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- <h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
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<h4>What is JABAWS?</h4>\r
-<p><span class="u">JA</span>va <span class="u">B</span>ioinformatics <span class="u">A</span>nalysis <span class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a collection of <a href="http://www.w3schools.com/SOAP/soap_intro.asp">SOAP</a> web services for bioinformatics. Web services make it easy to access well-known tools from anywhere anytime. SOAP Web Services are designed for use by other programmes, rather than people. Current version of JABA web services integrates with <a href="http://www.jalview.org">Jalview</a> and provides five web services for multiple sequence alignment. They are: </p>\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 and databases over the web from anywhere, at\r
+anytime. Unlike other web services, JABAWS can be easily installed on different platforms and work straight out of the box with minimum configuration. JABA Web Services are designed for use by other programs rather\r
+than people.\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/">ClustalW</a></li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a></li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a></li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a></li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a></li>\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
-<p> JABA Web Services have a number of distinct features not found elsewhere. \r
-<p>In particular JABAWS\r
-<ol>\r
- <li>gives uniform remote access for a number of command line tools <span class="box"> This allows you to access a number of programmes anywhere anytime. All multiple sequence alignment services comply with a single interface, simplifying command invocation. Most of the command line programmes' options are supported, so you have the same level of control as with the command line. </span></li>\r
- <li>enables Jalview to perform variety of analysis (more to come in the future) on the alignments <span class="box">It is very easy to connect the different instances of JABAWS. So if one is off line, another one will do the job for you. If you use it in your software it is only the matter of a server name change, no other magic is required. </span> </li>\r
- <li>can be easily deployed on a large variety of platforms and run on a single server or on the cluster. <span class="box"><a href="howto.html#clustsubsys">JABAWS integrates with a large number of cluster job management systems.</a>This eliminates the scalability issues and let you focus on your research, JABAWS will take care of the task management. </span></li>\r
- <li> services are <a href="http://www.ws-i.org/">WS-I basic profile</a> v. 1.1 compatible<span class="box">This means that programmes or other web services written in almost any programming languages should have no difficulties using JABA web services.</span></li>\r
- </ol>\r
-<p>Below are the examples of things that you can do with JABAWS</p>\r
-<ul>\r
- <li>\r
- <p><strong>Unhappy with the defaults settings? </strong><br /> \r
- Want to use PAM200 substitution matrix, set the number of iterations, or sequence clustering method? No problems, JABAWS can do that. Any additional parameters or combinations of where of can be defined. You are no longer limited to defaults!</p>\r
- </li>\r
- <li>\r
- <p><strong>JABAWS in Dundee is not available? </strong>No problem, choose a different service provider and off you go. We hope that other major service providers like EBI will soon be housing JABAWS. </p>\r
- </li>\r
- <li>\r
- <p><strong>Worried about sending your data to the internet?</strong> Install JABAWS in your lab. Point your Jalview client to the services in your lab, and no data will leave you lab any longer.</p>\r
- </li>\r
- <li>\r
- <p><strong>Want to install JABAWS but are not sure what is required? </strong>JABA Web Services will work happily on a single server as well as on the cluster. For large number of request of cause it is better to use a cluster. Little configuration is involved. </p>\r
- </li>\r
- </ul>\r
-<h3> Public JABAWS Server</a></h3>\r
- <table>\r
- <tbody>\r
- <tr>\r
- <th> Feature </th>\r
- <th> Description </th>\r
- </tr>\r
- <tr>\r
- <td><acronym title="Uniform Resource Locator">URL</acronym> </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba" title="http://www.compbio.dundee.ac.uk/jaba" rel="nofollow">http://www.compbio.dundee.ac.uk/jaba</a> </td>\r
- </tr>\r
- <tr>\r
- <td> Execution limits </td>\r
- <td> Local execution limit is 40 sequnces with no more than 500 letters average length. Larger tasks are send to the cluster. Tasks exceeding 1000×1000 (sequences per letters) will not be accepted for alignment. If you would like to work with bigger alignments consider installing JABAWS in your lab. </td>\r
- </tr>\r
- <tr>\r
- <td> Web Services Description </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" title="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" rel="nofollow">WSDL List</a> </td>\r
- </tr>\r
- </tbody>\r
- </table>\r
\r
+<p> JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to <a href="http://www.drmaa.org/">DRMAA</a> it integrates well with a large variety of cluster job management systems. <a href="http://www.jalview.org">Jalview</a> from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on <a href="howto.html#wjaba">JABAWS benefits</a>. </p>\r
+<h4>Public JABAWS Server</h4>\r
+<table>\r
+<tbody>\r
+<tr>\r
+<th width="22%">Feature</th>\r
+<th width="78%">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>JABAWS installation is backed up by 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
+For programmatic access to JABAWS please refer to the How To section <a href="howto.html#connectto">using JABAWS in your program</a>. \r
<h4>Authors</h4>\r
-<p>Conceptually, Java Bioinformatics Analysis Web Services are the successor of the Jalview Web Services. At the code level, however, JABA Web Services do not contain any code from Jalview Web Services because of the complete change of technologies in time of coding. Jim Procter and Geoff Barton are the authors of Jalview Web Services. Peter Troshin and Geoff Barton are the authors of the JABA Web Services. Jim Procter has contributed to JABAWS development by making useful suggestions, integrating JABAWS with Jalview, and correcting some of its configuration files.</p>\r
-</div><!-- content end--> \r
-<div id="copyright">Last update: 9 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
-</div><!-- wrapper end-->\r
-</div> <!-- page end-->\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
\r
+<!-- content end-->\r
+<div id="copyright">Last update: 17 November 2010<br />\r
+ Peter Troshin and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
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+\r
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