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23 <title>The JABAWS system</title>
27 <strong>The</strong> <strong><em>JA</em></strong>va <strong><em>B</em></strong>ioinformatics
28 <strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
29 <strong>system</strong> (<strong>JABAWS</strong>)<br> Jalview
30 includes a client for interacting with programmatic (SOAP) web
31 services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
32 service model, developed at the University of Dundee by Peter
33 Troshin and Geoff Barton. This is an open source system that
34 provides a framework for wrapping command line bioinformatics
35 analysis programs that enables them to be executed locally or on a
36 cluster using data and analysis parameters provided by a program
37 linked with the JABA engine directly or accessing it remotely <em>via</em>
38 its web services interface.
41 The list of JABAWS servers known to the Jalview desktop is shown in
42 the <a href="webServicesPrefs.html">Web Services Preferences
43 Panel</a>, and detailed information about a particular service is
44 available from the help text and web pages accessible from its <a
45 href="webServicesParams.html"
46 >job parameters dialog box</a>.
49 <strong>Obtaining JABAWS</strong><br> One of the aims of JABAWS
50 is to enable you to easily perform computationally intensive
51 bioinformatics analysis tasks using your own computational
52 facilities. It can be installed on a workstation to provide
53 stand-alone execution of analysis programs, or as a job submission
54 engine - enabling larger numbers of jobs to be handled. If you would
55 like to download and install JABAWS for your own use, please go to <a
56 href="http://www.compbio.dundee.ac.uk/jabaws"
57 >http://www.compbio.dundee.ac.uk/jabaws</a> for more information.
60 <strong>Configuring your own JABAWS services for use by
61 Jalview</strong><br> Once you have downloaded and installed JABAWS,
62 and verified it is working, all that is needed is to add the URL for
63 your JABAWS server(s) to the list in the <a
64 href="webServicesPrefs.html"
65 >Web Services Preferences Panel</a>. After adding your service and
66 saving your preferences or hitting the 'refresh web services'
67 button, you should be able to submit jobs to the server via the
68 alignment window's web services menu. Your JABAWS servers list is
69 stored in your Jalview preferences, so you will only have to
70 configure Jalview once for each new server.
73 <em>Support for accessing JABAWS servers was introduced in
77 <em>Option for adding JABAWS servers which fails validation was
78 introduced from version 2.8.2 </em>