Architecture for Provenance Systems

This document covers the logical and process architectures of provenance systems. The logical architecture identifies key roles and their interactions, whereas the process architecture discusses distribution and security. A fundamental aspect of our presentation is its technology-independent nature, which makes it reusable: the principles that are exposed in this document may be applied to different technologies

Sensor-Driven, Spatially Explicit Agent-Based Models

Conventionally, agent-based models (ABMs) are specified from well-established theory about the systems under investigation. For such models, data is only introduced to ensure the validity of the specified models. In cases where the underlying mechanisms of the system of interest are unknown, rich datasets about the system can reveal patterns and processes of the systems. Sensors have become ubiquitous allowing researchers to capture precise characteristics of entities in both time and space. The combination of data from in situ sensors to geospatial outputs provides a rich resource for characterising geospatial environments and entities on earth. More importantly, the sensor data can capture behaviours and interactions of entities allowing us to visualise emerging patterns from the interactions. However, there is a paucity of standardised methods for the integration of dynamic sensor data streams into ABMs. Further, only few models have attempted to incorporate spatial and temporal data dynamically from sensors for model specification, calibration and validation. This chapter documents the state of the art of methods for bridging the gap between sensor data observations and specification of accurate spatially explicit agent-based models. In addition, this work proposes a conceptual framework for dynamic validation of sensor-driven spatial ABMs to address the risk of model overfitting

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

Redesigning an Undergraduate Software Engineering Course for a Large Cohort

Teaching Software Engineering on an undergraduate programme is challenging, particularly when dealing with large numbers of stu- dents. On one hand, a strong understanding of software and good programming skills are prerequisites. On the other hand, the scale of the projects developed as part of undergraduate programmes do not always make the need for engineering obvious. Encourag- ing teamwork when students have little professional experience also adds to the level of complexity when delivering material. In this paper, we present a study on the redesign of a second year undergraduate course on Software Engineering for a large cohort