From 05c695da50cc7ac1bd759ed5c58b3d5d7a9d0085 Mon Sep 17 00:00:00 2001
From: jprocter The JAva Bioinformatics
+Analysis Web Services
+system (JABAWS) The list of JABAWS servers known to the Jalview desktop is shown
+in the Web Services Preferences
+Panel, and detailed information about a particular service is available
+from the help text and web pages accessible from its job parameters dialog box. Obtaining JABAWS Configuring your own JABAWS services for use by
+Jalview Support for accessing JABAWS servers was introduced in
+Jalview 2.6.
+Jalview includes a client for interacting with programmatic (SOAP) web
+services for the JABAWS
+service model, developed at the University of Dundee by Peter Troshin
+and Geoff Barton. This is an open source system that provides a
+framework for wrapping command line bioinformatics analysis programs
+that enables them to be executed locally or on a cluster using data and
+analysis parameters provided by a program linked with JABAWS directly or
+accessing it remotely via its web services interface.
+One of the aims of JABAWS is to enable you to easily perform
+computationally intensive bioinformatics analysis tasks using your own
+computational facilities. It can be installed on a workstation to
+provide stand-alone execution of analysis programs, or as a job
+submission engine - enabling larger numbers of jobs to be handled. If
+you would like to download and install JABAWS for your own use, please
+go to http://www.compbio.dundee.ac.uk/jabaws
+for more information.
+Once you have downloaded and installed JABAWS, and verified it is
+working, all that is needed is to add your new JABAWS server's URL to
+the list in the Web Services
+Preferences Panel. After adding your service and saving your preferences
+or hitting the 'refresh web services' button, you should be able to
+submit jobs to the server via the alignment window's web services menu.
+Your JABAWS servers list is stored in your Jalview preferences, so you
+will only have to configure Jalview once for each new server.
+
+ The Web Services Preference panel
+ controls the display and appearance of the submission and analysis
+ services in the Web Services menu.
Jalview's distributed computations are SOAP based services @@ -47,12 +59,13 @@ programs. These services actually run on the cluster based in the School of Life Sciences, University of Dundee, and are maintained by the Barton group.
-Jalview 2.5 includes a client to enable the user to submit one or -more sequences or sequence IDs to analysis workflows provided by the 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 EnVision2 web application. This allows Jalview users to easily access the EnCore -network of databases and analysis services developed by members of ENFIN.
+network of databases and analysis services developed by ENFIN (www.enfin.org).Web Service Dialog Box
@@ -78,28 +91,22 @@ permanently cancel the job, but this is only possible for some services. Multiple Alignment with Fast Fourier Transforms - a highly accurate and high throughput dna and amino acid alignment method, performing at least as well as ClustalW and Muscle. +