2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Web Services</title>
27 <strong>Web services</strong>
30 <p>Jalview includes clients for a variety of web services for both
31 bioinformatic data retrieval and analysis.
33 <li>The <a href="../features/seqfetch.html">Sequence
34 Fetcher</a> utilises web services for sequence, alignment and
35 structure retrieval provided by the European Bioinformatics
36 Institute (EBI) and Distributed Annotation System servers that are
37 capable of serving sequences.
39 <li>The <a href="../features/dasfeatures.html">DAS Feature
40 Fetcher</a> enables the retrieval and visualization of features from
41 DAS annotation sources
43 <li>The <a href="dbreffetcher.html">Database Reference
44 Fetcher</a> transfers database references from records available
45 from DAS or the public sequence databases.
47 <li>The <strong>Web Services</strong> menu in each alignment
48 window also provides access to the following:
50 <li>Programs for <a href="msaclient.html">multiple
51 sequence alignment</a>, made available <em>via</em> <a
52 href="JABAWS.html">Java Bioinformatic Analysis
53 Web Service (JABAWS)</a> servers.
55 <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
56 structure prediction</a> based at the University of Dundee.
58 <li>Services for alignment analysis, such as <a
59 href="shmr.html">Multi-Harmony</a>.
62 <strong>Web Service Dialog Box</strong>
63 </p> <img src="clwqueued.gif">
64 <p>This dialog box is displayed when a web service job is
65 submitted. It gives the name of the service and any method
66 citation information, and monitors the progress of the
67 calculation. The cancel button will permanently cancel the job,
68 but this is only possible for some services.</p> The <a
69 href="webServicesPrefs.html">Web Services Preference
70 panel</a> controls the display and appearance of the submission and
71 analysis services in the <strong>Web Services</strong> menu.
73 <li>If Jalview encounters problems accessing any services, it
74 may display a <a href="webServicesPrefs.html#wswarnings">warning
75 dialog box</a> (this can be turned off using the web services
81 <strong>More about Jalview's Web Services</strong> <br>
82 Jalview's distributed computations utilise <a
83 href="http://en.wikipedia.org/wiki/SOAP">SOAP</a> and <a
84 href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
85 web services exposing sequence alignment, analysis, and secondary
86 structure prediction programs. Originally, Jalview 2's services were
87 maintained by the Barton group at the University of Dundee, and ran
88 programs on the Life Sciences High-performance Computing Cluster.
89 With the advent of <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>,
90 however, it is possible for anyone to host Jalview web services.