<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="#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
\r
<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
<p>\r
(see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
Future versions of JABAWS will incorporate many other tools.\r
</p>\r
-\r
<h4>Getting JABAWS</h4>\r
<p>\r
JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and \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>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> JABAWS currently provides access to the following programs:</p>\r
<p>Multiple Sequence Alignement </p>\r
<ul>\r
<li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\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
-<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>\r
-<p>This release of JABAWS 2.0.1 is mostly bug fixing release. This is a list of bugs which have been fixed in JABAWS 2.0.1:</p>\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 the '>' symbols in the record identificator</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>JABAW 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>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>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 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
+\r
+\r
\r
<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
<p>\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
-\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\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
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git://source.jalview.org / jabaws.git / blobdiff