Computational inference in systems biology

Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem. The computational costs associated with repeatedly solving the ODEs are often high. Aimed at reducing this cost, new concepts using gradient matching have been proposed. This paper combines current adaptive gradient matching approaches, using Gaussian processes, with a parallel tempering scheme, and conducts a comparative evaluation with current methods used for parameter inference in ODEs

Newly qualified physical education teachers’ experiences of developing subject knowledge prior to, during and after a Postgraduate Certificate in Education course

Office for Standards in Education (OFSTED) inspections of secondary Postgraduate Certificate in Education (PGCE) physical education courses in England between 1996 and 1998 (OFSTED, 1999) were critical of student teachers' subject knowledge. The purpose of this study was to investigate the development of subject knowledge and influences on the development of that subject knowledge in a sample of three newly qualified teachers (NQTs) who had completed a PGCE physical education course in England. The research comprised semi-structured interviews and analysis of documentation. Among these three NQTs there were some similarities, but more differences in terms of the development of subject knowledge as well as different influences on the development of subject knowledge. These results suggest that teacher educators may need to be flexible in how they approach and support the development of student teachers' subject knowledge. Results also suggest that teacher educators should work more closely with colleagues teaching sports-related undergraduate degree courses to support the development of subject knowledge for those students who wish to progress to a PGCE physical education course

3D Hydrogeological Model Building Using Airborne Electromagnetic Data

We develop a 3D geological modelling procedure supported by the combination of helicopter time-domain electromagnetic data, seismic reflection data, and water well records for the Spiritwood buried valley aquifer system in Manitoba, Canada. Our procedure is an innovative hybrid of knowledge-driven and data-driven schemes that provides a clear protocol for incorporating different types of geophysical data into a 3D stratigraphic model framework. The limited spatial density of water well bedrock observations precludes detection of the buried valley bedrock topography and renders the water well records alone inadequate for accurate hydrogeological model building. The expert interpretation of the geophysical data allows for leveraging of a spatially extensive dataset with rich information content that would be otherwise difficult to utilize for lithostratigraphic classification

Reflective Journaling: A Theoretical Model and Digital Prototype for Developing Resilience and Creativity

Reflection is commonly discussed as a tool for personal and professional development that is becoming increasingly important in today’s global and digital world. In this paper, we propose a model that suggests ways in which reflection, in the form of Reflective Journaling, can support the development of creativity and resilience, which are needed to enable individuals to function effectively in a fast-changing environment. In addition, the model proposes ways in which external support and progress monitoring can be used in conjunction with skills in adaptive resilience and structured creativity, to support the maintenance of reflective journaling as a habit, in the longer term, thus creating virtuous cycles of skills and behaviours that can reinforce each other. Based on our model, and additional user research, we describe the design of a first digital prototype that aims to support the use of Reflective Journaling and to develop creativity and resilience through suggested mechanisms. Initial evaluations of our prototype are positive. It has been well-received by early test users, and has the potential to address all the connections defined. We therefore suggest that the theoretical model can be used to develop digital tools, such as the one included, to help those who wish to develop the habit of reflective journaling, and through that a range of other skills associated with resilience and creative thinking. We see this as a starting point for investigating this potential in more depth

An integrated strategy for prediction uncertainty analysis

Motivation: To further our understanding of the mechanisms underlying biochemical pathways mathematical modelling is used. Since many parameter values are unknown they need to be estimated using experimental observations. The complexity of models necessary to describe biological pathways in combination with the limited amount of quantitative data results in large parameter uncertainty which propagates into model predictions. Therefore prediction uncertainty analysis is an important topic that needs to be addressed in Systems Biology modelling

A Bayesian approach to targeted experiment design

Motivation: Systems biology employs mathematical modelling to further our understanding of biochemical pathways. Since the amount of experimental data on which the models are parameterized is often limited, these models exhibit large uncertainty in both parameters and predictions. Statistical methods can be used to select experiments that will reduce such uncertainty in an optimal manner. However, existing methods for optimal experiment design (OED) rely on assumptions that are inappropriate when data are scarce considering model complexity

Changing how Earth System Modelling is done to provide more useful information for decision making, science and society

New details about natural and anthropogenic processes are continually added to models of the Earth system, anticipating that the increased realism will increase the accuracy of their predictions. However, perspectives differ about whether this approach will improve the value of the information the models provide to decision makers, scientists, and societies. The present bias toward increasing realism leads to a range of updated projections, but at the expense of uncertainty quantification and model tractability. This bias makes it difficult to quantify the uncertainty associated with the projections from any one model or to the distribution of projections from different models. This in turn limits the utility of climate model outputs for deriving useful information such as in the design of effective climate change mitigation and adaptation strategies or identifying and prioritizing sources of uncertainty for reduction. Here we argue that a new approach to model development is needed, focused on the delivery of information to support specific policy decisions or science questions. The central tenet of this approach is the assessment and justification of the overall balance of model detail that reflects the question posed, current knowledge, available data, and sources of uncertainty. This differs from contemporary practices by explicitly seeking to quantify both the benefits and costs of details at a systemic level, taking into account the precision and accuracy with which predictions are made when compared to existing empirical evidence. We specify changes to contemporary model development practices that would help in achieving this goal.</jats:p

The initial education of high school teachers : a critical review of major issues and trends

This paper draws on major research findings in international literature in order to provide a critical review of a number of key issues and trends in the initial education of high school teachers. Firstly, this paper contextualizes the prevalent discourse surrounding the field of initial teacher education (ITE) and explores the effect that this discourse has on the conceptualization of teachers’ work. Secondly, this paper focuses on the debates regarding the most propitious site for the teacher education enterprise, the programme structure for ITE, the field placement or practicum, the relationship between subject study and pedagogy, and the overall effectiveness of teacher education. The paper concludes by considering the new challenges that the field of initial teacher education must confront and the implications of such challenges for the ITE curriculum.peer-reviewe