Seeing the forest through the trees: A review of integrated environmental modelling tools
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paper_title: Uncertainty Management in Integrated Assessment Modeling: Towards a Pluralistic Approach

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Integrated Assessment (IA) is an evolving research community that aims to address complex societal issues through an interdisciplinary process. The most-widely used method in Integrated Assessment is modeling. The state of the art in Integrated Assessment modeling is described in this paper in terms of history, general features, classes of models, and in terms of the strengths and weaknesses, and the dilemmasand challenges modelers face. One of the key challenges is the issue of uncertainty management. The paper outlines the sources and types of uncertainty modelers are confronted with. It then discusses how uncertainties are currently managed inIntegrated Assessment modeling, on which evaluation it is argued that complementary methods are needed that allow for pluralistic uncertainty management. The paperfinalises with discussing pluralistic concepts and approaches that are currently explored in the IA community and that seem promising in view of the challenge to incorporate explicitly more than one hidden perspective in models.
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paper_title: Integrated environmental modeling: A vision and roadmap for the future

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Integrated environmental modeling (IEM) is inspired by modern environmental problems, decisions, and policies and enabled by transdisciplinary science and computer capabilities that allow the environment to be considered in a holistic way. The problems are characterized by the extent of the environmental system involved, dynamic and interdependent nature of stressors and their impacts, diversity of stakeholders, and integration of social, economic, and environmental considerations. IEM provides a science-based structure to develop and organize relevant knowledge and information and apply it to explain, explore, and predict the behavior of environmental systems in response to human and natural sources of stress. During the past several years a number of workshops were held that brought IEM practitioners together to share experiences and discuss future needs and directions. In this paper we organize and present the results of these discussions. IEM is presented as a landscape containing four interdependent elements: applications, science, technology, and community. The elements are described from the perspective of their role in the landscape, current practices, and challenges that must be addressed. Workshop participants envision a global scale IEM community that leverages modern technologies to streamline the movement of science-based knowledge from its sources in research, through its organization into databases and models, to its integration and application for problem solving purposes. Achieving this vision will require that the global community of IEM stakeholders transcend social, and organizational boundaries and pursue greater levels of collaboration. Among the highest priorities for community action are the development of standards for publishing IEM data and models in forms suitable for automated discovery, access, and integration; education of the next generation of environmental stakeholders, with a focus on transdisciplinary research, development, and decision making; and providing a web-based platform for community interactions (e.g., continuous virtual workshops).
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paper_title: Again, and Again, and Again …

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. . . ::: ::: Replication—The confirmation of results and conclusions from one study obtained independently in another—is considered the scientific gold standard. New tools and technologies, massive amounts of data, long-term studies, interdisciplinary approaches, and the complexity of the questions being asked are complicating replication efforts, as are increased pressures on scientists to advance their research. The five Perspectives in this section (and associated News and Careers stories, Readers' Poll, and Editorial) explore some of the issues associated with replicating results across various fields. ::: ::: Ryan (p. 1229) highlights the excitement and challenges that come with field-based research. In particular, observing processes as they occur in nature allows for discovery but makes replication difficult, because the precise conditions surrounding the observations are unique. Further, although laboratory research allows for the specification of experimental conditions, the conclusions may not apply to the real world. Debate about the merits of lab-based and field-based studies has been a persistent theme over time. Tomasello and Call (p. 1227) further contribute to this debate in their discussion of some obvious barriers to replication in primate cognition and behavior research (small numbers of subjects, expense, and ethics issues) as well as more subtle ones, such as the nontrivial challenge of designing tasks that elicit complex cognitive behaviors. ::: ::: New technologies continue to produce a deluge of data of different varieties, raising expectations for new knowledge that will translate into meaningful therapeutics and insights into health. Ioannidis and Khoury (p. 1230) outline multiple steps for validating such large-scale data on the path to clinical utility and make suggestions for incentives (and penalties) that could enhance the availability of reliable data and analyses. ::: ::: Peng (p. 1226) discusses the need for a minimum standard of reproducibility in computer sciences, arguing that enough information about methods and code should be available for independent researchers to reach consistent conclusions using original raw data. Specifically, he describes a model that one journal has used to make this a reality. ::: ::: The need to convince the public that data are replicable has grown as science and public policy-making intersect, an issue that has has beset climate change studies. As Santer et al. (p. 1232) describe, having multiple groups examining the same data and generating new data has led to robust conclusions. ::: ::: The importance of replication and reproducibility for scientists is unquestioned. Sometimes attempts to replicate reveal scientific uncertainties. This is one of the main ways that science progresses (see associated News stories of faster-than-light neutrinos and sirtuins, pp. 1200 and 1194). Unfortunately, in rare instances (compared to the body of scientific work), it can also indicate fraud (see the Editorial by Crocker and Cooper, p. 1182). How do we promote the publication of replicable data? The authors in this section come up with possibilities that are targeted at funders, journals, and the research culture itself. In the Readers'Poll, you can make your views known as well.
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paper_title: Bridging the Gaps Between Design and Use: Developing Tools to Support Environmental Management and Policy

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A method is provided for compensating an output signal of an electronic device having an input end electrically connected to a feedback device and an output end electrically connected to a load. This method includes steps of (a) measuring a standard voltage Vo of the load, (b) determining an input voltage Vi and an input current Ii of the electronic device, and (c) generating a feedback signal based on said input voltage Vi. The method further includes steps of (d) determining a maximum current Imax and a minimum current Imin of the feedback signal passing through the feedback device, (e) defining an estimated output current Io of the electronic device based on the maximum current Imax and the minimum current Imin, and (f) compensating the output signal of the electronic device according to a compensating factor d determined by the standard voltage Vo, the input voltage Vi, the input current Ii, and the estimated output current Io, of the electronic device. The estimated output current Io is calculated according to the maximum current Imax and the minimum current Imin by a first equation of Io=Imax+kImin where k is a constant.
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paper_title: Integrated Assessment and Modelling: Features, Principles and Examples for Catchment Management

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Abstract To meet the challenges of sustainability and catchment management requires an approach that assesses resource usage options and environmental impacts integratively. Assessment must be able to integrate several dimensions: the consideration of multiple issues and stakeholders, the key disciplines within and between the human and natural sciences, multiple scales of system behaviour, cascading effects both spatially and temporally, models of the different system components, and multiple databases. Integrated assessment (IA) is an emerging discipline and process that attempts to address the demands of decision makers for management that has ecological, social and economic values and considerations. This paper summarises the features of IA and argues the role for models and information systems as a prime activity. Given the complex nature of IA problems, the broad objectives of IA modelling should be to understand the directions and magnitudes of change in relation to management interventions so as to be able to differentiate between associated outcome sets. Central to this broad objective is the need for improved techniques of uncertainty and sensitivity analysis that can provide a measure of confidence in the ability to differentiate between different decisions. Three examples of problems treated with an IA approach are presented. The variations in the way that the different dimensions are integrated in the modelling are discussed to highlight the sorts of choices that can be made in model construction. The conclusions stress the importance of IA as a process, not just as a set of outcomes, and define some of the deficiencies to be overcome.
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paper_title: Accessible Reproducible Research

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As use of computation in research grows, new tools are needed to expand recording, reporting, and reproduction of methods and data.
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paper_title: Standards-Based Computing Capabilities for Distributed Geospatial Applications

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Researchers face increasingly large repositories of geospatial data stored in different locations and in various formats. To address this problem, the Open Geospatial Consortium and the Open Grid Forum are collaborating to develop standards for distributed geospatial computing.
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paper_title: An IT perspective on integrated environmental modelling: The SIAT case

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Policy makers have a growing interest in integrated assessments of policies. The Integrated Assessment Modelling (IAM) community is reacting to this interest by extending the application of model development from pure scientific analysis towards application in decision making or policy context by giving tools a higher capability for analysis targeted at non-experts, but intelligent users. Many parties are involved in the construction of such tools including modellers, domain experts and tool users, resulting in as many views on the proposed tool. During tool development research continues which leads to advanced understanding of the system and may alter early specifications. Accumulation of changes to the initial design obscures the design, usually vastly increasing the number of defects in the software. The software engineering community uses concepts, methods and practices to deal with ambiguous specifications, changing requirements and incompletely conceived visions, and to design and develop maintainable/extensible quality software. The aim of this paper is to introduce modellers to software engineering concepts and methods which have the potential to improve model and tool development using experiences from the development of the Sustainability Impact Assessment Tool. These range from choosing a software development methodology for planning activities and coordinating people, technical design principles impacting maintainability, quality and reusability of the software to prototyping and user involvement. It is argued that adaptive development methods seem to best fit research projects, that typically have unclear upfront and changing requirements. The break-down of a system into elements that overlap as little as possible in features and behaviour helps to divide the work across teams and to achieve a modular and flexible system. However, this must be accompanied by proper automated testing methods and automated continuous integration of the elements. Prototypes, screen sketches and mock-ups are useful to align the different views, build a shared vision of required functionality and to match expectations.
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paper_title: Taverna , lessons in creating a workflow environment for the life sciences

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Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co-ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science.
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paper_title: Comparing modelling frameworks- A workshop approach.

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Abstract Of concern to the environmental modelling community is the proliferation of individual, and individualistic, models and the time associated with common model development tasks such as data transformation, coding of models, and visualisation. One way of addressing this problem is the adoption of modelling frameworks. These frameworks, or environments, support modular model development through provision of libraries of core environmental modelling modules, as well as reusable tools for data manipulation, analysis and visualisation. Such frameworks have a range of features and requirements related to the architecture, protocols and methods of operation, and it is difficult to compare the modelling workload and performance of alternative frameworks without using them to undertake identical, or similar modelling tasks. This paper describes the outcomes of a workshop to compare three frameworks – the Spatial Modelling Environment (SME), Tarsier and the Integrated Component Modelling System (ICMS). A simple environmental problem linking hillslope flow and soil erosion processes with a receiving water store was designed and then implemented in the three frameworks. It was found that the SME and Tarsier contained many components well suited to handling complex spatial and temporal models, with ICMS being an integrated framework tailored for smaller scale problems. Of the three tested frameworks, the SME proved superior in supporting problem description, Tarsier provided more flexibility in linking and validating the model components, and ICMS served as an effective prototyping tool. The test problem, and associated data and parameters, are described in detail to allow others to undertake this test.
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paper_title: An overview of model integration for environmental applications—components, frameworks and semantics

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Abstract In recent years, pressure has increased on environmental scientist/modellers to both undertake good science in an efficient and timely manner, under increasing resource constraints, and also to ensure that the science being performed is immediately relevant to a particular environmental management context. At the same time, environmental management is changing, with increasing requirements for multi-scale and multi-objective assessment and decision making that considers economic and social systems, as well as the ecosystem. Integration of management activities, and also of the modelling undertaken to support management, has become a high priority. To solve the problems of application and integration, knowledge encapsulation in models is being undertaken in a way that both meets the needs for good science, and also provides the conceptual and technical structures required for broader and more integrated application of that knowledge by managers. To support this modelling, tools and technologies from computer science and software engineering are being transferred to applied environmental science fields, and a range of new modelling and software development approaches are being pursued. The papers in this Special Issue provide examples of the integrated modelling concepts and applications that have been, or are being, developed. These include the use of object-oriented concepts, component-based modelling techniques and modelling frameworks, as well as the emerging use of integrated modelling platforms and metadata support for modelling semantics. This paper provides an overview of the science and management imperatives underlying recent developments, discusses the technological and conceptual developments that have taken place, and highlights some of the semantic, operational and process requirements that need to be addressed now that the technological aspects of integrated modelling are well advanced.
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paper_title: An overview of the open modelling interface and environment (the OpenMI)

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Abstract The paper reports on a Framework 5 project, HarmonIT, which is developing an open modelling interface and environment (the OpenMI) to simplify the linking of water related simulation models. Its purpose is to support the implementation of the Water Framework Directive. If successful, it will facilitate the simulation of process interactions and make it easier for catchment managers to explore the wider implications of the policy options open to them. The main deliverable of the project is the definition of a standard interface that will allow new and existing models to exchange data at run time. To help users adapt their models to use the interface, and then link and run them with other models, the standard will be supported by software tools for migration, linking, monitoring performance and displaying results. The paper describes the work to date, outlines the key features of the OpenMI's architecture and explains the actions being taken to sustain the OpenMI into the future.
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paper_title: A component-Based Framework for Simulating Agricultural Production and Externalities

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Although existing simulation tools can be used to study the impact of agricultural management on production activities in specific environments, they suffer from several limitations. They are largely specialized for specific production activities: arable crops/cropping systems, grassland, orchards, agro-forestry, livestock etc. Also, they often have a restricted ability to simulate system externalities which may have a negative environmental impact. Furthermore, the structure of such systems neither allows an easy plug-in of modules for other agricultural production activities, nor the use of alternative components for simulating processes. Finally, such systems are proprietary systems of either research groups or projects which inhibits further development by third parties.
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paper_title: Integrated Modelling Frameworks for Environmental Assessment and Decision Support

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Modern management of environmental resources defines problems from a holistic and integrated perspective, imposing strong requirements to Environmental Decision Support Systems (EDSSs) and Integrated Assessment Tools (IATs), which tend to be increasingly complex in terms of software architecture and computational power in order to cope with the type of problems they must solve. Such systems need to support methodologies and techniques ranging from agent-based modelling to participatory decision-making. Sometimes EDSSs and IATs are built from scratch, often with limited resources, by non-programmers. The disadvantages of this approach, which can quickly become overly expensive in terms of delivery time and resources required, have been addressed by the development of suites of software engineering tools called Environmental Integrated Modelling Frameworks (EIMFs). EIMFs have typically been designed as a response to the increasing complexity of building and delivering EDSSs and IATs. Modelling and simulation tools and frameworks have been adopted at a large scale in the management science and operations research disciplines, and standards for developing and expanding them have been developed. In contrast, no modelling framework has been universally adopted within the environmental modelling domain, and the number of environmental modelling frameworks is still growing. In this book chapter, we strive to address the above issues and clearly identify the essential characteristics of an EIMF. This book chapter also advocates the development of open standards for the exchange and re-use of modelling knowledge, including data sets, models, and procedures in order to facilitate improved communication among the leading EIMFs
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paper_title: The architecture of the Earth System Modeling Framework

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The Earth System Modeling Framework (ESMF) project is developing a standard software platform for Earth system models. The standard, which defines a component architecture and a support infrastructure, is being developed under open-software practices. Target applications range from operational numerical weather prediction to climate-system change and predictability studies.
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paper_title: The Common Modelling Protocol: A hierarchical framework for simulation of agricultural and environmental systems

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Abstract A modular approach to simulation modelling offers significant advantages for its application to agricultural and environmental questions, including re-use of model equations in different contexts and with different user-interfaces; configuration of model structures that are most appropriate to a given problem; and facilitation of collaboration between modelling teams. This paper describes the Common Modelling Protocol (CMP), a generic, open and platform-independent framework for modular simulation modelling that is in widespread use. The CMP is distinguished from existing simulation frameworks by taking an explicitly hierarchical view of the biophysical system being simulated and by representing continuous and discontinuous processes equally naturally. Modules of model logic are represented in the CMP by entities known as “components”. Each component may possess “properties” that convey the value of the quantities in its equations and “event handlers” that compute model logic. Low-level information-transfers in the CMP are carried out by means of a message-passing system. Co-ordinated sequences of messages carry out tasks such as initialization, exchange of variable values and the control of computation order. Extensible Markup Language (XML) is used in the protocol for tasks such as denoting data types, submitting simulations for execution and describing components to user-interface software. Examples are presented showing how the CMP can be used to couple modules developed by different teams and to configure a complex model structure. The choices and trade-offs encountered when building a framework for modular simulation are analyzed, using the CMP and other simulation frameworks as examples. The kinds of scientific issues that arise when the CMP is used to realize collaboration between modelling groups are discussed.
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paper_title: A Component Architecture for High-Performance Scientific Computing

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The Common Component Architecture (CCA) provides a means for software developers to manage the complexity of large-scale scientific simulations and to move toward a plug-and-play environment for high-performance coputing. In the scientific computing context, component models also promote collaboration using independently developed software, thereby allowing particular individals or groups to focus on the aspects of greatest interest to them. The CCA supports parallel and distributed coputing as well as local high-performance connections between components in a language-independent manner. The design places minimal requirements on components and thus facilitates the integration of existing code into the CCA environment. The CCA model imposes minimal ovehead to minimize the impact on application performance. The focus on high performance distinguishes the CCA from most other component models. The CCA is being applied within an increasing range of disciplines, including cobustion research, global climate simulation, and computtional chemistry.
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paper_title: OpenMI: Open modelling interface

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Management issues in many sectors of society demand integrated analysis that can be supported by integrated modelling. Since all-inclusive modelling software is difficult to achieve, and possibly even undesirable, integrated modelling requires the linkage of individual models or model components that address specific domains. Emerging from the water sector, the OpenMI has been developed with the purpose of being the glue that can link together model components from various origins. The OpenMI provides a standardized interface to define, describe and transfer data on a time basis between software components that run simultaneously, thus supporting systems where feedback between the modelled processes is necessary in order to achieve physically sound results. The OpenMI allows the linking of models with different spatial and temporal representations: for example, linking river models and groundwater models, where the river model typically uses a one-dimensional grid and a short timestep and the groundwater model uses a two- or three-dimensional grid and a longer timestep. The OpenMI is designed to accommodate the easy migration of existing modelling systems, since their re-implementation may not be economically feasible due to the large investments that have been put into the development and testing of these systems.
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paper_title: A taxonomy of scientific workflow systems for grid computing

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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. 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.
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paper_title: Guest editors' introduction to the special section on scientific workflows

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Business-oriented workflows have been studied since the 70's under various names (office automation, workflow management, business process management) and by different communities, including the database community. Much basic and applied research has been conducted over the years, e.g. theoretical studies of workflow languages and models (based on Petri-nets or process calculi), their properties, transactional behavior, etc.
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paper_title: Workflows and e-Science: An overview of workflow system features and capabilities

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Scientific workflow systems have become a necessary tool for many applications, enabling the composition and execution of complex analysis on distributed resources. Today there are many workflow systems, often with overlapping functionality. A key issue for potential users of workflow systems is the need to be able to compare the capabilities of the various available tools. There can be confusion about system functionality and the tools are often selected without a proper functional analysis. In this paper we extract a taxonomy of features from the way scientists make use of existing workflow systems and we illustrate this feature set by providing some examples taken from existing workflow systems. The taxonomy provides end users with a mechanism by which they can assess the suitability of workflow in general and how they might use these features to make an informed choice about which workflow system would be a good choice for their particular application.
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paper_title: A taxonomy and survey on autonomic management of applications in grid computing environments

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In Grid computing environments, the availability, performance, and state of resources, applications, services, and data undergo continuous changes during the life cycle of an application. Uncertainty is a fact in Grid environments, which is triggered by multiple factors, including: (1) failures, (2) dynamism, (3) incomplete global knowledge, and (4) heterogeneity. Unfortunately, the existing Grid management methods, tools, and application composition techniques are inadequate to handle these resource, application and environment behaviors. The aforementioned characteristics impose serious requirements on the Grid programming and runtime systems if they wish to deliver efficient performance to scientific and commercial applications. To overcome the above challenges, the Grid programming and runtime systems must become autonomic or self-managing in accordance with the high-level behavior specified by system administrators. Autonomic systems are inspired by biological systems that deal with similar challenges of complexity, dynamism, heterogeneity, and uncertainty. To this end, we propose a comprehensive taxonomy that characterizes and classifies different software components and high-level methods that are required for autonomic management of applications in Grids. We also survey several representative Grid computing systems that have been developed by various leading research groups in the academia and industry. The taxonomy not only highlights the similarities and differences of state-of-the-art technologies utilized in autonomic application management from the perspective of Grid computing, but also identifies the areas that require further research initiatives. We believe that this taxonomy and its mapping to relevant systems would be highly useful for academic- and industry-based researchers, who are engaged in the design of Autonomic Grid and more recently, Cloud computing systems. Copyright © 2011 John Wiley & Sons, Ltd.
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paper_title: Taverna: A tool for the composition and enactment of bioinformatics workflows

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Motivation:In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. ::: ::: Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application. ::: ::: Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net
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paper_title: VisMashup: Streamlining the Creation of Custom Visualization Applications

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Visualization is essential for understanding the increasing volumes of digital data. However, the process required to create insightful visualizations is involved and time consuming. Although several visualization tools are available, including tools with sophisticated visual interfaces, they are out of reach for users who have little or no knowledge of visualization techniques and/or who do not have programming expertise. In this paper, we propose VisMashup, a new framework for streamlining the creation of customized visualization applications. Because these applications can be customized for very specific tasks, they can hide much of the complexity in a visualization specification and make it easier for users to explore visualizations by manipulating a small set of parameters. We describe the framework and how it supports the various tasks a designer needs to carry out to develop an application, from mining and exploring a set of visualization specifications (pipelines), to the creation of simplified views of the pipelines, and the automatic generation of the application and its interface. We also describe the implementation of the system and demonstrate its use in two real application scenarios.
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paper_title: Scientific Workflow Management and the Kepler System

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Many scientific disciplines are now data and information driven, and new scientific knowledge is often gained by scientists putting together data analysis and knowledge discovery “pipelines”. A related trend is that more and more scientific communities realize the benefits of sharing their data and computational services, and are thus contributing to a distributed data and computational community infrastructure (a.k.a. “the Grid”). However, this infrastructure is only a means to an end and scientists ideally should be bothered little with its existence. The goal is for scientists to focus on development and use of what we call scientific workflows. These are networks of analytical steps that may involve, e.g., database access and querying steps, data analysis and mining steps, and many other steps including computationally intensive jobs on high performance cluster computers. In this paper we describe characteristics of and requirements for scientific workflows as identified in a number of our application projects. We then elaborate on Kepler, a particular scientific workflow system, currently under development across a number of scientific data management projects. We describe some key features of Kepler and its underlying Ptolemyii system, planned extensions, and areas of future research. Kepler is a communitydriven, open source project, and we always welcome related projects and new contributors to join.
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paper_title: Programming Scientific and Distributed Workflow with Triana Services

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In this paper, we discuss a real-world application scenario that uses three distinct types of workflow within the Triana problem-solving environment: serial scientific workflow for the data processing of gravitational wave signals; job submission workflows that execute Triana services on a testbed; and monitoring workflows that examine and modify the behaviour of the executing application. We briefly describe the Triana distribution mechanisms and the underlying architectures that we can support. Our middleware independent abstraction layer, called the Grid Application Prototype (GAP), enables us to advertise, discover and communicate with Web and peer-to-peer (P2P) services. We show how gravitational wave search algorithms have been implemented to distribute both the search computation and data across the European GridLab testbed, using a combination of Web services, Globus interaction and P2P infrastructures.
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paper_title: Triana Applications within Grid Computing and Peer to Peer Environments

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An overview of the Triana Problem Solving Environment is provided – with a particular focus on the GAP application-level interface, for integration with Grid Computing and Peer-to-Peer infrastructure. GAP is a Java-based subset of the Grid Application Toolkit interface (being implemented in the GridLab project), and an outline of its current functionality, usage and mappings to three supported underlying middleware derivatives: JXTA, Web Services, and P2PS (a simplified Peer-to-Peer platform) are provided. The motivation behind the development of P2PS is given – emphasising its minimal, but effective Peer-to-Peer mechanisms that allow scalable, decentralized discovery and communication amongst cooperating P2PS peers within highly unstable environments. A summary of three application use cases illustrating the range of scenarios that such a system addresses is also provided.
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paper_title: VisTrails: visualization meets data management

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Scientists are now faced with an incredible volume of data to analyze. To successfully analyze and validate various hypothesis, it is necessary to pose several queries, correlate disparate data, and create insightful visualizations of both the simulated processes and observed phenomena. Often, insight comes from comparing the results of multiple visualizations. Unfortunately, today this process is far from interactive and contains many error-prone and time-consuming tasks. As a result, the generation and maintenance of visualizations is a major bottleneck in the scientific process, hindering both the ability to mine scientific data and the actual use of the data. The VisTrails system represents our initial attempt to improve the scientific discovery process and reduce the time to insight. In VisTrails, we address the problem of visualization from a data management perspective: VisTrails manages the data and metadata of a visualization product. In this demonstration, we show the power and flexibility of our system by presenting actual scenarios in which scientific visualization is used and showing how our system improves usability, enables reproducibility, and greatly reduces the time required to create scientific visualizations.
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paper_title: Taverna , lessons in creating a workflow environment for the life sciences

paper_content:

Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co-ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science.
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paper_title: Virtual research environments in scholarly work and communications

paper_content:

Purpose – The purpose of this paper is to investigate the implications of the emergence of virtual research environments (VREs) and related e‐research tools for scholarly work and communications processes.Design/methodology/approach – The concepts of VREs and of e‐research more generally are introduced and relevant literature is reviewed. On this basis, the authors discuss the developing role they play in research practices across a number of disciplines and how scholarly communication is beginning to evolve in response to the opportunities these new tools open up and the challenges they raise.Findings – Virtual research environments are beginning to change the ways in which researchers go about their work and how they communicate with each other and with other stakeholders such as publishers and service providers. The changes are driven by the changing landscape of data production, curation and (re‐)use, by new scientific methods, by changes in technology supply and the increasingly interdisciplinary nat...
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paper_title: Why Linked Data is Not Enough for Scientists

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Scientific data represents a significant portion of the linked open data cloud and scientists stand to benefit from the data fusion capability this will afford. Publishing linked data into the cloud, however, does not ensure the required reusability. Publishing has requirements of provenance, quality, credit, attribution and methods to provide the reproducibility that enables validation of results. In this paper we make the case for a scientific data publication model on top of linked data and introduce the notion of Research Objects as first class citizens for sharing and publishing. Highlights? We identify and characterise different aspects of reuse and reproducibility. ? We examine requirements for such reuse. ? We propose a scientific data publication model that layers on top of linked data publishing.
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paper_title: Virtual research environments in scholarly work and communications

paper_content:

Purpose – The purpose of this paper is to investigate the implications of the emergence of virtual research environments (VREs) and related e‐research tools for scholarly work and communications processes.Design/methodology/approach – The concepts of VREs and of e‐research more generally are introduced and relevant literature is reviewed. On this basis, the authors discuss the developing role they play in research practices across a number of disciplines and how scholarly communication is beginning to evolve in response to the opportunities these new tools open up and the challenges they raise.Findings – Virtual research environments are beginning to change the ways in which researchers go about their work and how they communicate with each other and with other stakeholders such as publishers and service providers. The changes are driven by the changing landscape of data production, curation and (re‐)use, by new scientific methods, by changes in technology supply and the increasingly interdisciplinary nat...
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paper_title: Galaxy: A platform for interactive large-scale genome analysis

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Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.
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paper_title: Ecoinformatics: supporting ecology as a data-intensive science

paper_content:

Ecology is evolving rapidly and increasingly changing into a more open, accountable, interdisciplinary, collaborative and data-intensive science. Discovering, integrating and analyzing massive amounts of heterogeneous data are central to ecology as researchers address complex questions at scales from the gene to the biosphere. Ecoinformatics offers tools and approaches for managing ecological data and transforming the data into information and knowledge. Here, we review the state-of-the-art and recent advances in ecoinformatics that can benefit ecologists and environmental scientists as they tackle increasingly challenging questions that require voluminous amounts of data across disciplines and scales of space and time. We also highlight the challenges and opportunities that remain.
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paper_title: THE SEEK: A PLATFORM FOR SHARING DATA AND MODELS IN SYSTEMS BIOLOGY

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Abstract Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be heterogeneous and often involves high-throughput “omics” analyses. Models are developed iteratively from data generated in the projects and from the literature. Consequently, there is a growing requirement for exchanging experimental data, mathematical models, and scientific protocols between consortium members and a necessity to record and share the outcomes of experiments and the links between data and models. The overall output of a research consortium is also a valuable commodity in its own right. The research and associated data and models should eventually be available to the whole community for reuse and future analysis. The SEEK is an open-source, Web-based platform designed for the management and exchange of systems biology data and models. The SEEK was originally developed for the SysMO (systems biology of microorganisms) consortia, but the principles and objectives are applicable to any systems biology project. The SEEK provides an index of consortium resources and acts as gateway to other tools and services commonly used in the community. For example, the model simulation tool, JWS Online, has been integrated into the SEEK, and a plug-in to PubMed allows publications to be linked to supporting data and author profiles in the SEEK. The SEEK is a pragmatic solution to data management which encourages, but does not force, researchers to share and disseminate their data to community standard formats. It provides tools to assist with management and annotation as well as incentives and added value for following these recommendations. Data exchange and reuse rely on sufficient annotation, consistent metadata descriptions, and the use of standard exchange formats for models, data, and the experiments they are derived from. In this chapter, we present the SEEK platform, its functionalities, and the methods employed for lowering the barriers to adoption of standard formats. As the production of biological data continues to grow, in systems biology and in the life sciences in general, the need to record, manage, and exploit this wealth of information in the future is increasing. We promote the SEEK as a data and model management tool that can be adapted to the specific needs of a particular systems biology project.
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paper_title: A comparative evaluation of technical solutions for long-term data repositories in integrative biodiversity research

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Abstract The current study investigates existing infrastructure, its technical solutions and implemented standards for data repositories related to integrative biodiversity research. The storage and reuse of complex biodiversity data in central databases are becoming increasingly important, particularly in attempts to cope with the impacts of environmental change on biodiversity and ecosystems. From the data side, the main challenge of biodiversity repositories is to deal with the highly interdisciplinary and heterogeneous character of standardized and unstandardized data and metadata covering information from genes to ecosystems. Furthermore, the technical improvements in data acquisition techniques produce ever larger data volumes, which represent a challenge for database structure and proper data exchange. The current study is based on comprehensive in-depth interviews and an online survey addressing IT specialists involved in database development and operation. The results show that metadata are already well established, but that non-meta data still is largely unstandardized across various scientific communities. For example, only a third of all repositories in our investigation use internationally unified semantic standard checklists for taxonomy. The study also showed that database developers are mostly occupied with the implementation of state of the art technology and solving operational problems, leaving no time to implement user's requirements. One of the main reasons for this dissatisfying situation is the undersized and unreliable funding situation of most repositories, as reflected by the marginally small number of permanent IT staff members. We conclude that a sustainable data management system that fosters the future use and reuse of these valuable data resources requires the development of fewer, but more permanent data repositories using commonly accepted standards for their long-term data. This can only be accomplished through the consolidation of hitherto widely scattered small and non-permanent repositories.
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paper_title: Digital Earth 2020: towards the vision for the next decade

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Abstract This position paper is the outcome of a brainstorming workshop organised by the International Society for Digital Earth (ISDE) in Beijing in March 2011. It argues that the vision of Digital Earth (DE) put forward by Vice-President Al Gore 13 years ago needs to be re-evaluated in the light of the many developments in the fields of information technology, data infrastructures and earth observation that have taken place since. The paper identifies the main policy, scientific and societal drivers for the development of DE and illustrates the multi-faceted nature of a new vision of DE grounding it with a few examples of potential applications. Because no single organisation can on its own develop all the aspects of DE, it is essential to develop a series of collaborations at the global level to turn the vision outlined in this paper into reality.
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paper_title: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

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Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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paper_title: Progress in integrated assessment and modelling

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Environmental processes have been modelled for decades. However. the need for integrated assessment and modeling (IAM) has,town as the extent and severity of environmental problems in the 21st Century worsens. The scale of IAM is not restricted to the global level as in climate change models, but includes local and regional models of environmental problems. This paper discusses various definitions of IAM and identifies five different types of integration that Lire needed for the effective solution of environmental problems. The future is then depicted in the form of two brief scenarios: one optimistic and one pessimistic. The current state of IAM is then briefly reviewed. The issues of complexity and validation in IAM are recognised as more complex than in traditional disciplinary approaches. Communication is identified as a central issue both internally among team members and externally with decision-makers. stakeholders and other scientists. Finally it is concluded that the process of integrated assessment and modelling is considered as important as the product for any particular project. By learning to work together and recognise the contribution of all team members and participants, it is believed that we will have a strong scientific and social basis to address the environmental problems of the 21st Century.
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paper_title: Standards-Based Computing Capabilities for Distributed Geospatial Applications

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Researchers face increasingly large repositories of geospatial data stored in different locations and in various formats. To address this problem, the Open Geospatial Consortium and the Open Grid Forum are collaborating to develop standards for distributed geospatial computing.
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paper_title: Service chaining architectures for applications implementing distributed geographic information processing

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Service-Oriented Architectures can be used as a framework for enabling distributed geographic information processing (DGIP). The Open Geospatial Consortium (OGC) has published several standards for services. These can be composed into service chains that support the execution of workflows constituting complex DGIP applications. In this paper, we introduce a basic architecture and building blocks for building DGIP applications based on service chains. We investigate the issues arising from the composition of OGC services into such service chains. We study various architectural patterns in order to guide application developers in their task of implementing DGIP applications based on service chains. More specifically, we focus on the control flow and data flow patterns in the execution of a workflow. These issues are illustrated with an example from the domain of risk management-a forest fire risk mapping scenario.
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paper_title: Which Service Interfaces fit the Model Web

paper_content:

The Model Web has been proposed as a concept for integrating scientific models in an interoperable and collaborative manner. However, four years after the initial idea was formulated, there is still no stable long term solution. Multiple authors propose Web Service based approaches to model publication and chaining, but current implementations are highly case specific and lack flexibility. This paper discusses the Web Service interfaces, which are required for supporting integrated environmental modeling in a sustainable manner. We explore ways to expose environmental models and their components using Web Service interfaces. Our discussions present work in progress for establishing the Web Services technological grounds for simplifying information publication and exchange within the Model Web. As a main outcome, this contribution identifies challenges in respect to the required geo- processing and relates them to currently available Web Service standards.
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paper_title: Measuring complexity in OGC web services XML schemas: pragmatic use and solutions

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The use of standards in the geospatial domain, such as those defined by the Open Geospatial Consortium (OGC), for exchanging data has brought a great deal of interoperability upon which systems can be built in a reliable way. Unfortunately, these standards are becoming increasingly complex, making their implementation an arduous task. The use of appropriate software metrics can be very useful to quantify different properties of the standards that ultimately may suggest different solutions to deal with problems related to their complexity. In this regard, we present in this article an attempt to measure the complexity of the schemas associated with the OGC implementation specifications. We use a comprehensive set of metrics to provide a multidimensional view of this complexity. These metrics can be used to evaluate the impact of design decisions, study the evolution of schemas, and so on. We also present and evaluate different solutions that could be applied to overcome some of the problems associated with the complexity of the schemas.
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paper_title: BPELPower-A BPEL execution engine for geospatial web services

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The Business Process Execution Language (BPEL) has become a popular choice for orchestrating and executing workflows in the Web environment. As one special kind of scientific workflow, geospatial Web processing workflows are data-intensive, deal with complex structures in data and geographic features, and execute automatically with limited human intervention. To enable the proper execution and coordination of geospatial workflows, a specially enhanced BPEL execution engine is required. BPELPower was designed, developed, and implemented as a generic BPEL execution engine with enhancements for executing geospatial workflows. The enhancements are especially in its capabilities in handling Geography Markup Language (GML) and standard geospatial Web services, such as the Web Processing Service (WPS) and the Web Feature Service (WFS). BPELPower has been used in several demonstrations over the decade. Two scenarios were discussed in detail to demonstrate the capabilities of BPELPower. That study showed a standard-compliant, Web-based approach for properly supporting geospatial processing, with the only enhancement at the implementation level. Pattern-based evaluation and performance improvement of the engine are discussed: BPELPower directly supports 22 workflow control patterns and 17 workflow data patterns. In the future, the engine will be enhanced with high performance parallel processing and broad Web paradigms.
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paper_title: Scientific versus Business Workflows

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The formal concept of a workflow has existed in the business world for a long time. An entire industry of tools and technology devoted to workflow management has been developed and marketed to meet the needs of commercial enterprises. The Workflow Management Coalition (WfMC) has existed for over ten years and has developed a large set of reference models, documents, and standards. Why has the scientific community not adopted these existing standards? While it is not uncommon for the scientific community to reinvent technology rather than purchase existing solutions, there are issues involved in the technical applications that are unique to science, and we will attempt to characterize some of these here. There are, however, many core concepts that have been developed in the business workflow community that directly relate to science, and we will outline them below.
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paper_title: Service-Oriented Computing: State of the Art and Research Challenges

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Service-oriented computing promotes the idea of assembling application components into a network of services that can be loosely coupled to create flexible, dynamic business processes and agile applications that span organizations and computing platforms. An SOC research road map provides a context for exploring ongoing research activities.
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paper_title: WPS mediation: An approach to process geospatial data on different computing backends

paper_content:

The OGC Web Processing Service (WPS) specification allows generating information by processing distributed geospatial data made available through Spatial Data Infrastructures (SDIs). However, current SDIs have limited analytical capacities and various problems emerge when trying to use them in data and computing-intensive domains such as environmental sciences. These problems are usually not or only partially solvable using single computing resources. Therefore, the Geographic Information (GI) community is trying to benefit from the superior storage and computing capabilities offered by distributed computing (e.g., Grids, Clouds) related methods and technologies. Currently, there is no commonly agreed approach to grid-enable WPS. No implementation allows one to seamlessly execute a geoprocessing calculation following user requirements on different computing backends, ranging from a stand-alone GIS server up to computer clusters and large Grid infrastructures. Considering this issue, this paper presents a proof of concept by mediating different geospatial and Grid software packages, and by proposing an extension of WPS specification through two optional parameters. The applicability of this approach will be demonstrated using a Normalized Difference Vegetation Index (NDVI) mediated WPS process, highlighting benefits, and issues that need to be further investigated to improve performances.
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paper_title: REST-based semantic feature catalogue services

paper_content:

The exchange of scientific datasets online and their subsequent use by service-centric applications requires semantic description of the data objects, or features, being transacted. This is particularly the case in the Earth Systems Sciences. Semantic repositories provide a partial answer to generating rich content. Ideally these repositories should be founded in a framework that permits cross-referencing between independently established semantic data-stores and which provides for a loose coupling between repositories and the agents or clients that will use them. We investigated the applicability of using an ISO 19110-based Feature Catalogue as a cross-domain, semantic repository for various Earth Systems Science communities of interest. Our aim was to develop a repository and a set of services capable of providing semantic content for consumption by smart clients. The constraint applied throughout the research was to develop a set of tools that would present a very low uptake barrier for programmers and domain specialists alike. To meet this challenge, we used Representational State Transfer (REST)-based services to expose content from an enhanced implementation of an ISO 19110-based Feature Catalogue. This article describes how the ISO 19110 conceptual model was augmented during implementation to cater for the requirements of two large multi-disciplinary science groups: the Scientific Committee on Antarctic Research and the Australian Ocean Data Network. The reasons for opting for a REST-based service pattern are discussed and the three REST service types that were developed are described.
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paper_title: Linked Data: Evolving the Web Into a Global Data Space

paper_content:

The World Wide Web has enabled the creation of a global information space comprising linked documents. As the Web becomes ever more enmeshed with our daily lives, there is a growing desire for direct access to raw data not currently available on the Web or bound up in hypertext documents. Linked Data provides a publishing paradigm in which not only documents, but also data, can be a first class citizen of the Web, thereby enabling the extension of the Web with a global data space based on open standards - the Web of Data. In this Synthesis lecture we provide readers with a detailed technical introduction to Linked Data. We begin by outlining the basic principles of Linked Data, including coverage of relevant aspects of Web architecture. The remainder of the text is based around two main themes - the publication and consumption of Linked Data. Drawing on a practical Linked Data scenario, we provide guidance and best practices on: architectural approaches to publishing Linked Data; choosing URIs and vocabularies to identify and describe resources; deciding what data to return in a description of a resource on the Web; methods and frameworks for automated linking of data sets; and testing and debugging approaches for Linked Data deployments. We give an overview of existing Linked Data applications and then examine the architectures that are used to consume Linked Data from the Web, alongside existing tools and frameworks that enable these. Readers can expect to gain a rich technical understanding of Linked Data fundamentals, as the basis for application development, research or further study.
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paper_title: A RESTful proxy and data model for linked sensor data

paper_content:

Abstract The vision of a Digital Earth calls for more dynamic information systems, new sources of information, and stronger capabilities for their integration. Sensor networks have been identified as a major information source for the Digital Earth, while Semantic Web technologies have been proposed to facilitate integration. So far, sensor data are stored and published using the Observations & Measurements standard of the Open Geospatial Consortium (OGC) as data model. With the advent of Volunteered Geographic Information and the Semantic Sensor Web, work on an ontological model gained importance within Sensor Web Enablement (SWE). In contrast to data models, an ontological approach abstracts from implementation details by focusing on modeling the physical world from the perspective of a particular domain. Ontologies restrict the interpretation of vocabularies toward their intended meaning. The ongoing paradigm shift to Linked Sensor Data complements this attempt. Two questions have to be addressed: (1) ...
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paper_title: Enhancing integrated environmental modelling by designing resource-oriented interfaces

paper_content:

Integrated environmental modelling is gaining momentum for addressing grand scientific challenges such as monitoring the environment for change detection and forecasting environmental conditions along with the consequences for society. Such challenges can only be addressed by a multi-disciplinary approach, in which socio-economic, geospatial, and environmental information becomes inter-connected. However, existing solutions cannot be seamlessly integrated and current interaction paradigms prevent mainstream usage of the existing technology. In particular, it is still difficult to access and join harmonized data and processing algorithms that are provided by different environmental information infrastructures. In this paper we take a novel approach for integrated environmental modelling based on the notion of inter-linked resources on the Web. We present design practices for creating resource-oriented interfaces, driven by an interaction protocol built on the combination of valid linkages to enhance resource integration, accompanied by associated recommendations for implementation. The suggested resource-oriented approach provides a solution to the problems identified above, but still requires intense prototyping and experimentation. We discuss the central open issues and present a roadmap for future research. Highlights? Resource-oriented interfaces for linking of environmental resources and models. ? Design practices for creating resource-oriented interfaces. ??Implementation recommendations for inter-linked resources.
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paper_title: Integrated environmental modeling: A vision and roadmap for the future

paper_content:

Integrated environmental modeling (IEM) is inspired by modern environmental problems, decisions, and policies and enabled by transdisciplinary science and computer capabilities that allow the environment to be considered in a holistic way. The problems are characterized by the extent of the environmental system involved, dynamic and interdependent nature of stressors and their impacts, diversity of stakeholders, and integration of social, economic, and environmental considerations. IEM provides a science-based structure to develop and organize relevant knowledge and information and apply it to explain, explore, and predict the behavior of environmental systems in response to human and natural sources of stress. During the past several years a number of workshops were held that brought IEM practitioners together to share experiences and discuss future needs and directions. In this paper we organize and present the results of these discussions. IEM is presented as a landscape containing four interdependent elements: applications, science, technology, and community. The elements are described from the perspective of their role in the landscape, current practices, and challenges that must be addressed. Workshop participants envision a global scale IEM community that leverages modern technologies to streamline the movement of science-based knowledge from its sources in research, through its organization into databases and models, to its integration and application for problem solving purposes. Achieving this vision will require that the global community of IEM stakeholders transcend social, and organizational boundaries and pursue greater levels of collaboration. Among the highest priorities for community action are the development of standards for publishing IEM data and models in forms suitable for automated discovery, access, and integration; education of the next generation of environmental stakeholders, with a focus on transdisciplinary research, development, and decision making; and providing a web-based platform for community interactions (e.g., continuous virtual workshops).
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paper_title: A scientific workflow environment for Earth system related studies

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Many separate tasks must be performed to configure, run, and analyze Earth system modeling applications. This work is motivated by the complexities of running a large modeling system on a high performance network and the need to reduce those complexities, particularly for the average user. Scientific workflow systems can be used to simplify these task and their relationships, although how to implement such systems is still an open research area. In this paper, we present a methodology to combine a scientific workflow and modeling framework approach to create a standardized work environment and provide a first example of a self-describing Earth system model. We then show the results of an example workflow that is based on the proposed methodology. The example workflow allows running and analyzing a global circulation model on both a grid computing environment and a cluster system, with meaningful abstractions for the model and computing environment. As can be seen through this example, a layered approach to collecting provenance and metadata information has the added benefit of documenting a run in far greater detail than before. This approach facilitates exploration of runs and leads to possible reproducibility.
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Title: Seeing the forest through the trees: A review of integrated environmental modelling tools

Section 1: Introduction
Description 1: This section introduces the background of natural hazards, the need for integrated modelling (IM), and the aims and structure of this review.

Section 2: Engineering concepts of reuse
Description 2: This section discusses the challenges and concepts related to importing and reusing existing models or components into IM tools, including white-box and black-box approaches.

Section 3: Methodology and data
Description 3: This section explains the methodology employed in the review, including literature search and selection processes, and the classification of IM tools by viewpoints.

Section 4: Viewpoint-based analysis of IM tools
Description 4: This section analyzes the selected IM tools by different viewpoints, including component-based modelling frameworks, scientific workflow systems, virtual research environments, service-based modelling, and resource-based modelling.

Section 5: Cross-viewpoint discussion
Description 5: This section discusses the potential relationships and connections between various viewpoints in terms of reusability.

Section 6: Concluding remarks
Description 6: This section summarizes the findings, presents concluding remarks on the reusability in IM, and suggests future research directions.