WPS orchestration using the Taverna workbench: The eScience approach

eScience is an umbrella concept which covers internet technologies, such as web service orchestration that involves manipulation and processing of high volumes of data, using simple and efficient methodologies. This concept is normally associated with bioinformatics, but nothing prevents the use of an identical approach for geoinfomatics and OGC (Open Geospatial Consortium) web services like WPS (Web Processing Service). In this paper we present an extended WPS implementation based on the PyWPS framework using an automatically generated WSDL (Web Service Description Language) XML document that replicates the WPS input/output document structure used during an Execute request to a server. Services are accessed using a modified SOAP (Simple Object Access Protocol) interface provided by PyWPS, that uses service and input/outputs identifiers as element names. The WSDL XML document is dynamically generated by applying XSLT (Extensible Stylesheet Language Transformation) to the getCapabilities XML document that is generated by PyWPS. The availability of the SOAP interface and WSDL description allows WPS instances to be accessible to workflow development software like Taverna, enabling users to build complex workflows using web services represented by interconnecting graphics. Taverna will transform the visual representation of the workflow into a SCUFL (Simple Conceptual Unified Flow Language) based XML document that can be run internally or sent to a Taverna orchestration server. SCUFL uses a dataflow-centric orchestration model as opposed to the more commonly used orchestration language BPEL (Business Process Execution Language) which is process-centric.

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.