2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Web Services</title>
24 <strong>Web services</strong>
27 <p>Jalview includes clients for a variety of web services for both
28 bioinformatic data retrieval and analysis.
30 <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
31 utilises web services for sequence, alignment and structure retrieval
32 provided by the European Bioinformatics Institute (EBI) and
33 Distributed Annotation System servers that are capable of serving
35 <li>The <a href="../features/dasfeatures.html">DAS Feature
36 Fetcher</a> enables the retrieval and visualization of features from DAS
37 annotation sources</li>
38 <li>The <a href="dbreffetcher.html">Database Reference
39 Fetcher</a> transfers database references from records available from
40 DAS or the public sequence databases.</li>
41 <li>The <strong>Web Services</strong> menu in each alignment
42 window also provides access to the following:
44 <li>Programs for <a href="msaclient.html">multiple sequence
45 alignment</a>, made available <em>via</em> <a href="JABAWS.html">Java
46 Bioinformatic Analysis Web Service (JABAWS)</a> servers.</li>
47 <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
48 structure prediction</a> based at the University of Dundee.</li>
49 <li>Services for alignment analysis, such as <a
50 href="shmr.html">Multi-Harmony</a>.
51 <li>Services for submitting IDs and sequences to external
52 bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
55 <strong>Web Service Dialog Box</strong>
56 </p> <img src="clwqueued.gif">
57 <p>This dialog box is displayed when a web service job is
58 submitted. It gives the name of the service and any method citation
59 information, and monitors the progress of the calculation. The
60 cancel button will permanently cancel the job, but this is only
61 possible for some services.</p> The <a href="webServicesPrefs.html">Web
62 Services Preference panel</a> controls the display and appearance of the
63 submission and analysis services in the <strong>Web Services</strong>
65 <li>If Jalview encounters problems accessing any services, it may
66 display a <a href="webServicesPrefs.html#wswarnings">warning
67 dialog box</a> (this can be turned off using the web services
68 preferences tab).</li>
72 <strong>More about Jalview's Web Services</strong> <br> Jalview's
73 distributed computations utilise <a
74 href="http://en.wikipedia.org/wiki/SOAP">SOAP</a> and <a
75 href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
76 web services exposing sequence alignment, analysis, and secondary
77 structure prediction programs. Originally, Jalview 2's services were
78 maintained by the Barton group at the University of Dundee, and ran
79 programs on the Life Sciences High-performace Computing Cluster. With
80 the advent of <a href="http://www.compbio.dundee.ac.uk/JABAWS">JABAWS</a>,
81 however, it is possible for anyone to host Jalview web services.
84 <strong><a name="envision2">Envision2 Services</a>
88 Since version 2.5, Jalview has included a client to enable the user to
89 submit one or more sequences or sequence IDs to analysis workflows
90 provided by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
91 web application</a>. This allows Jalview users to easily access the
92 EnCore network of databases and analysis services developed by ENFIN (<a
93 href="http://www.enfin.org">www.enfin.org</a>).