your needs you can download and run JABAWS Server on your own hardware. This also applies if the privacy is a concern or an Internet connection is a problem. </p>\r
+<ul>\r
+ <li>The JABAWS public web services address is <strong>http://www.combio.dundee.ac.uk/jabaws</strong> </li>\r
+ <li>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> </td>\r
-</tr>\r
-</tbody>\r
-</table>\r
-\r
-<h4>Authors</h4>\r
-\r
+"nofollow">WSDL List</a></li>\r
+</ul>\r
+<h3>Contact Us </h3>\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
+<h3>Authors</h3>\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
</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: 11 January 2011<br />\r
+ This site is best viewed in Firefox 3.6, Google Chrome 8 or Internet Explorer 8 </div>\r
</div>\r
\r
<!-- wrapper end-->\r
git://source.jalview.org / jabaws.git / blobdiff