Beyond representations: towards an action-centric perspective on tangible interaction

In the light of theoretical as well as concrete technical development, we discuss a conceptual shift from an information-centric to an action-centric perspective on tangible interactive technology. We explicitly emphasise the qualities of shareable use, and the importance of designing tangibles that allow for meaningful manipulation and control of the digital material. This involves a broadened focus from studying properties of the interface, to instead aim for qualities of the activity of using a system, a general tendency towards designing for social and sharable use settings and an increased openness towards multiple and subjective interpretations. An effect of this is that tangibles are not designed as representations of data, but as resources for action. We discuss four ways that tangible artefacts work as resources for action: (1) for physical manipulation; (2) for referential, social and contextually oriented action; (3) for perception and sensory experience; (4) for digitally mediated action

BRAHMS: Novel middleware for integrated systems computation

Biological computational modellers are becoming increasingly interested in building large, eclectic models, including components on many different computational substrates, both biological and non-biological. At the same time, the rise of the philosophy of embodied modelling is generating a need to deploy biological models as controllers for robots in real-world environments. Finally, robotics engineers are beginning to find value in seconding biomimetic control strategies for use on practical robots. Together with the ubiquitous desire to make good on past software development effort, these trends are throwing up new challenges of intellectual and technological integration (for example across scales, across disciplines, and even across time) - challenges that are unmet by existing software frameworks. Here, we outline these challenges in detail, and go on to describe a newly developed software framework, BRAHMS. that meets them. BRAHMS is a tool for integrating computational process modules into a viable, computable system: its generality and flexibility facilitate integration across barriers, such as those described above, in a coherent and effective way. We go on to describe several cases where BRAHMS has been successfully deployed in practical situations. We also show excellent performance in comparison with a monolithic development approach. Additional benefits of developing in the framework include source code self-documentation, automatic coarse-grained parallelisation, cross-language integration, data logging, performance monitoring, and will include dynamic load-balancing and 'pause and continue' execution. BRAHMS is built on the nascent, and similarly general purpose, model markup language, SystemML. This will, in future, also facilitate repeatability and accountability (same answers ten years from now), transparent automatic software distribution, and interfacing with other SystemML tools. (C) 2009 Elsevier Ltd. All rights reserved

The role of the RM-ODP computational viewpoint concepts in the MDA approach

An MDA design approach should be able to accommodate designs at different levels of platform-independence. We have proposed a design approach previously (in [2]), which allows these levels to be identified. An important feature of this approach is the notion of abstract platform. An abstract platform is determined by the platform characteristics that are relevant for applications at a certain level of platform-independence, and must be established by considering various design goals. In this paper, we define a framework that makes it possible to use RM-ODP concepts in our MDA design approach. This framework allows a recursive application of the computational viewpoint at different levels of platform-independence. This is obtained by equating the RM-ODP notion of infrastructure to our notion of abstract platform

Enabling High-Level Application Development for the Internet of Things

Application development in the Internet of Things (IoT) is challenging because it involves dealing with a wide range of related issues such as lack of separation of concerns, and lack of high-level of abstractions to address both the large scale and heterogeneity. Moreover, stakeholders involved in the application development have to address issues that can be attributed to different life-cycles phases. when developing applications. First, the application logic has to be analyzed and then separated into a set of distributed tasks for an underlying network. Then, the tasks have to be implemented for the specific hardware. Apart from handling these issues, they have to deal with other aspects of life-cycle such as changes in application requirements and deployed devices. Several approaches have been proposed in the closely related fields of wireless sensor network, ubiquitous and pervasive computing, and software engineering in general to address the above challenges. However, existing approaches only cover limited subsets of the above mentioned challenges when applied to the IoT. This paper proposes an integrated approach for addressing the above mentioned challenges. The main contributions of this paper are: (1) a development methodology that separates IoT application development into different concerns and provides a conceptual framework to develop an application, (2) a development framework that implements the development methodology to support actions of stakeholders. The development framework provides a set of modeling languages to specify each development concern and abstracts the scale and heterogeneity related complexity. It integrates code generation, task-mapping, and linking techniques to provide automation. Code generation supports the application development phase by producing a programming framework that allows stakeholders to focus on the application logic, while our mapping and linking techniques together support the deployment phase by producing device-specific code to result in a distributed system collaboratively hosted by individual devices. Our evaluation based on two realistic scenarios shows that the use of our approach improves the productivity of stakeholders involved in the application development

KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624

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

The Astrophysical Multipurpose Software Environment

We present the open source Astrophysical Multi-purpose Software Environment (AMUSE, www.amusecode.org), a component library for performing astrophysical simulations involving different physical domains and scales. It couples existing codes within a Python framework based on a communication layer using MPI. The interfaces are standardized for each domain and their implementation based on MPI guarantees that the whole framework is well-suited for distributed computation. It includes facilities for unit handling and data storage. Currently it includes codes for gravitational dynamics, stellar evolution, hydrodynamics and radiative transfer. Within each domain the interfaces to the codes are as similar as possible. We describe the design and implementation of AMUSE, as well as the main components and community codes currently supported and we discuss the code interactions facilitated by the framework. Additionally, we demonstrate how AMUSE can be used to resolve complex astrophysical problems by presenting example applications.Comment: 23 pages, 25 figures, accepted for A&