-<html>\r
-\r
-<body>\r
-<p><strong>Web services </strong></p>\r
-<p>Originally Jalview used SRS server to retrieve sequence features for a given \r
- alignment. In addition certain remote alignment programs could be called from \r
- the Jalview interface and the results displayed in a new alignment panel. </p>\r
-<p>The main emphasis of the current development of the Jalview Project is to implement \r
- various sequence alignment programs, tree analysis, PCA algorithms on a large \r
- cluster based witihin the Barton Group. Jalview will be able to call these remote \r
- procedures without the user having to install any new software. <br>\r
- The main advantage of using these remote web services is that the computing \r
- power available is much greater than that of the users work station.</p>\r
-</body>\r
-</html>\r
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<html>
+<head>
+<title>Web Services</title>
+</head>
+<body>
+ <p>
+ <strong>Web services</strong>
+ </p>
+
+ <p>Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
+ <ul>
+ <li>The <a href="../features/seqfetch.html">Sequence
+ Fetcher</a> utilises web services for sequence, alignment and
+ structure retrieval provided by the European Bioinformatics
+ Institute (EBI) and Distributed Annotation System servers that are
+ capable of serving sequences.
+ </li>
+ <li>The <a href="../features/dasfeatures.html">DAS Feature
+ Fetcher</a> enables the retrieval and visualization of features from
+ DAS annotation sources
+ </li>
+ <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>The <strong>Web Services</strong> menu in each alignment
+ window also provides access to the following:
+ <ul>
+ <li>Programs for <a href="msaclient.html">multiple
+ sequence alignment</a>, made available <em>via</em> <a
+ href="JABAWS.html"
+ >Java Bioinformatic Analysis Web Service (JABAWS)</a> servers.
+ </li>
+ <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
+ structure prediction</a> based at the University of Dundee.
+ </li>
+ <li>Services for alignment analysis, such as <a
+ href="shmr.html"
+ >Multi-Harmony</a>.
+ </ul>
+ <p>
+ <strong>Web Service Dialog Box</strong>
+ </p> <img src="clwqueued.gif">
+ <p>This dialog box is displayed when a web service job is
+ submitted. It gives the name of the service and any method
+ citation information, and monitors the progress of the
+ calculation. The cancel button will permanently cancel the job,
+ but this is only possible for some services.</p> 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>
+ <li>If Jalview encounters problems accessing any services, it
+ may display a <a href="webServicesPrefs.html#wswarnings">warning
+ dialog box</a> (this can be turned off using the web services
+ preferences tab).
+ </li>
+ </ul>
+ </p>
+ <p>
+ <strong>More about Jalview's Web Services</strong> <br>
+ Jalview's distributed computations utilise <a
+ href="http://en.wikipedia.org/wiki/SOAP"
+ >SOAP</a> and <a
+ href="http://en.wikipedia.org/wiki/Representational_State_Transfer"
+ >REST</a> web services exposing sequence alignment, analysis, and
+ secondary structure prediction programs. Originally, Jalview 2's
+ services were maintained by the Barton group at the University of
+ Dundee, and ran programs on the Life Sciences High-performace
+ Computing Cluster. With the advent of <a
+ href="http://www.compbio.dundee.ac.uk/JABAWS"
+ >JABAWS</a>, however, it is possible for anyone to host Jalview web
+ services.
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff