WSRF-based modeling of clinical trial information for collaborative cancer research

The CancerGrid consortium is developing open-standards cancer informatics to address the challenges posed by modern cancer clinical trials. This paper presents the service-oriented software paradigm implemented in CancerGrid to derive clinical trial information management systems for collaborative cancer research across multiple institutions. Our proposal is founded on a combination of a clinical trial (meta)model and WSRF (Web Services Resource Framework), and is currently being evaluated for use in early phase trials. Although primarily targeted at cancer research, our approach is readily applicable to other areas for which a similar information model is available.

Goal-based modeling of dynamically adaptive system requirements

Self-adaptation is emerging as an increasingly important capability for many applications, particularly those deployed in dynamically changing environments, such as ecosystem monitoring and disaster management. One key challenge posed by Dynamically Adaptive Systems (DASs) is the need to handle changes to the requirements and corresponding behavior of a DAS in response to varying environmental conditions. Berry et al. previously identified four levels of RE that should be performed for a DAS. In this paper, we propose the Levels of RE for Modeling that reify the original levels to describe RE modeling work done by DAS developers. Specifically, we identify four types of developers: the system developer, the adaptation scenario developer, the adaptation infrastructure developer, and the DAS research community. Each level corresponds to the work of a different type of developer to construct goal model(s) specifying their requirements. We then leverage the Levels of RE for Modeling to propose two complementary processes for performing RE for a DAS. We describe our experiences with applying this approach to GridStix, an adaptive flood warning system, deployed to monitor the River Ribble in Yorkshire, England.

A goal-based modeling approach to develop requirements of an adaptive system with environmental uncertainty

Dynamically adaptive systems (DASs) are intended to monitor the execution environment and then dynamically adapt their behavior in response to changing environmental conditions. The uncertainty of the execution environment is a major motivation for dynamic adaptation; it is impossible to know at development time all of the possible combinations of environmental conditions that will be encountered. To date, the work performed in requirements engineering for a DAS includes requirements monitoring and reasoning about the correctness of adaptations, where the DAS requirements are assumed to exist. This paper introduces a goal-based modeling approach to develop the requirements for a DAS, while explicitly factoring uncertainty into the process and resulting requirements. We introduce a variation of threat modeling to identify sources of uncertainty and demonstrate how the RELAX specification language can be used to specify more flexible requirements within a goal model to handle the uncertainty. © 2009 Springer Berlin Heidelberg.

Modeling of spectral and statistical properties of a random distributed feedback fiber laser

For the first time we report full numerical NLSE-based modeling of generation properties of random distributed feedback fiber laser based on Rayleigh scattering. The model which takes into account the random backscattering via its average strength only describes well power and spectral properties of random DFB fiber lasers. The influence of dispersion and nonlinearity on spectral and statistical properties is investigated. The evidence of non-gaussian intensity statistics is found. © 2013 Optical Society of America.

A three dimensional numerical investigation of hillslope flow processes

Physically based distributed models of catchment hydrology are likely to be made available as engineering tools in the near future. Although these models are based on theoretically acceptable equations of continuity, there are still limitations in the present modelling strategy. Of interest to this thesis are the current modelling assumptions made concerning the effects of soil spatial variability, including formations producing distinct zones of preferential flow. The thesis contains a review of current physically based modelling strategies and a field based assessment of soil spatial variability. In order to investigate the effects of soil nonuniformity a fully three dimensional model of variability saturated flow in porous media is developed. The model is based on a Galerkin finite element approximation to Richards equation. Accessibility to a vector processor permits numerical solutions on grids containing several thousand node points. The model is applied to a single hillslope segment under various degrees of soil spatial variability. Such variability is introduced by generating random fields of saturated hydraulic conductivity using the turning bands method. Similar experiments are performed under conditions of preferred soil moisture movement. The results show that the influence of soil variability on subsurface flow may be less significant than suggested in the literature, due to the integrating effects of three dimensional flow. Under conditions of widespread infiltration excess runoff, the results indicate a greater significance of soil nonuniformity. The recognition of zones of preferential flow is also shown to be an important factor in accurate rainfall-runoff modelling. Using the results of various fields of soil variability, experiments are carried out to assess the validity of the commonly used concept of `effective parameters'. The results of these experiments suggest that such a concept may be valid in modelling subsurface flow. However, the effective parameter is observed to be event dependent when the dominating mechanism is infiltration excess runoff.

Advances in decision support systems on the endeavour for supply chain optimality

Industry practitioners are seeking to create optimal logistics networks through more efficient decision-making leading to a shift of power from a centralized position to a more decentralized approach. This has led to researchers, exploring with vigor, the application of agent based modeling (ABM) in supply chains and more recently, its impact on decision-making. This paper investigates reasons for the shift to decentralized decision-making and the impact on supply chains. Effective decentralization of decision-making with ABM and hybrid modeling is investigated, observing the methods and potential of achieving optimality.

Modeling geometric rules in object based models:an XML / GML approach

Most object-based approaches to Geographical Information Systems (GIS) have concentrated on the representation of geometric properties of objects in terms of fixed geometry. In our road traffic marking application domain we have a requirement to represent the static locations of the road markings but also enforce the associated regulations, which are typically geometric in nature. For example a give way line of a pedestrian crossing in the UK must be within 1100-3000 mm of the edge of the crossing pattern. In previous studies of the application of spatial rules (often called 'business logic') in GIS emphasis has been placed on the representation of topological constraints and data integrity checks. There is very little GIS literature that describes models for geometric rules, although there are some examples in the Computer Aided Design (CAD) literature. This paper introduces some of the ideas from so called variational CAD models to the GIS application domain, and extends these using a Geography Markup Language (GML) based representation. In our application we have an additional requirement; the geometric rules are often changed and vary from country to country so should be represented in a flexible manner. In this paper we describe an elegant solution to the representation of geometric rules, such as requiring lines to be offset from other objects. The method uses a feature-property model embraced in GML 3.1 and extends the possible relationships in feature collections to permit the application of parameterized geometric constraints to sub features. We show the parametric rule model we have developed and discuss the advantage of using simple parametric expressions in the rule base. We discuss the possibilities and limitations of our approach and relate our data model to GML 3.1. © 2006 Springer-Verlag Berlin Heidelberg.

Three-dimensional modeling of the human eye based on magnetic resonance imaging

PURPOSE. A methodology for noninvasively characterizing the three-dimensional (3-D) shape of the complete human eye is not currently available for research into ocular diseases that have a structural substrate, such as myopia. A novel application of a magnetic resonance imaging (MRI) acquisition and analysis technique is presented that, for the first time, allows the 3-D shape of the eye to be investigated fully. METHODS. The technique involves the acquisition of a T2-weighted MRI, which is optimized to reveal the fluid-filled chambers of the eye. Automatic segmentation and meshing algorithms generate a 3-D surface model, which can be shaded with morphologic parameters such as distance from the posterior corneal pole and deviation from sphericity. Full details of the method are illustrated with data from 14 eyes of seven individuals. The spatial accuracy of the calculated models is demonstrated by comparing the MRI-derived axial lengths with values measured in the same eyes using interferometry. RESULTS. The color-coded eye models showed substantial variation in the absolute size of the 14 eyes. Variations in the sphericity of the eyes were also evident, with some appearing approximately spherical whereas others were clearly oblate and one was slightly prolate. Nasal-temporal asymmetries were noted in some subjects. CONCLUSIONS. The MRI acquisition and analysis technique allows a novel way of examining 3-D ocular shape. The ability to stratify and analyze eye shape, ocular volume, and sphericity will further extend the understanding of which specific biometric parameters predispose emmetropic children subsequently to develop myopia. Copyright © Association for Research in Vision and Ophthalmology.

High performance numerical modeling of ultra-short laser pulse propagation based on multithreaded parallel hardware

The focus of this study is development of parallelised version of severely sequential and iterative numerical algorithms based on multi-threaded parallel platform such as a graphics processing unit. This requires design and development of a platform-specific numerical solution that can benefit from the parallel capabilities of the chosen platform. Graphics processing unit was chosen as a parallel platform for design and development of a numerical solution for a specific physical model in non-linear optics. This problem appears in describing ultra-short pulse propagation in bulk transparent media that has recently been subject to several theoretical and numerical studies. The mathematical model describing this phenomenon is a challenging and complex problem and its numerical modeling limited on current modern workstations. Numerical modeling of this problem requires a parallelisation of an essentially serial algorithms and elimination of numerical bottlenecks. The main challenge to overcome is parallelisation of the globally non-local mathematical model. This thesis presents a numerical solution for elimination of numerical bottleneck associated with the non-local nature of the mathematical model. The accuracy and performance of the parallel code is identified by back-to-back testing with a similar serial version.

Modeling contention based bandwidth request scheme for IEEE 802.16 networks

IEEE 802.16 standard specifies a contention based bandwidth request scheme for best-effort and non-real time polling services in Point-to-MultiPoint (PMP) architecture. In this letter we propose an analytical model for the scheme and study how the performances of bandwidth efficiency and channel access delay change with the contention window size, the number of contending subscriber stations, the number of slots allocated for bandwidth request and data transmission. Simulations validate its high accuracy. © 2007 IEEE.

Modeling 2R regenerator based on High Nonlinear Dispersion Imbalanced Loop Mirror (HN-DILM)

The model of Reshaping and Re-amplification (2R) regenerator based on High Nonlinear Dispersion Imbalanced Loop Mirror (HN-DILM) has been designed to examine its capability to reduce the necessary of fiber loop length and input peak power by deploying High Non linear Fiber (HNLF) compared to Dispersion Shifted Fiber (DSF). The simulation results show by deployed a HNLF as a nonlinear element in Dispersion Imbalanced Loop Mirror (DILM) requires only 400mW peak powers to obtain a peak of transmission compared to DSF which requires a higher peak power at 2000mW to obtain a certain transmissivity. It also shows that HNLF required shorter fiber length to achieve the highest transmission. The 2R regenerator also increases the extinction ratio (ER) of the entire system. © 2010 IEEE.