- <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.
+
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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/seqfetcher.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 DAS Feature Fetcher enables the retrieval and visualization of features from DAS annotation sources</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></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>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>
+ <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>Jalview's distributed computations are SOAP based services exposing
- protein sequence alignment and secondary structure prediction 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>Web Service Dialog Box</strong></p>
+<p><strong>More about Jalview's Web Services</strong> <br>
+Jalview's distributed computations are SOAP based services exposing
+protein sequence alignment and secondary structure prediction 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>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>
+<br />
+<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>
- <p>Current services:
- <ul><a href="msaclient.html"><strong>Multiple
- Sequence Alignment Services</strong></a><ul>
- <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>
- The clustal W service remains one of the more
- popular Jalview features.
- </li>
- <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
- High Quality and High Throughput multiple alignments of proteins. This
- method can sometimes be more accurate than ClustalW when dealing with
- diverse sets of sequences.
- </li>
- <li><a href="mafft.html">MAFFT</a><br>
- 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>
- </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
- 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>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>
+<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>
+<p>Current services:
+<ul>
+ <a href="msaclient.html"><strong>Multiple Sequence
+ Alignment Services</strong></a>
+ <ul>
+ <li><a href="clustalw.html">ClustalW Multiple Alignment and
+ re-alignment</a><br>
+ The clustal W service remains one of the more popular Jalview
+ features.</li>
+ <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
+ High Quality and High Throughput multiple alignments of proteins. This
+ method can sometimes be more accurate than ClustalW when dealing with
+ diverse sets of sequences.</li>
+ <li><a href="mafft.html">MAFFT</a><br>
+ 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 <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>
+
</body>
</html>
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