What is JABAWS?
JAva Bioinformatics Analysis Web Services (JABAWS) is a
collection of SOAP web
services for bioinformatics.
JABAWS is designed to make it easy to access bioinformatics
analysis programs over the web, by providing web services, which
make it easy to access programs and databases from anywhere, at
anytime. The flavour of web services that JABAWS provides are SOAP
web services, which are designed for use by other programs, rather
than people.
The current version of JABAWS is compatible with version 2.6 of Jalview, and provides five web
services for multiple sequence alignment:
Why JABAWS?
JABA Web Services has a number of distinct features that are not found in other bioinformatics web services systems. In particular, JABAWS:
- Provides uniform remote access to a number of command line tools This allows you to access a number of programs anywhere, at any time. For instance, all multiple sequence alignment services can be accessed with a single command line interface, simplifying their invocation. However, most of the command line options for each program are supported, so you have nearly the same level of control as if you were running them on the command line yourself.
- Enables web based or stand-alone applications, like Jalview, to
access a variety of bioinformatics analysis methods The java web service client library makes it very easy to
connect to one or more instances of JABAWS, so if one server is off
line, all you need to know is the URL of another server that will
do the job for you.
JABAWS provides WS-I basic profile v. 1.1 compatible services, which means that clients can be created for them in almost any programming language. - Can be easily deployed as a server on a variety of platforms, with command line tools run on the same machine or on a cluster.JABAWS integrates with a number of cluster job management systems (e.g. GridEngine, PBS, LSF, Condor). It also intelligently manages task scheduling depending on their size, eliminatng the scalability issues and let you focus on your research.
Here are just some of the problems that JABAWS can solve:
-
The default settings for a program don't work for my data!
JABAWS includes a comprehensive parameter model and validation mechanism, allowing you to specify additional options and arguments. Want to use PAM200 substitution matrix, set the number of iterations, or sequence clustering method? No problem - JABAWS lets you do that. You are no longer limited to defaults! -
I don't want to send my data to the internet!
Simply download and install JABAWS on a trusted machine in your lab or institute, and use its web address instead of the public JABAWS services. No data will leave your lab any longer. -
Running programs using the public services is slower than using my own computer!
The JABAWS server can run programs on a single machine or on a cluster, and are easy to install. If your server is going to be heavily used, then it is better to configure JABAWS to access your cluster, which is straightforward.
Public JABAWS Server
| Feature | Description |
|---|---|
| URL | http://www.compbio.dundee.ac.uk/jabaws |
| Execution limits | Local execution limit is 40 sequnces with no more than 500 letters average length. Larger tasks are send to the College of Life Sciences HPC cluster. Tasks exceeding 1000×1000 (sequences per letters) will not be accepted for alignment. If you would like to work with bigger alignments consider installing JABAWS in your lab. |
| Web Services Description | WSDL List |
Authors
Peter Troshin and Geoff Barton are the authors of the JABA Web Services. Jim Procter helped with the JABAWS design process and web pages, and developed the interface and management components in Jalview to access JABAWS servers.