Visual Analytics to Support Atomistic Simulations Design

Nowadays, complex simulations of a variety of processes are extensively used in academia and industry. Particularly in academia, powerful scientific software tools are constantly developed to simulate complex systems; for instance, simulations of quantum transport using the non-equilibrium greens Function formalism. The potential impact of these scientific tools in industry is huge, but it is hindered by the lack of usability of the software by those who are not deeply familiar with it. Visual analytics is a new field that has shown the positive impact of interactive visualizations in software usability and the cognitive process of the user. This research investigates whether the implementation of interactive visual aids also improves the usability and the cognitive processes of research codes users, particularly those used for simulation design. To accomplish this goal, this study defines a framework for simulation design in scientific research, identifies the stages in which visual aids can be implemented to increase usability, and implements an interactive visualization system (NemoViz). NEMO5, a tool for designing atomistic simulation, is used as a case study to measure the effectiveness, efficiency, and user satisfaction of the use of visual aids in scientific simulation design. The results from this research provide a framework of reference for development of user-friendly simulation design tools, and will shed light on strategies that scientific developers might implement to broaden the impact of their simulation codes

The relationship between research data management and virtual research environments

The aim of the study was to compile a conceptual model of a Virtual Research Environment (VRE) that indicates the relationship between Research Data Management (RDM) and VREs. The outcome of this study was that VREs are ideal platforms for the management of research data. In the first part of the study, a literature review was conducted by focusing on four themes: VREs and other concepts related to VREs; VRE components and tools; RDM; and the relationship between VREs and RDM. The first theme included a discussion of definitions of concepts, approaches to VREs, their development, aims, characteristics, similarities and differences of concepts, an overview of the e-Research approaches followed in this study, as well as an overview of concepts used in this study. The second theme consisted of an overview of developments of VREs in four countries (United Kingdom, USA, The Netherlands, and Germany), an indication of the differences and similarities of these programmes, and a discussion on the concept of research lifecycles, as well as VRE components. These components were then matched with possible tools, as well as to research lifecycle stages, which led to the development of a first conceptual VRE framework. The third theme included an overview of the definitions of the concepts ‘data’ and ‘research data’, as well as RDM and related concepts, an investigation of international developments with regards to RDM, an overview of the differences and similarities of approaches followed internationally, and a discussion of RDM developments in South Africa. This was followed by a discussion of the concept ‘research data lifecycles’, their various stages, corresponding processes and the roles various stakeholders can play in each stage. The fourth theme consisted of a discussion of the relationship between research lifecycles and research data lifecycles, a discussion on the role of RDM as a component within a VRE, the management of research data by means of a VRE, as well as the presentation of a possible conceptual model for the management of research data by means of a VRE. This literature review was conducted as a background and basis for this study. In the second part of the study, the research methodology was outlined. The chosen methodology entailed a non-empirical part consisting of a literature study, and an empirical part consisting of two case studies from a South African University. The two case studies were specifically chosen because each used different methods in conducting research. The one case study used natural science oriented data and laboratory/experimental methods, and the other, human orientated data and survey instruments. The proposed conceptual model derived from the literature study was assessed through these case studies and feedback received was used to modify and/or enhance the conceptual model. The contribution of this study lies primarily in the presentation of a conceptual VRE model with distinct component layers and generic components, which can be used as technological and collaborative frameworks for the successful management of research data.Thesis (DPhil)--University of Pretoria, 2018.National Research FoundationInformation ScienceDPhilUnrestricte