The JABAWS system

From: jprocter Date: Wed, 22 Sep 2010 01:04:24 +0000 (+0000) Subject: new web service dialogs and JABA X-Git-Tag: Release_2_6~13 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=05c695da50cc7ac1bd759ed5c58b3d5d7a9d0085;p=jalview.git new web service dialogs and JABA --- diff --git a/help/help.jhm b/help/help.jhm index 865013b..0ed676c 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -11,6 +11,9 @@ + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index f0403e7..39b5561 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -44,6 +44,9 @@ + + + diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html new file mode 100644 index 0000000..a313b83 --- /dev/null +++ b/help/html/webServices/JABAWS.html @@ -0,0 +1,61 @@ + + + +The JABAWS system + + +

The JAva Bioinformatics +Analysis Web Services +system (JABAWS)
+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.

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
+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.

Configuring your own JABAWS services for use by +Jalview
+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.

Support for accessing JABAWS servers was introduced in +Jalview 2.6.

+ + diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 8e785dc..9d13906 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -36,9 +36,21 @@ bioinformatic data retrieval and analysis.

The Database Reference Fetcher transfers database references from records available from DAS or the public sequence databases.

Jalview SOAP Web Services for sequence and alignment analysis - are provided by the University of Dundee, and are available from the - Alignment window's Web Service menu.

The Web Services menu in each alignment + window also provides access to the following: +

Jalview SOAP Web Services for sequence alignment and + secondary structure prediction based at the University of Dundee.
Services for submitting IDs and sequences to external + bioinformatics services such as Envision2.
Programs for multiple sequence alignment, made available via + Java Bioinformatic + Analysis Web Service (JABAWS) servers.

+ 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.

Envision2 Services

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. +

Other alignment methods are also available via JABAWS. For more information about a + particular service, see the documentation available via the web services parameter dialog box.

Secondary Structure Prediction

JNet
- This is a front end to the existing JNet www server allowing single sequence or profile based prediction.

- + diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index 7f4bac9..d35a28e 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -33,8 +33,8 @@ available:

alignment - where a new alignment is constructed from the input
realignment - -where any existing alignments in the input are passed to the service -for profile based alignment. +where any aligned sequences will be used by the service +to construct a profile based alignment of the remaining unaligned sequences.

diff --git a/help/html/webServices/webServicesParams.html b/help/html/webServices/webServicesParams.html new file mode 100644 index 0000000..ebb8d1b --- /dev/null +++ b/help/html/webServices/webServicesParams.html @@ -0,0 +1,86 @@ + + + + +Web Service Job Parameter Dialog Box + + +

Web service Job Parameter Dialog box

+ +

Some Jalview services including those provided by JABAWS, support a range of parameters and +options, enabling you to employ the most appropriate settings for the +input data. In addition to any preset combinations provided by the +services themselves, the Web services parameters dialog box also allows +you to create and store your own parameter sets, so they can be accessed +quickly from the presets menu.

Accessing the parameter dialog box
+The parameters dialog box is opened by selecting the 'Edit and Run' menu +entries within the JABAWS analysis submenu of the alignment window's web +services menu. Once opened, it presents the parameters and options +available for the chosen analysis for you to modify, and and also +enables you to browse any available service presets and select, create +or modify your own user defined parameter sets. Once you are satisfied +with the analysis parameters, press the Start Job +button to initiate the analysis.

Getting help on the analysis parameters
+Each option or parameter shown in the dialog is accompanied by a brief +description, which is shown as a tooltip when the mouse is moved over +it. For some, a link symbol will also be shown (as in the example +below), indicating that further information is available online. In this +case, right-clicking (or command-click) will open a pop-up menu allowing +you to select a URL to open in your web browser.

Analysis Parameters Dialog Box for JABAWS Services

+
+Parameter settings dialog box for JABAWS MAFFT Service +

The menu and text box at the top of the dialog box displays the +name of the current parameter set. The name can be edited, should you +wish to change or create a new user defined set, or clicked to present a +menu enabling other sets to be browsed. The description shown below may +also be edited (and the box resized to facilitate this), allowing you to +provide notes to accompany the parameter set. The modification of these +or any of the option or parameter settings will enable one or more of +the following buttons, that allow you to: +

Revert the changes you have made. This will undo any + changes you have made to the parameters and options with respect to the + currently selected parameter set, reverting each setting to its default + or last saved value.
Create a new parameter set. Selecting this option + will create a new parameter set with the given name. New parameter sets + will be saved for the current session, but a file chooser will also + open which gives you the option to save the set for use in future + sessions.
Update an existing user defined parameter set. This + button will save any modifications you have made to the current + parameter set.
Rename the current user defined parameter set. This + will update the name recorded for the current parameter set.
Delete the current parameter set. Selecting this will + erase the current user defined parameter set from memory, and delete + its associated parameter file (if it exists).

Support for adjusting and saving web service parameter +sets was added in Jalview 2.6

+ + diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html new file mode 100644 index 0000000..a8cda34 --- /dev/null +++ b/help/html/webServices/webServicesPrefs.html @@ -0,0 +1,60 @@ + + + + +The Web Services Preferences Dialog Box + + +

The Web Services Preferences Dialog Box

+ +

Jalview includes a range of web services clients for data +retrieval and analysis. The Web Services menu found in each +alignment window provides access to some of these services, and is +configured via the web services preference dialog box, +available from the Preferences panel from the Tools→Preferences... +menu from the Jalview Desktop window's menu bar.

+Web Services Preference Panel +

Configuring the list of JABAWS servers
+The main area of the panel shows the list of JABAWS +servers that Jalview is currently aware of. A server's URL may be added, +edited by double clicking on it, or deleted by selecting it and using +the buttons below. After adding or editing a server's URL, you will be +asked if you wish to test the server. If you wish to do so, then first +ensure you can view the new server's test report, which will be output +on Jalview's standard console output (you can open Jalview's built in +console viewer via the Tools→Java Console menu +option).

Controlling the layout of the Web Services Menu
+The range of services that Jalview is able to access depends upon your +requirements, and local computational resources. However, when a large +number of resources are available, then the entries and sub menus in the +web services menu can quickly become unwieldly. The +options in the lower part of the dialog box enable you to control the +display of each type of analysis service client in the web services +menu. In addition, indexing options are provided that enable you to +define the layout of the menus provided for JABAWS services by sorting +them into submenus according to analysis type and/or host server.

The web services preferences panel was added in Jalview +2.6

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