X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fman_about.html;h=f3fcd22e69b1152f6537b2aa87c0c9e940c19497;hb=c46caed03164e4396eb55dc30e7db3558a7b06cc;hp=1f55cbc64b11f677cdbba7bb352f42b1a47b6318;hpb=65f579f3a0ff4e2626017be25f015ee5c6e39275;p=jabaws.git

diff --git a/website/man_about.html b/website/man_about.html
index 1f55cbc..f3fcd22 100644
--- a/website/man_about.html
+++ b/website/man_about.html
@@ -18,7 +18,7 @@
 <table>
   <tr>
     <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>
-    <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>
+    <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>
     <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
   </tr>
 </table>
@@ -46,6 +46,7 @@
   <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>
   <a href="contacts.html">Contact Us</a>
   <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>
+  <a href="jabaws_funding.html">Funding</a>
 </div>
 <!-- panel end-->
 
@@ -58,11 +59,13 @@
   <li><a href="#wisjaba">What is JABAWS?</a></li>
   <li><a href="#wjaba">JABAWS Benefits</a></li>
   <li><a href="#alprog">JABA Web Services Programs </a></li>
-  <li><a href="#jaba2">What is new in JABAWS 2?</a> </li>
+  <li><a href="#jaba2.5">What is new in JABAWS 2?</a> </li>
   <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
   <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
   <li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
-  </ul>
+</ul>
+
+
 
 <h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>
 <p>
@@ -72,7 +75,6 @@
   (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.
   Future versions of JABAWS will incorporate many other tools.
 </p>
-
 <h4>Getting JABAWS</h4>
 <p>
   JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and 
@@ -83,6 +85,8 @@
   in writing your own client, the JABAWS command line client is what you need.
 </p>
 
+
+
 <h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>
 <ul>
   <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
@@ -95,18 +99,19 @@
   <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>
 </ul>
 
+
+
 <h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>
-<p>JABAWS currently provides access to the following programs:</p>
+<p> JABAWS currently provides access to the following programs:</p>
 <p>Multiple Sequence Alignement </p>
 <ul>
   <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>
-  <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.0.12)</li>
+  <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>
   <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>
   <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>
   <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
-  </ul>
-
+</ul>
 <p>Protein disorder prediction</p>
 <ul>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>
@@ -117,19 +122,37 @@
 <p>Amino Acid conservation </p>
 <ul>
   <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>
-  </ul>
+</ul>
+
 
-<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>
-<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>
+
+<h3><a name="jaba2.5"/></a>What is new in JABAWS 2.5? </h3>
+<strong>JABAWS Version 2.5 (Released 2nd Jul 2013)</strong><p>JABAWS 2.5 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>
 <ul>
   <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
   <li>Jronn failed to process jobs with more than 3 sequences</li>
-  <li>JABAWS could not deal with FASTA records with the '&gt' symbols in the record identificator</li>
+  <li>JABAWS could not deal with FASTA records with '&gt' symbols in the record identificator</li>
   <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 
       in one call</li>
-  <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>
+  <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>
   <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
+  <li>Documentation has been updated</li>
   </ul>
+  <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>
+<ul><li>updates for all multiple sequence alignment services</li>
+  <li>four new protein disorder prediction services</li>
+  <li>Clustal Omega multiple sequence alignment web service</li>
+  <li>amino acid conservation service</li>
+  <li>web services execution statistics visualization </li>
+  <li>web services status check from a web page</li>
+  <li>VirtualBox support was dropped in favour of VMware</li>
+  <li>new WAR package for Mac users</li>
+  <li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>
+  <li>Improved web services client API</li>
+  <li>Simplified WAR package installation</li>
+</ul>
+
+
 
 <h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>
 <p>
@@ -144,26 +167,29 @@
   instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
 </p>
 
+
+
 <h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>
 <p>
-  JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and 
-  v2.0 clients should be able to use JABAWS 2.0.1 instead. To benefit of new web services introduced in JABAWS 2.0 
-  the clients compitible with JABAWS v1.0 have to be updated.
+  JABAWS version 2.5 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and 
+  v2.0 clients should also be able to use JABAWS 2.5 services. To access the analysis web services introduced in
+  JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.
 </p>
 
+
+
 <h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>
 <p>
-JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language 
-or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home 
-page, and you can use this to automatically generate service bindings for your program. If you use Java, however, 
-then you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. 
-This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which 
-is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify 
-working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
+  JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language 
+  or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home 
+  page, and you can use this to automatically generate service bindings for your program. If you use Java, however, 
+  then you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. 
+  This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which 
+  is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify 
+  working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
 </p>
-
 </div><!-- content end-->
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>
+<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>
 </div><!-- wrapper end-->
 </div><!-- page end-->