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JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of currently supported programs) from Jalview. Future versions of JABAWS will incorporate other tools.
Getting JABAWSJABAWS consists of a server and a client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need.
JABAWS currently provides access to the following programs:
Multiple Sequence AlignmentThe website was improved and several service programs were update:
Several new web services are available in this version of JABAWS:
Some bugs have been fixed and several improvements have been done:
JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0. These are listed below:
Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.
It contains:
A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web services on any instance of JABAWS Server available over the web. The basic client is useful if you would like to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle any web service specific details. The client is an open source software, so you can also use the source code to as an example how to manipulate with JABAWS web services in your own code. Jalview, a multiple sequence alignment and analysis application, is a good example of a graphical JABAWS client. This client uses 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 version 2.2 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0, 2.0, 2.0.1 and 2.1 clients should also be able to use JABAWS 2.2 services. To access the analysis web services introduced in JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.
JABAWS 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
you may wish to use our
client package to access JABAWS.
This package is based on the autogenerated source code produced by