From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 26 May 2017 16:37:07 +0000 (+0100)
Subject: JAL-2418 JAL-2549 JABAWS 2.2 release notes
X-Git-Tag: Release_2_10_2~3^2~69^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=766a0572d838364c12564440a2273ee4a193e608;p=jalview.git

JAL-2418 JAL-2549 JABAWS 2.2 release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 1fe2602..01fd6c2 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -90,7 +90,7 @@ li:before {
             <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
           <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>  
           <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
-          
+          <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>
           </ul>
           <em>Experimental features</em>
           <ul>
diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index f74e4c4..84b2b86 100644
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -28,10 +28,10 @@
     <strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
     <strong>system</strong> (<strong>JABAWS</strong>)<br> Jalview
     includes a client for interacting with programmatic (SOAP) web
-    services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
-    service model, developed at the University of Dundee by Peter
-    Troshin and Geoff Barton. This is an open source system that
-    provides a framework for wrapping command line bioinformatics
+    services provided by the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+    system, developed at the University of Dundee by Peter
+    Troshin, Sasha Sherstnev, Dan Barton, Fabio Madeira-Marquez, Jim Procter and Geoff Barton.
+    This is an open source system that provides a framework for wrapping command line bioinformatics
     analysis programs that enables them to be executed locally or on a
     cluster using data and analysis parameters provided by a program
     linked with the JABA engine directly or accessing it remotely <em>via</em>
@@ -69,12 +69,15 @@
     each new server.
   </p>
   <p>
-    <em>Support for accessing JABAWS servers was introduced in
-      Jalview 2.6.</em>
+    <em>JABAWS Client updated to version 2.2 in Jalview 2.10.2</em>
   </p>
   <p>
     <em>Option for adding JABAWS servers which fails validation was
       introduced from version 2.8.2 </em>
   </p>
+  <p>
+    <em>Support for accessing JABAWS servers was introduced in
+      Jalview 2.6.</em>
+  </p>
 </body>
 </html>
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index 2fbbdbc..d627c66 100644
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -52,21 +52,18 @@
   </p>
   <p>
     <strong>Alignment programs supported by JABAWS</strong>. <br />Versions
-    shown are those bundled with JABAWS 2.01 - if you are using a
+    shown are those bundled with JABAWS 2.2 - if you are using a
     different server, check its home page to find out which versions are
     provided.
-  <ul>
-    <li><a href="http://www.clustal.org/">Clustal Omega and
-        Clustal W</a> (version 2.0.12)</li>
-    <li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a>
-      (version 6.8.57b)</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>
+      <li><a href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
+      <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
+      <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</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">T-coffee</a> (version 11.00.8cbe486)</li>
+      <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
+      <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
+      <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>
   </ul>
   </p>
 
diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html
index 1c35bf3..a06b3a9 100644
--- a/help/html/webServices/proteinDisorder.html
+++ b/help/html/webServices/proteinDisorder.html
@@ -48,7 +48,7 @@
       By Annotation</a> dialog box to colour sequences according to the
     results of predictors shown as annotation rows.
   </p>
-  <p>JABAWS 2.0 provides four disorder predictors which are
+  <p>JABAWS 2.2 provides four disorder predictors which are
     described below:</p>
   <ul>
     <li><a href="#disembl">DisEMBL</a></li>
@@ -146,7 +146,7 @@
   </p>
   <p>
     <strong><a name="iupred"></a><a
-      href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br />
+      href="http://iupred.enzim.hu/">IUPred</a></strong><br />
     IUPred employs an empirical model to estimate likely regions of
     disorder. There are three different prediction types offered, each
     using different parameters optimized for slightly different