A methodology for developing scientific software applications in science gateways

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonDistributed Computing Infrastructures (DCIs) have emerged as a viable and affordable solution to the computing needs of communities of practice that may require the need to improve system performance or enhance the availability of their scientific applications. According to the literature, the ease of access and several other issues which relate to the interoperability among different resources are the biggest challenges surrounding the use of these infrastructures. The traditional method of using a Command Line Interface (CLI) to access these resources is difficult and can make the learning curve quite steep. This approach can result in the low uptake of DCIs as it prevents potential users of the infrastructures from adopting the technology. Science Gateways have emerged as a viable option that are used to realise the high-level scientific domain-specific user interfaces that hide all the details of the underlying infrastructures and expose only the science-specific aspects of the scientific applications to be executed in the various DCIs. A Science Gateway is a digital interface to advanced technologies which is used to provide adequate support for science and engineering research and education. The focus of this study therefore is to propose and implement a Methodology for dEveloping Scientific Software Applications in science GatEways (MESSAGE). This will be achieved by testing an approach which is considered to be appropriate for developing applications in Science Gateways. In the course of this study, several Science Gateway functionalities obtained from the review of literature which may be utilised to provide services for different communities of practice are highlighted. To implement the identified functionalities, this study utilises the methodology for developing scientific software applications in Science Gateways. In order to achieve this purpose, this research therefore adopts the Catania Science Gateway Framework (CSGF) and the Future Gateway approach to implement the methods and ideas described in the proposed methodology, as well the essential services of Science Gateways discussed throughout the thesis. In addition, three different set of scientific software applications are utilised for the implementation of the proposed methodology. While the first application primarily serves as the case study for implementing the methodology discussed in this thesis, a second application is used to evaluate the entire process. Furthermore, several other real-life scientific applications developed (using two distinctly different Science Gateway frameworks) are also utilised for the purpose of evaluation. Subsequently, a revised MESSAGE methodology for developing scientific software applications in Science Gateways is discussed in the latter Chapter of this thesis. Following from the implementation of both scientific software applications which sees the use of portlets to execute single experiments, a study was also conducted to investigate ways in which Science Gateways may be utilised for the execution of multiple experiments in a distributed environment. Finally, similar to making different scientific software applications accessible and available (worldwide) to the communities that need them, the processes involved in making their associated research outputs (such as data, software and results) easily accessible and readily available are also discussed. The main contribution of this thesis is the MESSAGE methodology for developing scientific software applications in Science Gateways. Other contributions which are also made in different aspects of this research include a framework of the essential services required in generic Science Gateways and an approach to developing and executing multiple experiments (via Science Gateway interfaces) within a distributed environment. To a lesser extent, this study also utilises the Open Access Document Repository (OADR) (and other related technologies) to demonstrate accessibility and availability of research outputs associated with specific scientific software applications, thereby introducing the concept (and thus laying the foundation) of an Open Science research

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

Concurrency and Computation: Practice and Experience CCLRC Portal Infrastructure to support Research Facilities

The CCLRC e-Science Centre is working on a number of UK e-Research projects supporting access to large research facilities such as the neutron spallation source ISIS, the Synchrotron Radiation Source (SRS) and the Central Laser Facility (CLF) and the new synchroton light source, Diamond, in addition to the National Grid Service and the HPCx supercomputing facility. The aim of this work is to create a