Soaplab
Encyclopedia
Soaplab is a Web Services software framework
specialised for bioinformatics
programs with command-line interface
. It includes a module for running command-line programs as Web Services jobs and provides support to generate Java Web Services web applications for them. It allows both synchronous and asynchronous execution of programs. Soaplab generic interface makes it possible to use one single interface when accessing any Soaplab Web Services regardless of the command line interface of underlying programs.
Soaplab is well known to many bioinformaticians since it has built-in support for EMBOSS
programs and also because the European Bioinformatics Institute
where Soaplab was developed has had an active Soaplab server since year 2003. The EBI Soaplab Web Services, includes most EMBOSS applications that are suitable for launching through Web Services. It can be said that initial development of Soaplab was supported by the UK e-Science program, and it was part of the myGrid
project.
Its latest version, Soaplab2, first released in late 2007, resolved the known maintainability problems and included several enhancements. For example, the legacy Applab layer, which required an additional CORBA
server running in parallel to Soaplab servers, was removed and its functionality re-implemented as part of Soaplab2. It allowed deployment of Web Services in two configurations:
Soaplab2 supports defining and running test suites and includes a predefined test suite for testing EMBOSS
Web Services. One important new feature in Soaplab2 was its new web-page front-end Spinet which allows running of underlying programs through usual HTML forms.
Software framework
In computer programming, a software framework is an abstraction in which software providing generic functionality can be selectively changed by user code, thus providing application specific software...
specialised for bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
programs with command-line interface
Command-line interface
A command-line interface is a mechanism for interacting with a computer operating system or software by typing commands to perform specific tasks...
. It includes a module for running command-line programs as Web Services jobs and provides support to generate Java Web Services web applications for them. It allows both synchronous and asynchronous execution of programs. Soaplab generic interface makes it possible to use one single interface when accessing any Soaplab Web Services regardless of the command line interface of underlying programs.
Soaplab is well known to many bioinformaticians since it has built-in support for EMBOSS
EMBOSS
EMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
programs and also because the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
where Soaplab was developed has had an active Soaplab server since year 2003. The EBI Soaplab Web Services, includes most EMBOSS applications that are suitable for launching through Web Services. It can be said that initial development of Soaplab was supported by the UK e-Science program, and it was part of the myGrid
MyGrid
The myGrid consortium is a multi-institutional, multi-disciplinary internationally leading research group focussing on the challenges of eScience...
project.
Its latest version, Soaplab2, first released in late 2007, resolved the known maintainability problems and included several enhancements. For example, the legacy Applab layer, which required an additional CORBA
Çorba
Chorba , ciorbă , shurpa , shorpo , or sorpa is one of various kinds of soup or stew found in national cuisines across Middle East...
server running in parallel to Soaplab servers, was removed and its functionality re-implemented as part of Soaplab2. It allowed deployment of Web Services in two configurations:
- Document/literal-wrapped Web Services interface, based on JAX-WS Web Services stack
- RPC/encoded Web Services interface, based on AxisApache AxisApache Axis is an open source, XML based Web service framework. It consists of a Java and a C++ implementation of the SOAP server, and various utilities and APIs for generating and deploying Web service applications. Using Apache Axis, developers can create interoperable, distributed computing...
-1 Web Services stack (for backward compatibility of the existing clients)
Soaplab2 supports defining and running test suites and includes a predefined test suite for testing EMBOSS
EMBOSS
EMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
Web Services. One important new feature in Soaplab2 was its new web-page front-end Spinet which allows running of underlying programs through usual HTML forms.
See also
- Official Soaplab website
- EMBL-EBIEuropean Bioinformatics InstituteThe European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
Soaplab based EMBOSS Web Services