JABAWS 2

JABAWS is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.0 includes new disorder prediction services based on DisEMBL, IUPred, Ronn, GlobPlot and protein sequence alignment conservation measures calculated by AACon. A new multiple sequence alignment service for Clustal Omega is also provided, in addition to standard JABAWS:MSA services for Clustal W, JABAWS is free software which provides web services for prediction of protein disorder, multiple sequence alignment and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.0 introduces protein disorder prediction services based on DisEMBL, IUPred, Ronn, GlobPlot and protein sequence alignment conservation measures calculated by AACon. A new multiple sequence alignment service for Clustal Omega is also provided, in addition to standard JABAWS:MSA services for Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. JABA Web Services can be accessed from the Jalview desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.

- +

Please note that JABAWS 2 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012.)Â In the meantime you can access all JABAWS2 services through the JABAWS command-line client.

@@ -74,11 +79,11 @@ page

For Bioinformaticians/Developers

The Server: JABAWS Web Application aRchive (55M) +"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)
The Client: - Command Line Client binary | source + Command Line Client binary | source @@ -92,16 +97,16 @@ Check out the quick start guide for furt

Public JABAWS Server

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview is configured to use this public JABAWS server by default.

You can access our public JABA Web Services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2. The latest versions of Jalview are configured to use public JABAWS server by default.

The JABAWS public web services address is http://www.compbio.dundee.ac.uk/jabaws
A detailed web services description is available from here: WSDL List

These web services will reject submissions containing more then one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

- - +

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

Previous versions of JABAWS

JABAWS 1 is available from here http://www.compbio.dundee.ac.uk/jabaws1. We advise you to update to the JABAWS 2 as this version is fully backward compatible with JABAWS 1 and contain numerous improvements. Please consult the manual for more information on versions compatibility.

Reference

Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.

diff --git a/website/man_about.html b/website/man_about.html index 9bfd4eb..e37fd95 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -37,7 +37,7 @@ JABAWSJABAWS Development - Download + Download Usage Statistics Services Status Contact Us @@ -53,7 +53,9 @@

What is JABAWS?

JABAWS Benefits

JABA Web Services Programs

What is new in JABAWS 2?

What is JABAWS Client?

JABAWS versions compatibility and Jalview support

Programmatic access to JABAWS

@@ -95,8 +97,24 @@

Amino Acid conservation

AACon (1.0)

What is JABAWS client?

+ +

What is new in JABAWS 2?

Comparing to previous version of JABAWS JABAWS 2 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains

updates for all multiple sequence alignment services
four new protein disorder prediction services
Clustal Omega multiple sequence alignment web service
amino acid conservation service
web services execution statistics visialization
web services status check from a web page
VirtualBox support was dropped in favour of VMware
new WAR package for Mac users
Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
Improved web services client API
Simplified WAR package installation

+ +

What is JABAWS client?

A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods on any instance of JABAWS Server that it can reach over the web. It is useful if you @@ -105,12 +123,15 @@ specific details. The client is open source, so you can also use its source code out how to work with JABA Web Services if you would like to write your own client software. Jalview, which is a multiple sequence alignment and analysis application, provides a graphical JABAWS client. This client has the same functionality as the command line client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

JABAWS versions compatibility and Jalview support

JABAWS version 2 is fully backward compatible with JABAWS version 1. That means that all JABAWS 1 clients should be able to use JABAWS 2 instead. However, they will be limited to the multiple sequence alignment web services only. To benefit of new web services introduced in JABAWS 2 the clients have to be updated.
+Jalview since version 2.6.1 integrates fully with JABAWS 1. Therefore it will be possible to use any versions of Jalview after 2.6.1 with JABAWS 1. However, the full support for JABAWS 2 is introduced in Jalview version 2.8 or later.Â

Programmatic access to JABAWS

JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java, however, then you may wish to use our -client package to access JABAWS. +client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify working with JABAWS. For more information please refer to the data model javadoc. diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 9b2c984..21cd30c 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_awscloud_bs.html b/website/man_awscloud_bs.html index c5ff4a8..16cbb87 100644 --- a/website/man_awscloud_bs.html +++ b/website/man_awscloud_bs.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_awscloud_ec2.html b/website/man_awscloud_ec2.html index edb1e9c..a1121b7 100644 --- a/website/man_awscloud_ec2.html +++ b/website/man_awscloud_ec2.html @@ -44,7 +44,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_client.html b/website/man_client.html index 33f0110..d84f2a6 100644 --- a/website/man_client.html +++ b/website/man_client.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us @@ -51,7 +51,7 @@

JABAWS MANUAL

JABAWS Command Line Client Usage

The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]
-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS] diff --git a/website/man_configuration.html b/website/man_configuration.html index 2605797..f5348ec 100644 --- a/website/man_configuration.html +++ b/website/man_configuration.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us diff --git a/website/man_dev.html b/website/man_dev.html index 7b7d944..f541bd4 100644 --- a/website/man_dev.html +++ b/website/man_dev.html @@ -39,7 +39,7 @@ JABAWS JABAWS Development -Download +Download Usage Statistics Services Status Contact Us @@ -107,7 +107,7 @@

Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
Please refer to a data model javadoc for a detailed description of each class and its methods.

Connecting to JABAWS

For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

import java.net.URL;
import javax.xml.namespace.QName;
@@ -214,7 +214,7 @@ FileOutputStream outStream = new FileOutputStream(file);
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);

A complete client example

Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a PDF version of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

 import java.io.ByteArrayInputStream;
 import java.io.FileNotFoundException;
diff --git a/website/man_server_dev.html b/website/man_server_dev.html
index 8eae77b..3edfaa2 100644
--- a/website/man_server_dev.html
+++ b/website/man_server_dev.html
@@ -38,7 +38,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_servervm.html b/website/man_servervm.html
index d678232..d2001f6 100644
--- a/website/man_servervm.html
+++ b/website/man_servervm.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_serverwar.html b/website/man_serverwar.html
index fec6e59..76c58f5 100644
--- a/website/man_serverwar.html
+++ b/website/man_serverwar.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/man_stats.html b/website/man_stats.html
index 1b2164e..487aa13 100644
--- a/website/man_stats.html
+++ b/website/man_stats.html
@@ -39,7 +39,7 @@
 		JABAWS	
 		JABAWS Development
 	
-Download 
+Download 
 Usage Statistics
  Services Status
 Contact Us
diff --git a/website/manual_qs_client.html b/website/manual_qs_client.html
index 62bfb18..49c926c 100644
--- a/website/manual_qs_client.html
+++ b/website/manual_qs_client.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -67,7 +67,7 @@
 
 The JABAWS command line client

 Download the Client Jar (80 K)
+"http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar (80 K)
 
 This is a single java archive which contains the JABAWS command line client. 
 It requires Java version 1.6 to run, and allows anyone who wants to connect 
diff --git a/website/manual_qs_va.html b/website/manual_qs_va.html
index 833c4de..cdae95a 100644
--- a/website/manual_qs_va.html
+++ b/website/manual_qs_va.html
@@ -24,7 +24,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -61,7 +61,7 @@
 
 
 
Running JABAWS on your local machine

-  Download JABAWS Virtual Appliance (520M) 
+  Download JABAWS Virtual Appliance (520M) 
 
 The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a virtual machine on your laptop or desktop computer. A complete guide to the JABAWS VA is given in the manual, but for the impatient, a brief instructions are given below:
 
diff --git a/website/manual_qs_war.html b/website/manual_qs_war.html
index f29b327..e3c0cc8 100644
--- a/website/manual_qs_war.html
+++ b/website/manual_qs_war.html
@@ -25,7 +25,7 @@
 Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	 Services Status
 	Contact Us
@@ -69,7 +69,7 @@
 
This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.
 
 
-Download the JABAWS WAR for your platform 
+Download the JABAWS WAR for your platform 
   Download and install Apache-Tomcat.

    You will need at least version 5.5 of Tomcat (we would recommend version 7.0) and at least version 1.6 (i.e. JAVA 6) of Java.
   Drop the JABAWS WAR file into tomcat/webapps directory.
diff --git a/website/quick_start.html b/website/quick_start.html
index f2302c6..415ab93 100644
--- a/website/quick_start.html
+++ b/website/quick_start.html
@@ -24,7 +24,7 @@
 	Home
     Getting Started 
     Manual 
-	Download
+	Download
     Usage Statistics
 	Services Status
 	Contact Us
-- 
1.7.10.2

For Users

- The Server: JABAWS Virtual Appliance: (520M) + The Server: JABAWS Virtual Appliance: (520M) or use JABAWS on Amazon Webservices Cloud
The Client: Jalview (18M)

To use JABA Web Services on most operating systems, just download and install the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!

@@ -64,7 +69,7 @@ page

For System Administrators

The Server: JABAWS Web Application aRchive (55M)

+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive (55M)

JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for installation instructions.