-JAva Bioinformatics Analysis Web Services (JABAWS) is a collection of SOAP web services for Bioinformatics. 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. Unlike other web services you can run JABAWS services from your own computer. This puts you in control of the web services - they will be where and when you need them, have no restrictions and your data privacy is guaranteed. JABAWS scales well from the single user single computer to the cluster with hundreds of users. Finally, you do not have to be an expert to use JABAWS - the installation is simple and you can use the services from the comfort of your desktop via Jalview. You can access our public JABA Web Services with our command line client, the Jalview, or write your own program. To guarantee a level service for everyone our public services impose some restrictions on the size and the number of the jobs you can submit. Currently we do not process tasks that exceed 1000 sequences per 1000 letters on average. Should you find this to be insufficient for your needs you can download and run JABAWS Server on your own hardware. This also applies if the privacy is a concern or an Internet connection is a problem.
-Currently JABAWS provides five web
-services for multiple sequence alignment Clustal W, JABAWS 2
+Public JABAWS Server
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+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.
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+ 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! + |
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+ For System Administrators
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+ 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. + |
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+ For Bioinformaticians/Developers
+The Server: JABAWS Web Application aRchive (55M)
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+ + 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. + + |
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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.
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- The JABAWS public web services address is http://www.combio.dundee.ac.uk/jabaws -
- Detailed web services description is available from here: 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
Contact Us
-Please feel free to post your questions/issues to the jabaws-discuss mailing 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.
+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.