MPWide: a light-weight library for efficient message passing over wide area networks

We present MPWide, a light weight communication library which allows efficient message passing over a distributed network. MPWide has been designed to connect application running on distributed (super)computing resources, and to maximize the communication performance on wide area networks for those without administrative privileges. It can be used to provide message-passing between application, move files, and make very fast connections in client-server environments. MPWide has already been applied to enable distributed cosmological simulations across up to four supercomputers on two continents, and to couple two different bloodflow simulations to form a multiscale simulation.Comment: accepted by the Journal Of Open Research Software, 13 pages, 4 figures, 1 tabl

OpenKnowledge at work: exploring centralized and decentralized information gathering in emergency contexts

Real-world experience teaches us that to manage emergencies, efficient crisis response coordination is crucial; ICT infrastructures are effective in supporting the people involved in such contexts, by supporting effective ways of interaction. They also should provide innovative means of communication and information management. At present, centralized architectures are mostly used for this purpose; however, alternative infrastructures based on the use of distributed information sources, are currently being explored, studied and analyzed. This paper aims at investigating the capability of a novel approach (developed within the European project OpenKnowledge1) to support centralized as well as decentralized architectures for information gathering. For this purpose we developed an agent-based e-Response simulation environment fully integrated with the OpenKnowledge infrastructure and through which existing emergency plans are modelled and simulated. Preliminary results show the OpenKnowledge capability of supporting the two afore-mentioned architectures and, under ideal assumptions, a comparable performance in both cases

Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

Supporting Cyber-Physical Systems with Wireless Sensor Networks: An Outlook of Software and Services

Sensing, communication, computation and control technologies are the essential building blocks of a cyber-physical system (CPS). Wireless sensor networks (WSNs) are a way to support CPS as they provide fine-grained spatial-temporal sensing, communication and computation at a low premium of cost and power. In this article, we explore the fundamental concepts guiding the design and implementation of WSNs. We report the latest developments in WSN software and services for meeting existing requirements and newer demands; particularly in the areas of: operating system, simulator and emulator, programming abstraction, virtualization, IP-based communication and security, time and location, and network monitoring and management. We also reflect on the ongoing efforts in providing dependable assurances for WSN-driven CPS. Finally, we report on its applicability with a case-study on smart buildings

Simulation of networks of spiking neurons: A review of tools and strategies

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments