<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
--->
+ * 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>
+ <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>
+ <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>.
+ </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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff