Academic Computing Newsletter: September 1989

The Academic Computing Newsletter (Volume 5, Number 1) is an important means of communicating to the college community issues, information about facilities, and what is happening in general in the computing field.https://digitalcommons.brockport.edu/lits_news/1036/thumbnail.jp

Understanding user requirements in context: A case study of developing a visualisation tool to map skills in an engineering organisation

We provide a case study of understanding the environment and work context of a visualisation tool used in a collaborative engineering organisation, in order to inform the design, development and evaluation of a software network tool that uses a novel algorithm to search knowledge topics in a document corpus. We utilise focus group and qualitative interview data to understand the dynamics of existing knowledge searches and the visual analytics process of collaborative working environments in an engineering domain. We discuss the enablers and functionality needed in the network tool, and the envisaged challenges in its implementation. These challenges and enablers of a knowledge management visualisation software are then discussed in relation to evaluating the tool in a way that is grounded in the contextual working environment in which it will be used

Reclaimed asphalt pavement with waste frying oil and crumb rubber

The application of Reclaimed Asphalt Pavement (RAP) has become a relatively standard material in the road industry in most countries. However, some of the problems associated with the addition of RAP to asphalt mixtures are the increase in moisture and cracking damage. The addition of rejuvenators into the recycled mixture containing RAP is also needed to enhance its performance although the rutting resistance remains a major issue. Therefore, there is a need to investigate the incorporation of other materials in the design of the asphalt mixture to achieve improved properties and better performance. This study was carried out to investigate the performance of the recycled asphalt mixture that consists of the conventional asphalt binder with 60/70 penetration grade, 25% and 40% RAP, and the incorporation of waste materials comprising 2.6% and 4.7% Waste Frying Oil (WFO) as the rejuvenator and 1.5% Crumb Rubber (CR) with sieve size of 0.15 mm as the modifier. The study was divided into three stages, namely evaluation of material properties, analysis of the asphalt binder properties, and determination and analysis of the asphalt mixture performance. Based on the results, the addition of 25% and 40% RAP in the asphalt mixture along with WFO and CR lowered the Indirect Tensile Strength (ITS) by 31.1% and 47.3%, respectively, which fulfilled the requirement of the ITS ratio test. The resilient modulus pattern for the recycled asphalt mixture containing WFO and CR was identical at 25 and 40 °C. When tested at 40 °C, the 25% and 40% RAP with incorporated WFO and CR generated a significant resilient modulus of 848 and 901 MPa, respectively. The recycled asphalt mixture with WFO and CR also exhibited a lower permanent strain than that of the virgin asphalt binder. The rutting values of all asphalt mixtures in the wheel tracking test demonstrated a similar pattern at 45 and 60 °C test temperatures. The rutting resistance of the recycled asphalt mixture with WFO and CR slightly improved compared to the virgin asphalt binder at 60 °C. Therefore, the incorporation of WFO and CR has a considerable influence on the RAP performance while preserving the environment and reducing pollution through the recycling of waste materials

Yabi: An online research environment for grid, high performance and cloud computing

Background There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as well as domain-specific workflow environments that are either complex desktop applications or Internet-based applications. Complexities can arise when configuring these applications in heterogeneous compute and storage environments if the execution and data access models are not designed appropriately. These complexities manifest themselves through limited access to available HPC resources, significant overhead required to configure tools and inability for users to simply manage files across heterogenous HPC storage infrastructure. Results In this paper, we describe the architecture of a software system that is adaptable to a range of both pluggable execution and data backends in an open source implementation called Yabi. Enabling seamless and transparent access to heterogenous HPC environments at its core, Yabi then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. Yabi can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. In this paper, we highlight Yabi's capabilities through a range of bioinformatics use cases that arise from large-scale biomedical data analysis. Conclusion The Yabi system encapsulates considered design of both execution and data models, while abstracting technical details away from users who are not skilled in HPC and providing an intuitive drag-and-drop scalable web-based workflow environment where the same tools can also be accessed via a command line. Yabi is currently in use and deployed at multiple institutions and is available at http://ccg.murdoch.edu.au/yabi

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Usability of immersive virtual reality input devices

This research conducts a usability analysis of human interface devices within an Immersive Virtual Reality Environment. The analysis is carried out for two different interface devices, a commercially available Intersense © Wand and a home built pinch glove and wireless receiver. Users were asked to carry out a series of minor tasks involving placement of shaped blocks into corresponding holes within an Immersive Virtual Reality Environment. Performance was evaluated in terms of speed, accuracy and precision via the collection of completion times, errors made and the precision of motion during the experiment

The negotiated order and electronic patient records:a sociomaterial perspective

In this article, we consider how the notion of the negotiated order can be reinterpreted by drawing on ideas from sociomateriality. We argue that the negotiated order is an ongoing accomplishment in which a heterogeneous set of situated sociomaterial practices (or actors) are implicated. To do this, we draw upon an in-depth study of the use of a computerised physician order entry system in a hospital in Saudi Arabia. We explore how a computerised physician order entry system, as a new sociomaterial actor, performatively repositions the actors involved and hence offers the conditions of possibility for medical work practices to be renegotiated. We show that it is often contingent, mundane, situated sociomaterial practices that enact the conditions under which the negotiated order becomes re-established in terms of division of labour, legitimacy, collaboration, and social capital. We argue that as the social and material are co-constitutive, or intra-actional, it makes more sense to talk about the negotiated intra-actional order rather than the negotiated order. Importantly, such a change in conceptual vocabulary reveals the empirical and ontological issues at stake; essential for a more nuanced understanding of change/becoming

Integrated multimodal interaction framework for virtual reality foot reflexology stress therapy

Frameworks in interaction research have seen varying compositions from numerous researchers, and have been applied for either a specific or general purposes in several domains. Previous studies have highlighted virtual reality (VR) in stress therapy, and revealed the potential of foot reflexology therapy using VR technology. However, the interaction framework for foot reflexology through virtual reality requires further investigation. This study presents the design and evaluation of an integrated multimodal interaction framework for virtual reality foot reflexology stress therapy. The components of the proposed framework were identified from the literature review and previous research, which included design principles, technology, structural components, multimodal interaction architecture, and segment composition. This formed the proposed integrated multimodal interaction framework for virtual reality foot reflexology stress therapy. The proposed framework was then validated using expert reviews. This was followed by prototype development, which explored the effectiveness of the virtual reality foot reflexology therapy application on relaxation and stress relief using Smith Relaxation States Inventory (SRSI-3). A pre and post-test intervention quasi experiment was employed in the study for the evaluation. The findings revealed that Virtual Reality Foot Reflexology Stress Therapy (VR–FRST) effectively evokes the relaxation state categories of transcendence, mindfulness, positive energy, and basic relaxation, and also reduces users stress state. This research provides a concise, organized, practical and validated integrated multimodal interaction framework for the design and development of foot reflexology therapy in a virtual environment. This contributes to the field of interaction design for virtual reality developers and complementary therapy for the alternative medical practitioners