Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Closing the loop of design and analysis: Parametric modelling tools for early decision support

There is a growing need for parametric design software that communicates building performance feedback in early architectural exploration to support decision-making. This paper examines how the circuit of design and analysis process can be closed to provide active and concurrent feedback between architecture and services engineering domains. It presents the structure for an openly customisable design system that couples parametric modelling and energy analysis software to allow designers to assess the performance of early design iterations quickly. Finally, it discusses how user interactions with the system foster information exchanges that facilitate the sharing of design intelligence across disciplines

Operational semantics for signal handling

Signals are a lightweight form of interprocess communication in Unix. When a process receives a signal, the control flow is interrupted and a previously installed signal handler is run. Signal handling is reminiscent both of exception handling and concurrent interleaving of processes. In this paper, we investigate different approaches to formalizing signal handling in operational semantics, and compare them in a series of examples. We find the big-step style of operational semantics to be well suited to modelling signal handling. We integrate exception handling with our big-step semantics of signal handling, by adopting the exception convention as defined in the Definition of Standard ML. The semantics needs to capture the complex interactions between signal handling and exception handling.Comment: In Proceedings EXPRESS/SOS 2012, arXiv:1208.244

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

Using protocol analysis to explore the creative requirements engineering process

Protocol analysis is an empirical method applied by researchers in cognitive psychology and behavioural analysis. Protocol analysis can be used to collect, document and analyse thought processes by an individual problem solver. In general, research subjects are asked to think aloud when performing a given task. Their verbal reports are transcribed and represent a sequence of their thoughts and cognitive activities. These verbal reports are analysed to identify relevant segments of cognitive behaviours by the research subjects. The analysis results may be cross-examined (or validated through retrospective interviews with the research subjects). This paper offers a critical analysis of this research method, its approaches to data collection and analysis, strengths and limitations, and discusses its use in information systems research. The aim is to explore the use of protocol analysis in studying the creative requirements engineering process.<br /

Modelling iteration in engineering design

This paper examines design iteration and its modelling in the simulation of New Product Development (NPD) processes. A framework comprising six perspectives of iteration is proposed and it is argued that the importance of each perspective depends upon domain-specific factors. Key challenges of modelling iteration in process simulation frameworks such as the Design Structure Matrix are discussed, and we argue that no single model or framework can fully capture the iterative dynamics of an NPD process. To conclude, we propose that consideration of iteration and its representation could help identify the most appropriate modelling framework for a given process and modelling objective, thereby improving the fidelity of design process simulation models and increasing their utility

Monitoring and control in scenario-based requirements analysis

Scenarios are an effective means for eliciting, validating and documenting requirements. At the requirements level, scenarios describe sequences of interactions between the software-to-be and agents in the environment. Interactions correspond to the occurrence of an event that is controlled by one agent and monitored by another.This paper presents a technique to analyse requirements-level scenarios for unforeseen, potentially harmful, consequences. Our aim is to perform analysis early in system development, where it is highly cost-effective. The approach recognises the importance of monitoring and control issues and extends existing work on implied scenarios accordingly. These so-called input-output implied scenarios expose problematic behaviours in scenario descriptions that cannot be detected using standard implied scenarios. Validation of these implied scenarios supports requirements elaboration. We demonstrate the relevance of input-output implied scenarios using a number of examples

A Calculus for Orchestration of Web Services

Service-oriented computing, an emerging paradigm for distributed computing based on the use of services, is calling for the development of tools and techniques to build safe and trustworthy systems, and to analyse their behaviour. Therefore, many researchers have proposed to use process calculi, a cornerstone of current foundational research on specification and analysis of concurrent, reactive, and distributed systems. In this paper, we follow this approach and introduce CWS, a process calculus expressly designed for specifying and combining service-oriented applications, while modelling their dynamic behaviour. We show that CWS can model all the phases of the life cycle of service-oriented applications, such as publication, discovery, negotiation, orchestration, deployment, reconfiguration and execution. We illustrate the specification style that CWS supports by means of a large case study from the automotive domain and a number of more specific examples drawn from it