Flux balance analysis of biological systems: applications and challenges

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.

Real-time locating systems applications in construction

Real-time locating systems (RTLSs) are considered an effective way to identify and track the location of an object in both indoor and outdoor environments. Various RTLSs have been developed and made commercially available in recent years. Research into RTLSs in the construction sector is ubiquitous and results have been published in many construction-related academic journals over the past decade. A succinct and systematic review of current applications would help academics, researchers and industry practitioners in identifying existing research deficiencies and therefore future research directions. However, such a review is lacking to date. This paper provides a framework for understanding RTLS research and development in the construction literature over the last decade. The research opportunities and directions of construction RTLS are highlighted. Background information relating to construction RTLS trends, accuracy, deployment, cost, purposes, advantages and limitations is provided. Four major research gaps are identified and research opportunities and directions are highlighted.

A practical taxonomy of methods and literature for managing uncertain spatial data in geographic information systems

Perfect information is seldom available to man or machines due to uncertainties inherent in real world problems. Uncertainties in geographic information systems (GIS) stem from either vague/ambiguous or imprecise/inaccurate/incomplete information and it is necessary for GIS to develop tools and techniques to manage these uncertainties. There is a widespread agreement in the GIS community that although GIS has the potential to support a wide range of spatial data analysis problems, this potential is often hindered by the lack of consistency and uniformity. Uncertainties come in many shapes and forms, and processing uncertain spatial data requires a practical taxonomy to aid decision makers in choosing the most suitable data modeling and analysis method. In this paper, we: (1) review important developments in handling uncertainties when working with spatial data and GIS applications; (2) propose a taxonomy of models for dealing with uncertainties in GIS; and (3) identify current challenges and future research directions in spatial data analysis and GIS for managing uncertainties.

Dual retrieval in conceptual information systems

Conceptual Information Systems provide a multi-dimensional conceptually structured view on data stored in relational databases. On restricting the expressiveness of the retrieval language, they allow the visualization of sets of realted queries in conceptual hierarchies, hence supporting the search of something one does not have a precise description, but only a vague idea of. Information Retrieval is considered as the process of finding specific objects (documents etc.) out of a large set of objects which fit to some description. In some data analysis and knowledge discovery applications, the dual task is of interest: The analyst needs to determine, for a subset of objects, a description for this subset. In this paper we discuss how Conceptual Information Systems can be extended to support also the second task.

A conceptual framework for aligning business and information systems from organisational learning perspective

The three decades of on-going executives’ concerns of how to achieve successful alignment between business and information technology shows the complexity of such a vital process. Most of the challenges of alignment are related to knowledge and organisational change and several researchers have introduced a number of mechanisms to address some of these challenges. However, these mechanisms pay less attention to multi-level effects, which results in a limited un-derstanding of alignment across levels. Therefore, we reviewed these challenges from a multi-level learning perspective and found that business and IT alignment is related to the balance of exploitation and exploration strategies with the intellec-tual content of individual, group and organisational levels.

Analysis of cultural conflict in the development of web-enabled information systems

The advent of the World Wide Web (WWW) and the emergence of Internet commerce have given rise to the web as a medium of information exchange. In recent years, the phenomenon has affected the realm of transaction processing systems, as organizations are moving from designing web pages for marketing purposes, to web-based applications that support business-to-business (WEB) and business-to-consumer (B2C) interactions, integrated with databases and other back-end systems (Isakowitz, Bieber et al., 1998). Furthermore, web-enabled applications are increasingly being used to facilitate transactions even between various business units within a single enterprise. Examples of some of the more popular web-enabled applications in use today include airline reservation systems, internet banking, student enrollment systems in universities, and Human Resource (HR) and payroll systems. The prime motive behind the adoption of web-enabled applications are productivity gains due to reduced processing time, decrease in the usage of paper-based documentation and conventional modes of communication (such as letters, fax, or telephone), and improved quality of services to clients. Indeed, web-based solutions are commonly referred to as customer-centric (Li, 2000), which means that they provide user interfaces that do not necessitate high level of computer proficiency. Thus, organizations implement such systems to streamline routine transactions and gain strategic benefits in the process (Nambisan & Wang, 1999), though the latter are to be expected in the long-term. Notwithstanding the benefits of web technology adoption, the web has ample share of challenges for initiators and developers. Many of these challenges are associated with the unique nature of web-enabled applications. Research in the area of web-enabled information systems has revealed several differences with traditional applications. These differences exist with regards to system development methodology, stakeholder involvement, tasks, and technology (Nazareth, 1998). According to Fraternali (1999), web applications are commonly developed using an evolutionary prototyping approach, whereby the simplified version of the application is deployed as a pilot first, in order to gather user feedback. Thus, web-enabled applications typically undergo continuous refinement and evolution (Ginige, 1998; Nazareth, 1998; Siau, 1998; Standing, 2001). Prototype-based development also leads web-enabled information systems to have much shorter development life cycles, but which, unlike traditional applications, are regrettably developed in a rather adhoc fashion (Carstensen & Vogelsang, 2001). However, the principal difference between the two kinds of applications lies in the broad and diverse group of stakeholders associated with web-based information systems (Gordijn, Akkermans, et al., 2000; Russo, 2000; Earl & Khan, 2001; Carter, 2002; Hasselbring, 2002; Standing, 2002; Stevens & Timbrell, 2002). Stakeholders, or organizational members participating in a common business process (Freeman, 1984), vary in their computer competency, business knowledge, language and culture. This diversity is capable of causing conflict between different stakeholder groups with regards to the establishment of system requirements (Pouloudi & Whitley, 1997; Stevens & Timbrell, 2002). Since, web-based systems transcend organizational, departmental, and even national boundaries, the issue of culture poses a significant challenge to the web systems’ initiators and developers (Miles & Snow, 1992; Kumar & van Dissel, 1996; Pouloudi & Whitley, 1996; Li & Williams, 1999).

Development of an instrument to evaluate the quality of delivered information systems

Delivered information systems are an integral part of many organisations’ information technology infrastructure. Their dynamic nature creates new challenges, not the least of which is the need to measure the quality/effectiveness of these systems. Given the size of investment in these systems, it would be invaluable for business to formulate a fresh, simple, easy to administer, multi-dimensional instrument capable of measuring the quality of delivered information systems or applications. Such an instrument would provide a practical and efficient means to pinpoint areas that key stakeholders, ranging from end-users to managers, perceive as requiring attention. In this paper, we report on the development of one such instrument. This instrument addresses key areas of performance and uses multiple statements to enhance stakeholders’ understanding of these areas.

Mobile healthcare information systems : thru' the ant lens

Deployment of mobile technologies and applications in health care are becoming prevalent worldwide. As mobile innovation and standards in wireless continue to evolve, so does the mobile health care information systems framework. In this paper, we explore this evolving framework by synthesising current technologies, applications, issues and examining this through the actor-network theory (ANT) which seeks to understand socio-technical change by adopting a symmetric treatment of people and technologies.

The negative impact on nurses of lack of alignment of information systems with public hospital strategic goals

The objectives of this study were to investigate the degree to which hospital information systems are aligned with hospital strategies and how they impact on nurses. Semi-structured interviews were conducted with nine hospital staff from a range of disciplines in a large public hospital in Australia. The interviews revealed that the focus of hospital information systems on administration has meant that applications to support the patient's clinical journey have been deemed unaffordable. A consequence is that the historic use of the nurses' station as a source of verbal information about patients has continued, with negative impacts on nurses' perceived role and status, and the possible exacerbation of the clash between administrative and clinical cultures. We conclude that hospitals need clear strategies, with alignment of information systems. To do otherwise can undermine culture and morale, while disrupting workflows and patients' clinical journeys.

Protecting information systems from DDoS attack using multicore methodology

Previous work, in the area of defense systems has focused on developing a firewall like structure, in order to protect applications from attacks. The major drawback for implementing security in general, is that it affects the performance of the application they are trying to protect. In fact, most developers avoid implementing security at all. With the coming of new multicore systems, we might at last be able to minimize the performance issues that security places on applications. In our bodyguard framework we propose a new kind of defense that acts alongside, not in front, of applications. This means that performance issues that effect system applications are kept to a minimum, but at the same time still provide high grade security. Our experimental results demonstrate that a ten to fifteen percent speedup in performance is possible, with the potential of greater speedup.

Quality as the criterion for delivered information systems effectiveness

One of the major challenges of MIS activities is the difficulty in measuring the effectiveness of delivered systems. The principal purpose of my research is to explore this field in order to develop an instrument by which to measure such effectiveness. Conceptualisation of Information System (IS) Effectiveness has been substantially framed by DeLone and McLean's (1992) Success; Model. But with the innovation in Information Technology (IT) over the past decade, and the constant pressure in IT to improve performance, there is merit in undertaking a fresh appraisal of the issue. This study built on the model of IS Success developed by DeLone and MeLean, but was broadened to include related research from the domains of IS, Management and Marketing. This analysis found that an effective IS function is built on three pillars: the systems implemented; the information held and delivered by these systems; and, the service provided in support of the IS function. A common foundation for these pillars is the concept of stakeholder needs. In seeking to appreciate the effectiveness: of delivered IS applications in relation to the job performance of stakeholders, this research developed an understanding of what quality means in an IT context I argue that quality is a more useful criterion for effectiveness than the more customary measures of use and user satisfaction. Respecification of the IS Success Model was then proposed. The second phase of the research was to test this model empirically through judgment panels, focus groups and interviews. Results consistently supported the structure and components of the respecified model. Quality was determined as a multi-dimensional construct, with the key dimensions for the quality of delivered IS differing from those used in the research from other disciplines. Empirical work indicated that end-user stakeholders derived their evaluations of quality by internally evaluating perceived performance of delivered IS in relation to their expectations for such performance. A short trial explored whether, when overt measurement of expectations was concurrent with the measurement of perceptions, a more revealing appraisal of delivered IS quality was provided than when perceptions alone were measured. Results revealed a difference between the two measures. Using the New IS Success Model as the foundation, and drawing upon the related theoretical and empirical research, an instrument was developed to measure the quality/effectiveness of delivered IS applications. Four trials of this instrument, QUALIT, are documented. Analysis of results from preliminary trials indicates promise in terms of business value: the instrument is simple to administer and has the capacity to pinpoint areas of weakness. The research related to the respecification of the New IS Success Model and the associated empirical studies, including the development of QTJALIT, have both contributed to the development of theory about IS Effectiveness. More precisely, my research has reviewed the components of an information system, the dimensions comprising these components and the indicators of each, and based upon these findings, formulated an instrument by which to measure the effectiveness of a delivered IS.