The Astrophysics Simulation Collaboratory: A Science Portal Enabling Community Software Development

Grid Portals, based on standard web technologies, are emerging as important and useful user interfaces to computational and data Grids. Grid Portals enable Virtual Organizations, comprised of distributed researchers to collaborate and access resources more efficiently and seamlessly. The Astrophysics Simulation Collaboratory (ASC) Grid Portal provides a framework to enable researchers in the field of numerical relativity to study astrophysical phenomenon by making use of the Cactus computational toolkit. We examine user requirements and describe the design and implementation of the ASC Grid Portal.     

A taxonomy of peer-to-peer desktop grid paradigms

Desktop grid systems and applications have generated significant impacts on science and engineering. The emerging convergence of grid and peer-to-peer (P2P) computing technologies further opens new opportunities for enabling P2P Desktop Grid systems. This paper presents a taxonomy for classifying P2P desktop grid implementation paradigms, aiming to summarize the state-of-the-art technologies and explore the current and potential solution space. To have a comprehensive taxonomy for P2P desktop grid paradigms, we investigate both computational and data grid systems. Moreover, to ease the understanding, the taxonomy is applied to selected case studies of P2P desktop grid systems. The taxonomy is expected to be used as a survey of the state-of-the-art, a design map, a guideline for novice researchers, a common vocabulary, or a design space for simulation and benchmark, and to be extended as the technologies rapidly evolve.     

On Building Parallel &; Grid Applications: Component Technology and Distributed Services

Software Component Frameworks are well known in the commercial business application world and now this technology is being explored with great interest as a way to build large-scale scientific applications on parallel computers. In the case of Grid systems, the current architectural model is based on the emerging web services framework. In this paper we describe progress that has been made on the Common Component Architecture model (CCA) and discuss its success and limitations when applied to problems in Grid computing. Our primary conclusion is that a component model fits very well with a services-oriented Grid, but the model of composition must allow for a very dynamic (both in space and in time) control of composition. We note that this adds a new dimension to conventional service workflow and it extends the “Inversion of Control” aspects of most component systems. Dennis Gannon is a professor of Computer Science at Indiana University. He received his Ph.D. in Computer Science from the University of Illinois in 1980 and his Ph.D. in Mathematics from the University of California in 1974. From 1980 to 1985, he was on the faculty at Purdue University. His research interests include software tools for high performance distributed systems and problem solving environments for scientific computation. Sriram Krishnan received his Ph.D. in Computer Science from Indiana University in 2004. He is currently in the Grid Development Group at the San Diego Supercomputer Center where he is working on designing a Web services based architecture for biomedical applications that is secure and scalable, and is conducive to the creation of complex workflows. He received my undergraduate degree in Computer Engineering from the University of Mumbai, India. Liang Fang is a Ph.D. student in Computer Science at Indiana University. His research interests include Grid computing, Web services, portals, their security and scalability issues. He is a Research Assistant in Computer Science at Indiana University, currently responsible for investigating authorization and other security solutions to the project of Linked Environments for Atmospheric Discovery (LEAD). Gopi Kandaswamy is a Ph.D. student in the Computer Science Department at Indiana University where he is current a Research Assistant. His research interests include Web services and workflow systems for the Grid. Yogesh Simmhan received his B.E. degree in Computer Science from Madras University, India in 2000, and is a doctoral candidate in Computer Science at Indiana University. He is currently working as a Research Assistant at Indiana University, investigating data management issues in the LEAD project. His interests lie in data provenance for workflow systems and its use in data quality estimation. Aleksander Slominski is a Ph.D. student in the Computer Science at Indiana University. His research interests include Grid and Web Services, streaming XML Pull Parsing and performance, Grid security, asynchronous messaging, events, and notifications brokers, component technologies, and workflow composition. He is currently working as a Research Assistant investigating creation and execution of dynamic workflows using Grid Process Execution Language (GPEL) based on WS-BPEL.     

Development of NPACI Grid Application Portals and Portal Web Services

Grid portals and services are emerging as convenient mechanisms for providing the scientific community with familiar and simplified interfaces to the Grid. Our experiences in implementing computational grid portals, and the services needed to support them, has led to the creation of GridPort: a unique, integrated, layered software system for building portals and hosting portal services that access Grid services. The usefulness of this system has been successfully demonstrated with the implementation of several application portals. This system has several unique features: the software is portable and runs on most webservers; written in Perl/CGI, it is easy to support and modify; a single API provides access to a host of Grid services; it is flexible and adaptable; it supports single login between multiple portals; and portals built with it may run across multiple sites and organizations. In this paper we summarize our experiences in building this system, including philosophy and design choices and we describe the software we are building that support portal development, portal services. Finally, we discuss our experiences in developing the GridPort Client Toolkit in support of remote Web client portals and Grid Web services.     

Programming the Grid: Distributed Software Components, P2P and Grid Web Services for Scientific Applications

Computational Grids [17,25] have become an important asset in large-scale scientific and engineering research. By providing a set of services that allow a widely distributed collection of resources to be tied together into a relatively seamless computing framework, teams of researchers can collaborate to solve problems that they could not have attempted before. Unfortunately the task of building Grid applications remains extremely difficult because there are few tools available to support developers. To build reliable and re-usable Grid applications, programmers must be equipped with a programming framework that hides the details of most Grid services and allows the developer a consistent, non-complex model in which applications can be composed from well tested, reliable sub-units. This paper describes experiences with using a software component framework for building Grid applications. The framework, which is based on the DOE Common Component Architecture (CCA) [1,2,3,8], allows individual components to export function/service interfaces that can be remotely invoked by other components. The framework also provides a simple messaging/event system for asynchronous notification between application components. The paper also describes how the emerging Web-services [52] model fits with a component-oriented application design philosophy. To illustrate the connection between Web services and Grid application programming we describe a simple design pattern for application factory services which can be used to simplify the task of building reliable Grid programs. Finally we address several issues of Grid programming that better understood from the perspective of Peer-to-Peer (P2P) systems. In particular we describe how models for collaboration and resource sharing fit well with many Grid application scenarios.     

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.     

A feedforward model for the formation of a grid field where spatial information is provided solely from place cells

Grid cells (GCs) in the medial entorhinal cortex (mEC) have the property of having their firing activity spatially tuned to a regular triangular lattice. Several theoretical models for grid field formation have been proposed, but most assume that place cells (PCs) are a product of the grid cell system. There is, however, an alternative possibility that is supported by various strands of experimental data. Here we present a novel model for the emergence of gridlike firing patterns that stands on two key hypotheses: (1) spatial information in GCs is provided from PC activity and (2) grid fields result from a combined synaptic plasticity mechanism involving inhibitory and excitatory neurons mediating the connections between PCs and GCs. Depending on the spatial location, each PC can contribute with excitatory or inhibitory inputs to GC activity. The nature and magnitude of the PC input is a function of the distance to the place field center, which is inferred from rate decoding. A biologically plausible learning rule drives the evolution of the connection strengths from PCs to a GC. In this model, PCs compete for GC activation, and the plasticity rule favors efficient packing of the space representation. This leads to gridlike firing patterns. In a new environment, GCs continuously recruit new PCs to cover the entire space. The model described here makes important predictions and can represent the feedforward connections from hippocampus CA1 to deeper mEC layers.     

Security Implications of Typical Grid Computing Usage Scenarios

Grid Computing consists of a collection of heterogeneous computers and resources spread across multiple administrative domains with the intent of providing users uniform access to these resources. There are many ways to access the resources of a Grid, each with unique security requirements and implications for both the resource user and the resource provider. A comprehensive set of Grid usage scenarios is presented and analyzed with regard to security requirements such as authentication, authorization, integrity, and confidentiality. The main value of these scenarios and the associated security discussions is to provide a library of situations against which an application designer can match, thereby facilitating security-aware application use and development from the initial stages of the application design and invocation. A broader goal of these scenarios is to increase the awareness of security issues in Grid Computing.     

基于多传感器的声景大数据在线采集与分析系统研究

声景包含重要的生态信息,具有实时性强、信息密度高的特点,有重要研究价值。现有的声景研究中,音频及相关环境参数采集和分析仍需要大量的人工作业,耗时耗力。基于多传感集成、边缘计算和深度学习技术,建立了一套声景大数据在线采集与分析系统,包括边缘计算节点和中心计算服务器。并通过3个实验站点,进行了近1年的技术验证,实现了声景大数据的自动化在线采集、传输和分析。该系统能适应户外恶劣的自然环境,能根据任务需求持续不断地进行声景大数据在线采集和分析,稳定性好。声学指数可以反映声景变化,但因指数侧重点不同,不同的声学指数之间变化特征差异较大,需要组合使用。通过声纹特征图能直观地识别出不同发声源,对物种的快速识别、声源的分类等具有较强的借鉴意义。系统借助VGGish网络提取的高维声景特征图能很好地识别不同站点和不同时间的声景变化,在不同站点和昼夜上具有较高的区分精度,有快速和直观地反映不同生态系统的类型特征、生态系统动态变化的潜力。丰富声纹特征库、优化声景特征分析神经网络、建设声景长期监测共享网络,有助于扩展系统在物种识别、生物多样性快速分析、生物与环境相互作用机制方面的应用。研究为声景大数据的在线采集...     

Forest vascular plants as indicators of plant species richness: A data analysis of a flora atlas from northwestern Germany

Abstract

Our study had the objective to examine whether the number of forest vascular plants in a forest-poor region may be indicative of total plant species richness and of the number of threatened plant species. We also related forest plant species richness to geological and soil variables. The analysis was based on a regional flora atlas from the Weser-Elbe region in northwestern Germany including incidence data of species in a total of 1109 grid cells (each ca. 2.8 × 2.8 km²). All taxa were classified either as forest or non-forest species. Total species richness in the grid cells ranged from 65 to 597, with a mean value of 308. The number of forest species varied between 20 and 309 (mean 176). Grid cells with or without particular geological units differed in total and forest species richness, with those containing peatland and marshland being particularly species-poor. Indicator value analysis showed that both total and forest species richness in the grid cells were related to soil acidity and nitrogen in a hump-backed manner, with the highest number of species found at moderately low values for nitrogen and at intermediate values of pH. Forest species richness was highly positively correlated with the number of non-forest species and threatened non-forest species. Indicators for high species richness were primarily those species that are confined to closed semi-natural forests with a varied topography and relatively base- and nutrient-rich soils. Grid cells including historically ancient forest exhibited a higher species richness than grid cells lacking ancient forest, indicating the importance of a long habitat continuity for a high phytodiversity. The “habitat coincidence” of high species richness is best explained by similar responses of forest species and species of other habitats to the main environmental gradients. It is suggested that the regional patterns found for the Weser-Elbe region can be transferred also to other forest-poor regions in Central Europe.     

Surface plasmon resonance sensors in cell biology: basics and application

Optical sensors based on the excitation of surface plasmons, referred to as surface plasmon resonance (SPR) sensors, have become a central analytical tool for characterizing and quantifying a wide variety of macromolecular interactions, like receptor–ligand contacts. Besides this classical field of application, in the last 15 years, the development of SPR sensors aiming for the detection and analysis of ligand/cell or host/pathogen interactions, cell/cell contacts, and cellular reactions gained considerable momentum. The number of publications reporting about applications of SPR sensors implementing vital prokaryotic or eukaryotic cells as biorecognition elements for medical diagnostics, environmental monitoring, or biological safety is steadily growing. This review gives a short introduction to the technique of surface plasmon resonance and the parameters that are important for its application in the field of vital cell sensors. Furthermore, the publications concerning the application of such sensors in the analysis of cellular interactions and cellular reactions to extra- and intracellular stimuli are summarized.     

网格技术在生命科学中的应用研究

生命科学尤其是生物信息学中庞大的数据处理和高性能计算大大超出了某一单个机构的计算能力,而网格技术的出现使这些困难应刃而解,并逐渐成为生命科学标准的网络基础.从计算网格、数据网格和知识网格3个方面综述了最新的网格技术.最后展望了网格技术在生命科学领域中广阔的应用前景.     

Passive wireless MEMS microphones for biomedical applications

This paper introduces passive wireless telemetry based operation for high frequency acoustic sensors. The focus is on the development, fabrication, and evaluation of wireless, battery-less SAW-IDT MEMS microphones for biomedical applications. Due to the absence of batteries, the developed sensors are small and as a result of the batch manufacturing strategy are inexpensive which enables their utilization as disposable sensors. A pulse modulated surface acoustic wave interdigital transducer (SAW-IDT) based sensing strategy has been formulated. The sensing strategy relies on detecting the ac component of the acoustic pressure signal only and does not require calibration. The proposed sensing strategy has been successfully implemented on an in-house fabricated SAW-IDT sensor and a variable capacitor which mimics the impedance change of a capacitive microphone. Wireless telemetry distances of up to 5 centimeters have been achieved. A silicon MEMS microphone which will be used with the SAW-IDT device is being microfabricated and tested. The complete passive wireless sensor package will include the MEMS microphone wire-bonded on the SAW substrate and interrogated through an on-board antenna. This work on acoustic sensors breaks new ground by introducing high frequency (i.e., audio frequencies) sensor measurement utilizing SAW-IDT sensors. The developed sensors can be used for wireless monitoring of body sounds in a number of different applications, including monitoring breathing sounds in apnea patients, monitoring chest sounds after cardiac surgery, and for feedback sensing in compression (HFCC) vests used for respiratory ventilation. Another promising application is monitoring chest sounds in neonatal care units where the miniature sensors will minimize discomfort for the newborns.     

GLAD: a system for developing and deploying large-scale bioinformatics grid

MOTIVATION: Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. RESULTS: GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.     

Estimating animal population density using passive acoustics

Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture‐recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast‐developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics‐based density estimation, illustrated with examples from real‐world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic‐based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture‐recapture. The methods are also applicable to other aquatic and terrestrial sound‐producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here.     

A survey of the 2006-2009 quartz crystal microbalance biosensor literature

Since the publication of the original review of piezoelectric acoustic sensors in this series there has been a consistent, gradual expansion in the number of published papers using 'quartz crystal microbalances' (QCM). Between 2001 and 2009, the number of QCM publications per annum has increased from 49 to 273, with a two-fold increase in papers per annum between 2004 and 2008. Within the field, comparing the time covered by the current to the previous review, there are trends towards increasing use of QCM in the study of protein adsorption to surfaces (93% increase), homeostasis (67% increase), protein-protein interactions (40% increase) and carbohydrates (43% increase). New commercial systems have been released that are driving the uptake of the technology for characterization of binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This paper highlights theoretical and practical aspects of the principles that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and membrane interfaces.     

Linking field-based ecological data with remotely sensed data using a geographic information system in two malaria endemic urban areas of Kenya

BACKGROUND: Remote sensing technology provides detailed spectral and thermal images of the earth's surface from which surrogate ecological indicators of complex processes can be measured. METHODS: Remote sensing data were overlaid onto georeferenced entomological and human ecological data randomly sampled during April and May 2001 in the cities of Kisumu (population asymptotically equal to 320,000) and Malindi (population asymptotically equal to 81,000), Kenya. Grid cells of 270 meters x 270 meters were used to generate spatial sampling units for each city for the collection of entomological and human ecological field-based data. Multispectral Thermal Imager (MTI) satellite data in the visible spectrum at five meter resolution were acquired for Kisumu and Malindi during February and March 2001, respectively. The MTI data were fit and aggregated to the 270 meter x 270 meter grid cells used in field-based sampling using a geographic information system. The normalized difference vegetation index (NDVI) was calculated and scaled from MTI data for selected grid cells. Regression analysis was used to assess associations between NDVI values and entomological and human ecological variables at the grid cell level. RESULTS: Multivariate linear regression showed that as household density increased, mean grid cell NDVI decreased (global F-test = 9.81, df 3,72, P-value = <0.01; adjusted R2 = 0.26). Given household density, the number of potential anopheline larval habitats per grid cell also increased with increasing values of mean grid cell NDVI (global F-test = 14.29, df 3,36, P-value = <0.01; adjusted R2 = 0.51). CONCLUSIONS: NDVI values obtained from MTI data were successfully overlaid onto georeferenced entomological and human ecological data spatially sampled at a scale of 270 meters x 270 meters. Results demonstrate that NDVI at such a scale was sufficient to describe variations in entomological and human ecological parameters across both cities.     

Cactus Tools for Grid Applications

Cactus is an open source problem solving environment designed for scientists and engineers. Its modular structure facilitates parallel computation across different architectures and collaborative code development between different groups. The Cactus Code originated in the academic research community, where it has been developed and used over many years by a large international collaboration of physicists and computational scientists. We discuss here how the intensive computing requirements of physics applications now using the Cactus Code encourage the use of distributed and metacomputing, and detail how its design makes it an ideal application test-bed for Grid computing. We describe the development of tools, and the experiments which have already been performed in a Grid environment with Cactus, including distributed simulations, remote monitoring and steering, and data handling and visualization. Finally, we discuss how Grid portals, such as those already developed for Cactus, will open the door to global computing resources for scientific users.     

Designing a Non-invasive Surface Acoustic Resonator for Ultra-high Sensitive Ethanol Detection for an On-the-spot Health Monitoring System

Surface acoustic wave (SAW) sensors–based on piezoelectric crystal resonators–are extremely sensitive to even very small perturbations in the external atmosphere, because the energy associated with the acoustic waves is confined to the crystal surface. In this study, we present a critical review of the recent researches and developments predominantly used for SAW-based organic vapor sensors, especially ethanol. Besides highlighting their potential to realize real-time ethanol sensing, their drawbacks such as indirect sensing, invasive, time initializing, and low reliability, are properly discussed. The study investigates a proposed YZ-lithium niobate piezoelectric substrate with interdigital transducers patterned on the surface. Design of the resonator plays an important role in improving mass sensitivity, particularly the sensing area. Accordingly, a tin dioxide (SnO₂) layer with a specific thickness is generated on the surface of the sensor because of its high affinity to ethanol molecules. To determine the values of sensor configuration without facing the practical problems and the long theoretical calculation time, it is shown that the mass sensitivity of SAW sensors can be calculated by a simple three-dimensional (3-D) finite element analysis (FEA) using a commercial finite-element platform. In design validation step, different concentrations of ethanol are applied to investigate the acoustic wave properties of the sensor. The FEA data are used to obtain the surface and bulk total displacements of the sensor and fast Fourier transform (FFT) on output spectrum. The sensor could develop into highly sensitive and fast responsive structure so that a positive intensity shift of 0.18e-2 RIU is observed when the sensor is exposed to 15 ppm ethanol. It is capable of continuously monitoring the ethanol gas whether as an ultra-high sensitive sensor or switching applications for medical and industrial purposes.