<a 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 href="contacts.html">Contact Us</a>\r
<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a href="jabaws_funding.html">Funding</a>\r
</div>\r
<!-- panel end-->\r
\r
<li><a href="#jabaclient">What is JABAWS Client</a>?</li>\r
<li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>\r
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>\r
- </ul>\r
+</ul>\r
+\r
+\r
\r
<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
<p>\r
in writing your own client, the JABAWS command line client is what you need.\r
</p>\r
\r
+\r
+\r
<h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\r
<ul>\r
-<li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>\r
-<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>\r
-<li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>\r
-<li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>\r
-<li>Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, \r
- your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>\r
-<li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>\r
-<li>Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.</li>\r
+ <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>\r
+ <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>\r
+ <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>\r
+ <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>\r
+ <li>Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, \r
+ your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>\r
+ <li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>\r
+ <li>Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.</li>\r
</ul>\r
+\r
+\r
+\r
<h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>\r
<p> JABAWS currently provides access to the following programs:</p>\r
<p>Multiple Sequence Alignement </p>\r
<li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
<li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
<li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
- </ul>\r
-\r
+</ul>\r
<p>Protein disorder prediction</p>\r
<ul>\r
<li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
<p>Amino Acid conservation </p>\r
<ul>\r
<li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>\r
- </ul>\r
+</ul>\r
+\r
+\r
+\r
<h3><a name="jaba2.0.1"/></a>What is new in JABAWS 2.0.1? </h3>\r
-<p>JABAWS Version 2.0.1 includes several minor updates and bug fixes for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>\r
+<p>JABAWS Version 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>\r
<ul>\r
<li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
<li>Jronn failed to process jobs with more than 3 sequences</li>\r
in one call</li>\r
<li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>\r
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>\r
+ <li>Documentation has been updated</li>\r
</ul>\r
<a name="jaba2"/><strong>JABAWS Version 2 (Released 16th Dec 2011)</strong><p>Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.</p><p>It contains:</p>\r
<ul><li>updates for all multiple sequence alignment services</li>\r
<li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>\r
<li>Improved web services client API</li>\r
<li>Simplified WAR package installation</li>\r
- </ul>\r
+</ul>\r
+\r
\r
-<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
\r
+<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
<p>\r
A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web \r
services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web \r
provides a graphical JABAWS client. This client has the same functionality as the command line client, but \r
instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.\r
</p>\r
+\r
+\r
+\r
<h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
<p>\r
JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
v2.0 clients should also be able to use JABAWS 2.0.1 services. To access the analysis web services introduced in\r
JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
</p>\r
+\r
+\r
+\r
<h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>\r
<p>\r
-JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
-or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home \r
-page, and you can use this to automatically generate service bindings for your program. If you use Java, however, \r
-then you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. \r
-This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
-is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify \r
-working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
+ JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
+ or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home \r
+ page, and you can use this to automatically generate service bindings for your program. If you use Java, however, \r
+ then you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. \r
+ This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
+ is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify \r
+ working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
</p>\r
</div><!-- content end-->\r
<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
git://source.jalview.org / jabaws.git / blobdiff