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"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
+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
<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
-\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>Feature</th>\r
-<th>Description</th>\r
+<th width="22%">Feature</th>\r
+<th width="78%">Description</th>\r
</tr>\r
\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
+<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
</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
-\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
+<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
</div>\r
git://source.jalview.org / jabaws.git / blobdiff