- <html>\r
- <head><title>Web Services</title></head>\r
- <body>\r
- <p><strong>Web services</strong></p>\r
- \r
-<p>A variety of web services are available from the Alignment window's <strong> \r
- Web Service</strong> menu. </p>\r
- <p>Jalview's distributed computations are SOAP based services exposing\r
- protein sequence alignment and secondary structure prediction programs. These services actually run\r
- on the cluster based in the School of Life Sciences, University of\r
- Dundee, and are maintained by the Barton group.\r
- </p>\r
- <p><strong>Web Service Dialog Box</strong></p>\r
-<img src="clwqueued.gif">\r
-<p>\r
- This dialog box is displayed when a web service job\r
- is submitted. It gives the name of the service and\r
- any method citation information, and monitors the\r
- progress of the calculation. The cancel button will\r
- permanently cancel the job, but this is only\r
- possible for some services.\r
- </p>\r
- <p>Current services:\r
- <ul><a href="msaclient.html"><strong>Multiple\r
- Sequence Alignment Services</strong></a><ul>\r
- <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>\r
- The clustal W service remains one of the more\r
- popular Jalview features.\r
- </li>\r
- <li><a href="muscle.html">Muscle Multiple Alignment</a><br>\r
- High Quality and High Throughput multiple alignments of proteins. This\r
- method can sometimes be more accurate than ClustalW when dealing with\r
- diverse sets of sequences.\r
- </li>\r
- <li><a href="mafft.html">MAFFT</a><br>\r
- Multiple Alignment with Fast Fourier Transforms -\r
- a highly accurate and high throughput dna and amino\r
- acid alignment method, performing at least as well\r
- as ClustalW and Muscle.\r
- </li>\r
- </ul> \r
- </li>\r
- <li><strong>Secondary Structure Prediction</strong>\r
- <ul>\r
- <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a\r
- href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet\r
- www server</a> allowing single sequence or profile\r
- based prediction.\r
- </li>\r
- </ul>\r
- </li>\r
- </ul>\r
- </p>\r
- <p>Watch this space! These are some of the services\r
- planned to be released soon:<ul>\r
- <li>Repeat analysis\r
- </li>\r
- <li>Remote Homology Detection<br>\r
- </li>\r
- </ul>\r
- In the future, Jalview will also be able to new discover services\r
- dynamically, and distribute expensive analysis functions like <a\r
- href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>\r
-</body>\r
-</html>\r
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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>.
+ <li>Services for submitting IDs and sequences to external
+ bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
+ </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>
+ <p>
+ <strong><a name="envision2">Envision2 Services</a>
+ </strong>
+ </p>
+ <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 ENFIN (<a
+ href="http://www.enfin.org">www.enfin.org</a>).
+ </p>
+</body>
+</html>
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