Getting Started
===============
-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`_). Future versions of JABAWS will incorporate other tools.
+*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`_). Future versions of JABAWS will incorporate other tools.
JABAWS 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 (VA)`_. 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 (WAR)`_. 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 Interface (CLI)`_ client is what you need.
+The public server based on JABAWS 2.1 at the `University of Dundee`_ has been in production since October 2013 and serviced over 442,000 jobs for users worldwide.
+
+**New:** You can now run JABAWS with `Docker`_. `Click here to learn more`_.
------------
JABAWS Distributions
--------------------
-.. tip:: To help you choose the JABAWS distribution that better suits your needs and read on the quickstart guides below.
+.. tip:: To help you choose the JABAWS distribution that better suits your needs read on the quickstart guides below.
**I want to use JABAWS for...**
`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 `JABAWS Command Line Interface (CLI)`_ client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface. In this way, this is the easiest way to run JABAWS web services. Simply launch `Jalview`_ and run any of the methods provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default. If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can either setup a local `JABAWS Virtual Appliance (VA)`_ or configure the `JABAWS Web Application aRchive (WAR)`_ in your infrastructure.
+.. image:: ../../website/static/img/aligment.png
+ :height: 318
+ :width: 608
+ :scale: 100 %
+ :align: left
+
------------
.. _jabaws-cli:
.. code:: bash
- java -jar jaba-client.jar
+ java -jar jabaws-full-client-2.2.0.jar
The JABA Web Services are WS-I compliant. This means that you can access them from any language that has libraries or functions for consuming interoperable SOAP web services. More information on how to develop software that access JABAWS services is provided in the `documentation pages`_.
.. _VMWare Player: http://www.vmware.com/products/player
.. _VMWare Fusion: http://www.vmware.com/products/fusion/overview.html
.. _VA documentation pages: va.html
+.. _Docker: https://www.docker.com/
+.. _Click here to learn more: docker.html
git://source.jalview.org / jabaws.git / blobdiff