Goal-based analytic composition for on- and off-line execution at scale

Crafting scalable analytics in order to extract actionable business intelligence is a challenging endeavour, requiring multiple layers of expertise and experience. Often, this expertise is irreconcilably split between an organisation’s engineers and subject matter or domain experts. Previous approaches to this problem have relied on technically adept users with tool-specific training. These approaches have generally not targeted the levels of performance and scalability required to harness the sheer volume and velocity of large-scale data analytics. In this paper, we present a novel approach to the automated planning of scalable analytics using a semantically rich type system, the use of which requires little programming expertise from the user. This approach is the first of its kind to permit domain experts with little or no technical expertise to assemble complex and scalable analytics, for execution both on- and offline, with no lower-level engineering support. We describe in detail (i) an abstract model of analytic assembly and execution; (ii) goal-based planning and (iii) code generation using this model for both on- and off-line analytics. Our implementation of this model, MENDELEEV, is used to (iv) demonstrate the applicability of our approach through a series of case studies, in which a single interface is used to create analytics that can be run in real-time (on-line) and batch (off-line) environments. We (v) analyse the performance of the planner, and (vi) show that the performance of MENDELEEV’s generated code is comparable with that of hand-written analytics

Goal-based composition of scalable hybrid analytics for heterogeneous architectures

Crafting scalable analytics in order to extract actionable business intelligence is a challenging endeavour, requiring multiple layers of expertise and experience. Often, this expertise is irreconcilably split between an organisation’s engineers and subject matter domain experts. Previous approaches to this problem have relied on technically adept users with tool-specific training. Such an approach has a number of challenges: Expertise — There are few data-analytic subject domain experts with in-depth technical knowledge of compute architectures; Performance — Analysts do not generally make full use of the performance and scalability capabilities of the underlying architectures; Heterogeneity — calculating the most performant and scalable mix of real-time (on-line) and batch (off-line) analytics in a problem domain is difficult; Tools — Supporting frameworks will often direct several tasks, including, composition, planning, code generation, validation, performance tuning and analysis, but do not typically provide end-to-end solutions embedding all of these activities. In this paper, we present a novel semi-automated approach to the composition, planning, code generation and performance tuning of scalable hybrid analytics, using a semantically rich type system which requires little programming expertise from the user. This approach is the first of its kind to permit domain experts with little or no technical expertise to assemble complex and scalable analytics, for hybrid on- and off-line analytic environments, with no additional requirement for low-level engineering support. This paper describes (i) an abstract model of analytic assembly and execution, (ii) goal-based planning and (iii) code generation for hybrid on- and off-line analytics. An implementation, through a system which we call Mendeleev, is used to (iv) demonstrate the applicability of this technique through a series of case studies, where a single interface is used to create analytics that can be run simultaneously over on- and off-line environments. Finally, we (v) analyse the performance of the planner, and (vi) show that the performance of Mendeleev’s generated code is comparable with that of hand-written analytics

Engineering Secure Adaptable Web Services Compositions

Service-oriented architecture defines a paradigm for building applications by assembling autonomous components such as web services to create web service compositions. Web services are executed in complex contexts where unforeseen events may compromise the security of the web services composition. If such compositions perform critical functions, prompt action may be required as new security threats may arise at runtime. Manual interventions may not be ideal or feasible. To automatically decide on valid security changes to make at runtime, the composition needs to make use of current security context information. Such security changes are referred to as dynamic adaptation. This research proposes a framework to develop web services compositions that can dynamically adapt to maintain the same level of security when unforeseen security events occur at runtime. The framework is supported by mechanisms that map revised security requirements arising at runtime to a new security configuration plan that is used to adapt the web services composition

Molecular epidemiology of rabies in Kwazulu-Natal, South Africa

In South Africa, two biotypes of type species 1 of the Lyssavirus genus are maintained independently among the members of the Herpestidae and Canidae families, respectively. Canid rabies is a relatively new addition to the African subcontinent, having been introduced from infectious cycles, which had existed among dogs in Angola, in the early 1940s. Two epidemics, believed to have originated from dog endemic regions which had existed in the southern Maputo district of Mozambique since 1952, have occurred among domestic dogs in the KwaZulu Natal province in recent years. The first of these epidemics started in 1964, and ended by 1968, while the second epidemic which started in 1976, has proven to be intractable, despite the concerted efforts which have been implemented to bring it under control. In order to contribute to the understanding of the molecular epidemiology of rabies in the KwaZulu Natal province, and to thereby assist in future surveillance and control efforts, we conducted a molecular sequence analysis of representative panel of viral isolates which were obtained from the province during the year 2003. A 591 nt. sequence encompassing the G-L intergenic region and glycoprotein cytoplasmic domain was sequenced for 128 viral isolates, which were obtained from the different magisterial districts and affected host species of the province, and was subsequently used to characterize these viruses phylogenetically. Characterization of the KwaZulu Natal variants, and comparison of the obtained sequence data, to sequences data which was obtained from rabies endemic regions from elsewhere in South Africa and Zimbabwe, in general supported the pattern of spread which led to the introduction of rabies into the province, as was previously suggested from the literature. The phylogeny which was established from the analyses, indicated that the viral isolates from the province were highly related to each other, and could be divided into two groups, which although belonging to the canid biotype, were in general distinguishable from canid rabies virus isolates which were obtained from elsewhere in South Africa and Zimbabwe. The observation that these subfamilies showed a low genetic divergence, as well as that they shared a unique recent common ancestor, suggested that they were introduced recently into the northern reaches of the province, probably from the same geographical region (i.e. southern Mozambique). logenetic characterization of the KwaZulu Natal isolates further suggested that at least three enzootic fronts are currently responsible for the introduction of rabies into the northern and southern regions of the province. The first of these fronts was hypothesized to have spread directly across the southern Mozambique border (possibly via southeastern Swaziland), into the northeastern coastal regions of KwaZulu Natal, while the second front represented the south-eastwards spread of synergistic dog-jackal cycles from southeastern Mpumalanga, into the northern and northeastern regions of the province. The third front on the other hand, represented the possible spread of a remnant infectious cycle, left over from the 1964-1968 epidemic, from the northern region of the Eastern Cape, into southern KwaZulu Natal. logenetic characterization further proved useful for identifying the distribution of viral variants, and allowed us to propose a pathway by which the disease might have spread throughout the province. The proposed pathway of spread suggested that viral variants may have been translocated over long distances, and highlighted the role that major routes of human transportation may play in the dissemination of the disease. The regional characterization of viral variants from KwaZulu Natal, further demarked the location where the identified viral variants circulated in individual host populations, allowing us to place the current epidemic into an epidemiological framework which attempts to explain the long term persistence of the disease. This provided clues as to the intractability of the second epidemic, and allowed us to develop a proposal as to how current control strategies may be altered, in order to contain the current outbreak in the province. initial phylogeny which was established from the study provides an epidemiological framework, which will play an important role in determining the origin of future human spillover cases, and for tracking the spread of viral variants throughout the affected regions of the province. It is further envisaged that the data which was generated during the course of the project will be utilized in future surveillance efforts, targeted to the evaluation of the efficacy of potentially implemented control campaigns.Dissertation (MSc (Microbiology))--University of Pretoria, 2007.Microbiology and Plant Pathologyunrestricte

Kriteria van die nuut geopenbaarde verborgenheid van Kolossense en Efesiërs : 'n dispensionele benadering

Deur na die kriteria en uitsprake rondom die voorkomstes van die term 'Verborgenheid' in die Tweelingbriewe Kolossense en Efesiers te kyk, teen die agtergrond van die 'Toekomstige Dinge' (Jh 16.13) wat deur die Heilige Gees in die Progressiewe Openbaring van God aan die skrywers van die Nuwe Testament bekend gemaak was, word dit ontdek dat daar 'n splintemuwe skepping, die Corpus Christi, waarvan Christus die Hoof is, as hierdie Verborgenheid aan Paulus, na Handelinge 28 in die i gevangenis geopenbaar was, naamlik die Kerk wat daar I eers tot stand gekom het. Die Kerk, wat hoofsaaklik uit gelowige Heidene bestaan, het sedertdien as God se kanaal van heil tot die wereld gedien in die plek en onafhanklik van nasionale Israel, wat volgens Ou Testa- mentiese profesie, God se kanaal van Heil tot die wereld moes wees, onder en saam met wie die Heidene die Here moes dien. God het dus tot op Handelinge 28 steeds verbondmatig met Israel omgegaan om hulle tot bekering te probeer lei en het dit gevolglik tot op daardie stadium uitsluitlik gegaan om dit wat die Ou Testament geprofeteer het, naamlik die Koninkryk van God vir Israel. Maar weens hulle onboetvaardigheid, is Israel deur God verhard en in Handelinge 28 ter syde gestel as Sy kanaal en het Hy Sy Koninkryk program opgeskort en het God Hom tot die Heiden gewend. Daar was dus geen sprake van 'n 'Kerk' in die Handelinge tydperk gewees nie!Biblical and Ancient StudiesM. Th. (New Testament

Platforms for deployment of scalable on- and off-line data analytics.

The ability to exploit the intelligence concealed in bulk data to generate actionable insights is increasingly providing competitive advantages to businesses, government agencies, and charitable organisations. The burgeoning field of Data Science, and its related applications in the field of Data Analytics, finds broader applicability with each passing year. This expansion of users and applications is matched by an explosion in tools, platforms, and techniques designed to exploit more types of data in larger volumes, with more techniques, and at higher frequencies than ever before. This diversity in platforms and tools presents a new challenge for organisations aiming to integrate Data Science into their daily operations. Designing an analytic for a particular platform necessarily involves “lock-in” to that specific implementation – there are few opportunities for algorithmic portability. It is increasingly challenging to find engineers with experience in the diverse suite of tools available as well as understanding the precise details of the domain in which they work: the semantics of the data, the nature of queries and analyses to be executed, and the interpretation and presentation of results. The work presented in this thesis addresses these challenges by introducing a number of techniques to facilitate the creation of analytics for equivalent deployment across a variety of runtime frameworks and capabilities. In the first instance, this capability is demonstrated using the first Domain Specific Language and associated runtime environments to target multiple best-in-class frameworks for data analysis from the streaming and off-line paradigms. This capability is extended with a new approach to modelling analytics based around a semantically rich type system. An analytic planner using this model is detailed, thus empowering domain experts to build their own scalable analyses, without any specific programming or distributed systems knowledge. This planning technique is used to assemble complex ensembles of hybrid analytics: automatically applying multiple frameworks in a single workflow. Finally, this thesis demonstrates a novel approach to the speculative construction, compilation, and deployment of analytic jobs based around the observation of user interactions with an analytic planning system

Bluetongue: a historical and epidemiological perspective with the emphasis on South Africa

Bluetongue (BT) is a non-contagious, infectious, arthropod transmitted viral disease of domestic and wild ruminants that is caused by the bluetongue virus (BTV), the prototype member of the Orbivirus genus in the family Reoviridae. Bluetongue was first described in South Africa, where it has probably been endemic in wild ruminants since antiquity. Since its discovery BT has had a major impact on sheep breeders in the country and has therefore been a key focus of research at the Onderstepoort Veterinary Research Institute in Pretoria, South Africa. Several key discoveries were made at this Institute, including the demonstration that the aetiological agent of BT was a dsRNA virus that is transmitted by Culicoides midges and that multiple BTV serotypes circulate in nature. It is currently recognized that BT is endemic throughout most of South Africa and 22 of the 26 known serotypes have been detected in the region. Multiple serotypes circulate each vector season with the occurrence of different serotypes depending largely on herd-immunity. Indigenous sheep breeds, cattle and wild ruminants are frequently infected but rarely demonstrate clinical signs, whereas improved European sheep breeds are most susceptible. The immunization of susceptible sheep remains the most effective and practical control measure against BT. In order to protect sheep against multiple circulating serotypes, three pentavalent attenuated vaccines have been developed. Despite the proven efficacy of these vaccines in protecting sheep against the disease, several disadvantages are associated with their use in the field

Widespread Reassortment Contributes to Antigenic Shift in Bluetongue Viruses from South Africa

Bluetongue (BT), a viral disease of ruminants, is endemic throughout South Africa, where outbreaks of different serotypes occur. The predominant serotypes can differ annually due to herd immunity provided by annual vaccinations using a live attenuated vaccine (LAV). This has led to both wild-type and vaccine strains co-circulating in the field, potentially leading to novel viral strains due to reassortment and recombination. Little is known about the molecular evolution of the virus in the field in South Africa. The purpose of this study was to investigate the genetic diversity of field strains of BTV in South Africa and to provide an initial assessment of the evolutionary processes shaping BTV genetic diversity in the field. Complete genomes of 35 field viruses belonging to 11 serotypes, collected from different regions of the country between 2011 and 2017, were sequenced. The sequences were phylogenetically analysed in relation to all the BTV sequences available from GenBank, including the LAVs and reference strains, resulting in the analyses and reassortment detection of 305 BTVs. Phylogenomic analysis indicated a geographical selection of the genome segments, irrespective of the serotype. Based on the initial assessment of the current genomic clades that circulate in South Africa, the selection for specific clades is prevalent in directing genome segment reassortment, which seems to exclude the vaccine strains and in multiple cases involves Segment-2 resulting in antigenic shift

Editorial : OpenStreetMap research in the COVID-19 era

Minghini, M., Coetzee, S., Grinberger, A. Y., Yeboah, G., Juhász, L., & Mooney, P. (2020). Editorial: OpenStreetMap research in the COVID-19 era In: Minghini, M., Coetzee, S., Juhász, L., Yeboah, G., Mooney, P., Grinberger, A.Y. (Eds.). Proceedings of the Academic Track at the State of the Map 2020 Online Conference, July 04-05 2020. Available at https://zenodo.org/communities/sotm-202

Proceedings of the Academic Track at the State of the Map 2020

Proceedings of the Academic Track at the State of the Map 2020 - Online (originally planned in Cape Town, South Africa) July 4-6, 2020