Turning Models Inside Out

We present an approach for change-based (as opposed to state-based) model persistence that can facilitate highperformance incremental model processing (e.g. validation, transformation) by minimising the cost of change identification when models evolve. We illustrate a prototype that implements the proposed approach on top of the Eclipse Modelling Framework and we present a roadmap for further work in this direction

Using argument notation to engineer biological simulations with increased confidence

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions

Simulation validation: exploring the suitability of a simulation of cell division and differentiation in the prostate

Individual or agent-based simulation is an important tool for research involving understanding of complex systems. For a research tool to be useful, its use must be understood, and it must be possible to interpret the results of using the tool in the context of the research. This paper presents the partial validity argument for ongoing work on prostate cell simulation (a companion paper describes the models and implementation of the simulation). This is the basis for a discussion of issues in the validation of complex systems simulations used as scientific research tools