Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges--management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu

Running parallel applications on a heterogeneous environment with accessible development practices and automatic scalability

Grid computing makes it possible to gather large quantities of resources to work on a problem. In order to exploit this potential, a framework that presents the resources to the user programmer in a form that maintains productivity is necessary. The framework must not only provide accessible development, but it must make efficient use of the resources. The Seeds framework is proposed. It uses the current Grid and distributed computing middleware to provide a parallel programming environment to a wider community of programmers. The framework was used to investigate the feasibility of scaling skeleton/pattern parallel programming into Grid computing. The research accomplished two goals: it made parallel programming on the Grid more accessible to domain­specific programmers, and it made parallel programs scale on a heterogeneous resource environ­ ment. Programming is made easier to the programmer by using skeleton and pat­ tern­based programming approaches that effectively isolate the program from the envi­ ronment. To extend the pattern approach, the pattern adder operator is proposed, imple­ mented and tested. The results show the pattern operator can reduce the number of lines of code when compared with an MPJ­Express implementation for a stencil algorithm while having an overhead of at most ten microseconds per iteration. The research in scal­ ability involved adapting existing load­balancing techniques to skeletons and patterns re­ quiring little additional configuration on the part of the programmer. The hierarchical de­ pendency concept is proposed as well, which uses a streamed data flow programming model. The concept introduces data flow computation hibernation and dependencies that can split to accommodate additional processors. The results from implementing skeleton/patterns on hierarchical dependencies show an 18.23% increase in code is neces­ sary to enable automatic scalability. The concept can increase speedup depending on the algorithm and grain size

High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies

Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by multiple organizations. Grid applications often involve large amounts of data and/or computing resources that require secure resource sharing across organizational boundaries. This makes Grid application management and deployment a complex undertaking. Grid middlewares provide users with seamless computing ability and uniform access to resources in the heterogeneous Grid environment. Several software toolkits and systems have been developed, most of which are results of academic research projects, all over the world. This chapter will focus on four of these middlewares--UNICORE, Globus, Legion and Gridbus. It also presents our implementation of a resource broker for UNICORE as this functionality was not supported in it. A comparison of these systems on the basis of the architecture, implementation model and several other features is included.Comment: 19 pages, 10 figure

A Review on Energy Consumption Optimization Techniques in IoT Based Smart Building Environments

In recent years, due to the unnecessary wastage of electrical energy in residential buildings, the requirement of energy optimization and user comfort has gained vital importance. In the literature, various techniques have been proposed addressing the energy optimization problem. The goal of each technique was to maintain a balance between user comfort and energy requirements such that the user can achieve the desired comfort level with the minimum amount of energy consumption. Researchers have addressed the issue with the help of different optimization algorithms and variations in the parameters to reduce energy consumption. To the best of our knowledge, this problem is not solved yet due to its challenging nature. The gap in the literature is due to the advancements in the technology and drawbacks of the optimization algorithms and the introduction of different new optimization algorithms. Further, many newly proposed optimization algorithms which have produced better accuracy on the benchmark instances but have not been applied yet for the optimization of energy consumption in smart homes. In this paper, we have carried out a detailed literature review of the techniques used for the optimization of energy consumption and scheduling in smart homes. The detailed discussion has been carried out on different factors contributing towards thermal comfort, visual comfort, and air quality comfort. We have also reviewed the fog and edge computing techniques used in smart homes

MAGDA: A Mobile Agent based Grid Architecture

Mobile agents mean both a technology and a programming paradigm. They allow for a flexible approach which can alleviate a number of issues present in distributed and Grid-based systems, by means of features such as migration, cloning, messaging and other provided mechanisms. In this paper we describe an architecture (MAGDA – Mobile Agent based Grid Architecture) we have designed and we are currently developing to support programming and execution of mobile agent based application upon Grid systems

State-of-the-Art in Parallel Computing with R

R is a mature open-source programming language for statistical computing and graphics. Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel computing. This paper presents an overview of techniques for parallel computing with R on computer clusters, on multi-core systems, and in grid computing. It reviews sixteen different packages, comparing them on their state of development, the parallel technology used, as well as on usability, acceptance, and performance. Two packages (snow, Rmpi) stand out as particularly useful for general use on computer clusters. Packages for grid computing are still in development, with only one package currently available to the end user. For multi-core systems four different packages exist, but a number of issues pose challenges to early adopters. The paper concludes with ideas for further developments in high performance computing with R. Example code is available in the appendix

Advanced security infrastructures for grid education

This paper describes the research conducted into advanced authorization infrastructures at the National e-Science Centre (NeSC) at the University of Glasgow and their application to support a teaching environment as part of the Dynamic Virtual Organisations in e-Science Education (DyVOSE) project. We outline the lessons learnt in teaching Grid computing and rolling out the associated security authorisation infrastructures, and describe our plans for a future, extended security infrastructure for dynamic establishment of inter-institutional virtual organisations (VO) in the education domain