Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

A System for Deduction-based Formal Verification of Workflow-oriented Software Models

The work concerns formal verification of workflow-oriented software models using deductive approach. The formal correctness of a model's behaviour is considered. Manually building logical specifications, which are considered as a set of temporal logic formulas, seems to be the significant obstacle for an inexperienced user when applying the deductive approach. A system, and its architecture, for the deduction-based verification of workflow-oriented models is proposed. The process of inference is based on the semantic tableaux method which has some advantages when compared to traditional deduction strategies. The algorithm for an automatic generation of logical specifications is proposed. The generation procedure is based on the predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea for the approach is to consider patterns, defined in terms of temporal logic,as a kind of (logical) primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between intuitiveness of the deductive reasoning and the difficulty of its practical application in the case when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing our understanding of, the deduction-based formal verification of workflow-oriented models.Comment: International Journal of Applied Mathematics and Computer Scienc

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

Automatic case acquisition from texts for process-oriented case-based reasoning

This paper introduces a method for the automatic acquisition of a rich case representation from free text for process-oriented case-based reasoning. Case engineering is among the most complicated and costly tasks in implementing a case-based reasoning system. This is especially so for process-oriented case-based reasoning, where more expressive case representations are generally used and, in our opinion, actually required for satisfactory case adaptation. In this context, the ability to acquire cases automatically from procedural texts is a major step forward in order to reason on processes. We therefore detail a methodology that makes case acquisition from processes described as free text possible, with special attention given to assembly instruction texts. This methodology extends the techniques we used to extract actions from cooking recipes. We argue that techniques taken from natural language processing are required for this task, and that they give satisfactory results. An evaluation based on our implemented prototype extracting workflows from recipe texts is provided.Comment: Sous presse, publication pr\'evue en 201

The Evolution of myExperiment

The myExperiment social website for sharing scientific workflows, designed according to Web 2.0 principles, has grown to be the largest public repository of its kind. It is distinctive for its focus on sharing methods, its researcher-centric design and its facility to aggregate content into sharable 'research objects'. This evolution of myExperiment has occurred hand in hand with its users. myExperiment now supports Linked Data as a step toward our vision of the future research environment, which we categorise here as '3rd generation e-Research'

Extending OWL-S for the Composition of Web Services Generated With a Legacy Application Wrapper

Despite numerous efforts by various developers, web service composition is still a difficult problem to tackle. Lot of progressive research has been made on the development of suitable standards. These researches help to alleviate and overcome some of the web services composition issues. However, the legacy application wrappers generate nonstandard WSDL which hinder the progress. Indeed, in addition to their lack of semantics, WSDLs have sometimes different shapes because they are adapted to circumvent some technical implementation aspect. In this paper, we propose a method for the semi automatic composition of web services in the context of the NeuroLOG project. In this project the reuse of processing tools relies on a legacy application wrapper called jGASW. The paper describes the extensions to OWL-S in order to introduce and enable the composition of web services generated using the jGASW wrapper and also to implement consistency checks regarding these services.Comment: ICIW 2012, The Seventh International Conference on Internet and Web Applications and Services, Stuttgart : Germany (2012

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions