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 and databases over the web from anywhere, at
-anytime. Unlike other web services, JABAWS can be easily installed on different platforms and work straight out of the box with minimum configuration. JABA Web Services 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?
- -JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to DRMAA it integrates well with a large variety of cluster job management systems. Jalview from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on JABAWS benefits.
-Public JABAWS Server
+JABAWS 2
+JABAWS is free software which provides web services for multiple sequence alignment, prediction of protein disorder, 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). In the meantime you can access all JABAWS2 services through the JABAWS command-line client.
| Feature | -Description | -
|---|---|
| URL | -http://www.compbio.dundee.ac.uk/jabaws | -
| Execution limits | -JABAWS installation is backed up by 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 | -
|
+
+
+ For Users
+ 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! + |
+ |
+ For System Administrators
+
+ The Server: 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. + |
+ |
+ For Bioinformaticians/Developers
+The Server: JABAWS Web Application aRchive (55M)
+
+ + The Client: + Command Line Client binary | source + + + + You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public server (see below) with the command line client or you own script. +Check out the quick start guide for further details. + + |
+
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.
+Public JABAWS Server
+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 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.