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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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/>.
--->
+ * 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="dbreffetcher.html">Database Reference
+ Fetcher</a> transfers database references and annotation from 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-performance 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