Software and Space: Investigating How a Cosmology Research Group Enacts Infrastructure by Producing Software

Thesis (Ph.D.)--University of Washington, 2016-08

L’encadrement juridique des biobanques populationnelles et leurs obligations au Québec

La mise en banque d’échantillons humains et de données connexes n’est pas une pratique récente. Toutefois, dans les dernières décennies, ce phénomène a pris une ampleur sans précédent avec la création des biobanques populationnelles. Défini comme étant des infrastructures de recherche conçues pour durer plusieurs décennies, ce type de biobanques invite des milliers et, dans certains cas, des centaines de milliers de personnes à y participer en fournissant des échantillons, en se soumettant à des tests physiques et biochimiques, et en répondant à diverses questions sur leur santé et leur environnement sociodémographique. Mais quelles sont les obligations des biobanques et de leurs chercheurs face aux participants? Considérant leur longue durée, quel est l’encadrement juridique de ces biobanques populationnelles au Québec? Ce sont les deux questions que pose ce mémoire. Quant à l’encadrement, nous utilisons trois axes d’analyse : i) les lois, les règlements, la déontologie professionnelle et les normes applicables; ii) la qualification juridique de l’acte de mise en banque d’échantillons et de données; et iii) les obligations découlant de la nature même de l’objet de la relation juridique. Notre analyse révèle que cet encadrement est une mosaïque législative, contractuelle, déontologique et normative qui, malgré ses complexités et ses défis d’accessibilité pour les participants, assure une certaine protection pour ces derniers. Quant aux obligations incombant à la biobanque et à ses chercheurs, elles sont pour la majorité teintées par des caractéristiques particulières aux biobanques populationnelles. Ainsi, il existe des défis particuliers en ce qui concerne notamment le consentement, le devoir d’information, le retour de résultats et la sécurité des échantillons et des données. Étant donné la nature évolutive de ces obligations, nous proposons une approche basée sur le meilleur intérêt du participant pour déterminer la nature et l’intensité des obligations incombant à une biobanque et à ses chercheurs.

One- and two-center energy components in the atoms in molecules theory

The energy decomposition scheme proposed in a recent paper has been realized by performing numerical integrations. The sample calculations carried out for some simple molecules show excellent agreement with the chemical picture of molecules, indicating that such an energy decomposition analysis can be useful from the point of view of connecting quantum mechanics with the genuine chemical concepts

Parallel performance and scalability experiments with the Danish Eulerian Model on the EPCC supercomputers

The Danish Eulerian Model (DEM) is a powerful air pollution model, designed to calculate the concentrations of various dangerous species over a large geographical region (e.g. Europe). It takes into account the main physical and chemical processes between these species, the actual meteorological conditions, emissions, etc.. This is a huge computational task and requires significant resources of storage and CPU time. Parallel computing is essential for the efficient practical use of the model. Some efficient parallel versions of the model were created over the past several years. A suitable parallel version of DEM by using the Message Passing Interface library (AIPI) was implemented on two powerful supercomputers of the EPCC - Edinburgh, available via the HPC-Europa programme for transnational access to research infrastructures in EC: a Sun Fire E15K and an IBM HPCx cluster. Although the implementation is in principal, the same for both supercomputers, few modifications had to be done for successful porting of the code on the IBM HPCx cluster. Performance analysis and parallel optimization was done next. Results from bench marking experiments will be presented in this paper. Another set of experiments was carried out in order to investigate the sensitivity of the model to variation of some chemical rate constants in the chemical submodel. Certain modifications of the code were necessary to be done in accordance with this task. The obtained results will be used for further sensitivity analysis Studies by using Monte Carlo simulation.

Paving the way for methane hydrate formation on metal–organic frameworks (MOFs)

The presence of a highly tunable porous structure and surface chemistry makes metal–organic framework (MOF) materials excellent candidates for artificial methane hydrate formation under mild temperature and pressure conditions (2 °C and 3–5 MPa). Experimental results using MOFs with a different pore structure and chemical nature (MIL-100 (Fe) and ZIF-8) clearly show that the water–framework interactions play a crucial role in defining the extent and nature of the gas hydrates formed. Whereas the hydrophobic MOF promotes methane hydrate formation with a high yield, the hydrophilic one does not. The formation of these methane hydrates on MOFs has been identified for the first time using inelastic neutron scattering (INS) and synchrotron X-ray powder diffraction (SXRPD). The results described in this work pave the way towards the design of new MOF structures able to promote artificial methane hydrate formation upon request (confined or non-confined) and under milder conditions than in nature.

eHabitat, a multi-purpose Web Processing Service for ecological modeling

The number of interoperable research infrastructures has increased significantly with the growing awareness of the efforts made by the Global Earth Observation System of Systems (GEOSS). One of the Societal Benefit Areas (SBA) that is benefiting most from GEOSS is biodiversity, given the costs of monitoring the environment and managing complex information, from space observations to species records including their genetic characteristics. But GEOSS goes beyond simple data sharing to encourage the publishing and combination of models, an approach which can ease the handling of complex multi-disciplinary questions. It is the purpose of this paper to illustrate these concepts by presenting eHabitat, a basic Web Processing Service (WPS) for computing the likelihood of finding ecosystems with equal properties to those specified by a user. When chained with other services providing data on climate change, eHabitat can be used for ecological forecasting and becomes a useful tool for decision-makers assessing different strategies when selecting new areas to protect. eHabitat can use virtually any kind of thematic data that can be considered as useful when defining ecosystems and their future persistence under different climatic or development scenarios. The paper will present the architecture and illustrate the concepts through case studies which forecast the impact of climate change on protected areas or on the ecological niche of an African bird.

The impact of the MARINET initiative on the development of Marine Renewable Energy

Marine Renewable Energy Conversion systems comprise wave energy and tidal stream converters as well as offshore-wind turbines for electrical generation. These technologies are currently at different stages of development but are mostly at the pre-commercial stage and require research to be undertaken at a series of scales along the path to commercialization. However each of these technologies also needs specific research infrastructures in order to conduct this research. The aim of the MARINET initiative is to coordinate research and development at all scales (small models through to prototype scales, from laboratories through to open sea tests) and to allow access for researchers and developers to infrastructures which are not available universally in Europe, including test facilities for components such as power take-off systems, grid integration, moorings and environmental monitoring so as to ensure a focusing of activities in this area. The initiative offers researchers and developers access to 45 research facilities as well as to the associated network of expertise at all scales in Offshore Marine Renewable Energy technology research and development. The aim of this paper is to present this MARINET initiative that was started in 2011, bringing together a network of 29 partners spread across twelve countries. Details of the MARINET Transnational Access (TA) program are presented, for which over 260 applications were received throughout the 5 official calls for proposals. In particular, statistics on applications and completed projects are presented which provide an overview of the global development progress of the different offshore renewable energy conversion technologies at a European level. It also provides a good overview of the current research activity, as well as evidence of the requirement for specialised research facilities, in this burgeoning field.

An integrated approach to delimiting species borders in the genus Chrysotoxum Meigen, 1803 (Diptera: Syrphidae), with description of two new species

Integrative taxonomy tests the validity of taxa using methods additional to traditional morphology. The existence of two different morphotypes in specimens identified as Chrysotoxum vernale Loew (Diptera: Syrphidae) prompted their taxonomic study using an integrative approach that included morphology, wing and male-surstylus geometric morphometrics, genetic and ecological analyses. As a result, a new species is recognised, Chrysotoxum montanum Nedeljković & Vujić sp. nov., and C. vernale is re-defined. A lectotype and paralectotypes are designated for C. vernale to stabilize this concept. An additional species, Chrysotoxum orthostylum Vujić sp. nov., with distinctive male genitalia is also described. The three species share an antenna with the basoflagellomere shorter than the scape plus pedicel and terga with yellow fasciae not reaching the lateral margins. This study confirms the value of integrative approach for resolving species boundaries.

Developing spatial infrastructures for the Q.U.T. Samford Ecological Research Facility.

Staff and students of the Surveying and Spatial Sciences discipline at QUT have worked collaboratively with the Institute of Sustainable Resources in the creation and development of spatial information layers and infrastructure to support multi-disciplinary research efforts at the Samford Ecological Research Facility (SERF). The SERF property is unique in that it provides staff and students with a semi-rural controlled research base for multiple users. This paper aims to describe the development of a number of spatial information layers and network of survey monuments that assist and support research infrastructure at SERF. A brief historical background about the facility is presented along with descriptions of the surveying and mapping activities undertaken. These broad ranging activities include introducing monument infrastructure and a geodetic control network; surveying activities for aerial photography ground-control targets including precise levelling with barcode instruments; development of an ortho-rectified image spatial information layer; Real-Time-Kinematic Global Positioning Systems (RTK-GPS) surveying for constructing 100metre confluence points/monuments to support science-based disciplines to undertake environmental research transects and long-term ecological sampling; and real-world learning initiative to assist with water engineering projects and student experiential learning. The spatial information layers and physical infrastructure have been adopted by two specific yet diverse user groups with an interest in the long-term research focus of SERF.

The HWMD maturity model: a foundational framework to measure effectiveness of institutional research e-infrastructures

There is a nationally recognised need for a framework and tools to measure progress in implementing e-infrastructures for research from an institutional, organisational unit and service perspective. This paper describes the development of a prototype maturity model and self-assessment tool in response to that need. The authors present a background to the environment of technology enabling services for research and the challenges of fluidity of boundaries around traditional services and roles as institutions respond to the needs of the research community. The conceptual basis of the model is presented along with the model and its various elements that explain how the model is in its current form. The information provided in this paper, combined with field site test feedback, will promote discussion and debate amongst the community and opportunities will present to gather input to optimise the model. The next steps would be to further elaborate and test the constructs and indicators of the model in field test sites and to further develop the self -assessment tool.

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.

KE & Science Europe briefing paper: Funding Research Data Management and related infrastructures

Responsible Research Data Management (RDM) is a pillar of quality research. In practice good RDM requires the support of a well-functioning Research Data Infrastructure (RDI). One of the challenges the research community is facing is how to fund the management of research data and the required infrastructure. Knowledge Exchange and Science Europe have both defined activities to explore how RDM/RDI are, or can be, funded. Independently they each planned to survey users and providers of data services and on becoming aware of the similar objectives and approaches, the Science Europe Working Group on Research Data and the Knowledge Exchange Research Data expert group joined forces and devised a joint activity to to inform the discussion on the funding of RDM/RDI in Europe.

A review of models of spatial innovation infrastructures in support of high growth SMEs

This Paper first provides a review and analysis of the recent trends on innovation infrastructures developed in industrialised countries to promote innovation and competitiveness for high growth SMEs. It specifically aims to examine various spatial models developed to support provision of innovation infrastructure for high growth sector.

Exploring the needs for SMEs for mobile data technologies : the role of qualitative research techniques

The seemingly exponential nature of technological change provides SMEs with a complex and challenging operational context. The development of infrastructures capable of supporting the wireless application protocol (WAP) and associated 'wireless' applications represents the latest generation of technological innovation with potential appeals to SMEs and end-users alike. This paper aims to understand the mobile data technology needs of SMEs in a regional setting. The research was especially concerned with perceived needs across three market segments : non-adopters, partial-adopters and full-adopters of new technology. The research was exploratory in nature as the phenomenon under scrutiny is relatively new and the uses unclear, thus focus groups were conducted with each of the segments. The paper provides insights for business, industry and academics.