Geoscience after IT: Part J. Human requirements that shape the evolving geoscience information system

The geoscience record is constrained by the limitations of human thought and of the technology for handling information. IT can lead us away from the tyranny of older technology, but to find the right path, we need to understand our own limitations. Language, images, data and mathematical models, are tools for expressing and recording our ideas. Backed by intuition, they enable us to think in various modes, to build knowledge from information and create models as artificial views of a real world. Markup languages may accommodate more flexible and better connected records, and the object-oriented approach may help to match IT more closely to our thought processes

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Kassiopeia: A Modern, Extensible C++ Particle Tracking Package

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease of use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occuring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopei

Development of Distributed Research Center for analysis of regional climatic and environmental changes

We present an approach and first results of a collaborative project being carried out by a joint team of researchers from the Institute of Monitoring of Climatic and Ecological Systems, Russia and Earth Systems Research Center UNH, USA. Its main objective is development of a hardware and software platform prototype of a Distributed Research Center (DRC) for monitoring and projecting of regional climatic and environmental changes in the Northern extratropical areas. The DRC should provide the specialists working in climate related sciences and decision-makers with accurate and detailed climatic characteristics for the selected area and reliable and affordable tools for their in-depth statistical analysis and studies of the effects of climate change. Within the framework of the project, new approaches to cloud processing and analysis of large geospatial datasets (big geospatial data) inherent to climate change studies are developed and deployed on technical platforms of both institutions. We discuss here the state of the art in this domain, describe web based information-computational systems developed by the partners, justify the methods chosen to reach the project goal, and briefly list the results obtained so far

Geoscience after IT: Part L. Adjusting the emerging information system to new technology

Coherent development depends on following widely used standards that respect our vast legacy of existing entries in the geoscience record. Middleware ensures that we see a coherent view from our desktops of diverse sources of information. Developments specific to managing the written word, map content, and structured data come together in shared metadata linking topics and information types

Designing Improved Sediment Transport Visualizations

Monitoring, or more commonly, modeling of sediment transport in the coastal environment is a critical task with relevance to coastline stability, beach erosion, tracking environmental contaminants, and safety of navigation. Increased intensity and regularity of storms such as Superstorm Sandy heighten the importance of our understanding of sediment transport processes. A weakness of current modeling capabilities is the ability to easily visualize the result in an intuitive manner. Many of the available visualization software packages display only a single variable at once, usually as a two-dimensional, plan-view cross-section. With such limited display capabilities, sophisticated 3D models are undermined in both the interpretation of results and dissemination of information to the public. Here we explore a subset of existing modeling capabilities (specifically, modeling scour around man-made structures) and visualization solutions, examine their shortcomings and present a design for a 4D visualization for sediment transport studies that is based on perceptually-focused data visualization research and recent and ongoing developments in multivariate displays. Vector and scalar fields are co-displayed, yet kept independently identifiable utilizing human perception\u27s separation of color, texture, and motion. Bathymetry, sediment grain-size distribution, and forcing hydrodynamics are a subset of the variables investigated for simultaneous representation. Direct interaction with field data is tested to support rapid validation of sediment transport model results. Our goal is a tight integration of both simulated data and real world observations to support analysis and simulation of the impact of major sediment transport events such as hurricanes. We unite modeled results and field observations within a geodatabase designed as an application schema of the Arc Marine Data Model. Our real-world focus is on the Redbird Artificial Reef Site, roughly 18 nautical miles offshor- Delaware Bay, Delaware, where repeated surveys have identified active scour and bedform migration in 27 m water depth amongst the more than 900 deliberately sunken subway cars and vessels. Coincidently collected high-resolution multibeam bathymetry, backscatter, and side-scan sonar data from surface and autonomous underwater vehicle (AUV) systems along with complementary sub-bottom, grab sample, bottom imagery, and wave and current (via ADCP) datasets provide the basis for analysis. This site is particularly attractive due to overlap with the Delaware Bay Operational Forecast System (DBOFS), a model that provides historical and forecast oceanographic data that can be tested in hindcast against significant changes observed at the site during Superstorm Sandy and in predicting future changes through small-scale modeling around the individual reef objects

Virtue integrated platform : holistic support for distributed ship hydrodynamic design

Ship hydrodynamic design today is often still done in a sequential approach. Tools used for the different aspects of CFD (Computational Fluid Dynamics) simulation (e.g. wave resistance, cavitation, seakeeping, and manoeuvring), and even for the different levels of detail within a single aspect, are often poorly integrated. VIRTUE (the VIRtual Tank Utility in Europe) project has the objective to develop a platform that will enable various distributed CFD and design applications to be integrated so that they may operate in a unified and holistic manner. This paper presents an overview of the VIRTUE Integrated Platform (VIP), e.g. research background, objectives, current work, user requirements, system architecture, its implementation, evaluation, and current development and future work

An ECOOP web portal for visualising and comparing distributed coastal oceanography model and in situ data

As part of a large European coastal operational oceanography project (ECOOP), we have developed a web portal for the display and comparison of model and in situ marine data. The distributed model and in situ datasets are accessed via an Open Geospatial Consortium Web Map Service (WMS) and Web Feature Service (WFS) respectively. These services were developed independently and readily integrated for the purposes of the ECOOP project, illustrating the ease of interoperability resulting from adherence to international standards. The key feature of the portal is the ability to display co-plotted timeseries of the in situ and model data and the quantification of misfits between the two. By using standards-based web technology we allow the user to quickly and easily explore over twenty model data feeds and compare these with dozens of in situ data feeds without being concerned with the low level details of differing file formats or the physical location of the data. Scientific and operational benefits to this work include model validation, quality control of observations, data assimilation and decision support in near real time. In these areas it is essential to be able to bring different data streams together from often disparate locations

Digitometric Services for Open Archives Environments

We describe “digitometric” services and tools that add value to open-access eprint archives using the Open Archives Initiative (OAI) Protocol for Metadata Harvesting. Celestial is an OAI cache and gateway tool. Citebase Search enhances OAI-harvested metadata with linked references harvested from the full-text to provide a web service for citation navigation and research impact analysis. Digitometrics builds on data harvested using OAI to provide advanced visualisation and hypertext navigation for the research community. Together these services provide a modular, distributed architecture for building a “semantic web” for the research literature