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-<meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
+<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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<table>\r
<tr>\r
<td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.1" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<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
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<li><a href="#wisjaba">What is JABAWS?</a></li>\r
<li><a href="#wjaba">JABAWS Benefits</a></li>\r
<li><a href="#alprog">JABA Web Services Programs </a></li>\r
- <li><a href="#jaba2">What is new in JABAWS 2?</a> </li>\r
+ <li><a href="#jaba2.0.1">What is new in JABAWS 2?</a> </li>\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
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<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
<p>\r
Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your \r
lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure \r
but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested \r
- in writing your own client, the JABAWS command line client is what you need. </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
+\r
+\r
+\r
+<h3><a name="jaba2.0.1"/></a>What is new in JABAWS 2.0.1? </h3>\r
+<strong>JABAWS Version 2.0.1 (Released 2nd Jul 2013)</strong><p>JABAWS 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
+ <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
+ <li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores \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
-<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>\r
-<p>Comparing to previous version of JABAWS 2.0.1 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains </p>\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>four new protein disorder prediction services</li>\r
<li>Clustal Omega multiple sequence alignment web service</li>\r
<li>amino acid conservation service</li>\r
- <li>web services execution statistics visialization </li>\r
- <li>web services status check from a web page</li>\r
+ <li>web services execution statistics visualization </li>\r
+ <li>web services status check from a web page</li>\r
<li>VirtualBox support was dropped in favour of VMware</li>\r
<li>new WAR package for Mac users</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 be able to use JABAWS 2.0.1 instead. To benefit of new web services introduced in JABAWS 2.0 \r
- the clients compitible with JABAWS v1.0 have to be updated.\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> \r
-<!-- about end-->\r
-<!-- content end--> \r
-\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
+</div><!-- wrapper end-->\r
+</div><!-- page end-->\r
\r
-<div id="copyright">Last update: 16 September 2011<br /> Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\r
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-</div>\r
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