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

Enabling stream processing for people-centric IoT based on the fog computing paradigm

The world of machine-to-machine (M2M) communication is gradually moving from vertical single purpose solutions to multi-purpose and collaborative applications interacting across industry verticals, organizations and people - A world of Internet of Things (IoT). The dominant approach for delivering IoT applications relies on the development of cloud-based IoT platforms that collect all the data generated by the sensing elements and centrally process the information to create real business value. In this paper, we present a system that follows the Fog Computing paradigm where the sensor resources, as well as the intermediate layers between embedded devices and cloud computing datacenters, participate by providing computational, storage, and control. We discuss the design aspects of our system and present a pilot deployment for the evaluating the performance in a real-world environment. Our findings indicate that Fog Computing can address the ever-increasing amount of data that is inherent in an IoT world by effective communication among all elements of the architecture

Gaussian decomposition of HI surveys. V. Search for very cold clouds

In the previous papers of this series, we have decomposed into Gaussian components all the HI 21-cm line profiles of the Leiden-Argentina-Bonn (LAB) database, and studied statistical distributions of the obtained Gaussians. Now we are interested in separation from the general database of the components the "clouds" of closely spaced similar Gaussians. In this paper we describe the new cloud-finding algorithm. To separate the clouds of similar Gaussians, we start with the single-link hierarchical clustering procedure in five-dimensional (longitude, latitude, velocity, Gaussian width and height) space, but make some modifications to accommodate it to the large number of components. We also use the requirement that each cloud may be represented at any observed sky position by only one Gaussian and take into account the similarity of global properties of the merging clouds. As a test, we apply the algorithm for finding the clouds of the narrowest HI 21-cm line components. Using the full sky search for cold clouds, we easily detect the coldest known HI clouds and demonstrate that actually they are a part of a long narrow ribbon of cold clouds. We model these clouds as a part of a planar gas ring, deduce their spatial placement, and discuss their relation to supernova shells in the solar neighborhood. We conclude that the proposed algorithm satisfactorily solves the posed task. We guess that the study of the narrowest HI 21-cm line components may be a useful tool for finding the structure of neutral gas in solar neighborhood.Comment: 11 pages, 6 figures, short version will be published in "Astron. Astrophys", the version with full-resolution figures at http://www.aai.ee/~urmas/ast/Kits.pd

Attributes of Big Data Analytics for Data-Driven Decision Making in Cyber-Physical Power Systems

Big data analytics is a virtually new term in power system terminology. This concept delves into the way a massive volume of data is acquired, processed, analyzed to extract insight from available data. In particular, big data analytics alludes to applications of artificial intelligence, machine learning techniques, data mining techniques, time-series forecasting methods. Decision-makers in power systems have been long plagued by incapability and weakness of classical methods in dealing with large-scale real practical cases due to the existence of thousands or millions of variables, being time-consuming, the requirement of a high computation burden, divergence of results, unjustifiable errors, and poor accuracy of the model. Big data analytics is an ongoing topic, which pinpoints how to extract insights from these large data sets. The extant article has enumerated the applications of big data analytics in future power systems through several layers from grid-scale to local-scale. Big data analytics has many applications in the areas of smart grid implementation, electricity markets, execution of collaborative operation schemes, enhancement of microgrid operation autonomy, management of electric vehicle operations in smart grids, active distribution network control, district hub system management, multi-agent energy systems, electricity theft detection, stability and security assessment by PMUs, and better exploitation of renewable energy sources. The employment of big data analytics entails some prerequisites, such as the proliferation of IoT-enabled devices, easily-accessible cloud space, blockchain, etc. This paper has comprehensively conducted an extensive review of the applications of big data analytics along with the prevailing challenges and solutions

Fault Tolerant Adaptive Parallel and Distributed Simulation through Functional Replication

This paper presents FT-GAIA, a software-based fault-tolerant parallel and distributed simulation middleware. FT-GAIA has being designed to reliably handle Parallel And Distributed Simulation (PADS) models, which are needed to properly simulate and analyze complex systems arising in any kind of scientific or engineering field. PADS takes advantage of multiple execution units run in multicore processors, cluster of workstations or HPC systems. However, large computing systems, such as HPC systems that include hundreds of thousands of computing nodes, have to handle frequent failures of some components. To cope with this issue, FT-GAIA transparently replicates simulation entities and distributes them on multiple execution nodes. This allows the simulation to tolerate crash-failures of computing nodes. Moreover, FT-GAIA offers some protection against Byzantine failures, since interaction messages among the simulated entities are replicated as well, so that the receiving entity can identify and discard corrupted messages. Results from an analytical model and from an experimental evaluation show that FT-GAIA provides a high degree of fault tolerance, at the cost of a moderate increase in the computational load of the execution units.Comment: arXiv admin note: substantial text overlap with arXiv:1606.0731

Echo State Networks for Proactive Caching in Cloud-Based Radio Access Networks with Mobile Users

In this paper, the problem of proactive caching is studied for cloud radio access networks (CRANs). In the studied model, the baseband units (BBUs) can predict the content request distribution and mobility pattern of each user, determine which content to cache at remote radio heads and BBUs. This problem is formulated as an optimization problem which jointly incorporates backhaul and fronthaul loads and content caching. To solve this problem, an algorithm that combines the machine learning framework of echo state networks with sublinear algorithms is proposed. Using echo state networks (ESNs), the BBUs can predict each user's content request distribution and mobility pattern while having only limited information on the network's and user's state. In order to predict each user's periodic mobility pattern with minimal complexity, the memory capacity of the corresponding ESN is derived for a periodic input. This memory capacity is shown to be able to record the maximum amount of user information for the proposed ESN model. Then, a sublinear algorithm is proposed to determine which content to cache while using limited content request distribution samples. Simulation results using real data from Youku and the Beijing University of Posts and Telecommunications show that the proposed approach yields significant gains, in terms of sum effective capacity, that reach up to 27.8% and 30.7%, respectively, compared to random caching with clustering and random caching without clustering algorithm.Comment: Accepted in the IEEE Transactions on Wireless Communication