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

Simulation modelling and visualisation: toolkits for building artificial worlds

Simulations users at all levels make heavy use of compute resources to drive computational simulations for greatly varying applications areas of research using different simulation paradigms. Simulations are implemented in many software forms, ranging from highly standardised and general models that run in proprietary software packages to ad hoc hand-crafted simulations codes for very specific applications. Visualisation of the workings or results of a simulation is another highly valuable capability for simulation developers and practitioners. There are many different software libraries and methods available for creating a visualisation layer for simulations, and it is often a difficult and time-consuming process to assemble a toolkit of these libraries and other resources that best suits a particular simulation model. We present here a break-down of the main simulation paradigms, and discuss differing toolkits and approaches that different researchers have taken to tackle coupled simulation and visualisation in each paradigm

Knowledge Cartography: Software tools and mapping techniques

Knowledge Cartography is the discipline of mapping intellectual landscapes.The focus of this book is on the process by which manually crafting interactive, hypertextual maps clarifies one’s own understanding, as well as communicating it.The authors see mapping software as a set of visual tools for reading and writing in a networked age. In an information ocean, the primary challenge is to find meaningful patterns around which we can weave plausible narratives. Maps of concepts, discussions and arguments make the connections between ideas tangible and disputable. With 17 chapters from the leading researchers and practitioners, the reader will find the current state–of-the-art in the field. Part 1 focuses on educational applications in schools and universities, before Part 2 turns to applications in professional communitie

Producing place atmospheres digitally: Architecture, digital visualisations practices and the experience economy

Computer generated images have become the common means for architects and developers to visualise and market future urban developments. This article examines within the context of the experience economy how these digital images aim to evoke and manipulate specific place atmospheres to emphasize the experiential qualities of new buildings and urban environments. In particular, we argue that CGIs are far from ‘just’ glossy representations but are a new form of visualising the urban that captures and markets particular embodied sensations. Drawing on a two year qualitative study of architects’ practices that worked on the Msheireb project, a large scale redevelopment project in Doha (Qatar), we examine how digital visualisation technology enables the virtual engineering of sensory experiences using a wide range of graphic effects. We show how these CGIs are laboriously materialised in order to depict and present specific sensory, embodied regimes and affective experiences to appeal to clients and consumers. Such development has two key implications. Firstly, we demonstrate the importance of digital technologies in framing the ‘expressive infrastructure’ (Thrift 2012) of the experience economy. Secondly, we argue that although the Msheireb CGIs open up a field of negotiation between producers and the Qatari client, and work quite hard at being culturally specific, they ultimately draw “on a Westnocentric literary and sensory palette” (Tolia-Kelly 2006) that highlights the continuing influence of colonial sensibilities in supposedly postcolonial urban processes.This research was funded by the ESRC (RES-062-23-0223)

Key challenges in agent-based modelling for geo-spatial simulation

Agent-based modelling (ABM) is fast becoming the dominant paradigm in social simulation due primarily to a worldview that suggests that complex systems emerge from the bottom-up, are highly decentralised, and are composed of a multitude of heterogeneous objects called agents. These agents act with some purpose and their interaction, usually through time and space, generates emergent order, often at higher levels than those at which such agents operate. ABM however raises as many challenges as it seeks to resolve. It is the purpose of this paper to catalogue these challenges and to illustrate them using three somewhat different agent-based models applied to city systems. The seven challenges we pose involve: the purpose for which the model is built, the extent to which the model is rooted in independent theory, the extent to which the model can be replicated, the ways the model might be verified, calibrated and validated, the way model dynamics are represented in terms of agent interactions, the extent to which the model is operational, and the way the model can be communicated and shared with others. Once catalogued, we then illustrate these challenges with a pedestrian model for emergency evacuation in central London, a hypothetical model of residential segregation tuned to London data which elaborates the standard Schelling (1971) model, and an agent-based residential location built according to spatial interactions principles, calibrated to trip data for Greater London. The ambiguities posed by this new style of modelling are drawn out as conclusions

Steering in computational science: mesoscale modelling and simulation

This paper outlines the benefits of computational steering for high performance computing applications. Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to illustrate the substantial improvements which computational steering offers in terms of resource efficiency and time to discover new physics. We discuss details of our current steering implementations and describe their future outlook with the advent of computational grids.Comment: 40 pages, 11 figures. Accepted for publication in Contemporary Physic