Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model

Generating natural language specifications from UML class diagrams

Early phases of software development are known to be problematic, difficult to manage and errors occurring during these phases are expensive to correct. Many systems have been developed to aid the transition from informal Natural Language requirements to semistructured or formal specifications. Furthermore, consistency checking is seen by many software engineers as the solution to reduce the number of errors occurring during the software development life cycle and allow early verification and validation of software systems. However, this is confined to the models developed during analysis and design and fails to include the early Natural Language requirements. This excludes proper user involvement and creates a gap between the original requirements and the updated and modified models and implementations of the system. To improve this process, we propose a system that generates Natural Language specifications from UML class diagrams. We first investigate the variation of the input language used in naming the components of a class diagram based on the study of a large number of examples from the literature and then develop rules for removing ambiguities in the subset of Natural Language used within UML. We use WordNet,a linguistic ontology, to disambiguate the lexical structures of the UML string names and generate semantically sound sentences. Our system is developed in Java and is tested on an independent though academic case study

Quality-aware model-driven service engineering

Service engineering and service-oriented architecture as an integration and platform technology is a recent approach to software systems integration. Quality aspects ranging from interoperability to maintainability to performance are of central importance for the integration of heterogeneous, distributed service-based systems. Architecture models can substantially influence quality attributes of the implemented software systems. Besides the benefits of explicit architectures on maintainability and reuse, architectural constraints such as styles, reference architectures and architectural patterns can influence observable software properties such as performance. Empirical performance evaluation is a process of measuring and evaluating the performance of implemented software. We present an approach for addressing the quality of services and service-based systems at the model-level in the context of model-driven service engineering. The focus on architecture-level models is a consequence of the black-box character of services

Multilevel Coupled Model Transformations for Precise and Reusable Definition of Model Behaviour

The use of Domain-Specific Languages (DSLs) is a promising field for the development of tools tailored to specific problem spaces, effectively diminishing the complexity of hand-made software. With the goal of making models as precise, simple and reusable as possible, we augment DSLs with concepts from multilevel modelling, where the number of abstraction levels are not limited. This is particularly useful for DSL definitions with behaviour, whose concepts inherently belong to different levels of abstraction. Here, models can represent the state of the modelled system and evolve using model transformations. These transformations can benefit from a multilevel setting, becoming a precise and reusable definition of the semantics for behavioural modelling languages. We present in this paper the concept of Multilevel Coupled Model Transformations, together with examples, formal definitions and tools to assess their conceptual soundness and practical value.Comment: Journal of Logical and Algebraic Methods in Programming. Available online 11 January 2019. In Press, Accepted Manuscrip

A framework for effective management of condition based maintenance programs in the context of industrial development of E-Maintenance strategies

CBM (Condition Based Maintenance) solutions are increasingly present in industrial systems due to two main circumstances: rapid evolution, without precedents, in the capture and analysis of data and significant cost reduction of supporting technologies. CBM programs in industrial systems can become extremely complex, especially when considering the effective introduction of new capabilities provided by PHM (Prognostics and Health Management) and E-maintenance disciplines. In this scenario, any CBM solution involves the management of numerous technical aspects, that the maintenance manager needs to understand, in order to be implemented properly and effectively, according to the company’s strategy. This paper provides a comprehensive representation of the key components of a generic CBM solution, this is presented using a framework or supporting structure for an effective management of the CBM programs. The concept “symptom of failure”, its corresponding analysis techniques (introduced by ISO 13379-1 and linked with RCM/FMEA analysis), and other international standard for CBM open-software application development (for instance, ISO 13374 and OSA-CBM), are used in the paper for the development of the framework. An original template has been developed, adopting the formal structure of RCM analysis templates, to integrate the information of the PHM techniques used to capture the failure mode behaviour and to manage maintenance. Finally, a case study describes the framework using the referred template.Gobierno de Andalucía P11-TEP-7303 M

Evaluating the semantic web: a task-based approach

The increased availability of online knowledge has led to the design of several algorithms that solve a variety of tasks by harvesting the Semantic Web, i.e. by dynamically selecting and exploring a multitude of online ontologies. Our hypothesis is that the performance of such novel algorithms implicity provides an insight into the quality of the used ontologies and thus opens the way to a task-based evaluation of the Semantic Web. We have investigated this hypothesis by studying the lessons learnt about online ontologies when used to solve three tasks: ontology matching, folksonomy enrichment, and word sense disambiguation. Our analysis leads to a suit of conclusions about the status of the Semantic Web, which highlight a number of strengths and weaknesses of the semantic information available online and complement the findings of other analysis of the Semantic Web landscape

The AtollGame Experience: from Knowledge Engineering to a Computer-Assisted Role Playing Game

This paper presents the methodology developed to collect, understand and merge viewpoints coming from different stakeholders in order to build a shared and formal representation of the studied system dealing with groundwater management in the low-lying atoll of Tarawa (Republic of Kiribati). The methodology relies on three successive stages. First, a Global Targeted Appraisal focuses on social group leaders in order to collect different standpoints and their articulated mental models. These collective models are partly validated through Individual Activities Surveys focusing on behavioural patterns of individual islanders. Then, these models are merged into a single conceptual one using qualitative analysis software. This conceptual model is further simplified in order to create a computer-assisted role-playing game.Knowledge Elicitation, Associative Network, Ontology, Water Management, Pacific, Tarawa