Advanced computing for systems biology

Systems biology is based on computational modelling and simulation of large networks of interacting components. Models may be intended to capture processes, mechanisms, components and interactions at different levels of fidelity. Input data are often large and geographically disperse, and may require the computation to be moved to the data, not vice versa. In addition, complex system-level problems require collaboration across institutions and disciplines. Grid computing can offer robust, scaleable solutions for distributed data, compute and expertise. We illustrate some of the range of computational and data requirements in systems biology with three case studies: one requiring large computation but small data (orthologue mapping in comparative genomics), a second involving complex terabyte data (the Visible Cell project) and a third that is both computationally and data-intensive (simulations at multiple temporal and spatial scales). Authentication, authorisation and audit systems are currently not well scalable and may present bottlenecks for distributed collaboration particularly where outcomes may be commercialised. Challenges remain in providing lightweight standards to facilitate the penetration of robust, scalable grid-type computing into diverse user communities to meet the evolving demands of systems biology.

Modelling context information with ORM

Context-aware applications rely on implicit forms of input, such as sensor-derived data, in order to reduce the need for explicit input from users. They are especially relevant for mobile and pervasive computing environments, in which user attention is at a premium. To support the development of context-aware applications, techniques for modelling context information are required. These must address a unique combination of requirements, including the ability to model information supplied by both sensors and people, to represent imperfect information, and to capture context histories. As the field of context-aware computing is relatively new, mature solutions for context modelling do not exist, and researchers rely on information modelling solutions developed for other purposes. In our research, we have been using a variant of Object-Role Modeling (ORM) to model context. In this paper, we reflect on our experiences and outline some research challenges in this area.

A participatory design agenda for ubiquitous computing and multimodal interaction: A case study of dental practice

This paper reflects upon our attempts to bring a participatory design approach to design research into interfaces that better support dental practice. The project brought together design researchers, general and specialist dental practitioners, the CEO of a dental software company and, to a limited extent, dental patients. We explored the potential for deployment of speech and gesture technologies in the challenging and authentic context of dental practices. The paper describes the various motivations behind the project, the negotiation of access and the development of the participant relationships as seen from the researchers' perspectives. Conducting participatory design sessions with busy professionals demands preparation, improvisation, and clarity of purpose. The paper describes how we identified what went well and when to shift tactics. The contribution of the paper is in its description of what we learned in bringing participatory design principles to a project that spanned technical research interests, commercial objectives and placing demands upon the time of skilled professionals. Copyright © 2010 ACM, Inc

Career development and systems theory: Connecting theory and practice

The Systems Theory Framework was developed to produce a metatheoretical framework through which the contribution of all theories to our understanding of career behaviour could be recognised. In addition it emphasises the individual as the site for the integration of theory and practice. Its utility has become more broadly acknowledged through its application to a range of cultural groups and settings, qualitative assessment processes, career counselling, and multicultural career counselling. For these reasons, the STF is a very valuable addition to the field of career theory. In viewing the field of career theory as a system, open to changes and developments from within itself and through constantly interrelating with other systems, the STF and this book is adding to the pattern of knowledge and relationships within the career field. The contents of this book will be integrated within the field as representative of a shift in understanding existing relationships within and between theories. In the same way, each reader will integrate the contents of the book within their existing views about the current state of career theory and within their current theory-practice relationship. This book should be required reading for anyone involved in career theory. It is also highly suitable as a text for an advanced career counselling or theory course.

The Environment and the Selection of Aquaculture Species and Systems: An Economic Analysis

Environmental conditions play a significant role in the economic success of aquaculture. This article classifies environmental factors in a way that facilitates economic analysis of their implications for the selection of aquaculture species and systems. The implication of on-farm as on-site environmental conditions for this selection are considered first using profit-possibility frontiers and taking into account the biological law of environmental tolerance. However, in selecting, recommending and developing aquaculture species and systems, it is often unrealistic to assume the degree of managerial efficiency implied by the profit-possibility function. It is appropriate to take account of the degree of managerial inefficiency that actually exists, not all of which may be capable of being eliminated. Furthermore, experimental R&D should be geared to on-farm conditions, and the variability of these conditions needs to be taken into account. Particularly in shared water bodies, environmental spillovers between aquaculturalists can be important and as shown theoretically, can influence the socially optimal selection of aquaculture species and systems. Similarly, aquaculture can have environmental consequences for the rest of the community. The social economic implications of this for the selection of aquaculture species and systems are analyzed. Some paradoxical results are obtained. For example, if the quality of social governance of aquaculture is poor, aquaculture species and systems that cause a slow rate of environmental deterioration may be socially less satisfactory than those that cause a rapid rate of such deterioration. Socially optimal choice of aquaculture species and systems depends not only on their biophysical characteristics and market conditions but also on the prevailing state of governance of aquaculture. Failure to consider the last aspect can result in the introduction of new aquaculture species (and systems) doing more social harm than good.

Contingent on context? Social work and the state in Australia, Britain, and the USA

The notion that social work is an international profession, operating with generally similar goals, methodologies, and common values is considered critically. Examining the political and social contexts of three countries with liberal democratic governments-Australia, Britain and the United States-the role of social work within the welfare processes of each country is compared. While social work as an identifiable professional activity shares some features, it is argued that the idea of its having a core essence needs to be tempered with a realistic assessment of the importance of contextually created difference. Recent and rapid developments in the institutional context, such as those experienced in these three countries, further underscore the limited utility of the notion of a common professional project.

Applying ontologies to business and systems modelling techniques and perspectives: Lessons learned

For many years in the area of business systems analysis and design, practitioners and researchers alike have been searching for some comprehensive basis on which to evaluate, compare, and engineer techniques that are promoted for use in the modelling of systems' requirements. To date, while many frameworks, factors, and facets have been forthcoming, none appear to be based on a sound theory. In light of this dilemma, over the last 10 years, attention has been devoted by researchers to the use of ontology to provide some theoretical basis for the advancement of the business systems modelling discipline. This paper outlines how we have used a particular ontology for this purpose over the last five years. In particular we have learned that the understandability and the applicability of the selected ontology must be clear for IS professionals, the results of any ontological evaluation must be tempered by economic efficiency considerations of the stakeholders involved, and ontologies may have to be focused for the business purpose and type of user involved in the modelling situation.

Quantum computing and polynomial equations over the finite field Z(2)

What is the computational power of a quantum computer? We show that determining the output of a quantum computation is equivalent to counting the number of solutions to an easily computed set of polynomials defined over the finite field Z(2). This connection allows simple proofs to be given for two known relationships between quantum and classical complexity classes, namely BQP subset of P-#P and BQP subset of PP.

“Doing” Gender in Context: Household Bargaining and Risk of Divorce in Germany and the United States

Gender relations remain embedded in their sociopolitical context. Compared here using event-history analysis is how household divisions of paid and unpaid labor affect marital stability in the former West Germany, where policy reinforced male breadwinner families, and the United States, where policy remains silent regarding the private sphere. In Germany, any moves away from separate gendered spheres in terms of either wives' relative earnings or husbands' relative participation in housework increase the risk of divorce. In the United States, however, the more stable couples are those that adapt by displaying greater gender equity. These results highlight that policy shapes how gender gets done in the intimate sphere, and that reinforcement of a gendered division of labor may be detrimental to marital stability.