Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual

@@ -59,7 +61,7 @@ and sequence analysis calculations limited only by your own computing resources.

For Users

- The Server: JABAWS Virtual Appliance: (440M) + The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M)

To use JABA Web Services on most operating systems, just download and install diff --git a/website/jabaws_funding.html b/website/jabaws_funding.html new file mode 100644 index 0000000..18efa24 --- /dev/null +++ b/website/jabaws_funding.html @@ -0,0 +1,81 @@ + + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual + + + + + + +

+ + + + +

Home + Getting Started + Manual + Download + Usage Statistics + Services Status + Contact Us + Barton Group + Funding +

+ + + +

JABAWS FUNDING

+The primary funding for JABAWS development is provided by the BBSRC Bioinformatics and Biological Resources Grant: +"The Dundee Resource for Protein Structure Prediction and Sequence Analysis" 2013 to 2018 (BB/J019364/1) to Prof. +Geoff Barton. Further support comes from Wellcome Trust Strategic Grant: 100476. +

+ +

+ Initial development was funded from a mixture of sources including: BBSRC grants (BBS/B/14434, BB/G022682/1), + Wellcome Trust Strategic Grant (No. 083481), European Commision Framework of Excellence ENFIN + (LSHGCT-2005-518254) and the Scottish Universities Life Sciences Alliance (SULSA). +

+ + + + + + + +

Last update: 28 June 2013
Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK

+ + + + + + + diff --git a/website/man_about.html b/website/man_about.html index 9d644d4..55cdc98 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -46,6 +46,7 @@ Services Status Contact Us Barton Group + Funding

@@ -62,7 +63,9 @@

What is JABAWS Client?

JABAWS versions compatibility and Jalview support

Programmatic access to JABAWS

- + + +

What is JABAWS?

@@ -82,17 +85,22 @@ in writing your own client, the JABAWS command line client is what you need.

+ +

JABAWS Benefits

Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
Comes complete with sources and binaries for all the bioinformatics programs that it runs.
Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, - your lab's server, or the publicly available services at the University of Dundee.
Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.
Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.
Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.
Comes complete with sources and binaries for all the bioinformatics programs that it runs.
Can operate as a stand alone server or one that submits jobs to a cluster via DRMAA.
Easy to access from Jalview using its graphical client, or using the JABAWS command line client.
Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, + your lab's server, or the publicly available services at the University of Dundee.
Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.
Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.

+ + +

JABA Web Services Programs

JABAWS currently provides access to the following programs:

Multiple Sequence Alignement

@@ -103,8 +111,7 @@

Muscle (version 3.8.31)

Tcoffee (version 8.99)

Probcons (version 1.12)

- - +

Protein disorder prediction

DisEMBL (1.5)

Amino Acid conservation

AACon (1.0)

+ + +

What is new in JABAWS 2.0.1?

JABAWS Version 2.0.1 includes several minor updates and bug fixes for JABAWS Version 2. These are listed below:

JABAWS Version 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2. These are listed below:

Disembl returned swapped strings for HOTLOOPS and REM465
Jronn failed to process jobs with more than 3 sequences
JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties
Default web security has been incompatible with Tomcat 7.0.31 and newer
Documentation has been updated

JABAWS Version 2 (Released 16th Dec 2011)

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:

updates for all multiple sequence alignment services
Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
Improved web services client API
Simplified WAR package installation

+ + -

What is JABAWS client?

A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web @@ -154,21 +166,27 @@ provides a graphical JABAWS client. This client has 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 versions compatibility and Jalview support

JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and v2.0 clients should also be able to use JABAWS 2.0.1 services. To access the analysis web services introduced in JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.

+ + +

Programmatic access to JABAWS

-JABA 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, however, -then you may wish to use our client package to access JABAWS. -This package is based on the autogenerated source code produced by wsimport, which -is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify -working with JABAWS. For more information please refer to the data model javadoc. + JABA 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, however, + then you may wish to use our client package to access JABAWS. + This package is based on the autogenerated source code produced by wsimport, which + is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify + working with JABAWS. For more information please refer to the data model javadoc.

Last update: 28 June 2013
Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK

diff --git a/website/man_awscloud.html b/website/man_awscloud.html index 822ec3b..0a39b38 100644 --- a/website/man_awscloud.html +++ b/website/man_awscloud.html @@ -44,6 +44,7 @@ Services Status Contact Us Barton Group + Funding