Object-Oriented Paradigms for Modelling Vascular\ud Tumour Growth: a Case Study

Motivated by a family of related hybrid multiscale models, we have built an object-oriented framework for developing and implementing multiscale models of vascular tumour growth. The models are implemented in our framework as a case study to highlight how object-oriented programming techniques and good object-oriented design may be used effectively to develop hybrid multiscale models of vascular tumour growth. The intention is that this paper will serve as a useful reference for researchers modelling complex biological systems and that these researchers will employ some of the techniques presented herein in their own projects

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

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

Distribution of the Object Oriented Databases. A Viewpoint of the MVDB Model's Methodology and Architecture

In databases, much work has been done towards extending models with advanced tools such as view technology, schema evolution support, multiple classification, role modeling and viewpoints. Over the past years, most of the research dealing with the object multiple representation and evolution has proposed to enrich the monolithic vision of the classical object approach in which an object belongs to one hierarchy class. In particular, the integration of the viewpoint mechanism to the conventional object-oriented data model gives it flexibility and allows one to improve the modeling power of objects. The viewpoint paradigm refers to the multiple descriptions, the distribution, and the evolution of object. Also, it can be an undeniable contribution for a distributed design of complex databases. The motivation of this paper is to define an object data model integrating viewpoints in databases and to present a federated database architecture integrating multiple viewpoint sources following a local-as-extended-view data integration approach.object-oriented data model, OQL language, LAEV data integration approach, MVDB model, federated databases, Local-As-View Strategy.

Integration of the Gene Ontology into an object-oriented architecture

BACKGROUND: To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. RESULTS: Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). CONCLUSION: We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes

Abstracting object interactions using composition filters

It is generally claimed that object-based models are very suitable for building distributed system architectures since object interactions follow the client-server model. To cope with the complexity of today's distributed systems, however, we think that high-level linguistic mechanisms are needed to effectively structure, abstract and reuse object interactions. For example, the conventional object-oriented model does not provide high-level language mechanisms to model layered system architectures. Moreover, we consider the message passing model of the conventional object-oriented model as being too low-level because it can only specify object interactions that involve two partner objects at a time and its semantics cannot be extended easily. This paper introduces Abstract Communication Types (ACTs), which are objects that abstract interactions among objects. ACTs make it easier to model layered communication architectures, to enforce the invariant behavior among objects, to reduce the complexity of programs by hiding the interaction details in separate modules and to improve reusability through the application of object-oriented principles to ACT classes. We illustrate the concept of ACTs using the composition filters model

Combining Description Logics and object oriented models in an information integration framework

We present an information integration system called SINTAGMA which supports the semantic integration of heterogeneous information sources using a meta data driven approach. The main idea of SINTAGMA is to build a so called Model Warehouse, containing several layers of integrated models connected by mappings. At the bottom of this hierarchy there are the models representing the actual information sources. Higher level models represent virtual databases which can be queried, as the mappings provide a precise description of how to populate these virtual sources using the concrete ones. The implementation of SINTAGMA uses constraints and logic programming, for example, the complex queries are translated into Prolog goals. This paper focuses on a recent development in SINTAGMA allowing the information expert to use Description Logic (DL) based ontologies in the development of high abstraction level conceptual models. Querying these models is performed using the Closed World Assumption as we argue that traditional Open World DL reasoning is less appropriate in the context of database oriented information integration environments

High-Order Object Model Based Software Analysis

The integration of object oriented modeling and structured analysis (SA) for developing a well structured object oriented software system is a challenge for requirements analysts and software designers. Some of the existing object oriented modeling techniques adopt approaches that are very different from SA, and others have clumsily stayed with SA after a few modifications. Our High Order Object Modeling Technique (HOOMT) however, attempts to strike a mean between both extremes while at the same time provides an effective modeling method. HOOMT consists of two models, the High Order Object Model and the Object Information Flow Model. By using the familiar divide and conquer concept and functional decomposition, our approach also ensures a less stressful migration of SA analysts to object oriented platforms. The paper introduces HOOMT, its concepts, and notations

JBendge: An Object-Oriented System for Solving, Estimating and Selecting Nonlinear Dynamic Models

We present an object-oriented software framework allowing to specify, solve, and estimate nonlinear dynamic general equilibrium (DSGE) models. The imple- mented solution methods for nding the unknown policy function are the standard linearization around the deterministic steady state, and a function iterator using a multivariate global Chebyshev polynomial approximation with the Smolyak op- erator to overcome the course of dimensionality. The operator is also useful for numerical integration and we use it for the integrals arising in rational expecta- tions and in nonlinear state space lters. The estimation step is done by a parallel Metropolis-Hastings (MH) algorithm, using a linear or nonlinear lter. Implemented are the Kalman, Extended Kalman, Particle, Smolyak Kalman, Smolyak Sum, and Smolyak Kalman Particle lters. The MH sampling step can be interactively moni- tored and controlled by sequence and statistics plots. The number of parallel threads can be adjusted to benet from multiprocessor environments. JBendge is based on the framework JStatCom, which provides a standardized ap- plication interface. All tasks are supported by an elaborate multi-threaded graphical user interface (GUI) with project management and data handling facilities.Dynamic Stochastic General Equilibrium (DSGE) Models, Bayesian Time Series Econometrics, Java, Software Development

Integration testing of object-oriented software

This thesis examines integration testing of object-oriented software. The process of integrating and testing procedural programs is reviewed as foundation for testing object-oriented software. The complexity of object-oriented software is examined. The relationship of integration testing and the software development life cycle is presented. Scenarios are discussed which account for the introduction of defects into the software. The Unified Modeling Language (UML) is chosen for representing pre-implementation and post-implementation models of the software. A demonstration of the technique of using post-implementation models representing the logical and physical views as an aid in integration and system testing of the software is presented. The use of UML diagrams developed from the software is suggested as a technique for integration testing of object-oriented software. The need for automating the data collection and model building is recognized. The technique is integrated into the Revised Spiral Model for Object-Oriented Software Development developed by du Plessis and van der Walt.ComputingD.Phil. (Computer Science