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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 provided by the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
32 system, developed at the University of Dundee by Peter
33 Troshin, Sasha Sherstnev, Dan Barton, Fabio Madeira-Marquez, Jim Procter and Geoff Barton.
34 This is an open source system that 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">job parameters dialog box</a>.
48 <strong>Obtaining JABAWS</strong><br> One of the aims of JABAWS
49 is to enable you to easily perform computationally intensive
50 bioinformatics analysis tasks using your own computational
51 facilities. It can be installed on a workstation to provide
52 stand-alone execution of analysis programs, or as a job submission
53 engine - enabling larger numbers of jobs to be handled. If you would
54 like to download and install JABAWS for your own use, please go to <a
55 href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a>
59 <strong>Configuring your own JABAWS services for use by
60 Jalview</strong><br> Once you have downloaded and installed JABAWS,
61 and verified it is working, all that is needed is to add the URL for
62 your JABAWS server(s) to the list in the <a
63 href="webServicesPrefs.html">Web Services Preferences
64 Panel</a>. After adding your service and saving your preferences or
65 hitting the 'refresh web services' button, you should be able to
66 submit jobs to the server via the alignment window's web services
67 menu. Your JABAWS servers list is stored in your Jalview
68 preferences, so you will only have to configure Jalview once for
72 <em>JABAWS Client updated to version 2.2 in Jalview 2.10.2</em>
75 <em>Option for adding JABAWS servers which fails validation was
76 introduced from version 2.8.2 </em>
79 <em>Support for accessing JABAWS servers was introduced in