<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<title>Web Services</title>
</head>
<body>
- <p>
- <strong>Web services</strong>
- </p>
+ <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>
+ <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 from records available from
- DAS or the public sequence databases.</li>
+ 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-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>
+ 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>