<!--
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* 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/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>
-</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><a name="envision2">Envision2 Services</a></strong></p>
-<p>Jalview 2.5 includes 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 members of <a href="http://www.enfin.org">ENFIN</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>
+ <p>Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
<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>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>
- </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>More alignment services: PROBCONS, T-COFFEE</li>
- <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>
+ <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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