Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

Reconfigurable middleware architectures for large scale sensor networks

Wireless sensor networks, in an effort to be energy efficient, typically lack the high-level abstractions of advanced programming languages. Though strong, the dichotomy between these two paradigms can be overcome. The SENSIX software framework, described in this dissertation, uniquely integrates constraint-dominated wireless sensor networks with the flexibility of object-oriented programming models, without violating the principles of either. Though these two computing paradigms are contradictory in many ways, SENSIX bridges them to yield a dynamic middleware abstraction unifying low-level resource-aware task reconfiguration and high-level object recomposition. Through the layered approach of SENSIX, the software developer creates a domain-specific sensing architecture by defining a customized task specification and utilizing object inheritance. In addition, SENSIX performs better at large scales (on the order of 1000 nodes or more) than other sensor network middleware which do not include such unified facilities for vertical integration

Separating Agent-Functioning and Inter-Agent Coordination by Activated Modules: The DECOMAS Architecture

The embedding of self-organizing inter-agent processes in distributed software applications enables the decentralized coordination system elements, solely based on concerted, localized interactions. The separation and encapsulation of the activities that are conceptually related to the coordination, is a crucial concern for systematic development practices in order to prepare the reuse and systematic integration of coordination processes in software systems. Here, we discuss a programming model that is based on the externalization of processes prescriptions and their embedding in Multi-Agent Systems (MAS). One fundamental design concern for a corresponding execution middleware is the minimal-invasive augmentation of the activities that affect coordination. This design challenge is approached by the activation of agent modules. Modules are converted to software elements that reason about and modify their host agent. We discuss and formalize this extension within the context of a generic coordination architecture and exemplify the proposed programming model with the decentralized management of (web) service infrastructures

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

Taking Arduino to the Internet of things: the ASIP programming model

Micro-controllers such as Arduino are widely used by all kinds of makers worldwide. Popularity has been driven by Arduino’s simplicity of use and the large number of sensors and libraries available to extend the basic capabilities of these controllers. The last decade has witnessed a surge of software engineering solutions for “the Internet of Things”, but in several cases these solutions require computational resources that are more advanced than simple, resource-limited micro-controllers. Surprisingly, in spite of being the basic ingredients of complex hardware–software systems, there does not seem to be a simple and flexible way to (1) extend the basic capabilities of micro-controllers, and (2) to coordinate inter-connected micro-controllers in “the Internet of Things”. Indeed, new capabilities are added on a per-application basis and interactions are mainly limited to bespoke, point-to-point protocols that target the hardware I/O rather than the services provided by this hardware. In this paper we present the Arduino Service Interface Programming (ASIP) model, a new model that addresses the issues above by (1) providing a “Service” abstraction to easily add new capabilities to micro-controllers, and (2) providing support for networked boards using a range of strategies, including socket connections, bridging devices, MQTT-based publish–subscribe messaging, discovery services, etc. We provide an open-source implementation of the code running on Arduino boards and client libraries in Java, Python, Racket and Erlang. We show how ASIP enables the rapid development of non-trivial applications (coordination of input/output on distributed boards and implementation of a line-following algorithm for a remote robot) and we assess the performance of ASIP in several ways, both quantitative and qualitative

Taking Arduino to the Internet of things: the ASIP programming model

Micro-controllers such as Arduino are widely used by all kinds of makers worldwide. Popularity has been driven by Arduino’s simplicity of use and the large number of sensors and libraries available to extend the basic capabilities of these controllers. The last decade has witnessed a surge of software engineering solutions for “the Internet of Things”, but in several cases these solutions require computational resources that are more advanced than simple, resource-limited micro-controllers. Surprisingly, in spite of being the basic ingredients of complex hardware–software systems, there does not seem to be a simple and flexible way to (1) extend the basic capabilities of micro-controllers, and (2) to coordinate inter-connected micro-controllers in “the Internet of Things”. Indeed, new capabilities are added on a per-application basis and interactions are mainly limited to bespoke, point-to-point protocols that target the hardware I/O rather than the services provided by this hardware. In this paper we present the Arduino Service Interface Programming (ASIP) model, a new model that addresses the issues above by (1) providing a “Service” abstraction to easily add new capabilities to micro-controllers, and (2) providing support for networked boards using a range of strategies, including socket connections, bridging devices, MQTT-based publish–subscribe messaging, discovery services, etc. We provide an open-source implementation of the code running on Arduino boards and client libraries in Java, Python, Racket and Erlang. We show how ASIP enables the rapid development of non-trivial applications (coordination of input/output on distributed boards and implementation of a line-following algorithm for a remote robot) and we assess the performance of ASIP in several ways, both quantitative and qualitative