nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through ``multi-omics'' data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential gene expression analyses. The pipeline provides a quick and efficient way to obtain a matrix of read counts that can be used black with tools such as DESeq2 and edgeR for differential expression analysis. Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research.

Big Data Driven Decision Making Model: A case of the South African banking sector

The quest to develop a Big Data Driven Decision Making framework to support the incorporation of big data analytics into the decision-making process resulted in the development of a decision making model. The study was conducted within the banking sector of South Africa, with participants from three leading South African banking institutions. The conducted research followed the design science research process of awareness, suggestion, development, evaluation and conclusion. This study developed a theoretical Big Data Driven Decision Making model which illustrates the decision-making process in banking using big data. The study further determined the organizational supports that need to be in place to support the big data analytics decision-making process.

Consumer-centric factors for the implementation of smart meters in South Africa

Smart meter implementation is still in its infancy in many African countries, including South Africa. This is evident from the fact that most research studies are either Eurocentric or American-centric. Hence, this research aimed to identify consumer-centric factors for planning considerations in implementation of smart meters in South Africa. We used various behavioural theoretical models found in literature to identify potential factors relevant to this study. Based on quantitatively gathered data (n = 705), a structural equation model (SEM) was used to evaluate the identified factors. This study found that only ten consumer-centric factors were significant to smart meter consumers. These factors include behavioural intention, attitude, trust in technology, social norms, facilitating conditions, perceived usefulness, perceived ease of use, privacy risk, monetary cost, and perceived value. In conclusion, the study shows that not all factors suggested within the European and American context are relevant for smart meter implementation within the South African context. Hence, results of this study hold some practical implications in assisting utility companies in identifying consumer-centric factors that are relevant to the South African population. Finally, consumer-centric factors can be used by policy makers and energy regulators as baseline factors for future pervasive technology acceptance studies.

Creating pseudo-tactile feedback in virtual reality using shared crossmodal properties of audio and tactile feedback

Virtual reality has the potential to enhance a variety of real-world training and entertainment applications by creating the illusion that a user of virtual reality is physically present inside the digitally created environment. However, the use of tactile feedback to convey information about this environment is often lacking in VR applications. New methods for inducing a degree of tactile feedback in users are described, which induced the illusion of a tactile experience, referred to as pseudo-tactile feedback. These methods utilised shared properties between audio and tactile feedback that can be crossmodally mapped between the two modalities in the design of a virtual reality prototype for a qualitative usability study in order to test the effectiveness and underlying causes of such feedback in the total absence of any real-world tactile feedback. Results show that participants required believable audio stimuli that they could conceive as real-world textures as well a sense of hand-ownership to suspend disbelief and construct an internally consistent mental model of the virtual environment. This allowed them to conceive believable tactile sensations that result from interaction with virtual objects inside this environment.

The current state of measuring return on investment in user experience design

Incorporating user experience (UX) design into system development processes can give an organisation competitive advantage over its rivals. Embedding UX design into system development processes requires investment in skilled professionals, who in turn follow a methodical process to make UX design an integral part of the organisation. Despite the value that can be added by UX design, demonstrating the return on investment (ROI) in UX remains a perennial challenge because of the difficulty associated with explicitly linking UX design with good ROI, to the exclusion of other system development processes. In this paper, we report on the current state of measuring ROI in UX design in a selection of South African organisations. We interviewed 33 UX professionals from four organisations to get insight into how ROI in UX design is measured in their respective organisations. The results showed that some participants were aware of the metrics that could be used to measure ROI in UX design. However, none of the four organisations were specifically calculating ROI in UX. Rather, ROI was being calculated on entire project.

Architecture and Architectural Patterns for Mobile Augmented Reality

A software architecture codifies the design choices of software developers, which defines a modularorganizational spine for the design of a software artefact. Different architectures may bespecified for different types of artefacts, a real-time interactive artefact, for example, wouldhave markedly different requirements to those of a batch based transactional system. The use ofsoftware architecture becomes increasingly important as the complexity ofartefacts increases. Augmented Reality blends the real world observed through a computerinterface, with a computer generated virtual world. With the advent ofpowerful mobile devices, Mobile Augmented Reality (MAR)applications have become increasingly feasible, however the increased power hasled to increased complexity. Most MAR research has been directed towardstechnologies and not design resulting in a dearth of architecture and design literature for MAR. This research is targeted at addressing this void. The main requirement that a MAR architecture must meet isidentified as being the efficient real-time processing of data streams such asvideo frames and sensor data. A set of highly parallelised architecturalpatterns are documented within the context of MAR that meet thisrequirement. The contribution of this research is a software architecture, codifiedas architectural patterns, for MAR.

Editorial: Transitions

As of June 2022, SACJ will have a new editor-in-chief, Katherine Malan. In this editorial, I give a restrospective on progress with increasing the journal’s standing and visibility since I took over in June 2012.

A system architecture for ensuring interoperability in a South African national electronic health record system

ountries such as South Africa have attempted to leverage eHealth by digitising patients' medical records with the aim of improving the delivery of healthcare. This involves the use of an electronic health record (EHR) which is a longitudinal electronic record of a patient's information. The EHR includes all the patient's encounters that have been made with different health facilities. In the national context, the EHR is also known as a national EHR, which enables the sharing of patient information between points of care. However, a lack of interoperability exists between many South African health information systems making communication between these disparate systems impossible. As a result, the sharing of patient information is inhibited and the benefit of improving healthcare delivery cannot be realised. This paper proposes a system architecture for addressing interoperability challenges and indicates how interoperability can be ensured in a national EHR system. The proposed system architecture is differentiated from other national EHR system architectures found in the literature in order to emphasise its novelty. Secondary data obtained from a systematic literature review was analysed using content analysis, resulting in 9482 tags which informed the development of the proposed system architecture.