512,886 research outputs found

    A pattern-based approach to a cell tracking ontology

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    Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

    Model-based dependability analysis : state-of-the-art, challenges and future outlook

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    Abstract: Over the past two decades, the study of model-based dependability analysis has gathered significant research interest. Different approaches have been developed to automate and address various limitations of classical dependability techniques to contend with the increasing complexity and challenges of modern safety-critical system. Two leading paradigms have emerged, one which constructs predictive system failure models from component failure models compositionally using the topology of the system. The other utilizes design models - typically state automata - to explore system behaviour through fault injection. This paper reviews a number of prominent techniques under these two paradigms, and provides an insight into their working mechanism, applicability, strengths and challenges, as well as recent developments within these fields. We also discuss the emerging trends on integrated approaches and advanced analysis capabilities. Lastly, we outline the future outlook for model-based dependability analysis

    MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

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    Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

    Persistence and change in the spatio-temporal description of Sheffield Parish c.1750-1905

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    This paper brings a range of techniques from space syntax and fractal geometry to the question of the diachronic description of spatial structures that are usually considered in purely synchronic terms. Drawing on historical research into the growth of the English industrial city of Sheffield c.1770-1905 it asks how far the spatial configuration of the city’s rural hinterland (its ‘parish’) was implicated in the processes of social change and continuity that unfolded during this period. Time-series data on the development of Sheffield Parish is provided by the syntactical analysis of detailed historical maps, the routes taken by roadbased public transport systems and contemporary newspaper reports. The data is interpreted in the light of Hillier and Iida’s notion of angular, topological and metric “distance concepts” which are said to represent distinctive ‘modalities of scale’ in the emergence of an urban area embedded in the historical spatial configuration of its rural hinterland. In traditional urban geography the growth of cities is conventionally represented as the projection of an expanding built environment onto a blank surface. The discourse that accompanies this teleological notion of urbanization is typically one in which the countryside is ‘absorbed’ by the rapacious city. This language can be misleading, since urban areas whose growth can be regarded as ‘organic’ - in the sense of arising piecemeal over time - suggests the inadequacy of conceptualizing the built environment in a single (synchronic) dimension. The evidence from Sheffield Parish indicates how the differentiation of urban form is constituted both synchronically and diachronically in the description of spatial elements structured at different modalities of scale consistent with prevailing patterns of social practice, some of which relate to innovations in public transportation. The analysis of rural road networks represents a relatively new area of space syntax research. An historical study of this kind helps to ground future work by focusing on the emergent properties of space at the urban-rural periphery without also raising complex methodological questions relating to the application of space syntax methodology to large-scale contemporary urban regions. Rather, the emphasis is on drawing together the theoretical and analytical aspects of the Sheffield case study to assert that if the growing city is legitimately said to have ‘absorbed’ its rural hinterland then it is equally evident that this process of urban transformation can be also described in terms of the persistence of pre-urban road networks, historically embedded in local topography

    Internet enabled modelling of extended manufacturing enterprises using the process based techniques

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    The paper presents the preliminary results of an ongoing research project on Internet enabled process-based modelling of extended manufacturing enterprises. It is proposed to apply the Open System Architecture for CIM (CIMOSA) modelling framework alongside with object-oriented Petri Net models of enterprise processes and object-oriented techniques for extended enterprises modelling. The main features of the proposed approach are described and some components discussed. Elementary examples of object-oriented Petri Net implementation and real-time visualisation are presented

    Numerical implementation of the eXtended Finite Element Method for dynamic crack analysis

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    A numerical implementation of the eXtended Finite Element Method (X-FEM) to analyze crack propagation in a structure under dynamic loading is presented in this paper. The arbitrary crack is treated by the X-FEM method without re-meshing but using an enrichment of the classical displacement-based finite element approximation in the framework of the partition of unity method. Several algorithms have been implemented, within an Oriented Object framework in C++, in the home made explicit FEM code. The new module, called DynaCrack, included in the dynamic FEM code DynELA, evaluates the crack geometry, the propagation of the crack and allow the post-processing of the numerical results. The module solves the system of discrete equations using an explicit integration scheme. Some numerical examples illustrating the main features and the computational efficiency of the DynaCrack module for dynamic crack propagation are presented in the last section of the paper

    Web Services Support for Dynamic Business Process Outsourcing

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    Outsourcing of business processes is crucial for organizations to be effective, efficient and flexible. To meet fast-changing market conditions, dynamic outsourcing is required, in which business relationships are established and enacted on-the-fly in an adaptive, fine-grained way unrestricted by geographic distance. This requires automated means for both the establishment of outsourcing relationships and for the enactment of services performed in these relationships over electronic channels. Due to wide industry support and the underlying model of loose coupling of services, Web services increasingly become the mechanism of choice to connect organizations across organizational boundaries. This paper analyzes to which extent Web services support the dynamic process outsourcing paradigm. We discuss contract -based dynamic business process outsourcing to define requirements and then introduce the Web services framework. Based on this, we investigate the match between the two. We observe that the Web services framework requires further support for cross - organizational business processes and mechanisms for contracting, QoS management and process-based transaction support and suggest ways to fill those gaps
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