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.

Operational monitoring and forecasting of bathing water quality through exploiting satellite Earth observation and models: The AlgaRisk demonstration service

Coastal zones and shelf-seas are important for tourism, commercial fishing and aquaculture. As a result the importance of good water quality within these regions to support life is recognised worldwide and a number of international directives for monitoring them now exist. This paper describes the AlgaRisk water quality monitoring demonstration service that was developed and operated for the UK Environment Agency in response to the microbiological monitoring needs within the revised European Union Bathing Waters Directive. The AlgaRisk approach used satellite Earth observation to provide a near-real time monitoring of microbiological water quality and a series of nested operational models (atmospheric and hydrodynamic-ecosystem) provided a forecast capability. For the period of the demonstration service (2008–2013) all monitoring and forecast datasets were processed in near-real time on a daily basis and disseminated through a dedicated web portal, with extracted data automatically emailed to agency staff. Near-real time data processing was achieved using a series of supercomputers and an Open Grid approach. The novel web portal and java-based viewer enabled users to visualise and interrogate current and historical data. The system description, the algorithms employed and example results focussing on a case study of an incidence of the harmful algal bloom Karenia mikimotoi are presented. Recommendations and the potential exploitation of web services for future water quality monitoring services are discussed.

From plankton to top predators: bottom-up control of a marine food web across four trophic levels

1. Abundant mid-trophic pelagic fish often play a central role in marine ecosystems, both as links between zooplankton and top predators and as important fishery targets. In the North Sea, the lesser sandeel occupies this position, being the main prey of many bird, mammal and fish predators and the target of a major industrial fishery. However, since 2003, sandeel landings have decreased by > 50%, and many sandeel-dependent seabirds experienced breeding failures in 2004. 2. Despite the major economic implications, current understanding of the regulation of key constituents of this ecosystem is poor. Sandeel abundance may be regulated 'bottom-up' by food abundance, often thought to be under climatic control, or 'top-down' by natural or fishery predation. We tested predictions from these two hypotheses by combining unique long-term data sets (1973–2003) on seabird breeding productivity from the Isle of May, SE Scotland, and plankton and fish larvae from the Continuous Plankton Recorder survey. We also tested whether seabird breeding productivity was more tightly linked to sandeel biomass or quality (size) of individual fish. 3. The biomass of larval sandeels increased two- to threefold over the study period and was positively associated with proxies of the abundance of their plankton prey. Breeding productivity of four seabirds bringing multiple prey items to their offspring was positively related to sandeel larval biomass with a 1-year lag, indicating dependence on 1-year-old fish, but in one species bringing individual fish it was strongly associated with the size of adult sandeels. 4. These links are consistent with bottom-up ecosystem regulation and, with evidence from previous studies, indicate how climate-driven changes in plankton communities can affect top predators and potentially human fisheries through the dynamics of key mid-trophic fish. However, the failing recruitment to adult sandeel stocks and the exceptionally low seabird breeding productivity in 2004 were not associated with low sandeel larval biomass in 2003, so other mechanisms (e.g. predation, lack of suitable food after metamorphosis) must have been important in this case. Understanding ecosystem regulation is extremely important for predicting the fate of keystone species, such as sandeels, and their predators.