JAL-1503 documentation and release notes
[jalview.git] / help / html / whatsNew.html
index 639a2cf..21b67eb 100755 (executable)
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-               <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
+               <strong>What's new ?</strong></p>
+               <p>Jalview 2.8.1 includes a range of new features developed over the last 12 months. <br /> As usual you can find the
                highlights below, and the comprehensive list is given in the <a
                        href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
        </p>
-       <strong>Internationalisation</strong>
-       <p>
-               In August 2013, David Rold&aacute;n-Martinez took on the task of
+       <p>The Desktop and web based applet include new keystrokes for
+               defining and undefining groups, and PAM250 has been added to the range
+               of score models available for use by the tree and PCA calculations.
+               The Jalview project file format has also been extended for handling
+               RNA and protein secondary structure annotation, in anticipation for
+               new structure based secondary structure support in Jalview 2.8.2.</p>
+       <p><strong>Internationalisation</strong></p>
+       <p>Jalview 2.8.1 is the first release to include support for
+               displaying Jalview's user interface in different languages. In August
+               2013, David Rold&aacute;n-Martinez took on the task of
                internationalising Jalview's user interface. He also recruited Sara
-               Hern&aacute;ndez D&iacute;az and Laura Ferrandis Martinez who created Jalview's
-               first spanish user interface translation.</p><p>If you notice any
-               problems, or would like to help translate Jalview's user interface
-               into other languages, head over to <a href="http://issues.jalview.org">issues.jalview.org</a>
-               and put in a feature request describing the translations you can
-               provide to the <a
+               Hern&aacute;ndez D&iacute;az and Laura Ferrandis Martinez who created
+               Jalview's first spanish user interface translation.</p>
+       <p>
+               If you notice any problems, or would like to help translate Jalview's
+               user interface into other languages, head over to <a
+                       href="http://issues.jalview.org">issues.jalview.org</a> and put in a
+               feature request describing the translations you can provide to the <a
                        href="http://issues.jalview.org/browse/JAL/component/10682">i18n
-                       component</a>. David has also <a href="https://wiki.jalview.org/index.php/Development:i18n">documented the process of creating i18n translations</a> to help you get started.
+                       component</a>. David has also <a
+                       href="https://wiki.jalview.org/index.php/Development:i18n">documented
+                       the process of creating i18n translations</a> to help you get started.
+       </p>
+       <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
+       <p>
+               This version of Jalview includes a client to access the new services available in <a
+                       href="http://www.compbio.dundee.ac.uk/jaba">JABA v2.1</a> , which
+               provides services for RNA consensus secondary structure prediction and
+               two new alignment programs (<a
+                       href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
+                       href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
+       <p>
+               To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
+                       client documentation</a>. 
        </p>
-       <strong>Enhancements and new features</strong>
-       <ul>
-       <li>
-  <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
-       </ul>
-       <strong>Bug fixes</strong>
-       <ul>
-       </ul>
+  <div align="center">
+    <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
+                       summer student, Dan Barton.</em>
+       </div>
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