TumorML: Concept and requirements of an in silico cancer modelling markup language

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification

Errors and Artefacts in Agent-Based Modelling

The objectives of this paper are to define and classify different types of errors and artefacts that can appear in the process of developing an agent-based model, and to propose activities aimed at avoiding them during the model construction and testing phases. To do this in a structured way, we review the main concepts of the process of developing such a model – establishing a general framework that summarises the process of designing, implementing, and using agent-based models. Within this framework we identify the various stages where different types of errors and artefacts may appear. Finally we propose activities that could be used to detect (and hence eliminate) each type of error or artefact.Verification, Replication, Artefact, Error, Agent-Based Modelling, Modelling Roles

Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline

Metamodel-based model conformance and multiview consistency checking

Model-driven development, using languages such as UML and BON, often makes use of multiple diagrams (e.g., class and sequence diagrams) when modeling systems. These diagrams, presenting different views of a system of interest, may be inconsistent. A metamodel provides a unifying framework in which to ensure and check consistency, while at the same time providing the means to distinguish between valid and invalid models, that is, conformance. Two formal specifications of the metamodel for an object-oriented modeling language are presented, and it is shown how to use these specifications for model conformance and multiview consistency checking. Comparisons are made in terms of completeness and the level of automation each provide for checking multiview consistency and model conformance. The lessons learned from applying formal techniques to the problems of metamodeling, model conformance, and multiview consistency checking are summarized

Combining goal-oriented and model-driven approaches to solve the Payment Problem Scenario

Motivated by the objective to provide an improved participation of business domain experts in the design of service-oriented integration solutions, we extend our previous work on using the COSMO methodology for service mediation by introducing a goal-oriented approach to requirements engineering. With this approach, business requirements including the motivations behind the mediation solution are better understood, specified, and aligned with their technical implementations. We use the Payment Problem Scenario of the SWS Challenge to illustrate the extension

Towards a flexible service integration through separation of business rules

Driven by dynamic market demands, enterprises are continuously exploring collaborations with others to add value to their services and seize new market opportunities. Achieving enterprise collaboration is facilitated by Enterprise Application Integration and Business-to-Business approaches that employ architectural paradigms like Service Oriented Architecture and incorporate technological advancements in networking and computing. However, flexibility remains a major challenge related to enterprise collaboration. How can changes in demands and opportunities be reflected in collaboration solutions with minimum time and effort and with maximum reuse of existing applications? This paper proposes an approach towards a more flexible integration of enterprise applications in the context of service mediation. We achieve this by combining goal-based, model-driven and serviceoriented approaches. In particular, we pay special attention to the separation of business rules from the business process of the integration solution. Specifying the requirements as goal models, we separate those parts which are more likely to evolve over time in terms of business rules. These business rules are then made executable by exposing them as Web services and incorporating them into the design of the business process.\ud Thus, should the business rules change, the business process remains unaffected. Finally, this paper also provides an evaluation of the flexibility of our solution in relation to the current work in business process flexibility research

Modelling the relationship between planning, control, perception and execution behaviours in interactive worksystems

This paper presents a model of planning carried out by interactive worksystems which attempts: 1. To describe the relationship between planning, control, perception and execution behaviours; 2. To make explicit how these may be distributed across the user and physically separate devices. Such a model, it is argued, is more suitable to support HCI design practice than theories of planning in cognitive science which focus on problem-solving methods and representations. To demonstrate the application of the model to work situations, it is illustrated by examples drawn from an observational study of secretarial office administration

A software toolkit for web-based virtual environments based on a shared database

We propose a software toolkit for developing complex web-based user interfaces, incorporating such things as multi-user facilities, virtual environments (VEs), and interface agents. The toolkit is based on a novel software architecture that combines ideas from multi-agent platforms and user interface (UI) architectures. It provides a distributed shared database with publish-subscribe facilities. This enables UI components to observe the state and activities of any other components in the system easily. The system runs in a web-based environment. The toolkit is comprised of several programming and other specification languages, providing a complete suite of systems design languages. We illustrate the toolkit by means of a couple of examples

Goal-based self-contextualization

Abstract. System self-contextualizability is the system ability to autonomously adapt its behavior to the uncontrollable relevant context to keep its objectives satisfied. Self-contextualizable system must have alternative behaviors each fitting to a set of contexts. We propose to start considering context at the level of requirements engineering, adopting Tropos goal model to express requirements and complementing it with our proposed context analysis. We define variation points on goal model where a context-based decision might need to be taken, and propose constructs to analyze context. While goal analysis provides constructs to hierarchically analyze goals and discover alternative sets of tasks to be executed to satisfy a goal, our proposed context analysis provides constructs to hierarchically analyze context and discover alternative sets of facts to be monitored to verify a context.