new web service dialogs and JABA

[jalview.git] / help / html / webServices / index.html

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 8e785dc..9d13906 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -36,9 +36,21 @@ bioinformatic data retrieval and analysis.
        <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
        transfers database references from records available from DAS or the
        public sequence databases.</li>
-       <li>Jalview SOAP Web Services for sequence and alignment analysis
-       are provided by the University of Dundee, and are available from the
-       Alignment window's <strong> Web Service</strong> menu.</li>
+       <li>The <strong>Web Services</strong> menu in each alignment
+       window also provides access to the following:
+       <ul>
+               <li>Jalview SOAP Web Services for sequence alignment and
+               secondary structure prediction based at the University of Dundee.</li>
+               <li>Services for submitting IDs and sequences to external
+               bioinformatics services such as <a href="#envision2">Envision2</a>.</li>
+               <li>Programs for multiple sequence alignment, made available <em>via</em>
+               <a href="JABAWS.html">Java Bioinformatic
+               Analysis Web Service (JABAWS)</a> servers.</li>
+       </ul>
+       The <a href="webServicesPrefs.html">Web Services Preference panel</a>
+       controls the display and appearance of the submission and analysis
+       services in the <strong>Web Services</strong> menu.</li>
+
 </ul>
 </p>
 <p>Jalview's distributed computations are SOAP based services
@@ -47,12 +59,13 @@ programs. These services actually run on the cluster based in the School
 of Life Sciences, University of Dundee, and are maintained by the Barton
 group.</p>
 <p><strong><a name="envision2">Envision2 Services</a></strong></p>
-<p>Jalview 2.5 includes a client to enable the user to submit one or
-more sequences or sequence IDs to analysis workflows provided by the <a
+<p>Since version 2.5, Jalview has included a client to enable the
+user to submit one or more sequences or sequence IDs to analysis
+workflows provided by the <a
        href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
 application</a>. This allows Jalview users to easily access the EnCore
-network of databases and analysis services developed by members of <a
-       href="http://www.enfin.org">ENFIN</a>.</p>
+network of databases and analysis services developed by ENFIN (<a
+       href="http://www.enfin.org">www.enfin.org</a>).</p>
 <br />
 <p><strong>Web Service Dialog Box</strong></p>
 <img src="clwqueued.gif">
@@ -78,28 +91,22 @@ permanently cancel the job, but this is only possible for some services.
                Multiple Alignment with Fast Fourier Transforms - a highly accurate
                and high throughput dna and amino acid alignment method, performing at
                least as well as ClustalW and Muscle.</li>
+               <li>Other alignment methods are also available via <a
+                       href="JABAWS.html">JABAWS</a>. For more information about a
+               particular service, see the documentation available via the <a
+                       href="webServicesParams.html">web services parameter dialog box</a>.</li>
        </ul>
        </li>
        <li><strong>Secondary Structure Prediction</strong>
        <ul>
                <li><a href="jnet.html">JNet</a><br>
-               This is a front end to the existing <a
+               This is a front end to the <a
                        href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
                allowing single sequence or profile based prediction.</li>
        </ul>
        </li>
 </ul>
 </p>
-<!--                   <p>Watch this space! These are some of the services
-                  planned to be released soon:<ul>
-                  <li>More alignment services: PROBCONS, T-COFFEE</li>
-                  <li>Repeat analysis
-                  </li>
-                  <li>Remote Homology Detection<br>
-                  </li>
-                  </ul>
-                  In the future, Jalview will also be able to new discover services
-                  dynamically, and distribute expensive analysis functions like <a
-                  href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->
+
 </body>
 </html>