Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Requirement modeling for data warehouse using goal-UML approach: the case of health care

Decision makers use Data Warehouse (DW) for performing analysis on business information. DW development is a long term process with high risk of failure and it is difficult to estimate the future requirements for the decision-making. Further, the current DW design does not consider the early and late requirements analysis during its development, especially by using Unified Modeling Language (UML) approach. Due to this problem, it is crucial that current DW modeling approaches covered both early and late requirements analysis in the DW design. A case study was conducted on Malaysia Rural Health Care (MRH) to gather the requirements for DW design. The goal-oriented approach has been used to analyze the early requirements and later was mapped to UML approach to produce a new DW modeling called Goal-UML (G-UML). The proposed approach highlighted the mapping process of DW conceptual schema to a class diagram to produce a complete MRH-DW design. The correctness of the DW design was evaluated using expert reviews. The G-UML method can contribute to the development of DW and be a guideline to the DW developers to produce an improved DW design that meets all the user requirement

Evaluating methodologies: a requirements engineering approach through the use of an exemplar

Systems development methodologies continue to be a central area of research in software engineering. As the nature of applications and systems usage move increasingly towards open networked environments, not only are new methodologies required, but new ways for evaluating methodologies for these new environments are also required. The agent-oriented approach to software engineering introduces concepts such as pro-activeness and autonomy to achieve more flexible and robust systems for complex applications environments. A number of AOSE methodologies have been proposed. In order to evaluate and compare these methods in depth, we proposed the use of a common exemplar-a detailed application setting within which each of the methodologies will be worked out. The evaluation method emphasizes a requirements engineering perspective. In this paper we show how to apply this exemplar to evaluate three agentoriented methodologies.Facultad de Informátic

Interactive situation modelling in knowledge intensive domains

Interactive Situation Modelling (ISM) method, a semi-methodological approach, is proposed to tackle issues associated with modelling complex knowledge intensive domains, which cannot be easily modelled using traditional approaches. This paper presents the background and implementation of ISM within a complex domain, where synthesizing knowledge from various sources is critical, and is based on the principles of ethnography within a constructivist framework. Although the motivation for the reported work comes from the application presented in the paper, the actual scope of the paper covers a wide range of issues related to modelling complex systems. The author firstly reviews approaches used for modelling knowledge intensive domains, preceded by a brief discussion about two main issues: symmetry of ignorance and system behaviour, which are often confronted when applying modelling approaches to business domains. The ISM process is then characterized and critiqued with lessons from an exemplar presented to illustrate its effectiveness

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

Model Reka Bentuk Konseptual Operasian Storan Data Bagi Aplikasi Kepintaran Perniagaan

The development of business intelligence (BI) applications, involving of data sources, Data Warehouse (DW), Data Mart (DM) and Operational Data Store (ODS), imposes a major challenge to BI developers. This is mainly due to the lack of established models, guidelines and techniques in the development process as compared to system development in the discipline of software engineering. Furthermore, the present BI applications emphasize on the development of strategic information in contrast to operational and tactical. Therefore, the main aim of this study is to propose a conceptual design model for BI applications using ODS (CoDMODS). Through expert validation, the proposed conceptual design model that was developed by means of design science research approach, was found to satisfy nine quality model dimensions, which are, easy to understand, covers clear steps, is relevant and timeless, demonstrates flexibility, scalability, accuracy, completeness and consistency. Additionally, the two prototypes that were developed based on CoDMODS for water supply service (iUBIS) and telecommunication maintenance (iPMS) recorded a high usability average min value of 5.912 using Computer System Usability Questionnaire (CSUQ) instrument. The outcomes of this study, particularly the proposed model, contribute to the analysis and design method for the development of the operational and tactical information in BI applications. The model can be referred as guidelines by BI developers. Furthermore, the prototypes that were developed in the case studies can assist the organizations in using quality information for business operations