Triple-server blind quantum computation using entanglement swapping

NASA Astrophysics Data System (ADS)

Li, Qin; Chan, Wai Hong; Wu, Chunhui; Wen, Zhonghua

2014-04-01

Blind quantum computation allows a client who does not have enough quantum resources or technologies to achieve quantum computation on a remote quantum server such that the client's input, output, and algorithm remain unknown to the server. Up to now, single- and double-server blind quantum computation have been considered. In this work, we propose a triple-server blind computation protocol where the client can delegate quantum computation to three quantum servers by the use of entanglement swapping. Furthermore, the three quantum servers can communicate with each other and the client is almost classical since one does not require any quantum computational power, quantum memory, and the ability to prepare any quantum states and only needs to be capable of getting access to quantum channels.

Network issues for large mass storage requirements

NASA Technical Reports Server (NTRS)

Perdue, James

1992-01-01

File Servers and Supercomputing environments need high performance networks to balance the I/O requirements seen in today's demanding computing scenarios. UltraNet is one solution which permits both high aggregate transfer rates and high task-to-task transfer rates as demonstrated in actual tests. UltraNet provides this capability as both a Server-to-Server and Server-to-Client access network giving the supercomputing center the following advantages highest performance Transport Level connections (to 40 MBytes/sec effective rates); matches the throughput of the emerging high performance disk technologies, such as RAID, parallel head transfer devices and software striping; supports standard network and file system applications using SOCKET's based application program interface such as FTP, rcp, rdump, etc.; supports access to the Network File System (NFS) and LARGE aggregate bandwidth for large NFS usage; provides access to a distributed, hierarchical data server capability using DISCOS UniTree product; supports file server solutions available from multiple vendors, including Cray, Convex, Alliant, FPS, IBM, and others.

Data Storage and Transfer | High-Performance Computing | NREL

Science.gov Websites

High-Performance Computing (HPC) systems. Photo of computer server wiring and lights, blurred to show data. WinSCP for Windows File Transfers Use to transfer files from a local computer to a remote computer. Robinhood for File Management Use this tool to manage your data files on Peregrine. Best

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

Providing Internet Access to High-Resolution Mars Images

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2008-01-01

The OnMars server is a computer program that provides Internet access to high-resolution Mars images, maps, and elevation data, all suitable for use in geographical information system (GIS) software for generating images, maps, and computational models of Mars. The OnMars server is an implementation of the Open Geospatial Consortium (OGC) Web Map Service (WMS) server. Unlike other Mars Internet map servers that provide Martian data using an Earth coordinate system, the OnMars WMS server supports encoding of data in Mars-specific coordinate systems. The OnMars server offers access to most of the available high-resolution Martian image and elevation data, including an 8-meter-per-pixel uncontrolled mosaic of most of the Mars Global Surveyor (MGS) Mars Observer Camera Narrow Angle (MOCNA) image collection, which is not available elsewhere. This server can generate image and map files in the tagged image file format (TIFF), Joint Photographic Experts Group (JPEG), 8- or 16-bit Portable Network Graphics (PNG), or Keyhole Markup Language (KML) format. Image control is provided by use of the OGC Style Layer Descriptor (SLD) protocol. The OnMars server also implements tiled WMS protocol and super-overlay KML for high-performance client application programs.

Requirements for a network storage service

NASA Technical Reports Server (NTRS)

Kelly, Suzanne M.; Haynes, Rena A.

1992-01-01

Sandia National Laboratories provides a high performance classified computer network as a core capability in support of its mission of nuclear weapons design and engineering, physical sciences research, and energy research and development. The network, locally known as the Internal Secure Network (ISN), was designed in 1989 and comprises multiple distributed local area networks (LAN's) residing in Albuquerque, New Mexico and Livermore, California. The TCP/IP protocol suite is used for inner-node communications. Scientific workstations and mid-range computers, running UNIX-based operating systems, compose most LAN's. One LAN, operated by the Sandia Corporate Computing Directorate, is a general purpose resource providing a supercomputer and a file server to the entire ISN. The current file server on the supercomputer LAN is an implementation of the Common File System (CFS) developed by Los Alamos National Laboratory. Subsequent to the design of the ISN, Sandia reviewed its mass storage requirements and chose to enter into a competitive procurement to replace the existing file server with one more adaptable to a UNIX/TCP/IP environment. The requirements study for the network was the starting point for the requirements study for the new file server. The file server is called the Network Storage Services (NSS) and is requirements are described in this paper. The next section gives an application or functional description of the NSS. The final section adds performance, capacity, and access constraints to the requirements.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A configurable distributed high-performance computing framework for satellite's TDI-CCD imaging simulation

NASA Astrophysics Data System (ADS)

Xue, Bo; Mao, Bingjing; Chen, Xiaomei; Ni, Guoqiang

2010-11-01

This paper renders a configurable distributed high performance computing(HPC) framework for TDI-CCD imaging simulation. It uses strategy pattern to adapt multi-algorithms. Thus, this framework help to decrease the simulation time with low expense. Imaging simulation for TDI-CCD mounted on satellite contains four processes: 1) atmosphere leads degradation, 2) optical system leads degradation, 3) electronic system of TDI-CCD leads degradation and re-sampling process, 4) data integration. Process 1) to 3) utilize diversity data-intensity algorithms such as FFT, convolution and LaGrange Interpol etc., which requires powerful CPU. Even uses Intel Xeon X5550 processor, regular series process method takes more than 30 hours for a simulation whose result image size is 1500 * 1462. With literature study, there isn't any mature distributing HPC framework in this field. Here we developed a distribute computing framework for TDI-CCD imaging simulation, which is based on WCF[1], uses Client/Server (C/S) layer and invokes the free CPU resources in LAN. The server pushes the process 1) to 3) tasks to those free computing capacity. Ultimately we rendered the HPC in low cost. In the computing experiment with 4 symmetric nodes and 1 server , this framework reduced about 74% simulation time. Adding more asymmetric nodes to the computing network, the time decreased namely. In conclusion, this framework could provide unlimited computation capacity in condition that the network and task management server are affordable. And this is the brand new HPC solution for TDI-CCD imaging simulation and similar applications.

A performance analysis of advanced I/O architectures for PC-based network file servers

NASA Astrophysics Data System (ADS)

Huynh, K. D.; Khoshgoftaar, T. M.

1994-12-01

In the personal computing and workstation environments, more and more I/O adapters are becoming complete functional subsystems that are intelligent enough to handle I/O operations on their own without much intervention from the host processor. The IBM Subsystem Control Block (SCB) architecture has been defined to enhance the potential of these intelligent adapters by defining services and conventions that deliver command information and data to and from the adapters. In recent years, a new storage architecture, the Redundant Array of Independent Disks (RAID), has been quickly gaining acceptance in the world of computing. In this paper, we would like to discuss critical system design issues that are important to the performance of a network file server. We then present a performance analysis of the SCB architecture and disk array technology in typical network file server environments based on personal computers (PCs). One of the key issues investigated in this paper is whether a disk array can outperform a group of disks (of same type, same data capacity, and same cost) operating independently, not in parallel as in a disk array.

Installation and management of the SPS and LEP control system computers

NASA Astrophysics Data System (ADS)

Bland, Alastair

1994-12-01

Control of the CERN SPS and LEP accelerators and service equipment on the two CERN main sites is performed via workstations, file servers, Process Control Assemblies (PCAs) and Device Stub Controllers (DSCs). This paper describes the methods and tools that have been developed to manage the file servers, PCAs and DSCs since the LEP startup in 1989. There are five operational DECstation 5000s used as file servers and boot servers for the PCAs and DSCs. The PCAs consist of 90 SCO Xenix 386 PCs, 40 LynxOS 486 PCs and more than 40 older NORD 100s. The DSCs consist of 90 OS-968030 VME crates and 10 LynxOS 68030 VME crates. In addition there are over 100 development systems. The controls group is responsible for installing the computers, starting all the user processes and ensuring that the computers and the processes run correctly. The operators in the SPS/LEP control room and the Services control room have a Motif-based X window program which gives them, in real time, the state of all the computers and allows them to solve problems or reboot them.

Generic Divide and Conquer Internet-Based Computing

NASA Technical Reports Server (NTRS)

Follen, Gregory J. (Technical Monitor); Radenski, Atanas

2003-01-01

The growth of Internet-based applications and the proliferation of networking technologies have been transforming traditional commercial application areas as well as computer and computational sciences and engineering. This growth stimulates the exploration of Peer to Peer (P2P) software technologies that can open new research and application opportunities not only for the commercial world, but also for the scientific and high-performance computing applications community. The general goal of this project is to achieve better understanding of the transition to Internet-based high-performance computing and to develop solutions for some of the technical challenges of this transition. In particular, we are interested in creating long-term motivation for end users to provide their idle processor time to support computationally intensive tasks. We believe that a practical P2P architecture should provide useful service to both clients with high-performance computing needs and contributors of lower-end computing resources. To achieve this, we are designing dual -service architecture for P2P high-performance divide-and conquer computing; we are also experimenting with a prototype implementation. Our proposed architecture incorporates a master server, utilizes dual satellite servers, and operates on the Internet in a dynamically changing large configuration of lower-end nodes provided by volunteer contributors. A dual satellite server comprises a high-performance computing engine and a lower-end contributor service engine. The computing engine provides generic support for divide and conquer computations. The service engine is intended to provide free useful HTTP-based services to contributors of lower-end computing resources. Our proposed architecture is complementary to and accessible from computational grids, such as Globus, Legion, and Condor. Grids provide remote access to existing higher-end computing resources; in contrast, our goal is to utilize idle processor time of lower-end Internet nodes. Our project is focused on a generic divide and conquer paradigm and on mobile applications of this paradigm that can operate on a loose and ever changing pool of lower-end Internet nodes.

A study of kinematic cues and anticipatory performance in tennis using computational manipulation and computer graphics.

PubMed

Ida, Hirofumi; Fukuhara, Kazunobu; Kusubori, Seiji; Ishii, Motonobu

2011-09-01

Computer graphics of digital human models can be used to display human motions as visual stimuli. This study presents our technique for manipulating human motion with a forward kinematics calculation without violating anatomical constraints. A motion modulation of the upper extremity was conducted by proportionally modulating the anatomical joint angular velocity calculated by motion analysis. The effect of this manipulation was examined in a tennis situation--that is, the receiver's performance of predicting ball direction when viewing a digital model of the server's motion derived by modulating the angular velocities of the forearm or that of the elbow during the forward swing. The results showed that the faster the server's forearm pronated, the more the receiver's anticipation of the ball direction tended to the left side of the serve box. In contrast, the faster the server's elbow extended, the more the receiver's anticipation of the ball direction tended to the right. This suggests that tennis players are sensitive to the motion modulation of their opponent's racket-arm.

MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.

PubMed

Degroeve, Sven; Maddelein, Davy; Martens, Lennart

2015-07-01

We present an MS(2) peak intensity prediction server that computes MS(2) charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra. Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Flow Ambiguity: A Path Towards Classically Driven Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Mantri, Atul; Demarie, Tommaso F.; Menicucci, Nicolas C.; Fitzsimons, Joseph F.

2017-07-01

Blind quantum computation protocols allow a user to delegate a computation to a remote quantum computer in such a way that the privacy of their computation is preserved, even from the device implementing the computation. To date, such protocols are only known for settings involving at least two quantum devices: either a user with some quantum capabilities and a remote quantum server or two or more entangled but noncommunicating servers. In this work, we take the first step towards the construction of a blind quantum computing protocol with a completely classical client and single quantum server. Specifically, we show how a classical client can exploit the ambiguity in the flow of information in measurement-based quantum computing to construct a protocol for hiding critical aspects of a computation delegated to a remote quantum computer. This ambiguity arises due to the fact that, for a fixed graph, there exist multiple choices of the input and output vertex sets that result in deterministic measurement patterns consistent with the same fixed total ordering of vertices. This allows a classical user, computing only measurement angles, to drive a measurement-based computation performed on a remote device while hiding critical aspects of the computation.

Experimental evaluation of the impact of packet capturing tools for web services.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choe, Yung Ryn; Mohapatra, Prasant; Chuah, Chen-Nee

Network measurement is a discipline that provides the techniques to collect data that are fundamental to many branches of computer science. While many capturing tools and comparisons have made available in the literature and elsewhere, the impact of these packet capturing tools on existing processes have not been thoroughly studied. While not a concern for collection methods in which dedicated servers are used, many usage scenarios of packet capturing now requires the packet capturing tool to run concurrently with operational processes. In this work we perform experimental evaluations of the performance impact that packet capturing process have on web-based services;more » in particular, we observe the impact on web servers. We find that packet capturing processes indeed impact the performance of web servers, but on a multi-core system the impact varies depending on whether the packet capturing and web hosting processes are co-located or not. In addition, the architecture and behavior of the web server and process scheduling is coupled with the behavior of the packet capturing process, which in turn also affect the web server's performance.« less

Experience of public procurement of Open Compute servers

NASA Astrophysics Data System (ADS)

Bärring, Olof; Guerri, Marco; Bonfillou, Eric; Valsan, Liviu; Grigore, Alexandru; Dore, Vincent; Gentit, Alain; Clement, Benoît; Grossir, Anthony

2015-12-01

The Open Compute Project. OCP (http://www.opencompute.org/). was launched by Facebook in 2011 with the objective of building efficient computing infrastructures at the lowest possible cost. The technologies are released as open hardware. with the goal to develop servers and data centres following the model traditionally associated with open source software projects. In 2013 CERN acquired a few OCP servers in order to compare performance and power consumption with standard hardware. The conclusions were that there are sufficient savings to motivate an attempt to procure a large scale installation. One objective is to evaluate if the OCP market is sufficiently mature and broad enough to meet the constraints of a public procurement. This paper summarizes this procurement. which started in September 2014 and involved the Request for information (RFI) to qualify bidders and Request for Tender (RFT).

A Software Rejuvenation Framework for Distributed Computing

NASA Technical Reports Server (NTRS)

Chau, Savio

2009-01-01

A performability-oriented conceptual framework for software rejuvenation has been constructed as a means of increasing levels of reliability and performance in distributed stateful computing. As used here, performability-oriented signifies that the construction of the framework is guided by the concept of analyzing the ability of a given computing system to deliver services with gracefully degradable performance. The framework is especially intended to support applications that involve stateful replicas of server computers.

xDSL connection monitor

DOEpatents

Horton, John J.

2006-04-11

A system and method of maintaining communication between a computer and a server, the server being in communication with the computer via xDSL service or dial-up modem service, with xDSL service being the default mode of communication, the method including sending a request to the server via xDSL service to which the server should respond and determining if a response has been received. If no response has been received, displaying on the computer a message (i) indicating that xDSL service has failed and (ii) offering to establish communication between the computer and the server via the dial-up modem, and thereafter changing the default mode of communication between the computer and the server to dial-up modem service. In a preferred embodiment, an xDSL service provider monitors dial-up modem communications and determines if the computer dialing in normally establishes communication with the server via xDSL service. The xDSL service provider can thus quickly and easily detect xDSL failures.

SciServer: An Online Collaborative Environment for Big Data in Research and Education

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Souter, Barbara; Lemson, Gerard; Taghizadeh-Popp, Manuchehr

2017-01-01

For the past year, SciServer Compute (http://compute.sciserver.org) has offered access to big data resources running within server-side Docker containers. Compute has allowed thousands of researchers to bring advanced analysis to big datasets like the Sloan Digital Sky Survey and others, while keeping the analysis close to the data for better performance and easier read/write access. SciServer Compute is just one part of the SciServer system being developed at Johns Hopkins University, which provides an easy-to-use collaborative research environment for astronomy and many other sciences.SciServer enables these collaborative research strategies using Jupyter notebooks, in which users can write their own Python and R scripts and execute them on the same server as the data. We have written special-purpose libraries for querying, reading, and writing data. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files.SciServer Compute’s virtual research environment has grown with the addition of task management and access control functions, allowing collaborators to share both data and analysis scripts securely across the world. These features also open up new possibilities for education, allowing instructors to share datasets with students and students to write analysis scripts to share with their instructors. We are leveraging these features into a new system called “SciServer Courseware,” which will allow instructors to share assignments with their students, allowing students to engage with big data in new ways.SciServer has also expanded to include more datasets beyond the Sloan Digital Sky Survey. A part of that growth has been the addition of the SkyQuery component, which allows for simple, fast cross-matching between very large astronomical datasets.Demos, documentation, and more information about all these resources can be found at www.sciserver.org.

Vacation model for Markov machine repair problem with two heterogeneous unreliable servers and threshold recovery

NASA Astrophysics Data System (ADS)

Jain, Madhu; Meena, Rakesh Kumar

2018-03-01

Markov model of multi-component machining system comprising two unreliable heterogeneous servers and mixed type of standby support has been studied. The repair job of broken down machines is done on the basis of bi-level threshold policy for the activation of the servers. The server returns back to render repair job when the pre-specified workload of failed machines is build up. The first (second) repairman turns on only when the work load of N1 (N2) failed machines is accumulated in the system. The both servers may go for vacation in case when all the machines are in good condition and there are no pending repair jobs for the repairmen. Runge-Kutta method is implemented to solve the set of governing equations used to formulate the Markov model. Various system metrics including the mean queue length, machine availability, throughput, etc., are derived to determine the performance of the machining system. To provide the computational tractability of the present investigation, a numerical illustration is provided. A cost function is also constructed to determine the optimal repair rate of the server by minimizing the expected cost incurred on the system. The hybrid soft computing method is considered to develop the adaptive neuro-fuzzy inference system (ANFIS). The validation of the numerical results obtained by Runge-Kutta approach is also facilitated by computational results generated by ANFIS.

Automating NEURON Simulation Deployment in Cloud Resources.

PubMed

Stockton, David B; Santamaria, Fidel

2017-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the OpenStack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon's proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model.

Automating NEURON Simulation Deployment in Cloud Resources

PubMed Central

Santamaria, Fidel

2016-01-01

Simulations in neuroscience are performed on local servers or High Performance Computing (HPC) facilities. Recently, cloud computing has emerged as a potential computational platform for neuroscience simulation. In this paper we compare and contrast HPC and cloud resources for scientific computation, then report how we deployed NEURON, a widely used simulator of neuronal activity, in three clouds: Chameleon Cloud, a hybrid private academic cloud for cloud technology research based on the Open-Stack software; Rackspace, a public commercial cloud, also based on OpenStack; and Amazon Elastic Cloud Computing, based on Amazon’s proprietary software. We describe the manual procedures and how to automate cloud operations. We describe extending our simulation automation software called NeuroManager (Stockton and Santamaria, Frontiers in Neuroinformatics, 2015), so that the user is capable of recruiting private cloud, public cloud, HPC, and local servers simultaneously with a simple common interface. We conclude by performing several studies in which we examine speedup, efficiency, total session time, and cost for sets of simulations of a published NEURON model. PMID:27655341

48 CFR 1523.7002 - Waivers.

Code of Federal Regulations, 2011 CFR

2011-10-01

... ENVIRONMENTAL, CONSERVATION, OCCUPATIONAL SAFETY, AND DRUG-FREE WORKPLACE Energy-Efficient Computer Equipment 1523.7002 Waivers. (a) There are several types of computer equipment which technically fall under the... types of equipment: (1) LAN servers, including file servers; application servers; communication servers...

48 CFR 1523.7002 - Waivers.

Code of Federal Regulations, 2012 CFR

2012-10-01

... ENVIRONMENTAL, CONSERVATION, OCCUPATIONAL SAFETY, AND DRUG-FREE WORKPLACE Energy-Efficient Computer Equipment 1523.7002 Waivers. (a) There are several types of computer equipment which technically fall under the... types of equipment: (1) LAN servers, including file servers; application servers; communication servers...

48 CFR 1523.7002 - Waivers.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ENVIRONMENTAL, CONSERVATION, OCCUPATIONAL SAFETY, AND DRUG-FREE WORKPLACE Energy-Efficient Computer Equipment 1523.7002 Waivers. (a) There are several types of computer equipment which technically fall under the... types of equipment: (1) LAN servers, including file servers; application servers; communication servers...

PDS: A Performance Database Server

DOE PAGES

Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; ...

1994-01-01

The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore » benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

Characteristics and Energy Use of Volume Servers in the United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuchs, H.; Shehabi, A.; Ganeshalingam, M.

Servers’ field energy use remains poorly understood, given heterogeneous computing loads, configurable hardware and software, and operation over a wide range of management practices. This paper explores various characteristics of 1- and 2-socket volume servers that affect energy consumption, and quantifies the difference in power demand between higher-performing SPEC and ENERGY STAR servers and our best understanding of a typical server operating today. We first establish general characteristics of the U.S. installed base of volume servers from existing IDC data and the literature, before presenting information on server hardware configurations from data collection events at a major online retail website.more » We then compare cumulative distribution functions of server idle power across three separate datasets and explain the differences between them via examination of the hardware characteristics to which power draw is most sensitive. We find that idle server power demand is significantly higher than ENERGY STAR benchmarks and the industry-released energy use documented in SPEC, and that SPEC server configurations—and likely the associated power-scaling trends—are atypical of volume servers. Next, we examine recent trends in server power draw among high-performing servers across their full load range to consider how representative these trends are of all volume servers before inputting weighted average idle power load values into a recently published model of national server energy use. Finally, we present results from two surveys of IT managers (n=216) and IT vendors (n=178) that illustrate the prevalence of more-efficient equipment and operational practices in server rooms and closets; these findings highlight opportunities to improve the energy efficiency of the U.S. server stock.« less

Adaptive allocation of decisionmaking responsibility between human and computer in multitask situations

NASA Technical Reports Server (NTRS)

Chu, Y.-Y.; Rouse, W. B.

1979-01-01

As human and computer come to have overlapping decisionmaking abilities, a dynamic or adaptive allocation of responsibilities may be the best mode of human-computer interaction. It is suggested that the computer serve as a backup decisionmaker, accepting responsibility when human workload becomes excessive and relinquishing responsibility when workload becomes acceptable. A queueing theory formulation of multitask decisionmaking is used and a threshold policy for turning the computer on/off is proposed. This policy minimizes event-waiting cost subject to human workload constraints. An experiment was conducted with a balanced design of several subject runs within a computer-aided multitask flight management situation with different task demand levels. It was found that computer aiding enhanced subsystem performance as well as subjective ratings. The queueing model appears to be an adequate representation of the multitask decisionmaking situation, and to be capable of predicting system performance in terms of average waiting time and server occupancy. Server occupancy was further found to correlate highly with the subjective effort ratings.

Thirty Meter Telescope (TMT) Narrow Field Infrared Adaptive Optics System (NFIRAOS) real-time controller preliminary architecture

NASA Astrophysics Data System (ADS)

Kerley, Dan; Smith, Malcolm; Dunn, Jennifer; Herriot, Glen; Véran, Jean-Pierre; Boyer, Corinne; Ellerbroek, Brent; Gilles, Luc; Wang, Lianqi

2016-08-01

The Narrow Field Infrared Adaptive Optics System (NFIRAOS) is the first light Adaptive Optics (AO) system for the Thirty Meter Telescope (TMT). A critical component of NFIRAOS is the Real-Time Controller (RTC) subsystem which provides real-time wavefront correction by processing wavefront information to compute Deformable Mirror (DM) and Tip/Tilt Stage (TTS) commands. The National Research Council of Canada - Herzberg (NRC-H), in conjunction with TMT, has developed a preliminary design for the NFIRAOS RTC. The preliminary architecture for the RTC is comprised of several Linux-based servers. These servers are assigned various roles including: the High-Order Processing (HOP) servers, the Wavefront Corrector Controller (WCC) server, the Telemetry Engineering Display (TED) server, the Persistent Telemetry Storage (PTS) server, and additional testing and spare servers. There are up to six HOP servers that accept high-order wavefront pixels, and perform parallelized pixel processing and wavefront reconstruction to produce wavefront corrector error vectors. The WCC server performs low-order mode processing, and synchronizes and aggregates the high-order wavefront corrector error vectors from the HOP servers to generate wavefront corrector commands. The Telemetry Engineering Display (TED) server is the RTC interface to TMT and other subsystems. The TED server receives all external commands and dispatches them to the rest of the RTC servers and is responsible for aggregating several offloading and telemetry values that are reported to other subsystems within NFIRAOS and TMT. The TED server also provides the engineering GUIs and real-time displays. The Persistent Telemetry Storage (PTS) server contains fault tolerant data storage that receives and stores telemetry data, including data for Point-Spread Function Reconstruction (PSFR).

Development of a novel SCADA system for laboratory testing.

PubMed

Patel, M; Cole, G R; Pryor, T L; Wilmot, N A

2004-07-01

This document summarizes the supervisory control and data acquisition (SCADA) system that allows communication with, and controlling the output of, various I/O devices in the renewable energy systems and components test facility RESLab. This SCADA system differs from traditional SCADA systems in that it supports a continuously changing operating environment depending on the test to be performed. The SCADA System is based on the concept of having one Master I/O Server and multiple client computer systems. This paper describes the main features and advantages of this dynamic SCADA system, the connections of various field devices to the master I/O server, the device servers, and numerous software features used in the system. The system is based on the graphical programming language "LabVIEW" and its "Datalogging and Supervisory Control" (DSC) module. The DSC module supports a real-time database called the "tag engine," which performs the I/O operations with all field devices attached to the master I/O server and communications with the other tag engines running on the client computers connected via a local area network. Generic and detailed communication block diagrams illustrating the hierarchical structure of this SCADA system are presented. The flow diagram outlining a complete test performed using this system in one of its standard configurations is described.

Zebra: A striped network file system

NASA Technical Reports Server (NTRS)

Hartman, John H.; Ousterhout, John K.

1992-01-01

The design of Zebra, a striped network file system, is presented. Zebra applies ideas from log-structured file system (LFS) and RAID research to network file systems, resulting in a network file system that has scalable performance, uses its servers efficiently even when its applications are using small files, and provides high availability. Zebra stripes file data across multiple servers, so that the file transfer rate is not limited by the performance of a single server. High availability is achieved by maintaining parity information for the file system. If a server fails its contents can be reconstructed using the contents of the remaining servers and the parity information. Zebra differs from existing striped file systems in the way it stripes file data: Zebra does not stripe on a per-file basis; instead it stripes the stream of bytes written by each client. Clients write to the servers in units called stripe fragments, which are analogous to segments in an LFS. Stripe fragments contain file blocks that were written recently, without regard to which file they belong. This method of striping has numerous advantages over per-file striping, including increased server efficiency, efficient parity computation, and elimination of parity update.

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

PubMed

Wang, Lin; Zhang, Min; Alexov, Emil

2016-02-15

A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Cloud Computing with iPlant Atmosphere.

PubMed

McKay, Sheldon J; Skidmore, Edwin J; LaRose, Christopher J; Mercer, Andre W; Noutsos, Christos

2013-10-15

Cloud Computing refers to distributed computing platforms that use virtualization software to provide easy access to physical computing infrastructure and data storage, typically administered through a Web interface. Cloud-based computing provides access to powerful servers, with specific software and virtual hardware configurations, while eliminating the initial capital cost of expensive computers and reducing the ongoing operating costs of system administration, maintenance contracts, power consumption, and cooling. This eliminates a significant barrier to entry into bioinformatics and high-performance computing for many researchers. This is especially true of free or modestly priced cloud computing services. The iPlant Collaborative offers a free cloud computing service, Atmosphere, which allows users to easily create and use instances on virtual servers preconfigured for their analytical needs. Atmosphere is a self-service, on-demand platform for scientific computing. This unit demonstrates how to set up, access and use cloud computing in Atmosphere. Copyright © 2013 John Wiley & Sons, Inc.

The pepATTRACT web server for blind, large-scale peptide-protein docking.

PubMed

de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

2017-07-03

Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Parallel sort with a ranged, partitioned key-value store in a high perfomance computing environment

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary; Torres, Aaron; Poole, Stephen W.

2016-01-26

Improved sorting techniques are provided that perform a parallel sort using a ranged, partitioned key-value store in a high performance computing (HPC) environment. A plurality of input data files comprising unsorted key-value data in a partitioned key-value store are sorted. The partitioned key-value store comprises a range server for each of a plurality of ranges. Each input data file has an associated reader thread. Each reader thread reads the unsorted key-value data in the corresponding input data file and performs a local sort of the unsorted key-value data to generate sorted key-value data. A plurality of sorted, ranged subsets of each of the sorted key-value data are generated based on the plurality of ranges. Each sorted, ranged subset corresponds to a given one of the ranges and is provided to one of the range servers corresponding to the range of the sorted, ranged subset. Each range server sorts the received sorted, ranged subsets and provides a sorted range. A plurality of the sorted ranges are concatenated to obtain a globally sorted result.

Compute Server Performance Results

NASA Technical Reports Server (NTRS)

Stockdale, I. E.; Barton, John; Woodrow, Thomas (Technical Monitor)

1994-01-01

Parallel-vector supercomputers have been the workhorses of high performance computing. As expectations of future computing needs have risen faster than projected vector supercomputer performance, much work has been done investigating the feasibility of using Massively Parallel Processor systems as supercomputers. An even more recent development is the availability of high performance workstations which have the potential, when clustered together, to replace parallel-vector systems. We present a systematic comparison of floating point performance and price-performance for various compute server systems. A suite of highly vectorized programs was run on systems including traditional vector systems such as the Cray C90, and RISC workstations such as the IBM RS/6000 590 and the SGI R8000. The C90 system delivers 460 million floating point operations per second (FLOPS), the highest single processor rate of any vendor. However, if the price-performance ration (PPR) is considered to be most important, then the IBM and SGI processors are superior to the C90 processors. Even without code tuning, the IBM and SGI PPR's of 260 and 220 FLOPS per dollar exceed the C90 PPR of 160 FLOPS per dollar when running our highly vectorized suite,

PANNZER2: a rapid functional annotation web server.

PubMed

Törönen, Petri; Medlar, Alan; Holm, Liisa

2018-05-08

The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

Hiding the Disk and Network Latency of Out-of-Core Visualization

NASA Technical Reports Server (NTRS)

Ellsworth, David

2001-01-01

This paper describes an algorithm that improves the performance of application-controlled demand paging for out-of-core visualization by hiding the latency of reading data from both local disks or disks on remote servers. The performance improvements come from better overlapping the computation with the page reading process, and by performing multiple page reads in parallel. The paper includes measurements that show that the new multithreaded paging algorithm decreases the time needed to compute visualizations by one third when using one processor and reading data from local disk. The time needed when using one processor and reading data from remote disk decreased by two thirds. Visualization runs using data from remote disk actually ran faster than ones using data from local disk because the remote runs were able to make use of the remote server's high performance disk array.

78 FR 48821 - Energy Conservation Program for Consumer Products and Certain Commercial and Industrial Equipment...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-12

... Commercial and Industrial Equipment: Proposed Determination of Computer Servers as a Covered Consumer Product... comments on the proposed determination that computer servers (servers) qualify as a covered product. DATES: The comment period for the proposed determination relating to servers published on July 12, 2013 (78...

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

2014-12-01

Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

Enhanced delegated computing using coherence

NASA Astrophysics Data System (ADS)

Barz, Stefanie; Dunjko, Vedran; Schlederer, Florian; Moore, Merritt; Kashefi, Elham; Walmsley, Ian A.

2016-03-01

A longstanding question is whether it is possible to delegate computational tasks securely—such that neither the computation nor the data is revealed to the server. Recently, both a classical and a quantum solution to this problem were found [C. Gentry, in Proceedings of the 41st Annual ACM Symposium on the Theory of Computing (Association for Computing Machinery, New York, 2009), pp. 167-178; A. Broadbent, J. Fitzsimons, and E. Kashefi, in Proceedings of the 50th Annual Symposium on Foundations of Computer Science (IEEE Computer Society, Los Alamitos, CA, 2009), pp. 517-526]. Here, we study the first step towards the interplay between classical and quantum approaches and show how coherence can be used as a tool for secure delegated classical computation. We show that a client with limited computational capacity—restricted to an XOR gate—can perform universal classical computation by manipulating information carriers that may occupy superpositions of two states. Using single photonic qubits or coherent light, we experimentally implement secure delegated classical computations between an independent client and a server, which are installed in two different laboratories and separated by 50 m . The server has access to the light sources and measurement devices, whereas the client may use only a restricted set of passive optical devices to manipulate the information-carrying light beams. Thus, our work highlights how minimal quantum and classical resources can be combined and exploited for classical computing.

SciServer Compute brings Analysis to Big Data in the Cloud

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Medvedev, Dmitry; Lemson, Gerard; Souter, Barbara

2016-06-01

SciServer Compute uses Jupyter Notebooks running within server-side Docker containers attached to big data collections to bring advanced analysis to big data "in the cloud." SciServer Compute is a component in the SciServer Big-Data ecosystem under development at JHU, which will provide a stable, reproducible, sharable virtual research environment.SciServer builds on the popular CasJobs and SkyServer systems that made the Sloan Digital Sky Survey (SDSS) archive one of the most-used astronomical instruments. SciServer extends those systems with server-side computational capabilities and very large scratch storage space, and further extends their functions to a range of other scientific disciplines.Although big datasets like SDSS have revolutionized astronomy research, for further analysis, users are still restricted to downloading the selected data sets locally - but increasing data sizes make this local approach impractical. Instead, researchers need online tools that are co-located with data in a virtual research environment, enabling them to bring their analysis to the data.SciServer supports this using the popular Jupyter notebooks, which allow users to write their own Python and R scripts and execute them on the server with the data (extensions to Matlab and other languages are planned). We have written special-purpose libraries that enable querying the databases and other persistent datasets. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files. Communication between the various components of the SciServer system is managed through SciServer‘s new Single Sign-on Portal.We have created a number of demos to illustrate the capabilities of SciServer Compute, including Python and R scripts accessing a range of datasets and showing the data flow between storage and compute components.Demos, documentation, and more information can be found at www.sciserver.org.SciServer is funded by the National Science Foundation Award ACI-1261715.

A price and performance comparison of three different storage architectures for data in cloud-based systems

NASA Astrophysics Data System (ADS)

Gallagher, J. H. R.; Jelenak, A.; Potter, N.; Fulker, D. W.; Habermann, T.

2017-12-01

Providing data services based on cloud computing technology that is equivalent to those developed for traditional computing and storage systems is critical for successful migration to cloud-based architectures for data production, scientific analysis and storage. OPeNDAP Web-service capabilities (comprising the Data Access Protocol (DAP) specification plus open-source software for realizing DAP in servers and clients) are among the most widely deployed means for achieving data-as-service functionality in the Earth sciences. OPeNDAP services are especially common in traditional data center environments where servers offer access to datasets stored in (very large) file systems, and a preponderance of the source data for these services is being stored in the Hierarchical Data Format Version 5 (HDF5). Three candidate architectures for serving NASA satellite Earth Science HDF5 data via Hyrax running on Amazon Web Services (AWS) were developed and their performance examined for a set of representative use cases. The performance was based both on runtime and incurred cost. The three architectures differ in how HDF5 files are stored in the Amazon Simple Storage Service (S3) and how the Hyrax server (as an EC2 instance) retrieves their data. The results for both the serial and parallel access to HDF5 data in the S3 will be presented. While the study focused on HDF5 data, OPeNDAP and the Hyrax data server, the architectures are generic and the analysis can be extrapolated to many different data formats, web APIs, and data servers.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

SAME4HPC: A Promising Approach in Building a Scalable and Mobile Environment for High-Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karthik, Rajasekar

2014-01-01

In this paper, an architecture for building Scalable And Mobile Environment For High-Performance Computing with spatial capabilities called SAME4HPC is described using cutting-edge technologies and standards such as Node.js, HTML5, ECMAScript 6, and PostgreSQL 9.4. Mobile devices are increasingly becoming powerful enough to run high-performance apps. At the same time, there exist a significant number of low-end and older devices that rely heavily on the server or the cloud infrastructure to do the heavy lifting. Our architecture aims to support both of these types of devices to provide high-performance and rich user experience. A cloud infrastructure consisting of OpenStack withmore » Ubuntu, GeoServer, and high-performance JavaScript frameworks are some of the key open-source and industry standard practices that has been adopted in this architecture.« less

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Understanding Customer Dissatisfaction with Underutilized Distributed File Servers

NASA Technical Reports Server (NTRS)

Riedel, Erik; Gibson, Garth

1996-01-01

An important trend in the design of storage subsystems is a move toward direct network attachment. Network-attached storage offers the opportunity to off-load distributed file system functionality from dedicated file server machines and execute many requests directly at the storage devices. For this strategy to lead to better performance, as perceived by users, the response time of distributed operations must improve. In this paper we analyze measurements of an Andrew file system (AFS) server that we recently upgraded in an effort to improve client performance in our laboratory. While the original server's overall utilization was only about 3%, we show how burst loads were sufficiently intense to lead to period of poor response time significant enough to trigger customer dissatisfaction. In particular, we show how, after adjusting for network load and traffic to non-project servers, 50% of the variation in client response time was explained by variation in server central processing unit (CPU) use. That is, clients saw long response times in large part because the server was often over-utilized when it was used at all. Using these measures, we see that off-loading file server work in a network-attached storage architecture has to potential to benefit user response time. Computational power in such a system scales directly with storage capacity, so the slowdown during burst period should be reduced.

Secure Skyline Queries on Cloud Platform.

PubMed

Liu, Jinfei; Yang, Juncheng; Xiong, Li; Pei, Jian

2017-04-01

Outsourcing data and computation to cloud server provides a cost-effective way to support large scale data storage and query processing. However, due to security and privacy concerns, sensitive data (e.g., medical records) need to be protected from the cloud server and other unauthorized users. One approach is to outsource encrypted data to the cloud server and have the cloud server perform query processing on the encrypted data only. It remains a challenging task to support various queries over encrypted data in a secure and efficient way such that the cloud server does not gain any knowledge about the data, query, and query result. In this paper, we study the problem of secure skyline queries over encrypted data. The skyline query is particularly important for multi-criteria decision making but also presents significant challenges due to its complex computations. We propose a fully secure skyline query protocol on data encrypted using semantically-secure encryption. As a key subroutine, we present a new secure dominance protocol, which can be also used as a building block for other queries. Finally, we provide both serial and parallelized implementations and empirically study the protocols in terms of efficiency and scalability under different parameter settings, verifying the feasibility of our proposed solutions.

Two-Cloud-Servers-Assisted Secure Outsourcing Multiparty Computation

PubMed Central

Wen, Qiaoyan; Zhang, Hua; Jin, Zhengping; Li, Wenmin

2014-01-01

We focus on how to securely outsource computation task to the cloud and propose a secure outsourcing multiparty computation protocol on lattice-based encrypted data in two-cloud-servers scenario. Our main idea is to transform the outsourced data respectively encrypted by different users' public keys to the ones that are encrypted by the same two private keys of the two assisted servers so that it is feasible to operate on the transformed ciphertexts to compute an encrypted result following the function to be computed. In order to keep the privacy of the result, the two servers cooperatively produce a custom-made result for each user that is authorized to get the result so that all authorized users can recover the desired result while other unauthorized ones including the two servers cannot. Compared with previous research, our protocol is completely noninteractive between any users, and both of the computation and the communication complexities of each user in our solution are independent of the computing function. PMID:24982949

Two-cloud-servers-assisted secure outsourcing multiparty computation.

PubMed

Sun, Yi; Wen, Qiaoyan; Zhang, Yudong; Zhang, Hua; Jin, Zhengping; Li, Wenmin

2014-01-01

We focus on how to securely outsource computation task to the cloud and propose a secure outsourcing multiparty computation protocol on lattice-based encrypted data in two-cloud-servers scenario. Our main idea is to transform the outsourced data respectively encrypted by different users' public keys to the ones that are encrypted by the same two private keys of the two assisted servers so that it is feasible to operate on the transformed ciphertexts to compute an encrypted result following the function to be computed. In order to keep the privacy of the result, the two servers cooperatively produce a custom-made result for each user that is authorized to get the result so that all authorized users can recover the desired result while other unauthorized ones including the two servers cannot. Compared with previous research, our protocol is completely noninteractive between any users, and both of the computation and the communication complexities of each user in our solution are independent of the computing function.

Cloud Computing for Complex Performance Codes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Appel, Gordon John; Hadgu, Teklu; Klein, Brandon Thorin

This report describes the use of cloud computing services for running complex public domain performance assessment problems. The work consisted of two phases: Phase 1 was to demonstrate complex codes, on several differently configured servers, could run and compute trivial small scale problems in a commercial cloud infrastructure. Phase 2 focused on proving non-trivial large scale problems could be computed in the commercial cloud environment. The cloud computing effort was successfully applied using codes of interest to the geohydrology and nuclear waste disposal modeling community.

Design and Delivery of Multiple Server-Side Computer Languages Course

ERIC Educational Resources Information Center

Wang, Shouhong; Wang, Hai

2011-01-01

Given the emergence of service-oriented architecture, IS students need to be knowledgeable of multiple server-side computer programming languages to be able to meet the needs of the job market. This paper outlines the pedagogy of an innovative course of multiple server-side computer languages for the undergraduate IS majors. The paper discusses…

Virtual network computing: cross-platform remote display and collaboration software.

PubMed

Konerding, D E

1999-04-01

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

Implementation of an Embedded Web Server Application for Wireless Control of Brain Computer Interface Based Home Environments.

PubMed

Aydın, Eda Akman; Bay, Ömer Faruk; Güler, İnan

2016-01-01

Brain Computer Interface (BCI) based environment control systems could facilitate life of people with neuromuscular diseases, reduces dependence on their caregivers, and improves their quality of life. As well as easy usage, low-cost, and robust system performance, mobility is an important functionality expected from a practical BCI system in real life. In this study, in order to enhance users' mobility, we propose internet based wireless communication between BCI system and home environment. We designed and implemented a prototype of an embedded low-cost, low power, easy to use web server which is employed in internet based wireless control of a BCI based home environment. The embedded web server provides remote access to the environmental control module through BCI and web interfaces. While the proposed system offers to BCI users enhanced mobility, it also provides remote control of the home environment by caregivers as well as the individuals in initial stages of neuromuscular disease. The input of BCI system is P300 potentials. We used Region Based Paradigm (RBP) as stimulus interface. Performance of the BCI system is evaluated on data recorded from 8 non-disabled subjects. The experimental results indicate that the proposed web server enables internet based wireless control of electrical home appliances successfully through BCIs.

Quantum computing on encrypted data

NASA Astrophysics Data System (ADS)

Fisher, K. A. G.; Broadbent, A.; Shalm, L. K.; Yan, Z.; Lavoie, J.; Prevedel, R.; Jennewein, T.; Resch, K. J.

2014-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Quantum computing on encrypted data.

PubMed

Fisher, K A G; Broadbent, A; Shalm, L K; Yan, Z; Lavoie, J; Prevedel, R; Jennewein, T; Resch, K J

2014-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Software for Building Models of 3D Objects via the Internet

NASA Technical Reports Server (NTRS)

Schramer, Tim; Jensen, Jeff

2003-01-01

The Virtual EDF Builder (where EDF signifies Electronic Development Fixture) is a computer program that facilitates the use of the Internet for building and displaying digital models of three-dimensional (3D) objects that ordinarily comprise assemblies of solid models created previously by use of computer-aided-design (CAD) programs. The Virtual EDF Builder resides on a Unix-based server computer. It is used in conjunction with a commercially available Web-based plug-in viewer program that runs on a client computer. The Virtual EDF Builder acts as a translator between the viewer program and a database stored on the server. The translation function includes the provision of uniform resource locator (URL) links to other Web-based computer systems and databases. The Virtual EDF builder can be used in two ways: (1) If the client computer is Unix-based, then it can assemble a model locally; the computational load is transferred from the server to the client computer. (2) Alternatively, the server can be made to build the model, in which case the server bears the computational load and the results are downloaded to the client computer or workstation upon completion.

JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility.

PubMed

Jaschob, Daniel; Riffle, Michael

2012-07-30

Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, and many laboratories lack the expertise or resources to build and maintain a dedicated computer cluster. JobCenter is a client-server application and framework for job management and distributed job execution. The client and server components are both written in Java and are cross-platform and relatively easy to install. All communication with the server is client-driven, which allows worker nodes to run anywhere (even behind external firewalls or "in the cloud") and provides inherent load balancing. Adding a worker node to the worker pool is as simple as dropping the JobCenter client files onto any computer and performing basic configuration, which provides tremendous ease-of-use, flexibility, and limitless horizontal scalability. Each worker installation may be independently configured, including the types of jobs it is able to run. Executed jobs may be written in any language and may include multistep workflows. JobCenter is a versatile and scalable distributed job management system that allows laboratories to very efficiently distribute all computational work among available resources. JobCenter is freely available at http://code.google.com/p/jobcenter/.

The Red Atrapa Sismos (Quake Catcher Network in Mexico): assessing performance during large and damaging earthquakes.

USGS Publications Warehouse

Dominguez, Luis A.; Yildirim, Battalgazi; Husker, Allen L.; Cochran, Elizabeth S.; Christensen, Carl; Cruz-Atienza, Victor M.

2015-01-01

Each volunteer computer monitors ground motion and communicates using the Berkeley Open Infrastructure for Network Computing (BOINC, Anderson, 2004). Using a standard short‐term average, long‐term average (STLA) algorithm (Earle and Shearer, 1994; Cochran, Lawrence, Christensen, Chung, 2009; Cochran, Lawrence, Christensen, and Jakka, 2009), volunteer computer and sensor systems detect abrupt changes in the acceleration recordings. Each time a possible trigger signal is declared, a small package of information containing sensor and ground‐motion information is streamed to one of the QCN servers (Chung et al., 2011). Trigger signals, correlated in space and time, are then processed by the QCN server to look for potential earthquakes.

Predictors of Interpersonal Trust in Virtual Distributed Teams

DTIC Science & Technology

2008-09-01

understand systems that are very complex in nature . Such understanding is essential to facilitate building or maintaining operators’ mental models of the...a significant impact on overall system performance. Specifically, the level of automation that combined human generation of options with computer...and/or computer servers had a significant impact on automated system performance. Additionally, Parasuraman, Sheridan, & Wickens (2000) proposed

Unconditionally verifiable blind quantum computation

NASA Astrophysics Data System (ADS)

Fitzsimons, Joseph F.; Kashefi, Elham

2017-07-01

Blind quantum computing (BQC) allows a client to have a server carry out a quantum computation for them such that the client's input, output, and computation remain private. A desirable property for any BQC protocol is verification, whereby the client can verify with high probability whether the server has followed the instructions of the protocol or if there has been some deviation resulting in a corrupted output state. A verifiable BQC protocol can be viewed as an interactive proof system leading to consequences for complexity theory. We previously proposed [A. Broadbent, J. Fitzsimons, and E. Kashefi, in Proceedings of the 50th Annual Symposium on Foundations of Computer Science, Atlanta, 2009 (IEEE, Piscataway, 2009), p. 517] a universal and unconditionally secure BQC scheme where the client only needs to be able to prepare single qubits in separable states randomly chosen from a finite set and send them to the server, who has the balance of the required quantum computational resources. In this paper we extend that protocol with additional functionality allowing blind computational basis measurements, which we use to construct another verifiable BQC protocol based on a different class of resource states. We rigorously prove that the probability of failing to detect an incorrect output is exponentially small in a security parameter, while resource overhead remains polynomial in this parameter. This resource state allows entangling gates to be performed between arbitrary pairs of logical qubits with only constant overhead. This is a significant improvement on the original scheme, which required that all computations to be performed must first be put into a nearest-neighbor form, incurring linear overhead in the number of qubits. Such an improvement has important consequences for efficiency and fault-tolerance thresholds.

Some Programs Should Not Run on Laptops - Providing Programmatic Access to Applications Via Web Services

NASA Astrophysics Data System (ADS)

Gupta, V.; Gupta, N.; Gupta, S.; Field, E.; Maechling, P.

2003-12-01

Modern laptop computers, and personal computers, can provide capabilities that are, in many ways, comparable to workstations or departmental servers. However, this doesn't mean we should run all computations on our local computers. We have identified several situations in which it preferable to implement our seismological application programs in a distributed, server-based, computing model. In this model, application programs on the user's laptop, or local computer, invoke programs that run on an organizational server, and the results are returned to the invoking system. Situations in which a server-based architecture may be preferred include: (a) a program is written in a language, or written for an operating environment, that is unsupported on the local computer, (b) software libraries or utilities required to execute a program are not available on the users computer, (c) a computational program is physically too large, or computationally too expensive, to run on a users computer, (d) a user community wants to enforce a consistent method of performing a computation by standardizing on a single implementation of a program, and (e) the computational program may require current information, that is not available to all client computers. Until recently, distributed, server-based, computational capabilities were implemented using client/server architectures. In these architectures, client programs were often written in the same language, and they executed in the same computing environment, as the servers. Recently, a new distributed computational model, called Web Services, has been developed. Web Services are based on Internet standards such as XML, SOAP, WDSL, and UDDI. Web Services offer the promise of platform, and language, independent distributed computing. To investigate this new computational model, and to provide useful services to the SCEC Community, we have implemented several computational and utility programs using a Web Service architecture. We have hosted these Web Services as a part of the SCEC Community Modeling Environment (SCEC/CME) ITR Project (http://www.scec.org/cme). We have implemented Web Services for several of the reasons sited previously. For example, we implemented a FORTRAN-based Earthquake Rupture Forecast (ERF) as a Web Service for use by client computers that don't support a FORTRAN runtime environment. We implemented a Generic Mapping Tool (GMT) Web Service for use by systems that don't have local access to GMT. We implemented a Hazard Map Calculator Web Service to execute Hazard calculations that are too computationally intensive to run on a local system. We implemented a Coordinate Conversion Web Service to enforce a standard and consistent method for converting between UTM and Lat/Lon. Our experience developing these services indicates both strengths and weakness in current Web Service technology. Client programs that utilize Web Services typically need network access, a significant disadvantage at times. Programs with simple input and output parameters were the easiest to implement as Web Services, while programs with complex parameter-types required a significant amount of additional development. We also noted that Web services are very data-oriented, and adapting object-oriented software into the Web Service model proved problematic. Also, the Web Service approach of converting data types into XML format for network transmission has significant inefficiencies for some data sets.

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

Data decomposition of Monte Carlo particle transport simulations via tally servers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romano, Paul K.; Siegel, Andrew R.; Forget, Benoit

An algorithm for decomposing large tally data in Monte Carlo particle transport simulations is developed, analyzed, and implemented in a continuous-energy Monte Carlo code, OpenMC. The algorithm is based on a non-overlapping decomposition of compute nodes into tracking processors and tally servers. The former are used to simulate the movement of particles through the domain while the latter continuously receive and update tally data. A performance model for this approach is developed, suggesting that, for a range of parameters relevant to LWR analysis, the tally server algorithm should perform with minimal overhead on contemporary supercomputers. An implementation of the algorithmmore » in OpenMC is then tested on the Intrepid and Titan supercomputers, supporting the key predictions of the model over a wide range of parameters. We thus conclude that the tally server algorithm is a successful approach to circumventing classical on-node memory constraints en route to unprecedentedly detailed Monte Carlo reactor simulations.« less

Cybersecurity, massive data processing, community interaction, and other developments at WWW-based computational X-ray Server

NASA Astrophysics Data System (ADS)

Stepanov, Sergey

2013-03-01

X-Ray Server (x-server.gmca.aps.anl.gov) is a WWW-based computational server for modeling of X-ray diffraction, reflection and scattering data. The modeling software operates directly on the server and can be accessed remotely either from web browsers or from user software. In the later case the server can be deployed as a software library or a data fitting engine. As the server recently surpassed the milestones of 15 years online and 1.5 million calculations, it accumulated a number of technical solutions that are discussed in this paper. The developed approaches to detecting physical model limits and user calculations failures, solutions to spam and firewall problems, ways to involve the community in replenishing databases and methods to teach users automated access to the server programs may be helpful for X-ray researchers interested in using the server or sharing their own software online.

Secure Skyline Queries on Cloud Platform

PubMed Central

Liu, Jinfei; Yang, Juncheng; Xiong, Li; Pei, Jian

2017-01-01

Outsourcing data and computation to cloud server provides a cost-effective way to support large scale data storage and query processing. However, due to security and privacy concerns, sensitive data (e.g., medical records) need to be protected from the cloud server and other unauthorized users. One approach is to outsource encrypted data to the cloud server and have the cloud server perform query processing on the encrypted data only. It remains a challenging task to support various queries over encrypted data in a secure and efficient way such that the cloud server does not gain any knowledge about the data, query, and query result. In this paper, we study the problem of secure skyline queries over encrypted data. The skyline query is particularly important for multi-criteria decision making but also presents significant challenges due to its complex computations. We propose a fully secure skyline query protocol on data encrypted using semantically-secure encryption. As a key subroutine, we present a new secure dominance protocol, which can be also used as a building block for other queries. Finally, we provide both serial and parallelized implementations and empirically study the protocols in terms of efficiency and scalability under different parameter settings, verifying the feasibility of our proposed solutions. PMID:28883710

HPC: Rent or Buy

ERIC Educational Resources Information Center

Fredette, Michelle

2012-01-01

"Rent or buy?" is a question people ask about everything from housing to textbooks. It is also a question universities must consider when it comes to high-performance computing (HPC). With the advent of Amazon's Elastic Compute Cloud (EC2), Microsoft Windows HPC Server, Rackspace's OpenStack, and other cloud-based services, researchers now have…

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Vu, Quoc; Chao, Yi; Li, Zhi-Jin; Choi, Jei-Kook

2006-01-01

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Naver: a PC-cluster-based VR system

NASA Astrophysics Data System (ADS)

Park, ChangHoon; Ko, HeeDong; Kim, TaiYun

2003-04-01

In this paper, we present a new framework NAVER for virtual reality application. The NAVER is based on a cluster of low-cost personal computers. The goal of NAVER is to provide flexible, extensible, scalable and re-configurable framework for the virtual environments defined as the integration of 3D virtual space and external modules. External modules are various input or output devices and applications on the remote hosts. From the view of system, personal computers are divided into three servers according to its specific functions: Render Server, Device Server and Control Server. While Device Server contains external modules requiring event-based communication for the integration, Control Server contains external modules requiring synchronous communication every frame. And, the Render Server consists of 5 managers: Scenario Manager, Event Manager, Command Manager, Interaction Manager and Sync Manager. These managers support the declaration and operation of virtual environment and the integration with external modules on remote servers.

Generic Divide and Conquer Internet-Based Computing

NASA Technical Reports Server (NTRS)

Radenski, Atanas; Follen, Gregory J. (Technical Monitor)

2001-01-01

The rapid growth of internet-based applications and the proliferation of networking technologies have been transforming traditional commercial application areas as well as computer and computational sciences and engineering. This growth stimulates the exploration of new, internet-oriented software technologies that can open new research and application opportunities not only for the commercial world, but also for the scientific and high -performance computing applications community. The general goal of this research project is to contribute to better understanding of the transition to internet-based high -performance computing and to develop solutions for some of the difficulties of this transition. More specifically, our goal is to design an architecture for generic divide and conquer internet-based computing, to develop a portable implementation of this architecture, to create an example library of high-performance divide-and-conquer computing agents that run on top of this architecture, and to evaluate the performance of these agents. We have been designing an architecture that incorporates a master task-pool server and utilizes satellite computational servers that operate on the Internet in a dynamically changing large configuration of lower-end nodes provided by volunteer contributors. Our designed architecture is intended to be complementary to and accessible from computational grids such as Globus, Legion, and Condor. Grids provide remote access to existing high-end computing resources; in contrast, our goal is to utilize idle processor time of lower-end internet nodes. Our project is focused on a generic divide-and-conquer paradigm and its applications that operate on a loose and ever changing pool of lower-end internet nodes.

Incorporating client-server database architecture and graphical user interface into outpatient medical records.

PubMed Central

Fiacco, P. A.; Rice, W. H.

1991-01-01

Computerized medical record systems require structured database architectures for information processing. However, the data must be able to be transferred across heterogeneous platform and software systems. Client-Server architecture allows for distributive processing of information among networked computers and provides the flexibility needed to link diverse systems together effectively. We have incorporated this client-server model with a graphical user interface into an outpatient medical record system, known as SuperChart, for the Department of Family Medicine at SUNY Health Science Center at Syracuse. SuperChart was developed using SuperCard and Oracle SuperCard uses modern object-oriented programming to support a hypermedia environment. Oracle is a powerful relational database management system that incorporates a client-server architecture. This provides both a distributed database and distributed processing which improves performance. PMID:1807732

SPEER-SERVER: a web server for prediction of protein specificity determining sites

PubMed Central

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

2012-01-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry.

PubMed

Yan, Yumeng; Tao, Huanyu; Huang, Sheng-You

2018-05-26

A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 10∼20 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

PubMed

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

2012-07-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

Accelerating Demand Paging for Local and Remote Out-of-Core Visualization

NASA Technical Reports Server (NTRS)

Ellsworth, David

2001-01-01

This paper describes a new algorithm that improves the performance of application-controlled demand paging for the out-of-core visualization of data sets that are on either local disks or disks on remote servers. The performance improvements come from better overlapping the computation with the page reading process, and by performing multiple page reads in parallel. The new algorithm can be applied to many different visualization algorithms since application-controlled demand paging is not specific to any visualization algorithm. The paper includes measurements that show that the new multi-threaded paging algorithm decreases the time needed to compute visualizations by one third when using one processor and reading data from local disk. The time needed when using one processor and reading data from remote disk decreased by up to 60%. Visualization runs using data from remote disk ran about as fast as ones using data from local disk because the remote runs were able to make use of the remote server's high performance disk array.

Experimental Blind Quantum Computing for a Classical Client.

PubMed

Huang, He-Liang; Zhao, Qi; Ma, Xiongfeng; Liu, Chang; Su, Zu-En; Wang, Xi-Lin; Li, Li; Liu, Nai-Le; Sanders, Barry C; Lu, Chao-Yang; Pan, Jian-Wei

2017-08-04

To date, blind quantum computing demonstrations require clients to have weak quantum devices. Here we implement a proof-of-principle experiment for completely classical clients. Via classically interacting with two quantum servers that share entanglement, the client accomplishes the task of having the number 15 factorized by servers who are denied information about the computation itself. This concealment is accompanied by a verification protocol that tests servers' honesty and correctness. Our demonstration shows the feasibility of completely classical clients and thus is a key milestone towards secure cloud quantum computing.

Experimental Blind Quantum Computing for a Classical Client

NASA Astrophysics Data System (ADS)

Huang, He-Liang; Zhao, Qi; Ma, Xiongfeng; Liu, Chang; Su, Zu-En; Wang, Xi-Lin; Li, Li; Liu, Nai-Le; Sanders, Barry C.; Lu, Chao-Yang; Pan, Jian-Wei

2017-08-01

To date, blind quantum computing demonstrations require clients to have weak quantum devices. Here we implement a proof-of-principle experiment for completely classical clients. Via classically interacting with two quantum servers that share entanglement, the client accomplishes the task of having the number 15 factorized by servers who are denied information about the computation itself. This concealment is accompanied by a verification protocol that tests servers' honesty and correctness. Our demonstration shows the feasibility of completely classical clients and thus is a key milestone towards secure cloud quantum computing.

JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility

PubMed Central

2012-01-01

Background Laboratories engaged in computational biology or bioinformatics frequently need to run lengthy, multistep, and user-driven computational jobs. Each job can tie up a computer for a few minutes to several days, and many laboratories lack the expertise or resources to build and maintain a dedicated computer cluster. Results JobCenter is a client–server application and framework for job management and distributed job execution. The client and server components are both written in Java and are cross-platform and relatively easy to install. All communication with the server is client-driven, which allows worker nodes to run anywhere (even behind external firewalls or “in the cloud”) and provides inherent load balancing. Adding a worker node to the worker pool is as simple as dropping the JobCenter client files onto any computer and performing basic configuration, which provides tremendous ease-of-use, flexibility, and limitless horizontal scalability. Each worker installation may be independently configured, including the types of jobs it is able to run. Executed jobs may be written in any language and may include multistep workflows. Conclusions JobCenter is a versatile and scalable distributed job management system that allows laboratories to very efficiently distribute all computational work among available resources. JobCenter is freely available at http://code.google.com/p/jobcenter/. PMID:22846423

Surfing for Data: A Gathering Trend in Data Storage Is the Use of Web-Based Applications that Make It Easy for Authorized Users to Access Hosted Server Content with Just a Computing Device and Browser

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

In recent years, the widespread availability of networks and the flexibility of Web browsers have shifted the industry from a client-server model to a Web-based one. In the client-server model of computing, clients run applications locally, with the servers managing storage, printing functions, and network traffic. Because every client is…

Usage of Thin-Client/Server Architecture in Computer Aided Education

ERIC Educational Resources Information Center

Cimen, Caghan; Kavurucu, Yusuf; Aydin, Halit

2014-01-01

With the advances of technology, thin-client/server architecture has become popular in multi-user/single network environments. Thin-client is a user terminal in which the user can login to a domain and run programs by connecting to a remote server. Recent developments in network and hardware technologies (cloud computing, virtualization, etc.)…

Cryptanalysis and improvement of a biometrics-based authentication and key agreement scheme for multi-server environments.

PubMed

Yang, Li; Zheng, Zhiming

2018-01-01

According to advancements in the wireless technologies, study of biometrics-based multi-server authenticated key agreement schemes has acquired a lot of momentum. Recently, Wang et al. presented a three-factor authentication protocol with key agreement and claimed that their scheme was resistant to several prominent attacks. Unfortunately, this paper indicates that their protocol is still vulnerable to the user impersonation attack, privileged insider attack and server spoofing attack. Furthermore, their protocol cannot provide the perfect forward secrecy. As a remedy of these aforementioned problems, we propose a biometrics-based authentication and key agreement scheme for multi-server environments. Compared with various related schemes, our protocol achieves the stronger security and provides more functionality properties. Besides, the proposed protocol shows the satisfactory performances in respect of storage requirement, communication overhead and computational cost. Thus, our protocol is suitable for expert systems and other multi-server architectures. Consequently, the proposed protocol is more appropriate in the distributed networks.

A group communication approach for mobile computing mobile channel: An ISIS tool for mobile services

NASA Astrophysics Data System (ADS)

Cho, Kenjiro; Birman, Kenneth P.

1994-05-01

This paper examines group communication as an infrastructure to support mobility of users, and presents a simple scheme to support user mobility by means of switching a control point between replicated servers. We describe the design and implementation of a set of tools, called Mobile Channel, for use with the ISIS system. Mobile Channel is based on a combination of the two replication schemes: the primary-backup approach and the state machine approach. Mobile Channel implements a reliable one-to-many FIFO channel, in which a mobile client sees a single reliable server; servers, acting as a state machine, see multicast messages from clients. Migrations of mobile clients are handled as an intentional primary switch, and hand-offs or server failures are completely masked to mobile clients. To achieve high performance, servers are replicated at a sliding-window level. Our scheme provides a simple abstraction of migration, eliminates complicated hand-off protocols, provides fault-tolerance and is implemented within the existing group communication mechanism.

Cryptanalysis and improvement of a biometrics-based authentication and key agreement scheme for multi-server environments

PubMed Central

Zheng, Zhiming

2018-01-01

According to advancements in the wireless technologies, study of biometrics-based multi-server authenticated key agreement schemes has acquired a lot of momentum. Recently, Wang et al. presented a three-factor authentication protocol with key agreement and claimed that their scheme was resistant to several prominent attacks. Unfortunately, this paper indicates that their protocol is still vulnerable to the user impersonation attack, privileged insider attack and server spoofing attack. Furthermore, their protocol cannot provide the perfect forward secrecy. As a remedy of these aforementioned problems, we propose a biometrics-based authentication and key agreement scheme for multi-server environments. Compared with various related schemes, our protocol achieves the stronger security and provides more functionality properties. Besides, the proposed protocol shows the satisfactory performances in respect of storage requirement, communication overhead and computational cost. Thus, our protocol is suitable for expert systems and other multi-server architectures. Consequently, the proposed protocol is more appropriate in the distributed networks. PMID:29534085

Design and implementation of a reliable and cost-effective cloud computing infrastructure: the INFN Napoli experience

NASA Astrophysics Data System (ADS)

Capone, V.; Esposito, R.; Pardi, S.; Taurino, F.; Tortone, G.

2012-12-01

Over the last few years we have seen an increasing number of services and applications needed to manage and maintain cloud computing facilities. This is particularly true for computing in high energy physics, which often requires complex configurations and distributed infrastructures. In this scenario a cost effective rationalization and consolidation strategy is the key to success in terms of scalability and reliability. In this work we describe an IaaS (Infrastructure as a Service) cloud computing system, with high availability and redundancy features, which is currently in production at INFN-Naples and ATLAS Tier-2 data centre. The main goal we intended to achieve was a simplified method to manage our computing resources and deliver reliable user services, reusing existing hardware without incurring heavy costs. A combined usage of virtualization and clustering technologies allowed us to consolidate our services on a small number of physical machines, reducing electric power costs. As a result of our efforts we developed a complete solution for data and computing centres that can be easily replicated using commodity hardware. Our architecture consists of 2 main subsystems: a clustered storage solution, built on top of disk servers running GlusterFS file system, and a virtual machines execution environment. GlusterFS is a network file system able to perform parallel writes on multiple disk servers, providing this way live replication of data. High availability is also achieved via a network configuration using redundant switches and multiple paths between hypervisor hosts and disk servers. We also developed a set of management scripts to easily perform basic system administration tasks such as automatic deployment of new virtual machines, adaptive scheduling of virtual machines on hypervisor hosts, live migration and automated restart in case of hypervisor failures.

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-02-15

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 millionmore » vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-05-29

We present a new lock-free parallel algorithm for computing betweenness centrality of massive small-world networks. With minor changes to the data structures, our algorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in the HPCS SSCA#2 Graph Analysis benchmark, which has been extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the ThreadStorm processor, and a single-socket Sun multicore server with the UltraSparc T2 processor.more » For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

An Elliptic Curve Based Schnorr Cloud Security Model in Distributed Environment

PubMed Central

Muthurajan, Vinothkumar; Narayanasamy, Balaji

2016-01-01

Cloud computing requires the security upgrade in data transmission approaches. In general, key-based encryption/decryption (symmetric and asymmetric) mechanisms ensure the secure data transfer between the devices. The symmetric key mechanisms (pseudorandom function) provide minimum protection level compared to asymmetric key (RSA, AES, and ECC) schemes. The presence of expired content and the irrelevant resources cause unauthorized data access adversely. This paper investigates how the integrity and secure data transfer are improved based on the Elliptic Curve based Schnorr scheme. This paper proposes a virtual machine based cloud model with Hybrid Cloud Security Algorithm (HCSA) to remove the expired content. The HCSA-based auditing improves the malicious activity prediction during the data transfer. The duplication in the cloud server degrades the performance of EC-Schnorr based encryption schemes. This paper utilizes the blooming filter concept to avoid the cloud server duplication. The combination of EC-Schnorr and blooming filter efficiently improves the security performance. The comparative analysis between proposed HCSA and the existing Distributed Hash Table (DHT) regarding execution time, computational overhead, and auditing time with auditing requests and servers confirms the effectiveness of HCSA in the cloud security model creation. PMID:26981584

An Elliptic Curve Based Schnorr Cloud Security Model in Distributed Environment.

PubMed

Muthurajan, Vinothkumar; Narayanasamy, Balaji

2016-01-01

Cloud computing requires the security upgrade in data transmission approaches. In general, key-based encryption/decryption (symmetric and asymmetric) mechanisms ensure the secure data transfer between the devices. The symmetric key mechanisms (pseudorandom function) provide minimum protection level compared to asymmetric key (RSA, AES, and ECC) schemes. The presence of expired content and the irrelevant resources cause unauthorized data access adversely. This paper investigates how the integrity and secure data transfer are improved based on the Elliptic Curve based Schnorr scheme. This paper proposes a virtual machine based cloud model with Hybrid Cloud Security Algorithm (HCSA) to remove the expired content. The HCSA-based auditing improves the malicious activity prediction during the data transfer. The duplication in the cloud server degrades the performance of EC-Schnorr based encryption schemes. This paper utilizes the blooming filter concept to avoid the cloud server duplication. The combination of EC-Schnorr and blooming filter efficiently improves the security performance. The comparative analysis between proposed HCSA and the existing Distributed Hash Table (DHT) regarding execution time, computational overhead, and auditing time with auditing requests and servers confirms the effectiveness of HCSA in the cloud security model creation.

An incremental database access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, Nicholas; Sellis, Timos

1994-01-01

We investigated a number of design and performance issues of interoperable database management systems (DBMS's). The major results of our investigation were obtained in the areas of client-server database architectures for heterogeneous DBMS's, incremental computation models, buffer management techniques, and query optimization. We finished a prototype of an advanced client-server workstation-based DBMS which allows access to multiple heterogeneous commercial DBMS's. Experiments and simulations were then run to compare its performance with the standard client-server architectures. The focus of this research was on adaptive optimization methods of heterogeneous database systems. Adaptive buffer management accounts for the random and object-oriented access methods for which no known characterization of the access patterns exists. Adaptive query optimization means that value distributions and selectives, which play the most significant role in query plan evaluation, are continuously refined to reflect the actual values as opposed to static ones that are computed off-line. Query feedback is a concept that was first introduced to the literature by our group. We employed query feedback for both adaptive buffer management and for computing value distributions and selectivities. For adaptive buffer management, we use the page faults of prior executions to achieve more 'informed' management decisions. For the estimation of the distributions of the selectivities, we use curve-fitting techniques, such as least squares and splines, for regressing on these values.

On delay adjustment for dynamic load balancing in distributed virtual environments.

PubMed

Deng, Yunhua; Lau, Rynson W H

2012-04-01

Distributed virtual environments (DVEs) are becoming very popular in recent years, due to the rapid growing of applications, such as massive multiplayer online games (MMOGs). As the number of concurrent users increases, scalability becomes one of the major challenges in designing an interactive DVE system. One solution to address this scalability problem is to adopt a multi-server architecture. While some methods focus on the quality of partitioning the load among the servers, others focus on the efficiency of the partitioning process itself. However, all these methods neglect the effect of network delay among the servers on the accuracy of the load balancing solutions. As we show in this paper, the change in the load of the servers due to network delay would affect the performance of the load balancing algorithm. In this work, we conduct a formal analysis of this problem and discuss two efficient delay adjustment schemes to address the problem. Our experimental results show that our proposed schemes can significantly improve the performance of the load balancing algorithm with neglectable computation overhead.

Web-based system for surgical planning and simulation

NASA Astrophysics Data System (ADS)

Eldeib, Ayman M.; Ahmed, Mohamed N.; Farag, Aly A.; Sites, C. B.

1998-10-01

The growing scientific knowledge and rapid progress in medical imaging techniques has led to an increasing demand for better and more efficient methods of remote access to high-performance computer facilities. This paper introduces a web-based telemedicine project that provides interactive tools for surgical simulation and planning. The presented approach makes use of client-server architecture based on new internet technology where clients use an ordinary web browser to view, send, receive and manipulate patients' medical records while the server uses the supercomputer facility to generate online semi-automatic segmentation, 3D visualization, surgical simulation/planning and neuroendoscopic procedures navigation. The supercomputer (SGI ONYX 1000) is located at the Computer Vision and Image Processing Lab, University of Louisville, Kentucky. This system is under development in cooperation with the Department of Neurological Surgery, Alliant Health Systems, Louisville, Kentucky. The server is connected via a network to the Picture Archiving and Communication System at Alliant Health Systems through a DICOM standard interface that enables authorized clients to access patients' images from different medical modalities.

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

PubMed

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

2012-06-15

A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Client/Server data serving for high performance computing

NASA Technical Reports Server (NTRS)

Wood, Chris

1994-01-01

This paper will attempt to examine the industry requirements for shared network data storage and sustained high speed (10's to 100's to thousands of megabytes per second) network data serving via the NFS and FTP protocol suite. It will discuss the current structural and architectural impediments to achieving these sorts of data rates cost effectively today on many general purpose servers and will describe and architecture and resulting product family that addresses these problems. The sustained performance levels that were achieved in the lab will be shown as well as a discussion of early customer experiences utilizing both the HIPPI-IP and ATM OC3-IP network interfaces.

Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.

PubMed

Rey-Villamizar, Nicolas; Somasundar, Vinay; Megjhani, Murad; Xu, Yan; Lu, Yanbin; Padmanabhan, Raghav; Trett, Kristen; Shain, William; Roysam, Badri

2014-01-01

In this article, we describe the use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes, including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis tasks, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral images of brain tissue surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels. Each channel consists of 6000 × 10,000 × 500 voxels with 16 bits/voxel, implying image sizes exceeding 250 GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analysis for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN) capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment. Our Python script enables efficient data storage and movement between computers and storage servers, logs all the processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries.

Mobile cloud-computing-based healthcare service by noncontact ECG monitoring.

PubMed

Fong, Ee-May; Chung, Wan-Young

2013-12-02

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service.

Towards optimizing server performance in an educational MMORPG for teaching computer programming

NASA Astrophysics Data System (ADS)

Malliarakis, Christos; Satratzemi, Maya; Xinogalos, Stelios

2013-10-01

Web-based games have become significantly popular during the last few years. This is due to the gradual increase of internet speed, which has led to the ongoing multiplayer games development and more importantly the emergence of the Massive Multiplayer Online Role Playing Games (MMORPG) field. In parallel, similar technologies called educational games have started to be developed in order to be put into practice in various educational contexts, resulting in the field of Game Based Learning. However, these technologies require significant amounts of resources, such as bandwidth, RAM and CPU capacity etc. These amounts may be even larger in an educational MMORPG game that supports computer programming education, due to the usual inclusion of a compiler and the constant client/server data transmissions that occur during program coding, possibly leading to technical issues that could cause malfunctions during learning. Thus, the determination of the elements that affect the overall games resources' load is essential so that server administrators can configure them and ensure educational games' proper operation during computer programming education. In this paper, we propose a new methodology with which we can achieve monitoring and optimization of the load balancing, so that the essential resources for the creation and proper execution of an educational MMORPG for computer programming can be foreseen and bestowed without overloading the system.

Mobile Cloud-Computing-Based Healthcare Service by Noncontact ECG Monitoring

PubMed Central

Fong, Ee-May; Chung, Wan-Young

2013-01-01

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service. PMID:24316562

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

Development of a Real-Time GPS/Seismic Displacement Meter: GPS Component

NASA Astrophysics Data System (ADS)

Bock, Y.; Canas, J.; Andrew, A.; Vernon, F.

2002-12-01

We report on the status of the Orange County Real-Time GPS Network (OCRTN), an upgrade of the SCIGN sites in Orange County and Catalina Island to low latency (1 sec), high-rate (1 Hz) data streaming, analysis, and dissemination. The project is a collaborative effort of the California Spatial Reference Center (CSRC) and the Orange County Dept. of Geomatics, with partners from the geophysical community (SCIGN), local and state government, and the private sector. As part of Phase 1 of the project, nine sites are streaming data by dedicated, point-to-point radio modems to a central data server located in Santa Ana. Instantaneous positions are computed for each site. Data are converted from 1 Hz Ashtech binary MBEN format to (1) 1 Hz RTCM format, and (2) decimated (15 sec) RINEX format. A second computer outside a firewall and located in another building at the Orange County's Computer Center is a TCP-based client of RTCM data (messages 18, 19, 3, and 22) from the data server, as well as a TCP-based server of RTCM data to the outside world. An external computer can access the RTCM data from all active sites through an IP socket connection. Data latency, in the best case, is less than 1 sec from real-time. Once a day, the decimated RINEX data are transferred by ftp from the data server to the SOPAC-CSRC archive at Scripps. Data recovery is typically 99-100%. As part of the second phase of the project, the RTCM server provides data to field receivers to perform RTK surveying. On connection to the RTCM server the user gets a list of active stations, and can then choose from which site to retrieve RTCM data. This site then plays the role of the RTK base station and a CDPD-based wireless Internet device plays the role of the normal RTK radio link. If an Internet connection is available, we will demonstrate how the system operates. This system will serve as a prototype for the GPS component of the GPS/seismic displacement meter.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.

PubMed

Baek, Minkyung; Park, Taeyong; Heo, Lim; Park, Chiwook; Seok, Chaok

2017-07-03

Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure database or by ab initio docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Running GUI Applications on Peregrine from OSX | High-Performance Computing

Science.gov Websites

Learn how to use Virtual Network Computing to access a Linux graphical desktop environment on Peregrine local port (on, e.g., your laptop), starts a VNC server process that manages a virtual desktop on your virtual desktop. This is persistent, so remember it-you will use this password whenever accessing

Virtualizing access to scientific applications with the Application Hosting Environment

NASA Astrophysics Data System (ADS)

Zasada, S. J.; Coveney, P. V.

2009-12-01

The growing power and number of high performance computing resources made available through computational grids present major opportunities as well as a number of challenges to the user. At issue is how these resources can be accessed and how their power can be effectively exploited. In this paper we first present our views on the usability of contemporary high-performance computational resources. We introduce the concept of grid application virtualization as a solution to some of the problems with grid-based HPC usability. We then describe a middleware tool that we have developed to realize the virtualization of grid applications, the Application Hosting Environment (AHE), and describe the features of the new release, AHE 2.0, which provides access to a common platform of federated computational grid resources in standard and non-standard ways. Finally, we describe a case study showing how AHE supports clinical use of whole brain blood flow modelling in a routine and automated fashion. Program summaryProgram title: Application Hosting Environment 2.0 Catalogue identifier: AEEJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence, Version 2 No. of lines in distributed program, including test data, etc.: not applicable No. of bytes in distributed program, including test data, etc.: 1 685 603 766 Distribution format: tar.gz Programming language: Perl (server), Java (Client) Computer: x86 Operating system: Linux (Server), Linux/Windows/MacOS (Client) RAM: 134 217 728 (server), 67 108 864 (client) bytes Classification: 6.5 External routines: VirtualBox (server), Java (client) Nature of problem: The middleware that makes grid computing possible has been found by many users to be too unwieldy, and presents an obstacle to use rather than providing assistance [1,2]. Such problems are compounded when one attempts to harness the power of a grid, or a federation of different grids, rather than just a single resource on the grid. Solution method: To address the above problem, we have developed AHE, a lightweight interface, designed to simplify the process of running scientific codes on a grid of HPC and local resources. AHE does this by introducing a layer of middleware between the user and the grid, which encapsulates much of the complexity associated with launching grid applications. Unusual features: The server is distributed as a VirtualBox virtual machine. VirtualBox ( http://www.virtualbox.org) must be downloaded and installed in order to run the AHE server virtual machine. Details of how to do this are given in the AHE 2.0 Quick Start Guide. Running time: Not applicable References:J. Chin, P.V. Coveney, Towards tractable toolkits for the grid: A plea for lightweight, useable middleware, NeSC Technical Report, 2004, http://nesc.ac.uk/technical_papers/UKeS-2004-01.pdf. P.V. Coveney, R.S. Saksena, S.J. Zasada, M. McKeown, S. Pickles, The Application Hosting Environment: Lightweight middleware for grid-based computational science, Computer Physics Communications 176 (2007) 406-418.

3Drefine: an interactive web server for efficient protein structure refinement

PubMed Central

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-01-01

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

The FELICIA bulletin board system and the IRBIS anonymous FTP server: Computer security information sources for the DOE community. CIAC-2302

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orvis, W.J.

1993-11-03

The Computer Incident Advisory Capability (CIAC) operates two information servers for the DOE community, FELICIA (formerly FELIX) and IRBIS. FELICIA is a computer Bulletin Board System (BBS) that can be accessed by telephone with a modem. IRBIS is an anonymous ftp server that can be accessed on the Internet. Both of these servers contain all of the publicly available CIAC, CERT, NIST, and DDN bulletins, virus descriptions, the VIRUS-L moderated virus bulletin board, copies of public domain and shareware virus- detection/protection software, and copies of useful public domain and shareware utility programs. This guide describes how to connect these systemsmore » and obtain files from them.« less

Evaluation of Content-Matched Range Monitoring Queries over Moving Objects in Mobile Computing Environments.

PubMed

Jung, HaRim; Song, MoonBae; Youn, Hee Yong; Kim, Ung Mo

2015-09-18

A content-matched (CM) rangemonitoring query overmoving objects continually retrieves the moving objects (i) whose non-spatial attribute values are matched to given non-spatial query values; and (ii) that are currently located within a given spatial query range. In this paper, we propose a new query indexing structure, called the group-aware query region tree (GQR-tree) for efficient evaluation of CMrange monitoring queries. The primary role of the GQR-tree is to help the server leverage the computational capabilities of moving objects in order to improve the system performance in terms of the wireless communication cost and server workload. Through a series of comprehensive simulations, we verify the superiority of the GQR-tree method over the existing methods.

The SQL Server Database for Non Computer Professional Teaching Reform

ERIC Educational Resources Information Center

Liu, Xiangwei

2012-01-01

A summary of the teaching methods of the non-computer professional SQL Server database, analyzes the current situation of the teaching course. According to non computer professional curriculum teaching characteristic, put forward some teaching reform methods, and put it into practice, improve the students' analysis ability, practice ability and…

Multi-server blind quantum computation over collective-noise channels

NASA Astrophysics Data System (ADS)

Xiao, Min; Liu, Lin; Song, Xiuli

2018-03-01

Blind quantum computation (BQC) enables ordinary clients to securely outsource their computation task to costly quantum servers. Besides two essential properties, namely correctness and blindness, practical BQC protocols also should make clients as classical as possible and tolerate faults from nonideal quantum channel. In this paper, using logical Bell states as quantum resource, we propose multi-server BQC protocols over collective-dephasing noise channel and collective-rotation noise channel, respectively. The proposed protocols permit completely or almost classical client, meet the correctness and blindness requirements of BQC protocol, and are typically practical BQC protocols.

Measurement of Energy Performances for General-Structured Servers

NASA Astrophysics Data System (ADS)

Liu, Ren; Chen, Lili; Li, Pengcheng; Liu, Meng; Chen, Haihong

2017-11-01

Energy consumption of servers in data centers increases rapidly along with the wide application of Internet and connected devices. To improve the energy efficiency of servers, voluntary or mandatory energy efficiency programs for servers, including voluntary label program or mandatory energy performance standards have been adopted or being prepared in the US, EU and China. However, the energy performance of servers and testing methods of servers are not well defined. This paper presents matrices to measure the energy performances of general-structured servers. The impacts of various components of servers on their energy performances are also analyzed. Based on a set of normalized workload, the author proposes a standard method for testing energy efficiency of servers. Pilot tests are conducted to assess the energy performance testing methods of servers. The findings of the tests are discussed in the paper.

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

An Efficient and Practical Smart Card Based Anonymity Preserving User Authentication Scheme for TMIS using Elliptic Curve Cryptography.

PubMed

Amin, Ruhul; Islam, S K Hafizul; Biswas, G P; Khan, Muhammad Khurram; Kumar, Neeraj

2015-11-01

In the last few years, numerous remote user authentication and session key agreement schemes have been put forwarded for Telecare Medical Information System, where the patient and medical server exchange medical information using Internet. We have found that most of the schemes are not usable for practical applications due to known security weaknesses. It is also worth to note that unrestricted number of patients login to the single medical server across the globe. Therefore, the computation and maintenance overhead would be high and the server may fail to provide services. In this article, we have designed a medical system architecture and a standard mutual authentication scheme for single medical server, where the patient can securely exchange medical data with the doctor(s) via trusted central medical server over any insecure network. We then explored the security of the scheme with its resilience to attacks. Moreover, we formally validated the proposed scheme through the simulation using Automated Validation of Internet Security Schemes and Applications software whose outcomes confirm that the scheme is protected against active and passive attacks. The performance comparison demonstrated that the proposed scheme has lower communication cost than the existing schemes in literature. In addition, the computation cost of the proposed scheme is nearly equal to the exiting schemes. The proposed scheme not only efficient in terms of different security attacks, but it also provides an efficient login, mutual authentication, session key agreement and verification and password update phases along with password recovery.

Smart Cards and remote entrusting

NASA Astrophysics Data System (ADS)

Aussel, Jean-Daniel; D'Annoville, Jerome; Castillo, Laurent; Durand, Stephane; Fabre, Thierry; Lu, Karen; Ali, Asad

Smart cards are widely used to provide security in end-to-end communication involving servers and a variety of terminals, including mobile handsets or payment terminals. Sometime, end-to-end server to smart card security is not applicable, and smart cards must communicate directly with an application executing on a terminal, like a personal computer, without communicating with a server. In this case, the smart card must somehow trust the terminal application before performing some secure operation it was designed for. This paper presents a novel method to remotely trust a terminal application from the smart card. For terminals such as personal computers, this method is based on an advanced secure device connected through the USB and consisting of a smart card bundled with flash memory. This device, or USB dongle, can be used in the context of remote untrusting to secure portable applications conveyed in the dongle flash memory. White-box cryptography is used to set the secure channel and a mechanism based on thumbprint is described to provide external authentication when session keys need to be renewed. Although not as secure as end-to-end server to smart card security, remote entrusting with smart cards is easy to deploy for mass-market applications and can provide a reasonable level of security.

ACFIS: a web server for fragment-based drug discovery

PubMed Central

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-01-01

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. PMID:27150808

New Additions to the ClusPro Server Motivated by CAPRI

PubMed Central

Vajda, Sandor; Yueh, Christine; Beglov, Dmitri; Bohnuud, Tanggis; Mottarella, Scott E.; Xia, Bing; Hall, David R.; Kozakov, Dima

2016-01-01

The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for Small Angle X-ray Scattering (SAXS) data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. PMID:27936493

ACFIS: a web server for fragment-based drug discovery.

PubMed

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-07-08

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown 'chemical space' to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for 'chemical space', which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Performance of the High Sensitivity Open Source Multi-GNSS Assisted GNSS Reference Server.

NASA Astrophysics Data System (ADS)

Sarwar, Ali; Rizos, Chris; Glennon, Eamonn

2015-06-01

The Open Source GNSS Reference Server (OSGRS) exploits the GNSS Reference Interface Protocol (GRIP) to provide assistance data to GPS receivers. Assistance can be in terms of signal acquisition and in the processing of the measurement data. The data transfer protocol is based on Extensible Mark-up Language (XML) schema. The first version of the OSGRS required a direct hardware connection to a GPS device to acquire the data necessary to generate the appropriate assistance. Scenarios of interest for the OSGRS users are weak signal strength indoors, obstructed outdoors or heavy multipath environments. This paper describes an improved version of OSGRS that provides alternative assistance support from a number of Global Navigation Satellite Systems (GNSS). The underlying protocol to transfer GNSS assistance data from global casters is the Networked Transport of RTCM (Radio Technical Commission for Maritime Services) over Internet Protocol (NTRIP), and/or the RINEX (Receiver Independent Exchange) format. This expands the assistance and support model of the OSGRS to globally available GNSS data servers connected via internet casters. A variety of formats and versions of RINEX and RTCM streams become available, which strengthens the assistance provisioning capability of the OSGRS platform. The prime motivation for this work was to enhance the system architecture of the OSGRS to take advantage of globally available GNSS data sources. Open source software architectures and assistance models provide acquisition and data processing assistance for GNSS receivers operating in weak signal environments. This paper describes test scenarios to benchmark the OSGRSv2 performance against other Assisted-GNSS solutions. Benchmarking devices include the SPOT satellite messenger, MS-Based & MS-Assisted GNSS, HSGNSS (SiRFstar-III) and Wireless Sensor Networks Assisted-GNSS. Benchmarked parameters include the number of tracked satellites, the Time to Fix First (TTFF), navigation availability and accuracy. Three different configurations of Multi-GNSS assistance servers were used, namely Cloud-Client-Server, the Demilitarized Zone (DMZ) Client-Server and PC-Client-Server; with respect to the connectivity location of client and server. The impact on the performance based on server and/or client initiation, hardware capability, network latency, processing delay and computation times with their storage, scalability, processing and load sharing capabilities, were analysed. The performance of the OSGRS is compared against commercial GNSS, Assisted-GNSS and WSN-enabled GNSS devices. The OSGRS system demonstrated lower TTFF and higher availability.

Visualization of N-body Simulations in Virtual Worlds

NASA Astrophysics Data System (ADS)

Knop, Robert A.; Ames, J.; Djorgovski, G.; Farr, W.; Hut, P.; Johnson, A.; McMillan, S.; Nakasone, A.; Vesperini, E.

2010-01-01

We report on work to use virtual worlds for visualizing the results of N-body calculations, on three levels. First, we have written a demonstration 3-body solver entirely in the scripting language of the popularly used virtual world Second Life. Second, we have written a physics module for the open source virtual world OpenSim that performs N-body calculations as the physics engine for the server, allowing natural 3-d visualization of the solution as the solution is being performed. Finally, we give an initial report on the potential use of virtual worlds to visualize calculations which have previously been performed, or which are being performed in other processes and reported to the virtual world server. This work has been performed as part of the Meta-Institute of Computational Astrophysics (MICA). http://www.mica-vw.org

Connecting to HPC VPN | High-Performance Computing | NREL

Science.gov Websites

and password will match your NREL network account login/password. From OS X or Linux, open a terminal finalized. Open a Remote Desktop connection using server name WINHPC02 (this is the login node). Mac Mac

End-to-end performance measurement of Internet based medical applications.

PubMed

Dev, P; Harris, D; Gutierrez, D; Shah, A; Senger, S

2002-01-01

We present a method to obtain an end-to-end characterization of the performance of an application over a network. This method is not dependent on any specific application or type of network. The method requires characterization of network parameters, such as latency and packet loss, between the expected server or client endpoints, as well as characterization of the application's constraints on these parameters. A subjective metric is presented that integrates these characterizations and that operates over a wide range of applications and networks. We believe that this method may be of wide applicability as research and educational applications increasingly make use of computation and data servers that are distributed over the Internet.

A Robust and Effective Smart-Card-Based Remote User Authentication Mechanism Using Hash Function

PubMed Central

Odelu, Vanga; Goswami, Adrijit

2014-01-01

In a remote user authentication scheme, a remote server verifies whether a login user is genuine and trustworthy, and also for mutual authentication purpose a login user validates whether the remote server is genuine and trustworthy. Several remote user authentication schemes using the password, the biometrics, and the smart card have been proposed in the literature. However, most schemes proposed in the literature are either computationally expensive or insecure against several known attacks. In this paper, we aim to propose a new robust and effective password-based remote user authentication scheme using smart card. Our scheme is efficient, because our scheme uses only efficient one-way hash function and bitwise XOR operations. Through the rigorous informal and formal security analysis, we show that our scheme is secure against possible known attacks. We perform the simulation for the formal security analysis using the widely accepted AVISPA (Automated Validation Internet Security Protocols and Applications) tool to ensure that our scheme is secure against passive and active attacks. Furthermore, our scheme supports efficiently the password change phase always locally without contacting the remote server and correctly. In addition, our scheme performs significantly better than other existing schemes in terms of communication, computational overheads, security, and features provided by our scheme. PMID:24892078

A robust and effective smart-card-based remote user authentication mechanism using hash function.

PubMed

Das, Ashok Kumar; Odelu, Vanga; Goswami, Adrijit

2014-01-01

In a remote user authentication scheme, a remote server verifies whether a login user is genuine and trustworthy, and also for mutual authentication purpose a login user validates whether the remote server is genuine and trustworthy. Several remote user authentication schemes using the password, the biometrics, and the smart card have been proposed in the literature. However, most schemes proposed in the literature are either computationally expensive or insecure against several known attacks. In this paper, we aim to propose a new robust and effective password-based remote user authentication scheme using smart card. Our scheme is efficient, because our scheme uses only efficient one-way hash function and bitwise XOR operations. Through the rigorous informal and formal security analysis, we show that our scheme is secure against possible known attacks. We perform the simulation for the formal security analysis using the widely accepted AVISPA (Automated Validation Internet Security Protocols and Applications) tool to ensure that our scheme is secure against passive and active attacks. Furthermore, our scheme supports efficiently the password change phase always locally without contacting the remote server and correctly. In addition, our scheme performs significantly better than other existing schemes in terms of communication, computational overheads, security, and features provided by our scheme.

Demonstration of measurement-only blind quantum computing

NASA Astrophysics Data System (ADS)

Greganti, Chiara; Roehsner, Marie-Christine; Barz, Stefanie; Morimae, Tomoyuki; Walther, Philip

2016-01-01

Blind quantum computing allows for secure cloud networks of quasi-classical clients and a fully fledged quantum server. Recently, a new protocol has been proposed, which requires a client to perform only measurements. We demonstrate a proof-of-principle implementation of this measurement-only blind quantum computing, exploiting a photonic setup to generate four-qubit cluster states for computation and verification. Feasible technological requirements for the client and the device-independent blindness make this scheme very applicable for future secure quantum networks.

A biometric method to secure telemedicine systems.

PubMed

Zhang, G H; Poon, Carmen C Y; Li, Ye; Zhang, Y T

2009-01-01

Security and privacy are among the most crucial issues for data transmission in telemedicine systems. This paper proposes a solution for securing wireless data transmission in telemedicine systems, i.e. within a body sensor network (BSN), between the BSN and server as well as between the server and professionals who have assess to the server. A unique feature of this solution is the generation of random keys by physiological data (i.e. a biometric approach) for securing communication at all 3 levels. In the performance analysis, inter-pulse interval of photoplethysmogram is used as an example to generate these biometric keys to protect wireless data transmission. The results of statistical analysis and computational complexity suggest that this type of key is random enough to make telemedicine systems resistant to attacks.

Assessment of physical server reliability in multi cloud computing system

NASA Astrophysics Data System (ADS)

Kalyani, B. J. D.; Rao, Kolasani Ramchand H.

2018-04-01

Business organizations nowadays functioning with more than one cloud provider. By spreading cloud deployment across multiple service providers, it creates space for competitive prices that minimize the burden on enterprises spending budget. To assess the software reliability of multi cloud application layered software reliability assessment paradigm is considered with three levels of abstractions application layer, virtualization layer, and server layer. The reliability of each layer is assessed separately and is combined to get the reliability of multi-cloud computing application. In this paper, we focused on how to assess the reliability of server layer with required algorithms and explore the steps in the assessment of server reliability.

Quantum processing by remote quantum control

NASA Astrophysics Data System (ADS)

Qiang, Xiaogang; Zhou, Xiaoqi; Aungskunsiri, Kanin; Cable, Hugo; O'Brien, Jeremy L.

2017-12-01

Client-server models enable computations to be hosted remotely on quantum servers. We present a novel protocol for realizing this task, with practical advantages when using technology feasible in the near term. Client tasks are realized as linear combinations of operations implemented by the server, where the linear coefficients are hidden from the server. We report on an experimental demonstration of our protocol using linear optics, which realizes linear combination of two single-qubit operations by a remote single-qubit control. In addition, we explain when our protocol can remain efficient for larger computations, as well as some ways in which privacy can be maintained using our protocol.

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

NASA Astrophysics Data System (ADS)

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad

2015-05-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).

Secure Nearest Neighbor Query on Crowd-Sensing Data

PubMed Central

Cheng, Ke; Wang, Liangmin; Zhong, Hong

2016-01-01

Nearest neighbor queries are fundamental in location-based services, and secure nearest neighbor queries mainly focus on how to securely and quickly retrieve the nearest neighbor in the outsourced cloud server. However, the previous big data system structure has changed because of the crowd-sensing data. On the one hand, sensing data terminals as the data owner are numerous and mistrustful, while, on the other hand, in most cases, the terminals find it difficult to finish many safety operation due to computation and storage capability constraints. In light of they Multi Owners and Multi Users (MOMU) situation in the crowd-sensing data cloud environment, this paper presents a secure nearest neighbor query scheme based on the proxy server architecture, which is constructed by protocols of secure two-party computation and secure Voronoi diagram algorithm. It not only preserves the data confidentiality and query privacy but also effectively resists the collusion between the cloud server and the data owners or users. Finally, extensive theoretical and experimental evaluations are presented to show that our proposed scheme achieves a superior balance between the security and query performance compared to other schemes. PMID:27669253

Secure Nearest Neighbor Query on Crowd-Sensing Data.

PubMed

Cheng, Ke; Wang, Liangmin; Zhong, Hong

2016-09-22

Nearest neighbor queries are fundamental in location-based services, and secure nearest neighbor queries mainly focus on how to securely and quickly retrieve the nearest neighbor in the outsourced cloud server. However, the previous big data system structure has changed because of the crowd-sensing data. On the one hand, sensing data terminals as the data owner are numerous and mistrustful, while, on the other hand, in most cases, the terminals find it difficult to finish many safety operation due to computation and storage capability constraints. In light of they Multi Owners and Multi Users (MOMU) situation in the crowd-sensing data cloud environment, this paper presents a secure nearest neighbor query scheme based on the proxy server architecture, which is constructed by protocols of secure two-party computation and secure Voronoi diagram algorithm. It not only preserves the data confidentiality and query privacy but also effectively resists the collusion between the cloud server and the data owners or users. Finally, extensive theoretical and experimental evaluations are presented to show that our proposed scheme achieves a superior balance between the security and query performance compared to other schemes.

Cloud-based Predictive Modeling System and its Application to Asthma Readmission Prediction

PubMed Central

Chen, Robert; Su, Hang; Khalilia, Mohammed; Lin, Sizhe; Peng, Yue; Davis, Tod; Hirsh, Daniel A; Searles, Elizabeth; Tejedor-Sojo, Javier; Thompson, Michael; Sun, Jimeng

2015-01-01

The predictive modeling process is time consuming and requires clinical researchers to handle complex electronic health record (EHR) data in restricted computational environments. To address this problem, we implemented a cloud-based predictive modeling system via a hybrid setup combining a secure private server with the Amazon Web Services (AWS) Elastic MapReduce platform. EHR data is preprocessed on a private server and the resulting de-identified event sequences are hosted on AWS. Based on user-specified modeling configurations, an on-demand web service launches a cluster of Elastic Compute 2 (EC2) instances on AWS to perform feature selection and classification algorithms in a distributed fashion. Afterwards, the secure private server aggregates results and displays them via interactive visualization. We tested the system on a pediatric asthma readmission task on a de-identified EHR dataset of 2,967 patients. We conduct a larger scale experiment on the CMS Linkable 2008–2010 Medicare Data Entrepreneurs’ Synthetic Public Use File dataset of 2 million patients, which achieves over 25-fold speedup compared to sequential execution. PMID:26958172

Evaluation of Content-Matched Range Monitoring Queries over Moving Objects in Mobile Computing Environments

PubMed Central

Jung, HaRim; Song, MoonBae; Youn, Hee Yong; Kim, Ung Mo

2015-01-01

A content-matched (CM) range monitoring query over moving objects continually retrieves the moving objects (i) whose non-spatial attribute values are matched to given non-spatial query values; and (ii) that are currently located within a given spatial query range. In this paper, we propose a new query indexing structure, called the group-aware query region tree (GQR-tree) for efficient evaluation of CM range monitoring queries. The primary role of the GQR-tree is to help the server leverage the computational capabilities of moving objects in order to improve the system performance in terms of the wireless communication cost and server workload. Through a series of comprehensive simulations, we verify the superiority of the GQR-tree method over the existing methods. PMID:26393613

Client-Server: What Is It and Are We There Yet?

ERIC Educational Resources Information Center

Gershenfeld, Nancy

1995-01-01

Discusses client-server architecture in dumb terminals, personal computers, local area networks, and graphical user interfaces. Focuses on functions offered by client personal computers: individualized environments; flexibility in running operating systems; advanced operating system features; multiuser environments; and centralized data…

3Drefine: an interactive web server for efficient protein structure refinement.

PubMed

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-07-08

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

PubMed

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

PubMed Central

Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-01-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

RaptorX server: a resource for template-based protein structure modeling.

PubMed

Källberg, Morten; Margaryan, Gohar; Wang, Sheng; Ma, Jianzhu; Xu, Jinbo

2014-01-01

Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server ( http://raptorx.uchicago.edu ), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling.Given a target sequence, RaptorX server is able to detect even remotely related template sequences by means of a novel nonlinear context-specific alignment potential and probabilistic consistency algorithm. Using the protocol presented here it is thus possible to obtain high-quality structural models for many target protein sequences when only distantly related protein domains have experimentally solved structures. At present, RaptorX server can perform secondary and tertiary structure prediction of a 200 amino acid target sequence in approximately 30 min.

Exploiting volatile opportunistic computing resources with Lobster

NASA Astrophysics Data System (ADS)

Woodard, Anna; Wolf, Matthias; Mueller, Charles; Tovar, Ben; Donnelly, Patrick; Hurtado Anampa, Kenyi; Brenner, Paul; Lannon, Kevin; Hildreth, Mike; Thain, Douglas

2015-12-01

Analysis of high energy physics experiments using the Compact Muon Solenoid (CMS) at the Large Hadron Collider (LHC) can be limited by availability of computing resources. As a joint effort involving computer scientists and CMS physicists at Notre Dame, we have developed an opportunistic workflow management tool, Lobster, to harvest available cycles from university campus computing pools. Lobster consists of a management server, file server, and worker processes which can be submitted to any available computing resource without requiring root access. Lobster makes use of the Work Queue system to perform task management, while the CMS specific software environment is provided via CVMFS and Parrot. Data is handled via Chirp and Hadoop for local data storage and XrootD for access to the CMS wide-area data federation. An extensive set of monitoring and diagnostic tools have been developed to facilitate system optimisation. We have tested Lobster using the 20 000-core cluster at Notre Dame, achieving approximately 8-10k tasks running simultaneously, sustaining approximately 9 Gbit/s of input data and 340 Mbit/s of output data.

Performance Analysis of Cloud Computing Architectures Using Discrete Event Simulation

NASA Technical Reports Server (NTRS)

Stocker, John C.; Golomb, Andrew M.

2011-01-01

Cloud computing offers the economic benefit of on-demand resource allocation to meet changing enterprise computing needs. However, the flexibility of cloud computing is disadvantaged when compared to traditional hosting in providing predictable application and service performance. Cloud computing relies on resource scheduling in a virtualized network-centric server environment, which makes static performance analysis infeasible. We developed a discrete event simulation model to evaluate the overall effectiveness of organizations in executing their workflow in traditional and cloud computing architectures. The two part model framework characterizes both the demand using a probability distribution for each type of service request as well as enterprise computing resource constraints. Our simulations provide quantitative analysis to design and provision computing architectures that maximize overall mission effectiveness. We share our analysis of key resource constraints in cloud computing architectures and findings on the appropriateness of cloud computing in various applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadgu, Teklu; Appel, Gordon John

Sandia National Laboratories (SNL) continued evaluation of total system performance assessment (TSPA) computing systems for the previously considered Yucca Mountain Project (YMP). This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment (TSPA) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. This work is a continuation of the ongoing readiness evaluation reported in Lee and Hadgu (2014) and Hadgu et al. (2015). The TSPA computing hardware (CL2014) and storage system described in Hadgu et al. (2015) were used for the currentmore » analysis. One floating license of GoldSim with Versions 9.60.300, 10.5 and 11.1.6 was installed on the cluster head node, and its distributed processing capability was mapped on the cluster processors. Other supporting software were tested and installed to support the TSPA-type analysis on the server cluster. The current tasks included verification of the TSPA-LA uncertainty and sensitivity analyses, and preliminary upgrade of the TSPA-LA from Version 9.60.300 to the latest version 11.1. All the TSPA-LA uncertainty and sensitivity analyses modeling cases were successfully tested and verified for the model reproducibility on the upgraded 2014 server cluster (CL2014). The uncertainty and sensitivity analyses used TSPA-LA modeling cases output generated in FY15 based on GoldSim Version 9.60.300 documented in Hadgu et al. (2015). The model upgrade task successfully converted the Nominal Modeling case to GoldSim Version 11.1. Upgrade of the remaining of the modeling cases and distributed processing tasks will continue. The 2014 server cluster and supporting software systems are fully operational to support TSPA-LA type analysis.« less

BIO-Plex Information System Concept

NASA Technical Reports Server (NTRS)

Jones, Harry; Boulanger, Richard; Arnold, James O. (Technical Monitor)

1999-01-01

This paper describes a suggested design for an integrated information system for the proposed BIO-Plex (Bioregenerative Planetary Life Support Systems Test Complex) at Johnson Space Center (JSC), including distributed control systems, central control, networks, database servers, personal computers and workstations, applications software, and external communications. The system will have an open commercial computing and networking, architecture. The network will provide automatic real-time transfer of information to database server computers which perform data collection and validation. This information system will support integrated, data sharing applications for everything, from system alarms to management summaries. Most existing complex process control systems have information gaps between the different real time subsystems, between these subsystems and central controller, between the central controller and system level planning and analysis application software, and between the system level applications and management overview reporting. An integrated information system is vitally necessary as the basis for the integration of planning, scheduling, modeling, monitoring, and control, which will allow improved monitoring and control based on timely, accurate and complete data. Data describing the system configuration and the real time processes can be collected, checked and reconciled, analyzed and stored in database servers that can be accessed by all applications. The required technology is available. The only opportunity to design a distributed, nonredundant, integrated system is before it is built. Retrofit is extremely difficult and costly.

Advancing the Power and Utility of Server-Side Aggregation

NASA Technical Reports Server (NTRS)

Fulker, Dave; Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters.Topics 2 through 7 will be relevant to data consumers, data providers andnotably, due to the open-source nature of all OPeNDAP softwareto developers wishing to extend Hyrax, to build compatible clients and servers, andor to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

A daily living activity remote monitoring system for solitary elderly people.

PubMed

Maki, Hiromichi; Ogawa, Hidekuni; Matsuoka, Shingo; Yonezawa, Yoshiharu; Caldwell, W Morton

2011-01-01

A daily living activity remote monitoring system has been developed for supporting solitary elderly people. The monitoring system consists of a tri-axis accelerometer, six low-power active filters, a low-power 8-bit microcontroller (MC), a 1GB SD memory card (SDMC) and a 2.4 GHz low transmitting power mobile phone (PHS). The tri-axis accelerometer attached to the subject's chest can simultaneously measure dynamic and static acceleration forces produced by heart sound, respiration, posture and behavior. The heart rate, respiration rate, activity, posture and behavior are detected from the dynamic and static acceleration forces. These data are stored in the SD. The MC sends the data to the server computer every hour. The server computer stores the data and makes a graphic chart from the data. When the caregiver calls from his/her mobile phone to the server computer, the server computer sends the graphical chart via the PHS. The caregiver's mobile phone displays the chart to the monitor graphically.

Assessment of feasibility of running RSNA's MIRC on a Raspberry Pi: a cost-effective solution for teaching files in radiology.

PubMed

Pereira, Andre; Atri, Mostafa; Rogalla, Patrik; Huynh, Thien; O'Malley, Martin E

2015-11-01

The value of a teaching case repository in radiology training programs is immense. The allocation of resources for putting one together is a complex issue, given the factors that have to be coordinated: hardware, software, infrastructure, administration, and ethics. Costs may be significant and cost-effective solutions are desirable. We chose Medical Imaging Resource Center (MIRC) to build our teaching file. It is offered by RSNA for free. For the hardware, we chose the Raspberry Pi, developed by the Raspberry Foundation: a small control board developed as a low cost computer for schools also used in alternative projects such as robotics and environmental data collection. Its performance and reliability as a file server were unknown to us. For the operational system, we chose Raspbian, a variant of Debian Linux, along with Apache (web server), MySql (database server) and PHP, which enhance the functionality of the server. A USB hub and an external hard drive completed the setup. Installation of software was smooth. The Raspberry Pi was able to handle very well the task of hosting the teaching file repository for our division. Uptime was logged at 100 %, and loading times were similar to other MIRC sites available online. We setup two servers (one for backup), each costing just below $200.00 including external storage and USB hub. It is feasible to run RSNA's MIRC off a low-cost control board (Raspberry Pi). Performance and reliability are comparable to full-size servers for the intended purpose of hosting a teaching file within an intranet environment.

LocalMove: computing on-lattice fits for biopolymers

PubMed Central

Ponty, Y.; Istrate, R.; Porcelli, E.; Clote, P.

2008-01-01

Given an input Protein Data Bank file (PDB) for a protein or RNA molecule, LocalMove is a web server that determines an on-lattice representation for the input biomolecule. The web server implements a Markov Chain Monte-Carlo algorithm with simulated annealing to compute an approximate fit for either the coarse-grain model or backbone model on either the cubic or face-centered cubic lattice. LocalMove returns a PDB file as output, as well as dynamic movie of 3D images of intermediate conformations during the computation. The LocalMove server is publicly available at http://bioinformatics.bc.edu/clotelab/localmove/. PMID:18556754

Ecoupling server: A tool to compute and analyze electronic couplings.

PubMed

Cabeza de Vaca, Israel; Acebes, Sandra; Guallar, Victor

2016-07-05

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Implementation of Sensor Twitter Feed Web Service Server and Client

DTIC Science & Technology

2016-12-01

ARL-TN-0807 ● DEC 2016 US Army Research Laboratory Implementation of Sensor Twitter Feed Web Service Server and Client by...Implementation of Sensor Twitter Feed Web Service Server and Client by Bhagyashree V Kulkarni University of Maryland Michael H Lee Computational...

New additions to the ClusPro server motivated by CAPRI.

PubMed

Vajda, Sandor; Yueh, Christine; Beglov, Dmitri; Bohnuud, Tanggis; Mottarella, Scott E; Xia, Bing; Hall, David R; Kozakov, Dima

2017-03-01

The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X-ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435-444. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server

DTIC Science & Technology

2016-09-01

ARL-TR-7798 ● SEP 2016 US Army Research Laboratory Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server...for the Applied Anomaly Detection Tool (AADT) Web Server by Christian D Schlesiger Computational and Information Sciences Directorate, ARL...SUBTITLE Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

Remote Adaptive Communication System

DTIC Science & Technology

2001-10-25

manage several different devices using the software tool A. Client /Server Architecture The architecture we are proposing is based on the Client ...Server model (see figure 3). We want both client and server to be accessible from anywhere via internet. The computer, acting as a server, is in...the other hand, each of the client applications will act as sender or receiver, depending on the associated interface: user interface or device

Heterogeneous high throughput scientific computing with APM X-Gene and Intel Xeon Phi

DOE PAGES

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; ...

2015-05-22

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. As a result, we report our experience on software porting, performance and energy efficiency and evaluatemore » the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).« less

MATREX Leads the Way in Implementing New DOD VV&A Documentation Standards

DTIC Science & Technology

2007-05-24

Acquisition Operations & Support B C Sustainment FRP Decision Review FOC LRIP/IOT& ECritical Design Review Pre-Systems Acquisition Concept...Communications Human Performance Model • C3GRID – Command & Control, Computer GRID • CES – Communications Effects Server • CMS2 – Comprehensive

High Performance Computing Assets for Ocean Acoustics Research

DTIC Science & Technology

2016-11-18

independently on processing units with access to a typically available amount of memory, say 16 or 32 gigabytes. Our models require each processor to...allow results to be obtained with limited amounts of memory available to individual processing units (with no time frame for successful completion...put into use. One file server computer to store simulation output has also been purchased. The first workstation has 28 CPU cores, dual- thread , (56

Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing.

PubMed

Trudgian, David C; Mirzaei, Hamid

2012-12-07

We have extended the functionality of the Central Proteomics Facilities Pipeline (CPFP) to allow use of remote cloud and high performance computing (HPC) resources for shotgun proteomics data processing. CPFP has been modified to include modular local and remote scheduling for data processing jobs. The pipeline can now be run on a single PC or server, a local cluster, a remote HPC cluster, and/or the Amazon Web Services (AWS) cloud. We provide public images that allow easy deployment of CPFP in its entirety in the AWS cloud. This significantly reduces the effort necessary to use the software, and allows proteomics laboratories to pay for compute time ad hoc, rather than obtaining and maintaining expensive local server clusters. Alternatively the Amazon cloud can be used to increase the throughput of a local installation of CPFP as necessary. We demonstrate that cloud CPFP allows users to process data at higher speed than local installations but with similar cost and lower staff requirements. In addition to the computational improvements, the web interface to CPFP is simplified, and other functionalities are enhanced. The software is under active development at two leading institutions and continues to be released under an open-source license at http://cpfp.sourceforge.net.

Performance of a distributed superscalar storage server

NASA Technical Reports Server (NTRS)

Finestead, Arlan; Yeager, Nancy

1993-01-01

The RS/6000 performed well in our test environment. The potential exists for the RS/6000 to act as a departmental server for a small number of users, rather than as a high speed archival server. Multiple UniTree Disk Server's utilizing one UniTree Disk Server's utilizing one UniTree Name Server could be developed that would allow for a cost effective archival system. Our performance tests were clearly limited by the network bandwidth. The performance gathered by the LibUnix testing shows that UniTree is capable of exceeding ethernet speeds on an RS/6000 Model 550. The performance of FTP might be significantly faster if asked to perform across a higher bandwidth network. The UniTree Name Server also showed signs of being a potential bottleneck. UniTree sites that would require a high ratio of file creations and deletions to reads and writes would run into this bottleneck. It is possible to improve the UniTree Name Server performance by bypassing the UniTree LibUnix Library altogether and communicating directly with the UniTree Name Server and optimizing creations. Although testing was performed in a less than ideal environment, hopefully the performance statistics stated in this paper will give end-users a realistic idea as to what performance they can expect in this type of setup.

Mobile collaborative medical display system.

PubMed

Park, Sanghun; Kim, Wontae; Ihm, Insung

2008-03-01

Because of recent advances in wireless communication technologies, the world of mobile computing is flourishing with a variety of applications. In this study, we present an integrated architecture for a personal digital assistant (PDA)-based mobile medical display system that supports collaborative work between remote users. We aim to develop a system that enables users in different regions to share a working environment for collaborative visualization with the potential for exploring huge medical datasets. Our system consists of three major components: mobile client, gateway, and parallel rendering server. The mobile client serves as a front end and enables users to choose the visualization and control parameters interactively and cooperatively. The gateway handles requests and responses between mobile clients and the rendering server for efficient communication. Through the gateway, it is possible to share working environments between users, allowing them to work together in computer supported cooperative work (CSCW) mode. Finally, the parallel rendering server is responsible for performing heavy visualization tasks. Our experience indicates that some features currently available to our mobile clients for collaborative scientific visualization are limited due to the poor performance of mobile devices and the low bandwidth of wireless connections. However, as mobile devices and wireless network systems are experiencing considerable elevation in their capabilities, we believe that our methodology will be utilized effectively in building quite responsive, useful mobile collaborative medical systems in the very near future.

The effective use of virtualization for selection of data centers in a cloud computing environment

NASA Astrophysics Data System (ADS)

Kumar, B. Santhosh; Parthiban, Latha

2018-04-01

Data centers are the places which consist of network of remote servers to store, access and process the data. Cloud computing is a technology where users worldwide will submit the tasks and the service providers will direct the requests to the data centers which are responsible for execution of tasks. The servers in the data centers need to employ the virtualization concept so that multiple tasks can be executed simultaneously. In this paper we proposed an algorithm for data center selection based on energy of virtual machines created in server. The virtualization energy in each of the server is calculated and total energy of the data center is obtained by the summation of individual server energy. The tasks submitted are routed to the data center with least energy consumption which will result in minimizing the operational expenses of a service provider.

A distributed, graphical user interface based, computer control system for atomic physics experiments

NASA Astrophysics Data System (ADS)

Keshet, Aviv; Ketterle, Wolfgang

2013-01-01

Atomic physics experiments often require a complex sequence of precisely timed computer controlled events. This paper describes a distributed graphical user interface-based control system designed with such experiments in mind, which makes use of off-the-shelf output hardware from National Instruments. The software makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature should allow this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using a field programmable gate array-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100 ns achieved over effectively arbitrary sequence lengths.

A distributed, graphical user interface based, computer control system for atomic physics experiments.

PubMed

Keshet, Aviv; Ketterle, Wolfgang

2013-01-01

Atomic physics experiments often require a complex sequence of precisely timed computer controlled events. This paper describes a distributed graphical user interface-based control system designed with such experiments in mind, which makes use of off-the-shelf output hardware from National Instruments. The software makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature should allow this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using a field programmable gate array-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100 ns achieved over effectively arbitrary sequence lengths.

Near Real-Time Processing and Archiving of GPS Surveys for Crustal Motion Monitoring

NASA Astrophysics Data System (ADS)

Crowell, B. W.; Bock, Y.

2008-12-01

We present an inverse instantaneous RTK method for rapidly processing and archiving GPS data for crustal motion surveys that gives positional accuracy similar to traditional post-processing methods. We first stream 1 Hz data from GPS receivers over Bluetooth to Verizon XV6700 smartphones equipped with Geodetics, Inc. RTD Rover software. The smartphone transmits raw receiver data to a real-time server at the Scripps Orbit and Permanent Array Center (SOPAC) running RTD Pro. At the server, instantaneous positions are computed every second relative to the three closest base stations in the California Real Time Network (CRTN), using ultra-rapid orbits produced by SOPAC, the NOAATrop real-time tropospheric delay model, and ITRF2005 coordinates computed by SOPAC for the CRTN stations. The raw data are converted on-the-fly to RINEX format at the server. Data in both formats are stored on the server along with a file of instantaneous positions, computed independently at each observation epoch. The single-epoch instantaneous positions are continuously transmitted back to the field surveyor's smartphone, where RTD Rover computes a median position and interquartile range for each new epoch of observation. The best-fit solution is the last median position and is available as soon as the survey is completed. We describe how we used this method to process 1 Hz data from the February, 2008 Imperial Valley GPS survey of 38 geodetic monuments established by Imperial College, London in the 1970's, and previously measured by SOPAC using rapid-static GPS methods in 1993, 1999 and 2000, as well as 14 National Geodetic Survey (NGS) monuments. For redundancy, each monument was surveyed for about 15 minutes at least twice and at staggered intervals using two survey teams operating autonomously. Archiving of data and the overall project at SOPAC is performed using the PGM software, developed by the California Spatial Reference Center (CSRC) for the National Geodetic Survey (NGS). The importation of raw receiver data, site metadata and antenna height information is performed using PGM client software running on the same PDA running RTD Rover or laptop, and uploaded to the PGM server where the raw data are converted to RINEX format. The campaign information is then published online, where all of the campaign information can be accessed such as start and stop times, equipment information, RINEX and solution SINEX files, observer information and baseline information for network adjustments.

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

PubMed

Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

2010-07-01

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

Smart Grid Privacy through Distributed Trust

NASA Astrophysics Data System (ADS)

Lipton, Benjamin

Though the smart electrical grid promises many advantages in efficiency and reliability, the risks to consumer privacy have impeded its deployment. Researchers have proposed protecting privacy by aggregating user data before it reaches the utility, using techniques of homomorphic encryption to prevent exposure of unaggregated values. However, such schemes generally require users to trust in the correct operation of a single aggregation server. We propose two alternative systems based on secret sharing techniques that distribute this trust among multiple service providers, protecting user privacy against a misbehaving server. We also provide an extensive evaluation of the systems considered, comparing their robustness to privacy compromise, error handling, computational performance, and data transmission costs. We conclude that while all the systems should be computationally feasible on smart meters, the two methods based on secret sharing require much less computation while also providing better protection against corrupted aggregators. Building systems using these techniques could help defend the privacy of electricity customers, as well as customers of other utilities as they move to a more data-driven architecture.

An efficient quantum scheme for Private Set Intersection

NASA Astrophysics Data System (ADS)

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2016-01-01

Private Set Intersection allows a client to privately compute set intersection with the collaboration of the server, which is one of the most fundamental and key problems within the multiparty collaborative computation of protecting the privacy of the parties. In this paper, we first present a cheat-sensitive quantum scheme for Private Set Intersection. Compared with classical schemes, our scheme has lower communication complexity, which is independent of the size of the server's set. Therefore, it is very suitable for big data services in Cloud or large-scale client-server networks.

Blind Quantum Signature with Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Li, Wei; Shi, Ronghua; Guo, Ying

2017-04-01

Blind quantum computation allows a client without quantum abilities to interact with a quantum server to perform a unconditional secure computing protocol, while protecting client's privacy. Motivated by confidentiality of blind quantum computation, a blind quantum signature scheme is designed with laconic structure. Different from the traditional signature schemes, the signing and verifying operations are performed through measurement-based quantum computation. Inputs of blind quantum computation are securely controlled with multi-qubit entangled states. The unique signature of the transmitted message is generated by the signer without leaking information in imperfect channels. Whereas, the receiver can verify the validity of the signature using the quantum matching algorithm. The security is guaranteed by entanglement of quantum system for blind quantum computation. It provides a potential practical application for e-commerce in the cloud computing and first-generation quantum computation.

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

PubMed Central

2012-01-01

Background Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain. Results In this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model. Conclusions Our use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org. PMID:23281941

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

PubMed

El-Kalioby, Mohamed; Abouelhoda, Mohamed; Krüger, Jan; Giegerich, Robert; Sczyrba, Alexander; Wall, Dennis P; Tonellato, Peter

2012-01-01

Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain. In this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model. Our use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Verification for measurement-only blind quantum computing

NASA Astrophysics Data System (ADS)

Morimae, Tomoyuki

2014-06-01

Blind quantum computing is a new secure quantum computing protocol where a client who does not have any sophisticated quantum technology can delegate her quantum computing to a server without leaking any privacy. It is known that a client who has only a measurement device can perform blind quantum computing [T. Morimae and K. Fujii, Phys. Rev. A 87, 050301(R) (2013), 10.1103/PhysRevA.87.050301]. It has been an open problem whether the protocol can enjoy the verification, i.e., the ability of the client to check the correctness of the computing. In this paper, we propose a protocol of verification for the measurement-only blind quantum computing.

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2014-06-16

CFD analysis. Coupled simulations will be run at PSU on the COCOA -4 cluster, a high performance computing cluster. The CRUNCH CFD software has...been installed on the COCOA -4 servers and initial software tests are being conducted. Initial efforts will use the Generic Frigate Shape SFS-2 to

Economics of Computing: The Case of Centralized Network File Servers.

ERIC Educational Resources Information Center

Solomon, Martin B.

1994-01-01

Discusses computer networking and the cost effectiveness of decentralization, including local area networks. A planned experiment with a centralized approach to the operation and management of file servers at the University of South Carolina is described that hopes to realize cost savings and the avoidance of staffing problems. (Contains four…

Blind quantum computation with identity authentication

NASA Astrophysics Data System (ADS)

Li, Qin; Li, Zhulin; Chan, Wai Hong; Zhang, Shengyu; Liu, Chengdong

2018-04-01

Blind quantum computation (BQC) allows a client with relatively few quantum resources or poor quantum technologies to delegate his computational problem to a quantum server such that the client's input, output, and algorithm are kept private. However, all existing BQC protocols focus on correctness verification of quantum computation but neglect authentication of participants' identity which probably leads to man-in-the-middle attacks or denial-of-service attacks. In this work, we use quantum identification to overcome such two kinds of attack for BQC, which will be called QI-BQC. We propose two QI-BQC protocols based on a typical single-server BQC protocol and a double-server BQC protocol. The two protocols can ensure both data integrity and mutual identification between participants with the help of a third trusted party (TTP). In addition, an unjammable public channel between a client and a server which is indispensable in previous BQC protocols is unnecessary, although it is required between TTP and each participant at some instant. Furthermore, the method to achieve identity verification in the presented protocols is general and it can be applied to other similar BQC protocols.

Internet Distribution of Spacecraft Telemetry Data

NASA Technical Reports Server (NTRS)

Specht, Ted; Noble, David

2006-01-01

Remote Access Multi-mission Processing and Analysis Ground Environment (RAMPAGE) is a Java-language server computer program that enables near-real-time display of spacecraft telemetry data on any authorized client computer that has access to the Internet and is equipped with Web-browser software. In addition to providing a variety of displays of the latest available telemetry data, RAMPAGE can deliver notification of an alarm by electronic mail. Subscribers can then use RAMPAGE displays to determine the state of the spacecraft and formulate a response to the alarm, if necessary. A user can query spacecraft mission data in either binary or comma-separated-value format by use of a Web form or a Practical Extraction and Reporting Language (PERL) script to automate the query process. RAMPAGE runs on Linux and Solaris server computers in the Ground Data System (GDS) of NASA's Jet Propulsion Laboratory and includes components designed specifically to make it compatible with legacy GDS software. The client/server architecture of RAMPAGE and the use of the Java programming language make it possible to utilize a variety of competitive server and client computers, thereby also helping to minimize costs.

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

PubMed Central

Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang

2012-01-01

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users. PMID:23110173

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

PubMed

Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

2012-07-01

The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.

Group-oriented coordination models for distributed client-server computing

NASA Technical Reports Server (NTRS)

Adler, Richard M.; Hughes, Craig S.

1994-01-01

This paper describes group-oriented control models for distributed client-server interactions. These models transparently coordinate requests for services that involve multiple servers, such as queries across distributed databases. Specific capabilities include: decomposing and replicating client requests; dispatching request subtasks or copies to independent, networked servers; and combining server results into a single response for the client. The control models were implemented by combining request broker and process group technologies with an object-oriented communication middleware tool. The models are illustrated in the context of a distributed operations support application for space-based systems.

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

A convergent model for distributed processing of Big Sensor Data in urban engineering networks

NASA Astrophysics Data System (ADS)

Parygin, D. S.; Finogeev, A. G.; Kamaev, V. A.; Finogeev, A. A.; Gnedkova, E. P.; Tyukov, A. P.

2017-01-01

The problems of development and research of a convergent model of the grid, cloud, fog and mobile computing for analytical Big Sensor Data processing are reviewed. The model is meant to create monitoring systems of spatially distributed objects of urban engineering networks and processes. The proposed approach is the convergence model of the distributed data processing organization. The fog computing model is used for the processing and aggregation of sensor data at the network nodes and/or industrial controllers. The program agents are loaded to perform computing tasks for the primary processing and data aggregation. The grid and the cloud computing models are used for integral indicators mining and accumulating. A computing cluster has a three-tier architecture, which includes the main server at the first level, a cluster of SCADA system servers at the second level, a lot of GPU video cards with the support for the Compute Unified Device Architecture at the third level. The mobile computing model is applied to visualize the results of intellectual analysis with the elements of augmented reality and geo-information technologies. The integrated indicators are transferred to the data center for accumulation in a multidimensional storage for the purpose of data mining and knowledge gaining.

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

The ISMARA client

PubMed Central

Ioannidis, Vassilios; van Nimwegen, Erik; Stockinger, Heinz

2016-01-01

ISMARA ( ismara.unibas.ch) automatically infers the key regulators and regulatory interactions from high-throughput gene expression or chromatin state data. However, given the large sizes of current next generation sequencing (NGS) datasets, data uploading times are a major bottleneck. Additionally, for proprietary data, users may be uncomfortable with uploading entire raw datasets to an external server. Both these problems could be alleviated by providing a means by which users could pre-process their raw data locally, transferring only a small summary file to the ISMARA server. We developed a stand-alone client application that pre-processes large input files (RNA-seq or ChIP-seq data) on the user's computer for performing ISMARA analysis in a completely automated manner, including uploading of small processed summary files to the ISMARA server. This reduces file sizes by up to a factor of 1000, and upload times from many hours to mere seconds. The client application is available from ismara.unibas.ch/ISMARA/client. PMID:28232860

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments

PubMed Central

Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.’s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.’s scheme still has weaknesses. In this paper, we show that Moon et al.’s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient. PMID:29121050

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments.

PubMed

Guo, Hua; Wang, Pei; Zhang, Xiyong; Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.'s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.'s scheme still has weaknesses. In this paper, we show that Moon et al.'s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient.

Active Nodal Task Seeking for High-Performance, Ultra-Dependable Computing

DTIC Science & Technology

1994-07-01

implementation. Figure 1 shows a hardware organization of ANTS: stand-alone computing nodes inter - connected by buses. 2.1 Run Time Partitioning The...nodes in 14 respond to changing loads [27] or system reconfiguration [26]. Existing techniques are all source-initiated or server-initiated [27]. 5.1...short-running task segments. The task segments must be short-running in order that processors will become avalable often enough to satisfy changing

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

PubMed Central

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

PubMed

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

Selection of Server-Side Technologies for an E-Business Curriculum

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2007-01-01

The rapid growth of e-business and e-commerce has made server-side programming an increasingly important topic in information systems (IS) and computer science (CS) curricula. This article presents an overview of the major features of several popular server-side programming technologies and discusses the factors that influence the selection of…

Visits, Hits, Caching and Counting on the World Wide Web: Old Wine in New Bottles?

ERIC Educational Resources Information Center

Berthon, Pierre; Pitt, Leyland; Prendergast, Gerard

1997-01-01

Although web browser caching speeds up retrieval, reduces network traffic, and decreases the load on servers and browser's computers, an unintended consequence for marketing research is that Web servers undercount hits. This article explores counting problems, caching, proxy servers, trawler software and presents a series of correction factors…

Beating the tyranny of scale with a private cloud configured for Big Data

NASA Astrophysics Data System (ADS)

Lawrence, Bryan; Bennett, Victoria; Churchill, Jonathan; Juckes, Martin; Kershaw, Philip; Pepler, Sam; Pritchard, Matt; Stephens, Ag

2015-04-01

The Joint Analysis System, JASMIN, consists of a five significant hardware components: a batch computing cluster, a hypervisor cluster, bulk disk storage, high performance disk storage, and access to a tape robot. Each of the computing clusters consists of a heterogeneous set of servers, supporting a range of possible data analysis tasks - and a unique network environment makes it relatively trivial to migrate servers between the two clusters. The high performance disk storage will include the world's largest (publicly visible) deployment of the Panasas parallel disk system. Initially deployed in April 2012, JASMIN has already undergone two major upgrades, culminating in a system which by April 2015, will have in excess of 16 PB of disk and 4000 cores. Layered on the basic hardware are a range of services, ranging from managed services, such as the curated archives of the Centre for Environmental Data Archival or the data analysis environment for the National Centres for Atmospheric Science and Earth Observation, to a generic Infrastructure as a Service (IaaS) offering for the UK environmental science community. Here we present examples of some of the big data workloads being supported in this environment - ranging from data management tasks, such as checksumming 3 PB of data held in over one hundred million files, to science tasks, such as re-processing satellite observations with new algorithms, or calculating new diagnostics on petascale climate simulation outputs. We will demonstrate how the provision of a cloud environment closely coupled to a batch computing environment, all sharing the same high performance disk system allows massively parallel processing without the necessity to shuffle data excessively - even as it supports many different virtual communities, each with guaranteed performance. We will discuss the advantages of having a heterogeneous range of servers with available memory from tens of GB at the low end to (currently) two TB at the high end. There are some limitations of the JASMIN environment, the high performance disk environment is not fully available in the IaaS environment, and a planned ability to burst compute heavy jobs into the public cloud is not yet fully available. There are load balancing and performance issues that need to be understood. We will conclude with projections for future usage, and our plans to meet those requirements.

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Blind quantum computing with weak coherent pulses.

PubMed

Dunjko, Vedran; Kashefi, Elham; Leverrier, Anthony

2012-05-18

The universal blind quantum computation (UBQC) protocol [A. Broadbent, J. Fitzsimons, and E. Kashefi, in Proceedings of the 50th Annual IEEE Symposiumon Foundations of Computer Science (IEEE Computer Society, Los Alamitos, CA, USA, 2009), pp. 517-526.] allows a client to perform quantum computation on a remote server. In an ideal setting, perfect privacy is guaranteed if the client is capable of producing specific, randomly chosen single qubit states. While from a theoretical point of view, this may constitute the lowest possible quantum requirement, from a pragmatic point of view, generation of such states to be sent along long distances can never be achieved perfectly. We introduce the concept of ϵ blindness for UBQC, in analogy to the concept of ϵ security developed for other cryptographic protocols, allowing us to characterize the robustness and security properties of the protocol under possible imperfections. We also present a remote blind single qubit preparation protocol with weak coherent pulses for the client to prepare, in a delegated fashion, quantum states arbitrarily close to perfect random single qubit states. This allows us to efficiently achieve ϵ-blind UBQC for any ϵ>0, even if the channel between the client and the server is arbitrarily lossy.

Blind Quantum Computing with Weak Coherent Pulses

NASA Astrophysics Data System (ADS)

Dunjko, Vedran; Kashefi, Elham; Leverrier, Anthony

2012-05-01

The universal blind quantum computation (UBQC) protocol [A. Broadbent, J. Fitzsimons, and E. Kashefi, in Proceedings of the 50th Annual IEEE Symposiumon Foundations of Computer Science (IEEE Computer Society, Los Alamitos, CA, USA, 2009), pp. 517-526.] allows a client to perform quantum computation on a remote server. In an ideal setting, perfect privacy is guaranteed if the client is capable of producing specific, randomly chosen single qubit states. While from a theoretical point of view, this may constitute the lowest possible quantum requirement, from a pragmatic point of view, generation of such states to be sent along long distances can never be achieved perfectly. We introduce the concept of ɛ blindness for UBQC, in analogy to the concept of ɛ security developed for other cryptographic protocols, allowing us to characterize the robustness and security properties of the protocol under possible imperfections. We also present a remote blind single qubit preparation protocol with weak coherent pulses for the client to prepare, in a delegated fashion, quantum states arbitrarily close to perfect random single qubit states. This allows us to efficiently achieve ɛ-blind UBQC for any ɛ>0, even if the channel between the client and the server is arbitrarily lossy.

Mpeg2 codec HD improvements with medical and robotic imaging benefits

NASA Astrophysics Data System (ADS)

Picard, Wayne F. J.

2010-02-01

In this report, we propose an efficient scheme to use High Definition Television (HDTV) in a console or notebook format as a computer terminal in addition to their role as TV display unit. In the proposed scheme, we assume that the main computer is situated at a remote location. The computer raster in the remote server is compressed using an HD E- >Mpeg2 encoder and transmitted to the terminal at home. The built-in E->Mpeg2 decoder in the terminal decompresses the compressed bit stream, and displays the raster. The terminal will be fitted with a mouse and keyboard, through which the interaction with the remote computer server can be performed via a communications back channel. The terminal in a notebook format can thus be used as a high resolution computer and multimedia device. We will consider developments such as the required HD enhanced Mpeg2 resolution (E->Mpeg2) and its medical ramifications due to improvements on compressed image quality with 2D to 3D conversion (Mpeg3) and using the compressed Discrete Cosine Transform coefficients in the reality compression of vision and control of medical robotic surgeons.

Advanced technologies for scalable ATLAS conditions database access on the grid

NASA Astrophysics Data System (ADS)

Basset, R.; Canali, L.; Dimitrov, G.; Girone, M.; Hawkings, R.; Nevski, P.; Valassi, A.; Vaniachine, A.; Viegas, F.; Walker, R.; Wong, A.

2010-04-01

During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysis of server performance under stress tests indicates that Conditions Db data access is limited by the disk I/O throughput. An unacceptable side-effect of the disk I/O saturation is a degradation of the WLCG 3D Services that update Conditions Db data at all ten ATLAS Tier-1 sites using the technology of Oracle Streams. To avoid such bottlenecks we prototyped and tested a novel approach for database peak load avoidance in Grid computing. Our approach is based upon the proven idea of pilot job submission on the Grid: instead of the actual query, an ATLAS utility library sends to the database server a pilot query first.

Next Generation Multimedia Distributed Data Base Systems

NASA Technical Reports Server (NTRS)

Pendleton, Stuart E.

1997-01-01

The paradigm of client/server computing is changing. The model of a server running a monolithic application and supporting clients at the desktop is giving way to a different model that blurs the line between client and server. We are on the verge of plunging into the next generation of computing technology--distributed object-oriented computing. This is not only a change in requirements but a change in opportunities, and requires a new way of thinking for Information System (IS) developers. The information system demands caused by global competition are requiring even more access to decision making tools. Simply, object-oriented technology has been developed to supersede the current design process of information systems which is not capable of handling next generation multimedia.

GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

NASA Astrophysics Data System (ADS)

Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the distributed operation, reduplication operation transfer operation of spatial index in the grid environment. The design of GSHR-Tree has ensured the performance of the load balance in the parallel computation. This tree structure is fit for the parallel process of the spatial information in the distributed network environments. Instead of spatial object's recursive comparison where original R tree has been used, the algorithm builds the spatial index by applying binary code operation in which computer runs more efficiently, and extended dynamic hash code for bit comparison. In GSHR-Tree, a new server is assigned to the network whenever a split of a full node is required. We describe a more flexible allocation protocol which copes with a temporary shortage of storage resources. It uses a distributed balanced binary spatial tree that scales with insertions to potentially any number of storage servers through splits of the overloaded ones. The application manipulates the GSHR-Tree structure from a node in the grid environment. The node addresses the tree through its image that the splits can make outdated. This may generate addressing errors, solved by the forwarding among the servers. In this paper, a spatial index data distribution algorithm that limits the number of servers has been proposed. We improve the storage utilization at the cost of additional messages. The structure of GSHR-Tree is believed that the scheme of this grid spatial index should fit the needs of new applications using endlessly larger sets of spatial data. Our proposal constitutes a flexible storage allocation method for a distributed spatial index. The insertion policy can be tuned dynamically to cope with periods of storage shortage. In such cases storage balancing should be favored for better space utilization, at the price of extra message exchanges between servers. This structure makes a compromise in the updating of the duplicated index and the transformation of the spatial index data. Meeting the needs of the grid computing, GSHRTree has a flexible structure in order to satisfy new needs in the future. The GSHR-Tree provides the R-tree capabilities for large spatial datasets stored over interconnected servers. The analysis, including the experiments, confirmed the efficiency of our design choices. The scheme should fit the needs of new applications of spatial data, using endlessly larger datasets. Using the system response time of the parallel processing of spatial scope query algorithm as the performance evaluation factor, According to the result of the simulated the experiments, GSHR-Tree is performed to prove the reasonable design and the high performance of the indexing structure that the paper presented.

Diamond Eye: a distributed architecture for image data mining

NASA Astrophysics Data System (ADS)

Burl, Michael C.; Fowlkes, Charless; Roden, Joe; Stechert, Andre; Mukhtar, Saleem

1999-02-01

Diamond Eye is a distributed software architecture, which enables users (scientists) to analyze large image collections by interacting with one or more custom data mining servers via a Java applet interface. Each server is coupled with an object-oriented database and a computational engine, such as a network of high-performance workstations. The database provides persistent storage and supports querying of the 'mined' information. The computational engine provides parallel execution of expensive image processing, object recognition, and query-by-content operations. Key benefits of the Diamond Eye architecture are: (1) the design promotes trial evaluation of advanced data mining and machine learning techniques by potential new users (all that is required is to point a web browser to the appropriate URL), (2) software infrastructure that is common across a range of science mining applications is factored out and reused, and (3) the system facilitates closer collaborations between algorithm developers and domain experts.

Centralized Duplicate Removal Video Storage System with Privacy Preservation in IoT.

PubMed

Yan, Hongyang; Li, Xuan; Wang, Yu; Jia, Chunfu

2018-06-04

In recent years, the Internet of Things (IoT) has found wide application and attracted much attention. Since most of the end-terminals in IoT have limited capabilities for storage and computing, it has become a trend to outsource the data from local to cloud computing. To further reduce the communication bandwidth and storage space, data deduplication has been widely adopted to eliminate the redundant data. However, since data collected in IoT are sensitive and closely related to users' personal information, the privacy protection of users' information becomes a challenge. As the channels, like the wireless channels between the terminals and the cloud servers in IoT, are public and the cloud servers are not fully trusted, data have to be encrypted before being uploaded to the cloud. However, encryption makes the performance of deduplication by the cloud server difficult because the ciphertext will be different even if the underlying plaintext is identical. In this paper, we build a centralized privacy-preserving duplicate removal storage system, which supports both file-level and block-level deduplication. In order to avoid the leakage of statistical information of data, Intel Software Guard Extensions (SGX) technology is utilized to protect the deduplication process on the cloud server. The results of the experimental analysis demonstrate that the new scheme can significantly improve the deduplication efficiency and enhance the security. It is envisioned that the duplicated removal system with privacy preservation will be of great use in the centralized storage environment of IoT.

Application of Blind Quantum Computation to Two-Party Quantum Computation

NASA Astrophysics Data System (ADS)

Sun, Zhiyuan; Li, Qin; Yu, Fang; Chan, Wai Hong

2018-06-01

Blind quantum computation (BQC) allows a client who has only limited quantum power to achieve quantum computation with the help of a remote quantum server and still keep the client's input, output, and algorithm private. Recently, Kashefi and Wallden extended BQC to achieve two-party quantum computation which allows two parties Alice and Bob to perform a joint unitary transform upon their inputs. However, in their protocol Alice has to prepare rotated single qubits and perform Pauli operations, and Bob needs to have a powerful quantum computer. In this work, we also utilize the idea of BQC to put forward an improved two-party quantum computation protocol in which the operations of both Alice and Bob are simplified since Alice only needs to apply Pauli operations and Bob is just required to prepare and encrypt his input qubits.

Application of Blind Quantum Computation to Two-Party Quantum Computation

NASA Astrophysics Data System (ADS)

Sun, Zhiyuan; Li, Qin; Yu, Fang; Chan, Wai Hong

2018-03-01

Blind quantum computation (BQC) allows a client who has only limited quantum power to achieve quantum computation with the help of a remote quantum server and still keep the client's input, output, and algorithm private. Recently, Kashefi and Wallden extended BQC to achieve two-party quantum computation which allows two parties Alice and Bob to perform a joint unitary transform upon their inputs. However, in their protocol Alice has to prepare rotated single qubits and perform Pauli operations, and Bob needs to have a powerful quantum computer. In this work, we also utilize the idea of BQC to put forward an improved two-party quantum computation protocol in which the operations of both Alice and Bob are simplified since Alice only needs to apply Pauli operations and Bob is just required to prepare and encrypt his input qubits.

A visualization environment for supercomputing-based applications in computational mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavlakos, C.J.; Schoof, L.A.; Mareda, J.F.

1993-06-01

In this paper, we characterize a visualization environment that has been designed and prototyped for a large community of scientists and engineers, with an emphasis in superconducting-based computational mechanics. The proposed environment makes use of a visualization server concept to provide effective, interactive visualization to the user`s desktop. Benefits of using the visualization server approach are discussed. Some thoughts regarding desirable features for visualization server hardware architectures are also addressed. A brief discussion of the software environment is included. The paper concludes by summarizing certain observations which we have made regarding the implementation of such visualization environments.

Share Data with OPeNDAP Hyrax: New Features and Improvements

NASA Technical Reports Server (NTRS)

Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in 1. server installation, 2. server configuration, 3. Hyrax aggregation capabilities, 4. support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS), 5. support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.

PubMed

Zhou, Pei; Jin, Bowen; Li, Hao; Huang, Sheng-You

2018-05-09

Protein-peptide interactions are crucial in many cellular functions. Therefore, determining the structure of protein-peptide complexes is important for understanding the molecular mechanism of related biological processes and developing peptide drugs. HPEPDOCK is a novel web server for blind protein-peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a success rate of 33.3% in binding mode prediction on a benchmark of 57 unbound cases when the top 10 models were considered, compared to 21.1% for pepATTRACT server. HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions. For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top 10 predictions, compared to 45.2% for HADDOCK peptide protocol. Our HPEPDOCK server is computationally efficient and consumed an average of 29.8 mins for a global peptide docking job and 14.2 mins for a local peptide docking job. The HPEPDOCK web server is available at http://huanglab.phys.hust.edu.cn/hpepdock/.

Implementation of Multispectral Image Classification on a Remote Adaptive Computer

NASA Technical Reports Server (NTRS)

Figueiredo, Marco A.; Gloster, Clay S.; Stephens, Mark; Graves, Corey A.; Nakkar, Mouna

1999-01-01

As the demand for higher performance computers for the processing of remote sensing science algorithms increases, the need to investigate new computing paradigms its justified. Field Programmable Gate Arrays enable the implementation of algorithms at the hardware gate level, leading to orders of m a,gnitude performance increase over microprocessor based systems. The automatic classification of spaceborne multispectral images is an example of a computation intensive application, that, can benefit from implementation on an FPGA - based custom computing machine (adaptive or reconfigurable computer). A probabilistic neural network is used here to classify pixels of of a multispectral LANDSAT-2 image. The implementation described utilizes Java client/server application programs to access the adaptive computer from a remote site. Results verify that a remote hardware version of the algorithm (implemented on an adaptive computer) is significantly faster than a local software version of the same algorithm implemented on a typical general - purpose computer).

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

Optimal Discrete Event Supervisory Control of Aircraft Gas Turbine Engines

NASA Technical Reports Server (NTRS)

Litt, Jonathan (Technical Monitor); Ray, Asok

2004-01-01

This report presents an application of the recently developed theory of optimal Discrete Event Supervisory (DES) control that is based on a signed real measure of regular languages. The DES control techniques are validated on an aircraft gas turbine engine simulation test bed. The test bed is implemented on a networked computer system in which two computers operate in the client-server mode. Several DES controllers have been tested for engine performance and reliability.

Breaking through with Thin-Client Technologies: A Cost Effective Approach for Academic Libraries.

ERIC Educational Resources Information Center

Elbaz, Sohair W.; Stewart, Christofer

This paper provides an overview of thin-client/server computing in higher education. Thin-clients are like PCs in appearance, but they do not house hard drives or localized operating systems and cannot function without being connected to a server. Two types of thin-clients are described: the Network Computer (NC) and the Windows Terminal (WT).…

Performance Analysis of the Unitree Central File

NASA Technical Reports Server (NTRS)

Pentakalos, Odysseas I.; Flater, David

1994-01-01

This report consists of two parts. The first part briefly comments on the documentation status of two major systems at NASA#s Center for Computational Sciences, specifically the Cray C98 and the Convex C3830. The second part describes the work done on improving the performance of file transfers between the Unitree Mass Storage System running on the Convex file server and the users workstations distributed over a large georgraphic area.

Mobile object retrieval in server-based image databases

NASA Astrophysics Data System (ADS)

Manger, D.; Pagel, F.; Widak, H.

2013-05-01

The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

Mobile clusters of single board computers: an option for providing resources to student projects and researchers.

PubMed

Baun, Christian

2016-01-01

Clusters usually consist of servers, workstations or personal computers as nodes. But especially for academic purposes like student projects or scientific projects, the cost for purchase and operation can be a challenge. Single board computers cannot compete with the performance or energy-efficiency of higher-value systems, but they are an option to build inexpensive cluster systems. Because of the compact design and modest energy consumption, it is possible to build clusters of single board computers in a way that they are mobile and can be easily transported by the users. This paper describes the construction of such a cluster, useful applications and the performance of the single nodes. Furthermore, the clusters' performance and energy-efficiency is analyzed by executing the High Performance Linpack benchmark with a different number of nodes and different proportion of the systems total main memory utilized.

Wireless Acoustic Measurement System

NASA Technical Reports Server (NTRS)

Anderson, Paul D.; Dorland, Wade D.; Jolly, Ronald L.

2007-01-01

A prototype wireless acoustic measurement system (WAMS) is one of two main subsystems of the Acoustic Prediction/ Measurement Tool, which comprises software, acoustic instrumentation, and electronic hardware combined to afford integrated capabilities for predicting and measuring noise emitted by rocket and jet engines. The other main subsystem is described in the article on page 8. The WAMS includes analog acoustic measurement instrumentation and analog and digital electronic circuitry combined with computer wireless local-area networking to enable (1) measurement of sound-pressure levels at multiple locations in the sound field of an engine under test and (2) recording and processing of the measurement data. At each field location, the measurements are taken by a portable unit, denoted a field station. There are ten field stations, each of which can take two channels of measurements. Each field station is equipped with two instrumentation microphones, a micro- ATX computer, a wireless network adapter, an environmental enclosure, a directional radio antenna, and a battery power supply. The environmental enclosure shields the computer from weather and from extreme acoustically induced vibrations. The power supply is based on a marine-service lead-acid storage battery that has enough capacity to support operation for as long as 10 hours. A desktop computer serves as a control server for the WAMS. The server is connected to a wireless router for communication with the field stations via a wireless local-area network that complies with wireless-network standard 802.11b of the Institute of Electrical and Electronics Engineers. The router and the wireless network adapters are controlled by use of Linux-compatible driver software. The server runs custom Linux software for synchronizing the recording of measurement data in the field stations. The software includes a module that provides an intuitive graphical user interface through which an operator at the control server can control the operations of the field stations for calibration and for recording of measurement data. A test engineer positions and activates the WAMS. The WAMS automatically establishes the wireless network. Next, the engineer performs pretest calibrations. Then the engineer executes the test and measurement procedures. After the test, the raw measurement files are copied and transferred, through the wireless network, to a hard disk in the control server. Subsequently, the data are processed into 1.3-octave spectrograms.

Wireless Acoustic Measurement System

NASA Technical Reports Server (NTRS)

Anderson, Paul D.; Dorland, Wade D.

2005-01-01

A prototype wireless acoustic measurement system (WAMS) is one of two main subsystems of the Acoustic Prediction/Measurement Tool, which comprises software, acoustic instrumentation, and electronic hardware combined to afford integrated capabilities for predicting and measuring noise emitted by rocket and jet engines. The other main subsystem is described in "Predicting Rocket or Jet Noise in Real Time" (SSC-00215-1), which appears elsewhere in this issue of NASA Tech Briefs. The WAMS includes analog acoustic measurement instrumentation and analog and digital electronic circuitry combined with computer wireless local-area networking to enable (1) measurement of sound-pressure levels at multiple locations in the sound field of an engine under test and (2) recording and processing of the measurement data. At each field location, the measurements are taken by a portable unit, denoted a field station. There are ten field stations, each of which can take two channels of measurements. Each field station is equipped with two instrumentation microphones, a micro-ATX computer, a wireless network adapter, an environmental enclosure, a directional radio antenna, and a battery power supply. The environmental enclosure shields the computer from weather and from extreme acoustically induced vibrations. The power supply is based on a marine-service lead-acid storage battery that has enough capacity to support operation for as long as 10 hours. A desktop computer serves as a control server for the WAMS. The server is connected to a wireless router for communication with the field stations via a wireless local-area network that complies with wireless-network standard 802.11b of the Institute of Electrical and Electronics Engineers. The router and the wireless network adapters are controlled by use of Linux-compatible driver software. The server runs custom Linux software for synchronizing the recording of measurement data in the field stations. The software includes a module that provides an intuitive graphical user interface through which an operator at the control server can control the operations of the field stations for calibration and for recording of measurement data. A test engineer positions and activates the WAMS. The WAMS automatically establishes the wireless network. Next, the engineer performs pretest calibrations. Then the engineer executes the test and measurement procedures. After the test, the raw measurement files are copied and transferred, through the wireless network, to a hard disk in the control server. Subsequently, the data are processed into 1/3-octave spectrograms.

Investigation of Storage Options for Scientific Computing on Grid and Cloud Facilities

NASA Astrophysics Data System (ADS)

Garzoglio, Gabriele

2012-12-01

In recent years, several new storage technologies, such as Lustre, Hadoop, OrangeFS, and BlueArc, have emerged. While several groups have run benchmarks to characterize them under a variety of configurations, more work is needed to evaluate these technologies for the use cases of scientific computing on Grid clusters and Cloud facilities. This paper discusses our evaluation of the technologies as deployed on a test bed at FermiCloud, one of the Fermilab infrastructure-as-a-service Cloud facilities. The test bed consists of 4 server-class nodes with 40 TB of disk space and up to 50 virtual machine clients, some running on the storage server nodes themselves. With this configuration, the evaluation compares the performance of some of these technologies when deployed on virtual machines and on “bare metal” nodes. In addition to running standard benchmarks such as IOZone to check the sanity of our installation, we have run I/O intensive tests using physics-analysis applications. This paper presents how the storage solutions perform in a variety of realistic use cases of scientific computing. One interesting difference among the storage systems tested is found in a decrease in total read throughput with increasing number of client processes, which occurs in some implementations but not others.

Investigation of storage options for scientific computing on Grid and Cloud facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garzoglio, Gabriele

In recent years, several new storage technologies, such as Lustre, Hadoop, OrangeFS, and BlueArc, have emerged. While several groups have run benchmarks to characterize them under a variety of configurations, more work is needed to evaluate these technologies for the use cases of scientific computing on Grid clusters and Cloud facilities. This paper discusses our evaluation of the technologies as deployed on a test bed at FermiCloud, one of the Fermilab infrastructure-as-a-service Cloud facilities. The test bed consists of 4 server-class nodes with 40 TB of disk space and up to 50 virtual machine clients, some running on the storagemore » server nodes themselves. With this configuration, the evaluation compares the performance of some of these technologies when deployed on virtual machines and on bare metal nodes. In addition to running standard benchmarks such as IOZone to check the sanity of our installation, we have run I/O intensive tests using physics-analysis applications. This paper presents how the storage solutions perform in a variety of realistic use cases of scientific computing. One interesting difference among the storage systems tested is found in a decrease in total read throughput with increasing number of client processes, which occurs in some implementations but not others.« less

Large-Scale Astrophysical Visualization on Smartphones

NASA Astrophysics Data System (ADS)

Becciani, U.; Massimino, P.; Costa, A.; Gheller, C.; Grillo, A.; Krokos, M.; Petta, C.

2011-07-01

Nowadays digital sky surveys and long-duration, high-resolution numerical simulations using high performance computing and grid systems produce multidimensional astrophysical datasets in the order of several Petabytes. Sharing visualizations of such datasets within communities and collaborating research groups is of paramount importance for disseminating results and advancing astrophysical research. Moreover educational and public outreach programs can benefit greatly from novel ways of presenting these datasets by promoting understanding of complex astrophysical processes, e.g., formation of stars and galaxies. We have previously developed VisIVO Server, a grid-enabled platform for high-performance large-scale astrophysical visualization. This article reviews the latest developments on VisIVO Web, a custom designed web portal wrapped around VisIVO Server, then introduces VisIVO Smartphone, a gateway connecting VisIVO Web and data repositories for mobile astrophysical visualization. We discuss current work and summarize future developments.

The Czech National Grid Infrastructure

NASA Astrophysics Data System (ADS)

Chudoba, J.; Křenková, I.; Mulač, M.; Ruda, M.; Sitera, J.

2017-10-01

The Czech National Grid Infrastructure is operated by MetaCentrum, a CESNET department responsible for coordinating and managing activities related to distributed computing. CESNET as the Czech National Research and Education Network (NREN) provides many e-infrastructure services, which are used by 94% of the scientific and research community in the Czech Republic. Computing and storage resources owned by different organizations are connected by fast enough network to provide transparent access to all resources. We describe in more detail the computing infrastructure, which is based on several different technologies and covers grid, cloud and map-reduce environment. While the largest part of CPUs is still accessible via distributed torque servers, providing environment for long batch jobs, part of infrastructure is available via standard EGI tools in EGI, subset of NGI resources is provided into EGI FedCloud environment with cloud interface and there is also Hadoop cluster provided by the same e-infrastructure.A broad spectrum of computing servers is offered; users can choose from standard 2 CPU servers to large SMP machines with up to 6 TB of RAM or servers with GPU cards. Different groups have different priorities on various resources, resource owners can even have an exclusive access. The software is distributed via AFS. Storage servers offering up to tens of terabytes of disk space to individual users are connected via NFS4 on top of GPFS and access to long term HSM storage with peta-byte capacity is also provided. Overview of available resources and recent statistics of usage will be given.

Prototyping a 10 Gigabit-Ethernet Event-Builder for the CTA Camera Server

NASA Astrophysics Data System (ADS)

Hoffmann, Dirk; Houles, Julien

2012-12-01

While the Cherenkov Telescope Array will end its Preperatory Phase in 2012 or 2013 with the publication of a Technical Design Report, our lab has undertaken within the french CTA community the design and prototyping of a Camera-Server, which is a PC architecture based computer, used as a switchboard assigned to each of a hundred telescopes to handle a maximum amount of scientific data recorded by each telescope. Our work aims for a data acquisition hardware and software system for the scientific raw data at optimal speed. We have evaluated the maximum performance that can be obtained by choosing standard (COTS) hardware and software (Linux) in conjunction with a 10 Gb/s switch.

An Array Library for Microsoft SQL Server with Astrophysical Applications

NASA Astrophysics Data System (ADS)

Dobos, L.; Szalay, A. S.; Blakeley, J.; Falck, B.; Budavári, T.; Csabai, I.

2012-09-01

Today's scientific simulations produce output on the 10-100 TB scale. This unprecedented amount of data requires data handling techniques that are beyond what is used for ordinary files. Relational database systems have been successfully used to store and process scientific data, but the new requirements constantly generate new challenges. Moving terabytes of data among servers on a timely basis is a tough problem, even with the newest high-throughput networks. Thus, moving the computations as close to the data as possible and minimizing the client-server overhead are absolutely necessary. At least data subsetting and preprocessing have to be done inside the server process. Out of the box commercial database systems perform very well in scientific applications from the prospective of data storage optimization, data retrieval, and memory management but lack basic functionality like handling scientific data structures or enabling advanced math inside the database server. The most important gap in Microsoft SQL Server is the lack of a native array data type. Fortunately, the technology exists to extend the database server with custom-written code that enables us to address these problems. We present the prototype of a custom-built extension to Microsoft SQL Server that adds array handling functionality to the database system. With our Array Library, fix-sized arrays of all basic numeric data types can be created and manipulated efficiently. Also, the library is designed to be able to be seamlessly integrated with the most common math libraries, such as BLAS, LAPACK, FFTW, etc. With the help of these libraries, complex operations, such as matrix inversions or Fourier transformations, can be done on-the-fly, from SQL code, inside the database server process. We are currently testing the prototype with two different scientific data sets: The Indra cosmological simulation will use it to store particle and density data from N-body simulations, and the Milky Way Laboratory project will use it to store galaxy simulation data.

Twin-tailed fail-over for fileservers maintaining full performance in the presence of a failure

DOEpatents

Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Steinmacher-Burow, Burkhard D.

2008-02-12

A method for maintaining full performance of a file system in the presence of a failure is provided. The file system having N storage devices, where N is an integer greater than zero and N primary file servers where each file server is operatively connected to a corresponding storage device for accessing files therein. The file system further having a secondary file server operatively connected to at least one of the N storage devices. The method including: switching the connection of one of the N storage devices to the secondary file server upon a failure of one of the N primary file servers; and switching the connections of one or more of the remaining storage devices to a primary file server other than the failed file server as necessary so as to prevent a loss in performance and to provide each storage device with an operating file server.

The application of cloud computing to scientific workflows: a study of cost and performance.

PubMed

Berriman, G Bruce; Deelman, Ewa; Juve, Gideon; Rynge, Mats; Vöckler, Jens-S

2013-01-28

The current model of transferring data from data centres to desktops for analysis will soon be rendered impractical by the accelerating growth in the volume of science datasets. Processing will instead often take place on high-performance servers co-located with data. Evaluations of how new technologies such as cloud computing would support such a new distributed computing model are urgently needed. Cloud computing is a new way of purchasing computing and storage resources on demand through virtualization technologies. We report here the results of investigations of the applicability of commercial cloud computing to scientific computing, with an emphasis on astronomy, including investigations of what types of applications can be run cheaply and efficiently on the cloud, and an example of an application well suited to the cloud: processing a large dataset to create a new science product.

Reducing Time to Science: Unidata and JupyterHub Technology Using the Jetstream Cloud

NASA Astrophysics Data System (ADS)

Chastang, J.; Signell, R. P.; Fischer, J. L.

2017-12-01

Cloud computing can accelerate scientific workflows, discovery, and collaborations by reducing research and data friction. We describe the deployment of Unidata and JupyterHub technologies on the NSF-funded XSEDE Jetstream cloud. With the aid of virtual machines and Docker technology, we deploy a Unidata JupyterHub server co-located with a Local Data Manager (LDM), THREDDS data server (TDS), and RAMADDA geoscience content management system. We provide Jupyter Notebooks and the pre-built Python environments needed to run them. The notebooks can be used for instruction and as templates for scientific experimentation and discovery. We also supply a large quantity of NCEP forecast model results to allow data-proximate analysis and visualization. In addition, users can transfer data using Globus command line tools, and perform their own data-proximate analysis and visualization with Notebook technology. These data can be shared with others via a dedicated TDS server for scientific distribution and collaboration. There are many benefits of this approach. Not only is the cloud computing environment fast, reliable and scalable, but scientists can analyze, visualize, and share data using only their web browser. No local specialized desktop software or a fast internet connection is required. This environment will enable scientists to spend less time managing their software and more time doing science.

PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition.

PubMed

Zuo, Yongchun; Li, Yuan; Chen, Yingli; Li, Guangpeng; Yan, Zhenhe; Yang, Lei

2017-01-01

The reduced amino acids perform powerful ability for both simplifying protein complexity and identifying functional conserved regions. However, dealing with different protein problems may need different kinds of cluster methods. Encouraged by the success of pseudo-amino acid composition algorithm, we developed a freely available web server, called PseKRAAC (the pseudo K-tuple reduced amino acids composition). By implementing reduced amino acid alphabets, the protein complexity can be significantly simplified, which leads to decrease chance of overfitting, lower computational handicap and reduce information redundancy. PseKRAAC delivers more capability for protein research by incorporating three crucial parameters that describes protein composition. Users can easily generate many different modes of PseKRAAC tailored to their needs by selecting various reduced amino acids alphabets and other characteristic parameters. It is anticipated that the PseKRAAC web server will become a very useful tool in computational proteomics and protein sequence analysis. Freely available on the web at http://bigdata.imu.edu.cn/psekraac CONTACTS: yczuo@imu.edu.cn or imu.hema@foxmail.com or yanglei_hmu@163.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Measurements over distributed high performance computing and storage systems

NASA Technical Reports Server (NTRS)

Williams, Elizabeth; Myers, Tom

1993-01-01

A strawman proposal is given for a framework for presenting a common set of metrics for supercomputers, workstations, file servers, mass storage systems, and the networks that interconnect them. Production control and database systems are also included. Though other applications and third part software systems are not addressed, it is important to measure them as well.

ERDC MSRC Resource. High Performance Computing for the Warfighter. Spring 2006

DTIC Science & Technology

2006-01-01

named Ruby, and the HP/Compaq SC45, named Emerald , continue to add their unique sparkle to the ERDC MSRC computer infrastructure. ERDC invited the...configuration on B-52H purchased additional memory for the login nodes so that this part of the solution process could be done as a preprocessing step. On...application and system services. Of the service nodes, 10 are login nodes and 23 are input/output (I/O) server nodes for the Lustre file system (i.e., the

Design and implementation of streaming media server cluster based on FFMpeg.

PubMed

Zhao, Hong; Zhou, Chun-long; Jin, Bao-zhao

2015-01-01

Poor performance and network congestion are commonly observed in the streaming media single server system. This paper proposes a scheme to construct a streaming media server cluster system based on FFMpeg. In this scheme, different users are distributed to different servers according to their locations and the balance among servers is maintained by the dynamic load-balancing algorithm based on active feedback. Furthermore, a service redirection algorithm is proposed to improve the transmission efficiency of streaming media data. The experiment results show that the server cluster system has significantly alleviated the network congestion and improved the performance in comparison with the single server system.

Design and Implementation of Streaming Media Server Cluster Based on FFMpeg

PubMed Central

Zhao, Hong; Zhou, Chun-long; Jin, Bao-zhao

2015-01-01

Poor performance and network congestion are commonly observed in the streaming media single server system. This paper proposes a scheme to construct a streaming media server cluster system based on FFMpeg. In this scheme, different users are distributed to different servers according to their locations and the balance among servers is maintained by the dynamic load-balancing algorithm based on active feedback. Furthermore, a service redirection algorithm is proposed to improve the transmission efficiency of streaming media data. The experiment results show that the server cluster system has significantly alleviated the network congestion and improved the performance in comparison with the single server system. PMID:25734187

Hypertext-based computer vision teaching packages

NASA Astrophysics Data System (ADS)

Marshall, A. David

1994-10-01

The World Wide Web Initiative has provided a means for providing hypertext and multimedia based information across the whole INTERNET. Many applications have been developed on such http servers. At Cardiff we have developed a http hypertext based multimedia server, the Cardiff Information Server, using the widely available Mosaic system. The server provides a variety of information ranging from the provision of teaching modules, on- line documentation, timetables for departmental activities to more light hearted hobby interests. One important and novel development to the server has been the development of courseware facilities. This ranges from the provision of on-line lecture notes, exercises and their solutions to more interactive teaching packages. A variety of disciplines have benefitted notably Computer Vision, and Image Processing but also C programming, X Windows, Computer Graphics and Parallel Computing. This paper will address the issues of the implementation of the Computer Vision and Image Processing packages, the advantages gained from using a hypertext based system and also will relate practical experiences of using the packages in a class environment. The paper addresses issues of how best to provide information in such a hypertext based system and how interactive image processing packages can be developed and integrated into courseware. The suite of tools developed facilitates a flexible and powerful courseware package that has proved popular in the classroom and over the Internet. The paper will also detail many future developments we see possible. One of the key points raised in the paper is that Mosaic's hypertext language (html) is extremely powerful and yet relatively straightforward to use. It is also possible to link in Unix calls so that programs and shells can be executed. This provides a powerful suite of utilities that can be exploited to develop many packages.

IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)

PubMed Central

Kolekar, Pandurang; Pataskar, Abhijeet; Kulkarni-Kale, Urmila; Pal, Jayanta; Kulkarni, Abhijeet

2016-01-01

Cellular mRNAs are predominantly translated in a cap-dependent manner. However, some viral and a subset of cellular mRNAs initiate their translation in a cap-independent manner. This requires presence of a structured RNA element, known as, Internal Ribosome Entry Site (IRES) in their 5′ untranslated regions (UTRs). Experimental demonstration of IRES in UTR remains a challenging task. Computational prediction of IRES merely based on sequence and structure conservation is also difficult, particularly for cellular IRES. A web server, IRESPred is developed for prediction of both viral and cellular IRES using Support Vector Machine (SVM). The predictive model was built using 35 features that are based on sequence and structural properties of UTRs and the probabilities of interactions between UTR and small subunit ribosomal proteins (SSRPs). The model was found to have 75.51% accuracy, 75.75% sensitivity, 75.25% specificity, 75.75% precision and Matthews Correlation Coefficient (MCC) of 0.51 in blind testing. IRESPred was found to perform better than the only available viral IRES prediction server, VIPS. The IRESPred server is freely available at http://bioinfo.net.in/IRESPred/. PMID:27264539

Server-Based and Server-Less Byod Solutions to Support Electronic Learning

DTIC Science & Technology

2016-06-01

Knowledge Online NSD National Security Directive OS operating system OWA Outlook Web Access PC personal computer PED personal electronic device PDA...mobile devices, institute mobile device policies and standards, and promote the development and use of DOD mobile and web -enabled applications” (DOD...with an isolated BYOD web server, properly educated system administrators must carry out and execute the necessary, pre-defined network security

LDAP: a web server for lncRNA-disease association prediction.

PubMed

Lan, Wei; Li, Min; Zhao, Kaijie; Liu, Jin; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

2017-02-01

Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources. Then, we implement this method as a web server for lncRNA-disease association prediction (LDAP). The input of the LDAP server is the lncRNA sequence. The LDAP predicts potential lncRNA-disease associations by using a bagging SVM classifier based on lncRNA similarity and disease similarity. The web server is available at http://bioinformatics.csu.edu.cn/ldap jxwang@mail.csu.edu.cn. Supplementary data are available at Bioinformatics online.

Benchmark tests on the digital equipment corporation Alpha AXP 21164-based AlphaServer 8400, including a comparison of optimized vector and superscalar processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wasserman, H.J.

1996-02-01

The second generation of the Digital Equipment Corp. (DEC) DECchip Alpha AXP microprocessor is referred to as the 21164. From the viewpoint of numerically-intensive computing, the primary difference between it and its predecessor, the 21064, is that the 21164 has twice the multiply/add throughput per clock period (CP), a maximum of two floating point operations (FLOPS) per CP vs. one for 21064. The AlphaServer 8400 is a shared-memory multiprocessor server system that can accommodate up to 12 CPUs and up to 14 GB of memory. In this report we will compare single processor performance of the 8400 system with thatmore » of the International Business Machines Corp. (IBM) RISC System/6000 POWER-2 microprocessor running at 66 MHz, the Silicon Graphics, Inc. (SGI) MIPS R8000 microprocessor running at 75 MHz, and the Cray Research, Inc. CRAY J90. The performance comparison is based on a set of Fortran benchmark codes that represent a portion of the Los Alamos National Laboratory supercomputer workload. The advantage of using these codes, is that the codes also span a wide range of computational characteristics, such as vectorizability, problem size, and memory access pattern. The primary disadvantage of using them is that detailed, quantitative analysis of performance behavior of all codes on all machines is difficult. One important addition to the benchmark set appears for the first time in this report. Whereas the older version was written for a vector processor, the newer version is more optimized for microprocessor architectures. Therefore, we have for the first time, an opportunity to measure performance on a single application using implementations that expose the respective strengths of vector and superscalar architecture. All results in this report are from single processors. A subsequent article will explore shared-memory multiprocessing performance of the 8400 system.« less

Intro and Recent Advances: Remote Data Access via OPeNDAP Web Services

NASA Technical Reports Server (NTRS)

Fulker, David

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

PubMed Central

2013-01-01

Background The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms. Results We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set. Conclusions D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight. PMID:23617301

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

PubMed

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

The software analysis project for the Office of Human Resources

NASA Technical Reports Server (NTRS)

Tureman, Robert L., Jr.

1994-01-01

There were two major sections of the project for the Office of Human Resources (OHR). The first section was to conduct a planning study to analyze software use with the goal of recommending software purchases and determining whether the need exists for a file server. The second section was analysis and distribution planning for retirement planning computer program entitled VISION provided by NASA Headquarters. The software planning study was developed to help OHR analyze the current administrative desktop computing environment and make decisions regarding software acquisition and implementation. There were three major areas addressed by the study: current environment new software requirements, and strategies regarding the implementation of a server in the Office. To gather data on current environment, employees were surveyed and an inventory of computers were produced. The surveys were compiled and analyzed by the ASEE fellow with interpretation help by OHR staff. New software requirements represented a compilation and analysis of the surveyed requests of OHR personnel. Finally, the information on the use of a server represents research done by the ASEE fellow and analysis of survey data to determine software requirements for a server. This included selection of a methodology to estimate the number of copies of each software program required given current use and estimated growth. The report presents the results of the computing survey, a description of the current computing environment, recommenations for changes in the computing environment, current software needs, management advantages of using a server, and management considerations in the implementation of a server. In addition, detailed specifications were presented for the hardware and software recommendations to offer a complete picture to OHR management. The retirement planning computer program available to NASA employees will aid in long-range retirement planning. The intended audience is the NASA civil service employee with several years until retirement. The employee enters current salary and savings information as well as goals concerning salary at retirement, assumptions on inflation, and the return on investments. The program produces a picture of the employee's retirement income from all sources based on the assumptions entered. A session showing features of the program was conducted for key personnel at the Center. After analysis, it was decided to offer the program through the Learning Center starting in August 1994.

Development of a small-scale computer cluster

NASA Astrophysics Data System (ADS)

Wilhelm, Jay; Smith, Justin T.; Smith, James E.

2008-04-01

An increase in demand for computing power in academia has necessitated the need for high performance machines. Computing power of a single processor has been steadily increasing, but lags behind the demand for fast simulations. Since a single processor has hard limits to its performance, a cluster of computers can have the ability to multiply the performance of a single computer with the proper software. Cluster computing has therefore become a much sought after technology. Typical desktop computers could be used for cluster computing, but are not intended for constant full speed operation and take up more space than rack mount servers. Specialty computers that are designed to be used in clusters meet high availability and space requirements, but can be costly. A market segment exists where custom built desktop computers can be arranged in a rack mount situation, gaining the space saving of traditional rack mount computers while remaining cost effective. To explore these possibilities, an experiment was performed to develop a computing cluster using desktop components for the purpose of decreasing computation time of advanced simulations. This study indicates that small-scale cluster can be built from off-the-shelf components which multiplies the performance of a single desktop machine, while minimizing occupied space and still remaining cost effective.

Centralized Fabric Management Using Puppet, Git, and GLPI

NASA Astrophysics Data System (ADS)

Smith, Jason A.; De Stefano, John S., Jr.; Fetzko, John; Hollowell, Christopher; Ito, Hironori; Karasawa, Mizuki; Pryor, James; Rao, Tejas; Strecker-Kellogg, William

2012-12-01

Managing the infrastructure of a large and complex data center can be extremely difficult without taking advantage of recent technological advances in administrative automation. Puppet is a seasoned open-source tool that is designed for enterprise class centralized configuration management. At the RHIC and ATLAS Computing Facility (RACF) at Brookhaven National Laboratory, we use Puppet along with Git, GLPI, and some custom scripts as part of our centralized configuration management system. In this paper, we discuss how we use these tools for centralized configuration management of our servers and services, change management requiring authorized approval of production changes, a complete version controlled history of all changes made, separation of production, testing and development systems using puppet environments, semi-automated server inventory using GLPI, and configuration change monitoring and reporting using the Puppet dashboard. We will also discuss scalability and performance results from using these tools on a 2,000+ node cluster and 400+ infrastructure servers with an administrative staff of approximately 25 full-time employees (FTEs).

Infinite capacity multi-server queue with second optional service channel

NASA Astrophysics Data System (ADS)

Ke, Jau-Chuan; Wu, Chia-Huang; Pearn, Wen Lea

2013-02-01

This paper deals with an infinite-capacity multi-server queueing system with a second optional service (SOS) channel. The inter-arrival times of arriving customers, the service times of the first essential service (FES) and the SOS channel are all exponentially distributed. A customer may leave the system after the FES channel with probability (1-θ), or at the completion of the FES may immediately require a SOS with probability θ (0 <= θ <= 1). The formulae for computing the rate matrix and stationary probabilities are derived by means of a matrix analytical approach. A cost model is developed to determine the optimal values of the number of servers and the two service rates, simultaneously, at the minimal total expected cost per unit time. Quasi-Newton method are employed to deal with the optimization problem. Under optimal operating conditions, numerical results are provided in which several system performance measures are calculated based on assumed numerical values of the system parameters.

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

PubMed Central

2013-01-01

Background Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs. Results A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset. Conclusions Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html PMID:23815072

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

A General Purpose Connections type CTI Server Based on SIP Protocol and Its Implementation

NASA Astrophysics Data System (ADS)

Watanabe, Toru; Koizumi, Hisao

In this paper, we propose a general purpose connections type CTI (Computer Telephony Integration) server that provides various CTI services such as voice logging where the CTI server communicates with IP-PBX using the SIP (Session Initiation Protocol), and accumulates voice packets of external line telephone call flowing between an IP telephone for extension and a VoIP gateway connected to outside line networks. The CTI server realizes CTI services such as voice logging, telephone conference, or IVR (interactive voice response) with accumulating and processing voice packets sampled. Furthermore, the CTI server incorporates a web server function which can provide various CTI services such as a Web telephone directory via a Web browser to PCs, cellular telephones or smart-phones in mobile environments.

From honeybees to Internet servers: biomimicry for distributed management of Internet hosting centers.

PubMed

Nakrani, Sunil; Tovey, Craig

2007-12-01

An Internet hosting center hosts services on its server ensemble. The center must allocate servers dynamically amongst services to maximize revenue earned from hosting fees. The finite server ensemble, unpredictable request arrival behavior and server reallocation cost make server allocation optimization difficult. Server allocation closely resembles honeybee forager allocation amongst flower patches to optimize nectar influx. The resemblance inspires a honeybee biomimetic algorithm. This paper describes details of the honeybee self-organizing model in terms of information flow and feedback, analyzes the homology between the two problems and derives the resulting biomimetic algorithm for hosting centers. The algorithm is assessed for effectiveness and adaptiveness by comparative testing against benchmark and conventional algorithms. Computational results indicate that the new algorithm is highly adaptive to widely varying external environments and quite competitive against benchmark assessment algorithms. Other swarm intelligence applications are briefly surveyed, and some general speculations are offered regarding their various degrees of success.

How to secure your servers, code and data

ScienceCinema

Lopienski, Sebastian

2018-04-30

Oral presentation in English, slides in English. Advice and best practices regarding the security of your servers, code and data will be presented. We will also describe how the Computer Security Team can help you reduce the risks.

Implementing bioinformatic workflows within the bioextract server

USDA-ARS?s Scientific Manuscript database

Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

PubMed

Trepalin, S V; Yarkov, A V

2001-01-01

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Cloud Computing Trace Characterization and Synthetic Workload Generation

DTIC Science & Technology

2013-03-01

measurements [44]. Olio is primarily for learning Web 2.0 technologies, evaluating the three implementations (PHP, Java EE, and RubyOnRails (ROR...Add Event 17 Olio is well documented, but assumes prerequisite knowledge with setup and operation of apache web servers and MySQL databases. Olio...Faban supports numerous servers such as Apache httpd, Sun Java System Web, Portal and Mail Servers, Oracle RDBMS, memcached, and others [18]. Perhaps

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

PubMed

Hirsh, Layla; Paladin, Lisanna; Piovesan, Damiano; Tosatto, Silvio C E

2018-05-09

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.

NASA Langley Research Center's distributed mass storage system

NASA Technical Reports Server (NTRS)

Pao, Juliet Z.; Humes, D. Creig

1993-01-01

There is a trend in institutions with high performance computing and data management requirements to explore mass storage systems with peripherals directly attached to a high speed network. The Distributed Mass Storage System (DMSS) Project at NASA LaRC is building such a system and expects to put it into production use by the end of 1993. This paper presents the design of the DMSS, some experiences in its development and use, and a performance analysis of its capabilities. The special features of this system are: (1) workstation class file servers running UniTree software; (2) third party I/O; (3) HIPPI network; (4) HIPPI/IPI3 disk array systems; (5) Storage Technology Corporation (STK) ACS 4400 automatic cartridge system; (6) CRAY Research Incorporated (CRI) CRAY Y-MP and CRAY-2 clients; (7) file server redundancy provision; and (8) a transition mechanism from the existent mass storage system to the DMSS.

Robotic tape library system level testing at NSA: Present and planned

NASA Technical Reports Server (NTRS)

Shields, Michael F.

1994-01-01

In the present of declining Defense budgets, increased pressure has been placed on the DOD to utilize Commercial Off the Shelf (COTS) solutions to incrementally solve a wide variety of our computer processing requirements. With the rapid growth in processing power, significant expansion of high performance networking, and the increased complexity of applications data sets, the requirement for high performance, large capacity, reliable and secure, and most of all affordable robotic tape storage libraries has greatly increased. Additionally, the migration to a heterogeneous, distributed computing environment has further complicated the problem. With today's open system compute servers approaching yesterday's supercomputer capabilities, the need for affordable, reliable secure Mass Storage Systems (MSS) has taken on an ever increasing importance to our processing center's ability to satisfy operational mission requirements. To that end, NSA has established an in-house capability to acquire, test, and evaluate COTS products. Its goal is to qualify a set of COTS MSS libraries, thereby achieving a modicum of standardization for robotic tape libraries which can satisfy our low, medium, and high performance file and volume serving requirements. In addition, NSA has established relations with other Government Agencies to complete this in-house effort and to maximize our research, testing, and evaluation work. While the preponderance of the effort is focused at the high end of the storage ladder, considerable effort will be extended this year and next at the server class or mid range storage systems.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

PubMed

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E; Troein, Carl; Millar, Andrew J; Goryanin, Igor; Gilmore, Stephen

2013-03-01

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats. All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.

Distributing Data from Desktop to Hand-Held Computers

NASA Technical Reports Server (NTRS)

Elmore, Jason L.

2005-01-01

A system of server and client software formats and redistributes data from commercially available desktop to commercially available hand-held computers via both wired and wireless networks. This software is an inexpensive means of enabling engineers and technicians to gain access to current sensor data while working in locations in which such data would otherwise be inaccessible. The sensor data are first gathered by a data-acquisition server computer, then transmitted via a wired network to a data-distribution computer that executes the server portion of the present software. Data in all sensor channels -- both raw sensor outputs in millivolt units and results of conversion to engineering units -- are made available for distribution. Selected subsets of the data are transmitted to each hand-held computer via the wired and then a wireless network. The selection of the subsets and the choice of the sequences and formats for displaying the data is made by means of a user interface generated by the client portion of the software. The data displayed on the screens of hand-held units can be updated at rates from 1 to

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

NASA Technical Reports Server (NTRS)

Katz, Randy H.; Anderson, Thomas E.; Ousterhout, John K.; Patterson, David A.

1991-01-01

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications.

OPeNDAP Server4: Buidling a High-Performance Server for the DAP by Leveraging Existing Software

NASA Astrophysics Data System (ADS)

Potter, N.; West, P.; Gallagher, J.; Garcia, J.; Fox, P.

2006-12-01

OPeNDAP has been working in conjunction with NCAR/ESSL/HAO to develop a modular, high performance data server that will be the successor to the current OPeNDAP data server. The new server, called Server4, is really two servers: A 'Back-End' data server which reads information from various types of data sources and packages the results in DAP objects; and A 'Front-End' which receives client DAP request and then decides how use features of the Back-End data server to build the correct responses. This architecture can be configured in several interesting ways: The Front- and Back-End components can be run on either the same or different machines, depending on security and performance needs, new Front-End software can be written to support other network data access protocols and local applications can interact directly with the Back-End data server. This new server's Back-End component will use the server infrastructure developed by HAO for use with the Earth System Grid II project. Extensions needed to use it as part of the new OPeNDAP server were minimal. The HAO server was modified so that it loads 'data handlers' at run-time. Each data handler module only needs to satisfy a simple interface which both enabled the existing data handlers written for the old OPeNDAP server to be directly used and also simplifies writing new handlers from scratch. The Back-End server leverages high- performance features developed for the ESG II project, so applications that can interact with it directly can read large volumes of data efficiently. The Front-End module of Server4 uses the Java Servlet system in place of the Common Gateway Interface (CGI) used in the past. New front-end modules can be written to support different network data access protocols, so that same server will ultimately be able to support more than the DAP/2.0 protocol. As an example, we will discuss a SOAP interface that's currently in development. In addition to support for DAP/2.0 and prototypical support for a SOAP interface, the new server includes support for the THREDDS cataloging protocol. THREDDS is tightly integrated into the Front-End of Server4. The Server4 Front-End can make full use of the advanced THREDDS features such as attribute specification and inheritance, custom catalogs which segue into automatically generated catalogs as well as providing a default behavior which requires almost no catalog configuration.

Dynamic Web Pages: Performance Impact on Web Servers.

ERIC Educational Resources Information Center

Kothari, Bhupesh; Claypool, Mark

2001-01-01

Discussion of Web servers and requests for dynamic pages focuses on experimentally measuring and analyzing the performance of the three dynamic Web page generation technologies: CGI, FastCGI, and Servlets. Develops a multivariate linear regression model and predicts Web server performance under some typical dynamic requests. (Author/LRW)

Optimizing the Use of Storage Systems Provided by Cloud Computing Environments

NASA Astrophysics Data System (ADS)

Gallagher, J. H.; Potter, N.; Byrne, D. A.; Ogata, J.; Relph, J.

2013-12-01

Cloud computing systems present a set of features that include familiar computing resources (albeit augmented to support dynamic scaling of processing power) bundled with a mix of conventional and unconventional storage systems. The linux base on which many Cloud environments (e.g., Amazon) are based make it tempting to assume that any Unix software will run efficiently in this environment efficiently without change. OPeNDAP and NODC collaborated on a short project to explore how the S3 and Glacier storage systems provided by the Amazon Cloud Computing infrastructure could be used with a data server developed primarily to access data stored in a traditional Unix file system. Our work used the Amazon cloud system, but we strived for designs that could be adapted easily to other systems like OpenStack. Lastly, we evaluated different architectures from a computer security perspective. We found that there are considerable issues associated with treating S3 as if it is a traditional file system, even though doing so is conceptually simple. These issues include performance penalties because using a software tool that emulates a traditional file system to store data in S3 performs poorly when compared to a storing data directly in S3. We also found there are important benefits beyond performance to ensuring that data written to S3 can directly accessed without relying on a specific software tool. To provide a hierarchical organization to the data stored in S3, we wrote 'catalog' files, using XML. These catalog files map discrete files to S3 access keys. Like a traditional file system's directories, the catalogs can also contain references to other catalogs, providing a simple but effective hierarchy overlaid on top of S3's flat storage space. An added benefit to these catalogs is that they can be viewed in a web browser; our storage scheme provides both efficient access for the data server and access via a web browser. We also looked at the Glacier storage system and found that the system's response characteristics are very different from a traditional file system or database; it behaves like a near-line storage system. To be used by a traditional data server, the underlying access protocol must support asynchronous accesses. This is because the Glacier system takes a minimum of four hours to deliver any data object, so systems built with the expectation of instant access (i.e., most web systems) must be fundamentally changed to use Glacier. Part of a related project has been to develop an asynchronous access mode for OPeNDAP, and we have developed a design using that new addition to the DAP protocol with Glacier as a near-line mass store. In summary, we found that both S3 and Glacier require special treatment to be effectively used by a data server. It is important to add (new) interfaces to data servers that enable them to use these storage devices through their native interfaces. We also found that our designs could easily map to a cloud environment based on OpenStack. Lastly, we noted that while these designs invited more liberal use of remote references for data objects, that can expose software to new security risks.

EarthServer: Cross-Disciplinary Earth Science Through Data Cube Analytics

NASA Astrophysics Data System (ADS)

Baumann, P.; Rossi, A. P.

2016-12-01

The unprecedented increase of imagery, in-situ measurements, and simulation data produced by Earth (and Planetary) Science observations missions bears a rich, yet not leveraged potential for getting insights from integrating such diverse datasets and transform scientific questions into actual queries to data, formulated in a standardized way.The intercontinental EarthServer [1] initiative is demonstrating new directions for flexible, scalable Earth Science services based on innovative NoSQL technology. Researchers from Europe, the US and Australia have teamed up to rigorously implement the concept of the datacube. Such a datacube may have spatial and temporal dimensions (such as a satellite image time series) and may unite an unlimited number of scenes. Independently from whatever efficient data structuring a server network may perform internally, users (scientist, planners, decision makers) will always see just a few datacubes they can slice and dice.EarthServer has established client [2] and server technology for such spatio-temporal datacubes. The underlying scalable array engine, rasdaman [3,4], enables direct interaction, including 3-D visualization, common EO data processing, and general analytics. Services exclusively rely on the open OGC "Big Geo Data" standards suite, the Web Coverage Service (WCS). Conversely, EarthServer has shaped and advanced WCS based on the experience gained. The first phase of EarthServer has advanced scalable array database technology into 150+ TB services. Currently, Petabyte datacubes are being built for ad-hoc and cross-disciplinary querying, e.g. using climate, Earth observation and ocean data.We will present the EarthServer approach, its impact on OGC / ISO / INSPIRE standardization, and its platform technology, rasdaman.References: [1] Baumann, et al. (2015) DOI: 10.1080/17538947.2014.1003106 [2] Hogan, P., (2011) NASA World Wind, Proceedings of the 2nd International Conference on Computing for Geospatial Research & Applications ACM. [3] Baumann, Peter, et al. (2014) In Proc. 10th ICDM, 194-201. [4] Dumitru, A. et al. (2014) In Proc ACM SIGMOD Workshop on Data Analytics in the Cloud (DanaC'2014), 1-4.

Using FastX on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

with full 3D hardware acceleration. The traditional method of displaying graphics applications to a remote X server (indirect rendering) supports 3D hardware acceleration, but this approach causes all of the OpenGL commands and 3D data to be sent over the network to be rendered on the client machine. With

Modeling, Simulation and Analysis of Public Key Infrastructure

NASA Technical Reports Server (NTRS)

Liu, Yuan-Kwei; Tuey, Richard; Ma, Paul (Technical Monitor)

1998-01-01

Security is an essential part of network communication. The advances in cryptography have provided solutions to many of the network security requirements. Public Key Infrastructure (PKI) is the foundation of the cryptography applications. The main objective of this research is to design a model to simulate a reliable, scalable, manageable, and high-performance public key infrastructure. We build a model to simulate the NASA public key infrastructure by using SimProcess and MatLab Software. The simulation is from top level all the way down to the computation needed for encryption, decryption, digital signature, and secure web server. The application of secure web server could be utilized in wireless communications. The results of the simulation are analyzed and confirmed by using queueing theory.

Modeling And Simulation Of Multimedia Communication Networks

NASA Astrophysics Data System (ADS)

Vallee, Richard; Orozco-Barbosa, Luis; Georganas, Nicolas D.

1989-05-01

In this paper, we present a simulation study of a browsing system involving radiological image servers. The proposed IEEE 802.6 DQDB MAN standard is designated as the computer network to transfer radiological images from file servers to medical workstations, and to simultaneously support real time voice communications. Storage and transmission of original raster scanned images and images compressed according to pyramid data structures are considered. Different types of browsing as well as various image sizes and bit rates in the DQDB MAN are also compared. The elapsed time, measured from the time an image request is issued until the image is displayed on the monitor, is the parameter considered to evaluate the system performance. Simulation results show that image browsing can be supported by the DQDB MAN.

More Effective Distributed ML via a Stale Synchronous Parallel Parameter Server

PubMed Central

Ho, Qirong; Cipar, James; Cui, Henggang; Kim, Jin Kyu; Lee, Seunghak; Gibbons, Phillip B.; Gibson, Garth A.; Ganger, Gregory R.; Xing, Eric P.

2014-01-01

We propose a parameter server system for distributed ML, which follows a Stale Synchronous Parallel (SSP) model of computation that maximizes the time computational workers spend doing useful work on ML algorithms, while still providing correctness guarantees. The parameter server provides an easy-to-use shared interface for read/write access to an ML model’s values (parameters and variables), and the SSP model allows distributed workers to read older, stale versions of these values from a local cache, instead of waiting to get them from a central storage. This significantly increases the proportion of time workers spend computing, as opposed to waiting. Furthermore, the SSP model ensures ML algorithm correctness by limiting the maximum age of the stale values. We provide a proof of correctness under SSP, as well as empirical results demonstrating that the SSP model achieves faster algorithm convergence on several different ML problems, compared to fully-synchronous and asynchronous schemes. PMID:25400488

Universal blind quantum computation for hybrid system

NASA Astrophysics Data System (ADS)

Huang, He-Liang; Bao, Wan-Su; Li, Tan; Li, Feng-Guang; Fu, Xiang-Qun; Zhang, Shuo; Zhang, Hai-Long; Wang, Xiang

2017-08-01

As progress on the development of building quantum computer continues to advance, first-generation practical quantum computers will be available for ordinary users in the cloud style similar to IBM's Quantum Experience nowadays. Clients can remotely access the quantum servers using some simple devices. In such a situation, it is of prime importance to keep the security of the client's information. Blind quantum computation protocols enable a client with limited quantum technology to delegate her quantum computation to a quantum server without leaking any privacy. To date, blind quantum computation has been considered only for an individual quantum system. However, practical universal quantum computer is likely to be a hybrid system. Here, we take the first step to construct a framework of blind quantum computation for the hybrid system, which provides a more feasible way for scalable blind quantum computation.

System-Level Virtualization Research at Oak Ridge National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott, Stephen L; Vallee, Geoffroy R; Naughton, III, Thomas J

2010-01-01

System-level virtualization is today enjoying a rebirth as a technique to effectively share what were then considered large computing resources to subsequently fade from the spotlight as individual workstations gained in popularity with a one machine - one user approach. One reason for this resurgence is that the simple workstation has grown in capability to rival that of anything available in the past. Thus, computing centers are again looking at the price/performance benefit of sharing that single computing box via server consolidation. However, industry is only concentrating on the benefits of using virtualization for server consolidation (enterprise computing) whereas ourmore » interest is in leveraging virtualization to advance high-performance computing (HPC). While these two interests may appear to be orthogonal, one consolidating multiple applications and users on a single machine while the other requires all the power from many machines to be dedicated solely to its purpose, we propose that virtualization does provide attractive capabilities that may be exploited to the benefit of HPC interests. This does raise the two fundamental questions of: is the concept of virtualization (a machine sharing technology) really suitable for HPC and if so, how does one go about leveraging these virtualization capabilities for the benefit of HPC. To address these questions, this document presents ongoing studies on the usage of system-level virtualization in a HPC context. These studies include an analysis of the benefits of system-level virtualization for HPC, a presentation of research efforts based on virtualization for system availability, and a presentation of research efforts for the management of virtual systems. The basis for this document was material presented by Stephen L. Scott at the Collaborative and Grid Computing Technologies meeting held in Cancun, Mexico on April 12-14, 2007.« less

Computers in Small Libraries: Learning Server-Side Scripting

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

In this column, the author compares and contrasts the most popular scripting languages that are used to create truly dynamic service-oriented Web sites, building a conceptual framework that be can used as a starting point for specific server-side library projects.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair.

PubMed

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair

PubMed Central

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed. PMID:29706894

Openlobby: an open game server for lobby and matchmaking

NASA Astrophysics Data System (ADS)

Zamzami, E. M.; Tarigan, J. T.; Jaya, I.; Hardi, S. M.

2018-03-01

Online Multiplayer is one of the most essential feature in modern games. However, while developing a multiplayer feature can be done with a simple computer networking programming, creating a balanced multiplayer session requires more player management components such as game lobby and matchmaking system. Our objective is to develop OpenLobby, a server that available to be used by other developers to support their multiplayer application. The proposed system acts as a lobby and matchmaker where queueing players will be matched to other player according to a certain criteria defined by developer. The solution provides an application programing interface that can be used by developer to interact with the server. For testing purpose, we developed a game that uses the server as their multiplayer server.

I/O load balancing for big data HPC applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul, Arnab K.; Goyal, Arpit; Wang, Feiyi

High Performance Computing (HPC) big data problems require efficient distributed storage systems. However, at scale, such storage systems often experience load imbalance and resource contention due to two factors: the bursty nature of scientific application I/O; and the complex I/O path that is without centralized arbitration and control. For example, the extant Lustre parallel file system-that supports many HPC centers-comprises numerous components connected via custom network topologies, and serves varying demands of a large number of users and applications. Consequently, some storage servers can be more loaded than others, which creates bottlenecks and reduces overall application I/O performance. Existing solutionsmore » typically focus on per application load balancing, and thus are not as effective given their lack of a global view of the system. In this paper, we propose a data-driven approach to load balance the I/O servers at scale, targeted at Lustre deployments. To this end, we design a global mapper on Lustre Metadata Server, which gathers runtime statistics from key storage components on the I/O path, and applies Markov chain modeling and a minimum-cost maximum-flow algorithm to decide where data should be placed. Evaluation using a realistic system simulator and a real setup shows that our approach yields better load balancing, which in turn can improve end-to-end performance.« less

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cloudy Solar Software - Enhanced Capabilities for Finding, Pre-processing, and Visualizing Solar Data

NASA Astrophysics Data System (ADS)

Istvan Etesi, Laszlo; Tolbert, K.; Schwartz, R.; Zarro, D.; Dennis, B.; Csillaghy, A.

2010-05-01

In our project "Extending the Virtual Solar Observatory (VSO)” we have combined some of the features available in Solar Software (SSW) to produce an integrated environment for data analysis, supporting the complete workflow from data location, retrieval, preparation, and analysis to creating publication-quality figures. Our goal is an integrated analysis experience in IDL, easy-to-use but flexible enough to allow more sophisticated procedures such as multi-instrument analysis. To that end, we have made the transition from a locally oriented setting where all the analysis is done on the user's computer, to an extended analysis environment where IDL has access to services available on the Internet. We have implemented a form of Cloud Computing that uses the VSO search and a new data retrieval and pre-processing server (PrepServer) that provides remote execution of instrument-specific data preparation. We have incorporated the interfaces to the VSO search and the PrepServer into an IDL widget (SHOW_SYNOP) that provides user-friendly searching and downloading of raw solar data and optionally sends search results for pre-processing to the PrepServer prior to downloading the data. The raw and pre-processed data can be displayed with our plotting suite, PLOTMAN, which can handle different data types (light curves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. PLOTMAN is highly configurable and suited for visual data analysis and for creating publishable figures. PLOTMAN and SHOW_SYNOP work hand-in-hand for a convenient working environment. Our environment supports a growing number of solar instruments that currently includes RHESSI, SOHO/EIT, TRACE, SECCHI/EUVI, HINODE/XRT, and HINODE/EIS.

A Standardized Interface for Obtaining Digital Planetary and Heliophysics Time Series Data

NASA Astrophysics Data System (ADS)

Vandegriff, Jon; Weigel, Robert; Faden, Jeremy; King, Todd; Candey, Robert

2016-10-01

We describe a low level interface for accessing digital Planetary and Heliophysics data, focusing primarily on time-series data from in-situ instruments. As the volume and variety of planetary data has increased, it has become harder to merge diverse datasets into a common analysis environment. Thus we are building low-level computer-to-computer infrastructure to enable data from different missions or archives to be able to interoperate. The key to enabling interoperability is a simple access interface that standardizes the common capabilities available from any data server: 1. identify the data resources that can be accessed; 2. describe each resource; and 3. get the data from a resource. We have created a standardized way for data servers to perform each of these three activities. We are also developing a standard streaming data format for the actual data content to be returned (i.e., the result of item 3). Our proposed standard access interface is simple enough that it could be implemented on top of or beside existing data services, or it could even be fully implemented by a small data provider as a way to ensure that the provider's holdings can participate in larger data systems or joint analysis with other datasets. We present details of the interface and of the streaming format, including a sample server designed to illustrate the data request and streaming capabilities.

Preliminary Results on Design and Implementation of a Solar Radiation Monitoring System

PubMed Central

Balan, Mugur C.; Damian, Mihai; Jäntschi, Lorentz

2008-01-01

The paper presents a solar radiation monitoring system, using two scientific pyranometers and an on-line computer home-made data acquisition system. The first pyranometer measures the global solar radiation and the other one, which is shaded, measure the diffuse radiation. The values of total and diffuse solar radiation are continuously stored into a database on a server. Original software was created for data acquisition and interrogation of the created system. The server application acquires the data from pyranometers and stores it into a database with a baud rate of one record at 50 seconds. The client-server application queries the database and provides descriptive statistics. A web interface allow to any user to define the including criteria and to obtain the results. In terms of results, the system is able to provide direct, diffuse and total radiation intensities as time series. Our client-server application computes also derivate heats. The ability of the system to evaluate the local solar energy potential is highlighted. PMID:27879746

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

e-Stars Template Builder is a computer program that implements a concept of enabling users to rapidly gain access to information on projects of NASA's Jet Propulsion Laboratory. The information about a given project is not stored in a data base, but rather, in a network that follows the project as it develops. e-Stars Template Builder resides on a server computer, using Practical Extraction and Reporting Language (PERL) scripts to create what are called "e-STARS node templates," which are software constructs that allow for project-specific configurations. The software resides on the server and does not require specific software on the user machine except for an Internet browser. A user's computer need not be equipped with special software (other than an Internet-browser program). e-Stars Template Builder is compatible with Windows, Macintosh, and UNIX operating systems. A user invokes e-Stars Template Builder from a browser window. Operations that can be performed by the user include the creation of child processes and the addition of links and descriptions of documentation to existing pages or nodes. By means of this addition of "child processes" of nodes, a network that reflects the development of a project is generated.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Designing and Implementation of River Classification Assistant Management System

NASA Astrophysics Data System (ADS)

Zhao, Yinjun; Jiang, Wenyuan; Yang, Rujun; Yang, Nan; Liu, Haiyan

2018-03-01

In an earlier publication, we proposed a new Decision Classifier (DCF) for Chinese river classification based on their structures. To expand, enhance and promote the application of the DCF, we build a computer system to support river classification named River Classification Assistant Management System. Based on ArcEngine and ArcServer platform, this system implements many functions such as data management, extraction of river network, river classification, and results publication under combining Client / Server with Browser / Server framework.

Secure data aggregation in heterogeneous and disparate networks using stand off server architecture

NASA Astrophysics Data System (ADS)

Vimalathithan, S.; Sudarsan, S. D.; Seker, R.; Lenin, R. B.; Ramaswamy, S.

2009-04-01

The emerging global reach of technology presents myriad challenges and intricacies as Information Technology teams aim to provide anywhere, anytime and anyone access, for service providers and customers alike. The world is fraught with stifling inequalities, both from an economic as well as socio-political perspective. The net result has been large capability gaps between various organizational locations that need to work together, which has raised new challenges for information security teams. Similar issues arise, when mergers and acquisitions among and between organizations take place. While integrating remote business locations with mainstream operations, one or more of the issues including the lack of application level support, computational capabilities, communication limitations, and legal requirements cause a serious impediment thereby complicating integration while not violating the organizations' security requirements. Often resorted techniques like IPSec, tunneling, secure socket layer, etc. may not be always techno-economically feasible. This paper addresses such security issues by introducing an intermediate server between corporate central server and remote sites, called stand-off-server. We present techniques such as break-before-make connection, break connection after transfer, multiple virtual machine instances with different operating systems using the concept of a stand-off-server. Our experiments show that the proposed solution provides sufficient isolation for the central server/site from attacks arising out of weak communication and/or computing links and is simple to implement.

Computer Ethics and Cyber Laws to Mental Health Professionals

PubMed Central

Raveesh, B N; Pande, Sanjay

2004-01-01

The explosive growth of computer and communications technology raises new legal and ethical challenges that reflect tensions between individual rights and societal needs. For instance, should cracking into a computer system be viewed as a petty prank, as trespassing, as theft, or as espionage? Should placing copyrighted material onto a public file server be treated as freedom of expression or as theft? Should ordinary communications be encrypted using codes that make it impossible for law-enforcement agencies to perform wiretaps? As we develop shared understandings and norms of behaviour, we are setting standards that will govern the information society for decades to come. PMID:21408035

Computer ethics and cyber laws to mental health professionals.

PubMed

Raveesh, B N; Pande, Sanjay

2004-04-01

The explosive growth of computer and communications technology raises new legal and ethical challenges that reflect tensions between individual rights and societal needs. For instance, should cracking into a computer system be viewed as a petty prank, as trespassing, as theft, or as espionage? Should placing copyrighted material onto a public file server be treated as freedom of expression or as theft? Should ordinary communications be encrypted using codes that make it impossible for law-enforcement agencies to perform wiretaps? As we develop shared understandings and norms of behaviour, we are setting standards that will govern the information society for decades to come.

Multi-Core Processor Memory Contention Benchmark Analysis Case Study

NASA Technical Reports Server (NTRS)

Simon, Tyler; McGalliard, James

2009-01-01

Multi-core processors dominate current mainframe, server, and high performance computing (HPC) systems. This paper provides synthetic kernel and natural benchmark results from an HPC system at the NASA Goddard Space Flight Center that illustrate the performance impacts of multi-core (dual- and quad-core) vs. single core processor systems. Analysis of processor design, application source code, and synthetic and natural test results all indicate that multi-core processors can suffer from significant memory subsystem contention compared to similar single-core processors.

Converged photonic data storage and switch platform for exascale disaggregated data centers

NASA Astrophysics Data System (ADS)

Pitwon, R.; Wang, K.; Worrall, A.

2017-02-01

We report on a converged optically enabled Ethernet storage, switch and compute platform, which could support future disaggregated data center architectures. The platform includes optically enabled Ethernet switch controllers, an advanced electro-optical midplane and optically interchangeable generic end node devices. We demonstrate system level performance using optically enabled Ethernet disk drives and micro-servers across optical links of varied lengths.

Construction and application of Red5 cluster based on OpenStack

NASA Astrophysics Data System (ADS)

Wang, Jiaqing; Song, Jianxin

2017-08-01

With the application and development of cloud computing technology in various fields, the resource utilization rate of the data center has been improved obviously, and the system based on cloud computing platform has also improved the expansibility and stability. In the traditional way, Red5 cluster resource utilization is low and the system stability is poor. This paper uses cloud computing to efficiently calculate the resource allocation ability, and builds a Red5 server cluster based on OpenStack. Multimedia applications can be published to the Red5 cloud server cluster. The system achieves the flexible construction of computing resources, but also greatly improves the stability of the cluster and service efficiency.

Client/Server Architecture Promises Radical Changes.

ERIC Educational Resources Information Center

Freeman, Grey; York, Jerry

1991-01-01

This article discusses the emergence of the client/server paradigm for the delivery of computer applications, its emergence in response to the proliferation of microcomputers and local area networks, the applicability of the model in academic institutions, and its implications for college campus information technology organizations. (Author/DB)

Perspectives of IT Professionals on Employing Server Virtualization Technologies

ERIC Educational Resources Information Center

Sligh, Darla

2010-01-01

Server virtualization enables a physical computer to support multiple applications logically by decoupling the application from the hardware layer, thereby reducing operational costs and competitive in delivering IT services to their enterprise organizations. IT organizations continually examine the efficiency of their internal IT systems and…

Remote vibration monitoring system using wireless internet data transfer

NASA Astrophysics Data System (ADS)

Lemke, John

2000-06-01

Vibrations from construction activities can affect infrastructure projects in several ways. Within the general vicinity of a construction site, vibrations can result in damage to existing structures, disturbance to people, damage to sensitive machinery, and degraded performance of precision instrumentation or motion sensitive equipment. Current practice for monitoring vibrations in the vicinity of construction sites commonly consists of measuring free field or structural motions using velocity transducers connected to a portable data acquisition unit via cables. This paper describes an innovative way to collect, process, transmit, and analyze vibration measurements obtained at construction sites. The system described measures vibration at the sensor location, performs necessary signal conditioning and digitization, and sends data to a Web server using wireless data transmission and Internet protocols. A Servlet program running on the Web server accepts the transmitted data and incorporates it into a project database. Two-way interaction between the Web-client and the Web server is accomplished through the use of a Servlet program and a Java Applet running inside a browser located on the Web client's computer. Advantages of this system over conventional vibration data logging systems include continuous unattended monitoring, reduced costs associated with field data collection, instant access to data files and graphs by project team members, and the ability to remotely modify data sampling schemes.

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

PubMed

Margreitter, Christian; Lu, Hui-Chun; Townsend, Catherine; Stewart, Alexander; Dunn-Walters, Deborah K; Fraternali, Franca

2018-04-14

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server's functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

Viewing ISS Data in Real Time via the Internet

NASA Technical Reports Server (NTRS)

Myers, Gerry; Chamberlain, Jim

2004-01-01

EZStream is a computer program that enables authorized users at diverse terrestrial locations to view, in real time, data generated by scientific payloads aboard the International Space Station (ISS). The only computation/communication resource needed for use of EZStream is a computer equipped with standard Web-browser software and a connection to the Internet. EZStream runs in conjunction with the TReK software, described in a prior NASA Tech Briefs article, that coordinates multiple streams of data for the ground communication system of the ISS. EZStream includes server components that interact with TReK within the ISS ground communication system and client components that reside in the users' remote computers. Once an authorized client has logged in, a server component of EZStream pulls the requested data from a TReK application-program interface and sends the data to the client. Future EZStream enhancements will include (1) extensions that enable the server to receive and process arbitrary data streams on its own and (2) a Web-based graphical-user-interface-building subprogram that enables a client who lacks programming expertise to create customized display Web pages.

PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.

PubMed

Zhang, P; Tao, L; Zeng, X; Qin, C; Chen, S Y; Zhu, F; Yang, S Y; Li, Z R; Chen, W P; Chen, Y Z

2017-02-03

The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein-protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles. Copyright © 2016 Elsevier Ltd. All rights reserved.

SSRL Emergency Response Shore Tool

NASA Technical Reports Server (NTRS)

Mah, Robert W.; Papasin, Richard; McIntosh, Dawn M.; Denham, Douglas; Jorgensen, Charles; Betts, Bradley J.; Del Mundo, Rommel

2006-01-01

The SSRL Emergency Response Shore Tool (wherein SSRL signifies Smart Systems Research Laboratory ) is a computer program within a system of communication and mobile-computing software and hardware being developed to increase the situational awareness of first responders at building collapses. This program is intended for use mainly in planning and constructing shores to stabilize partially collapsed structures. The program consists of client and server components, runs in the Windows operating system on commercial off-the-shelf portable computers, and can utilize such additional hardware as digital cameras and Global Positioning System devices. A first responder can enter directly, into a portable computer running this program, the dimensions of a required shore. The shore dimensions, plus an optional digital photograph of the shore site, can then be uploaded via a wireless network to a server. Once on the server, the shore report is time-stamped and made available on similarly equipped portable computers carried by other first responders, including shore wood cutters and an incident commander. The staff in a command center can use the shore reports and photographs to monitor progress and to consult with structural engineers to assess whether a building is in imminent danger of further collapse.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Yahoo! Compute Coop (YCC). A Next-Generation Passive Cooling Design for Data Centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robison, AD; Page, Christina; Lytle, Bob

The purpose of the Yahoo! Compute Coop (YCC) project is to research, design, build and implement a greenfield "efficient data factory" and to specifically demonstrate that the YCC concept is feasible for large facilities housing tens of thousands of heat-producing computing servers. The project scope for the Yahoo! Compute Coop technology includes: - Analyzing and implementing ways in which to drastically decrease energy consumption and waste output. - Analyzing the laws of thermodynamics and implementing naturally occurring environmental effects in order to maximize the "free-cooling" for large data center facilities. "Free cooling" is the direct usage of outside air tomore » cool the servers vs. traditional "mechanical cooling" which is supplied by chillers or other Dx units. - Redesigning and simplifying building materials and methods. - Shortening and simplifying build-to-operate schedules while at the same time reducing initial build and operating costs. Selected for its favorable climate, the greenfield project site is located in Lockport, NY. Construction on the 9.0 MW critical load data center facility began in May 2009, with the fully operational facility deployed in September 2010. The relatively low initial build cost, compatibility with current server and network models, and the efficient use of power and water are all key features that make it a highly compatible and globally implementable design innovation for the data center industry. Yahoo! Compute Coop technology is designed to achieve 99.98% uptime availability. This integrated building design allows for free cooling 99% of the year via the building's unique shape and orientation, as well as server physical configuration.« less

Innovation Incubator: LiquidCool Solutions Technical Evaluation. Laboratory Study and Demonstration Results of a Directed-Flow, Liquid Submerged Server for High-Efficiency Data Centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozubal, Eric J

LiquidCool Solutions (LCS) has developed liquid submerged server (LSS) technology that changes the way computer electronics are cooled. The technology provides an option to cool electronics by the direct contact flow of dielectric fluid (coolant) into a sealed enclosure housing all the electronics of a single server. The intimate dielectric fluid contact with electronics improves the effectiveness of heat removal from the electronics.

FY17 Status Report on the Computing Systems for the Yucca Mountain Project TSPA-LA Models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Appel, Gordon John; Hadgu, Teklu; Appel, Gordon John

Sandia National Laboratories (SNL) continued evaluation of total system performance assessment (TSPA) computing systems for the previously considered Yucca Mountain Project (YMP). This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment (TSPA) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. This work is a continuation of the ongoing readiness evaluation reported in Lee and Hadgu (2014), Hadgu et al. (2015) and Hadgu and Appel (2016). The TSPA computing hardware (CL2014) and storage system described in Hadgu et al. (2015) weremore » used for the current analysis. One floating license of GoldSim with Versions 9.60.300, 10.5, 11.1 and 12.0 was installed on the cluster head node, and its distributed processing capability was mapped on the cluster processors. Other supporting software were tested and installed to support the TSPA- type analysis on the server cluster. The current tasks included preliminary upgrade of the TSPA-LA from Version 9.60.300 to the latest version 12.0 and address DLL-related issues observed in the FY16 work. The model upgrade task successfully converted the Nominal Modeling case to GoldSim Versions 11.1/12. Conversions of the rest of the TSPA models were also attempted but program and operational difficulties precluded this. Upgrade of the remaining of the modeling cases and distributed processing tasks is expected to continue. The 2014 server cluster and supporting software systems are fully operational to support TSPA-LA type analysis.« less

[Construction and analysis of a monitoring system with remote real-time multiple physiological parameters based on cloud computing].

PubMed

Zhu, Lingyun; Li, Lianjie; Meng, Chunyan

2014-12-01

There have been problems in the existing multiple physiological parameter real-time monitoring system, such as insufficient server capacity for physiological data storage and analysis so that data consistency can not be guaranteed, poor performance in real-time, and other issues caused by the growing scale of data. We therefore pro posed a new solution which was with multiple physiological parameters and could calculate clustered background data storage and processing based on cloud computing. Through our studies, a batch processing for longitudinal analysis of patients' historical data was introduced. The process included the resource virtualization of IaaS layer for cloud platform, the construction of real-time computing platform of PaaS layer, the reception and analysis of data stream of SaaS layer, and the bottleneck problem of multi-parameter data transmission, etc. The results were to achieve in real-time physiological information transmission, storage and analysis of a large amount of data. The simulation test results showed that the remote multiple physiological parameter monitoring system based on cloud platform had obvious advantages in processing time and load balancing over the traditional server model. This architecture solved the problems including long turnaround time, poor performance of real-time analysis, lack of extensibility and other issues, which exist in the traditional remote medical services. Technical support was provided in order to facilitate a "wearable wireless sensor plus mobile wireless transmission plus cloud computing service" mode moving towards home health monitoring for multiple physiological parameter wireless monitoring.

Beyond Electronic Forms: E-Mail as an Institution-Wide Information Server.

ERIC Educational Resources Information Center

Jacobson, Carl

1992-01-01

The University of Delaware developed an intelligent mail server to provide easy, inexpensive access to institutional information for faculty, staff, and students on any node, machine, or operating system on the campuswide computing network. Security concerns have been addressed. The small investment has returned immediate benefits. (MSE)

A Study of the Efficiency of Spatial Indexing Methods Applied to Large Astronomical Databases

NASA Astrophysics Data System (ADS)

Donaldson, Tom; Berriman, G. Bruce; Good, John; Shiao, Bernie

2018-01-01

Spatial indexing of astronomical databases generally uses quadrature methods, which partition the sky into cells used to create an index (usually a B-tree) written as database column. We report the results of a study to compare the performance of two common indexing methods, HTM and HEALPix, on Solaris and Windows database servers installed with a PostgreSQL database, and a Windows Server installed with MS SQL Server. The indexing was applied to the 2MASS All-Sky Catalog and to the Hubble Source catalog. On each server, the study compared indexing performance by submitting 1 million queries at each index level with random sky positions and random cone search radius, which was computed on a logarithmic scale between 1 arcsec and 1 degree, and measuring the time to complete the query and write the output. These simulated queries, intended to model realistic use patterns, were run in a uniform way on many combinations of indexing method and indexing level. The query times in all simulations are strongly I/O-bound and are linear with number of records returned for large numbers of sources. There are, however, considerable differences between simulations, which reveal that hardware I/O throughput is a more important factor in managing the performance of a DBMS than the choice of indexing scheme. The choice of index itself is relatively unimportant: for comparable index levels, the performance is consistent within the scatter of the timings. At small index levels (large cells; e.g. level 4; cell size 3.7 deg), there is large scatter in the timings because of wide variations in the number of sources found in the cells. At larger index levels, performance improves and scatter decreases, but the improvement at level 8 (14 min) and higher is masked to some extent in the timing scatter caused by the range of query sizes. At very high levels (20; 0.0004 arsec), the granularity of the cells becomes so high that a large number of extraneous empty cells begin to degrade performance. Thus, for the use patterns studied here the database performance is not critically dependent on the exact choices of index or level.

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

CTserver: A Computational Thermodynamics Server for the Geoscience Community

NASA Astrophysics Data System (ADS)

Kress, V. C.; Ghiorso, M. S.

2006-12-01

The CTserver platform is an Internet-based computational resource that provides on-demand services in Computational Thermodynamics (CT) to a diverse geoscience user base. This NSF-supported resource can be accessed at ctserver.ofm-research.org. The CTserver infrastructure leverages a high-quality and rigorously tested software library of routines for computing equilibrium phase assemblages and for evaluating internally consistent thermodynamic properties of materials, e.g. mineral solid solutions and a variety of geological fluids, including magmas. Thermodynamic models are currently available for 167 phases. Recent additions include Duan, Møller and Weare's model for supercritical C-O-H-S, extended to include SO2 and S2 species, and an entirely new associated solution model for O-S-Fe-Ni sulfide liquids. This software library is accessed via the CORBA Internet protocol for client-server communication. CORBA provides a standardized, object-oriented, language and platform independent, fast, low-bandwidth interface to phase property modules running on the server cluster. Network transport, language translation and resource allocation are handled by the CORBA interface. Users access server functionality in two principal ways. Clients written as browser- based Java applets may be downloaded which provide specific functionality such as retrieval of thermodynamic properties of phases, computation of phase equilibria for systems of specified composition, or modeling the evolution of these systems along some particular reaction path. This level of user interaction requires minimal programming effort and is ideal for classroom use. A more universal and flexible mode of CTserver access involves making remote procedure calls from user programs directly to the server public interface. The CTserver infrastructure relieves the user of the burden of implementing and testing the often complex thermodynamic models of real liquids and solids. A pilot application of this distributed architecture involves CFD computation of magma convection at Volcan Villarrica with magma properties and phase proportions calculated at each spatial node and at each time step via distributed function calls to MELTS-objects executing on the CTserver. Documentation and programming examples are provided at http://ctserver.ofm- research.org.

Availability of software services for a hospital information system.

PubMed

Sakamoto, N

1998-03-01

Hospital information systems (HISs) are becoming more important and covering more parts in daily hospital operations as order-entry systems become popular and electronic charts are introduced. Thus, HISs today need to be able to provide necessary services for hospital operations for a 24-h day, 365 days a year. The provision of services discussed here does not simply mean the availability of computers, in which all that matters is that the computer is functioning. It means the provision of necessary information for hospital operations by the computer software, and we will call it the availability of software services. HISs these days are mostly client-server systems. To increase availability of software services in these systems, it is not enough to just use system structures that are highly reliable in existing host-centred systems. Four main components which support availability of software services are network systems, client computers, server computers, and application software. In this paper, we suggest how to structure these four components to provide the minimum requested software services even if a part of the system stops to function. The network system should be double-protected in stratus using Asynchronous Transfer Mode (ATM) as its base network. Client computers should be fat clients with as much application logic as possible, and reference information which do not require frequent updates (master files, for example) should be replicated in clients. It would be best if all server computers could be double-protected. However, if that is physically impossible, one database file should be made accessible by several server computers. Still, at least the basic patients' information and the latest clinical records should be double-protected physically. Application software should be tested carefully before introduction. Different versions of the application software should always be kept and managed in case the new version has problems. If a hospital information system is designed and developed with these points in mind, it's availability of software services should increase greatly.

Integrated multimodal human-computer interface and augmented reality for interactive display applications

NASA Astrophysics Data System (ADS)

Vassiliou, Marius S.; Sundareswaran, Venkataraman; Chen, S.; Behringer, Reinhold; Tam, Clement K.; Chan, M.; Bangayan, Phil T.; McGee, Joshua H.

2000-08-01

We describe new systems for improved integrated multimodal human-computer interaction and augmented reality for a diverse array of applications, including future advanced cockpits, tactical operations centers, and others. We have developed an integrated display system featuring: speech recognition of multiple concurrent users equipped with both standard air- coupled microphones and novel throat-coupled sensors (developed at Army Research Labs for increased noise immunity); lip reading for improving speech recognition accuracy in noisy environments, three-dimensional spatialized audio for improved display of warnings, alerts, and other information; wireless, coordinated handheld-PC control of a large display; real-time display of data and inferences from wireless integrated networked sensors with on-board signal processing and discrimination; gesture control with disambiguated point-and-speak capability; head- and eye- tracking coupled with speech recognition for 'look-and-speak' interaction; and integrated tetherless augmented reality on a wearable computer. The various interaction modalities (speech recognition, 3D audio, eyetracking, etc.) are implemented a 'modality servers' in an Internet-based client-server architecture. Each modality server encapsulates and exposes commercial and research software packages, presenting a socket network interface that is abstracted to a high-level interface, minimizing both vendor dependencies and required changes on the client side as the server's technology improves.

Spontaneous Ad Hoc Mobile Cloud Computing Network

PubMed Central

Lacuesta, Raquel; Sendra, Sandra; Peñalver, Lourdes

2014-01-01

Cloud computing helps users and companies to share computing resources instead of having local servers or personal devices to handle the applications. Smart devices are becoming one of the main information processing devices. Their computing features are reaching levels that let them create a mobile cloud computing network. But sometimes they are not able to create it and collaborate actively in the cloud because it is difficult for them to build easily a spontaneous network and configure its parameters. For this reason, in this paper, we are going to present the design and deployment of a spontaneous ad hoc mobile cloud computing network. In order to perform it, we have developed a trusted algorithm that is able to manage the activity of the nodes when they join and leave the network. The paper shows the network procedures and classes that have been designed. Our simulation results using Castalia show that our proposal presents a good efficiency and network performance even by using high number of nodes. PMID:25202715

Spontaneous ad hoc mobile cloud computing network.

PubMed

Lacuesta, Raquel; Lloret, Jaime; Sendra, Sandra; Peñalver, Lourdes

2014-01-01

Cloud computing helps users and companies to share computing resources instead of having local servers or personal devices to handle the applications. Smart devices are becoming one of the main information processing devices. Their computing features are reaching levels that let them create a mobile cloud computing network. But sometimes they are not able to create it and collaborate actively in the cloud because it is difficult for them to build easily a spontaneous network and configure its parameters. For this reason, in this paper, we are going to present the design and deployment of a spontaneous ad hoc mobile cloud computing network. In order to perform it, we have developed a trusted algorithm that is able to manage the activity of the nodes when they join and leave the network. The paper shows the network procedures and classes that have been designed. Our simulation results using Castalia show that our proposal presents a good efficiency and network performance even by using high number of nodes.

The UK Human Genome Mapping Project online computing service.

PubMed

Rysavy, F R; Bishop, M J; Gibbs, G P; Williams, G W

1992-04-01

This paper presents an overview of computing and networking facilities developed by the Medical Research Council to provide online computing support to the Human Genome Mapping Project (HGMP) in the UK. The facility is connected to a number of other computing facilities in various centres of genetics and molecular biology research excellence, either directly via high-speed links or through national and international wide-area networks. The paper describes the design and implementation of the current system, a 'client/server' network of Sun, IBM, DEC and Apple servers, gateways and workstations. A short outline of online computing services currently delivered by this system to the UK human genetics research community is also provided. More information about the services and their availability could be obtained by a direct approach to the UK HGMP-RC.

How Does One Manage ’Information? Making Sense of the Information Being Received

DTIC Science & Technology

2012-12-01

to manage. (Photo by PFC Franklin E. Mercado .) Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of...in choosing the right application. Appli- cation software is written to perform a specific task or function, and it becomes increasingly difficult...common data, virtu- alizing machines for all software (using one computer/server, but dividing it into logical segments), and standardizing

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

PubMed

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

Defense strategies for cloud computing multi-site server infrastructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Nageswara S.; Ma, Chris Y. T.; He, Fei

We consider cloud computing server infrastructures for big data applications, which consist of multiple server sites connected over a wide-area network. The sites house a number of servers, network elements and local-area connections, and the wide-area network plays a critical, asymmetric role of providing vital connectivity between them. We model this infrastructure as a system of systems, wherein the sites and wide-area network are represented by their cyber and physical components. These components can be disabled by cyber and physical attacks, and also can be protected against them using component reinforcements. The effects of attacks propagate within the systems, andmore » also beyond them via the wide-area network.We characterize these effects using correlations at two levels using: (a) aggregate failure correlation function that specifies the infrastructure failure probability given the failure of an individual site or network, and (b) first-order differential conditions on system survival probabilities that characterize the component-level correlations within individual systems. We formulate a game between an attacker and a provider using utility functions composed of survival probability and cost terms. At Nash Equilibrium, we derive expressions for the expected capacity of the infrastructure given by the number of operational servers connected to the network for sum-form, product-form and composite utility functions.« less

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.

PubMed

Chang, Darby Tien-Hau; Chen, Chien-Yu; Chung, Wen-Chin; Oyang, Yen-Jen; Juan, Hsueh-Fen; Huang, Hsuan-Cheng

2004-07-01

Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the alpha-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/.

HIPAA-compliant automatic monitoring system for RIS-integrated PACS operation

NASA Astrophysics Data System (ADS)

Jin, Jin; Zhang, Jianguo; Chen, Xiaomeng; Sun, Jianyong; Yang, Yuanyuan; Liang, Chenwen; Feng, Jie; Sheng, Liwei; Huang, H. K.

2006-03-01

As a governmental regulation, Health Insurance Portability and Accountability Act (HIPAA) was issued to protect the privacy of health information that identifies individuals who are living or deceased. HIPAA requires security services supporting implementation features: Access control; Audit controls; Authorization control; Data authentication; and Entity authentication. These controls, which proposed in HIPAA Security Standards, are Audit trails here. Audit trails can be used for surveillance purposes, to detect when interesting events might be happening that warrant further investigation. Or they can be used forensically, after the detection of a security breach, to determine what went wrong and who or what was at fault. In order to provide security control services and to achieve the high and continuous availability, we design the HIPAA-Compliant Automatic Monitoring System for RIS-Integrated PACS operation. The system consists of two parts: monitoring agents running in each PACS component computer and a Monitor Server running in a remote computer. Monitoring agents are deployed on all computer nodes in RIS-Integrated PACS system to collect the Audit trail messages defined by the Supplement 95 of the DICOM standard: Audit Trail Messages. Then the Monitor Server gathers all audit messages and processes them to provide security information in three levels: system resources, PACS/RIS applications, and users/patients data accessing. Now the RIS-Integrated PACS managers can monitor and control the entire RIS-Integrated PACS operation through web service provided by the Monitor Server. This paper presents the design of a HIPAA-compliant automatic monitoring system for RIS-Integrated PACS Operation, and gives the preliminary results performed by this monitoring system on a clinical RIS-integrated PACS.

Autoplot and the HAPI Server

NASA Astrophysics Data System (ADS)

Faden, J.; Vandegriff, J. D.; Weigel, R. S.

2016-12-01

Autoplot was introduced in 2008 as an easy-to-use plotting tool for the space physics community. It reads data from a variety of file resources, such as CDF and HDF files, and a number of specialized data servers, such as the PDS/PPI's DIT-DOS, CDAWeb, and from the University of Iowa's RPWG Das2Server. Each of these servers have optimized methods for transmitting data to display in Autoplot, but require coordination and specialized software to work, limiting Autoplot's ability to access new servers and datasets. Likewise, groups who would like software to access their APIs must either write thier own clients, or publish a specification document in hopes that people will write clients. The HAPI specification was written so that a simple, standard API could be used by both Autoplot and server implementations, to remove these barriers to free flow of time series data. Autoplot's software for communicating with HAPI servers is presented, showing the user interface scientists will use, and how data servers might implement the HAPI specification to provide access to their data. This will also include instructions on how Autoplot is used and installed desktop computers, and used to view data from the RBSP, Juno, and other missions.

Pervasive brain monitoring and data sharing based on multi-tier distributed computing and linked data technology

PubMed Central

Zao, John K.; Gan, Tchin-Tze; You, Chun-Kai; Chung, Cheng-En; Wang, Yu-Te; Rodríguez Méndez, Sergio José; Mullen, Tim; Yu, Chieh; Kothe, Christian; Hsiao, Ching-Teng; Chu, San-Liang; Shieh, Ce-Kuen; Jung, Tzyy-Ping

2014-01-01

EEG-based Brain-computer interfaces (BCI) are facing basic challenges in real-world applications. The technical difficulties in developing truly wearable BCI systems that are capable of making reliable real-time prediction of users' cognitive states in dynamic real-life situations may seem almost insurmountable at times. Fortunately, recent advances in miniature sensors, wireless communication and distributed computing technologies offered promising ways to bridge these chasms. In this paper, we report an attempt to develop a pervasive on-line EEG-BCI system using state-of-art technologies including multi-tier Fog and Cloud Computing, semantic Linked Data search, and adaptive prediction/classification models. To verify our approach, we implement a pilot system by employing wireless dry-electrode EEG headsets and MEMS motion sensors as the front-end devices, Android mobile phones as the personal user interfaces, compact personal computers as the near-end Fog Servers and the computer clusters hosted by the Taiwan National Center for High-performance Computing (NCHC) as the far-end Cloud Servers. We succeeded in conducting synchronous multi-modal global data streaming in March and then running a multi-player on-line EEG-BCI game in September, 2013. We are currently working with the ARL Translational Neuroscience Branch to use our system in real-life personal stress monitoring and the UCSD Movement Disorder Center to conduct in-home Parkinson's disease patient monitoring experiments. We shall proceed to develop the necessary BCI ontology and introduce automatic semantic annotation and progressive model refinement capability to our system. PMID:24917804

Pervasive brain monitoring and data sharing based on multi-tier distributed computing and linked data technology.

PubMed

Zao, John K; Gan, Tchin-Tze; You, Chun-Kai; Chung, Cheng-En; Wang, Yu-Te; Rodríguez Méndez, Sergio José; Mullen, Tim; Yu, Chieh; Kothe, Christian; Hsiao, Ching-Teng; Chu, San-Liang; Shieh, Ce-Kuen; Jung, Tzyy-Ping

2014-01-01

EEG-based Brain-computer interfaces (BCI) are facing basic challenges in real-world applications. The technical difficulties in developing truly wearable BCI systems that are capable of making reliable real-time prediction of users' cognitive states in dynamic real-life situations may seem almost insurmountable at times. Fortunately, recent advances in miniature sensors, wireless communication and distributed computing technologies offered promising ways to bridge these chasms. In this paper, we report an attempt to develop a pervasive on-line EEG-BCI system using state-of-art technologies including multi-tier Fog and Cloud Computing, semantic Linked Data search, and adaptive prediction/classification models. To verify our approach, we implement a pilot system by employing wireless dry-electrode EEG headsets and MEMS motion sensors as the front-end devices, Android mobile phones as the personal user interfaces, compact personal computers as the near-end Fog Servers and the computer clusters hosted by the Taiwan National Center for High-performance Computing (NCHC) as the far-end Cloud Servers. We succeeded in conducting synchronous multi-modal global data streaming in March and then running a multi-player on-line EEG-BCI game in September, 2013. We are currently working with the ARL Translational Neuroscience Branch to use our system in real-life personal stress monitoring and the UCSD Movement Disorder Center to conduct in-home Parkinson's disease patient monitoring experiments. We shall proceed to develop the necessary BCI ontology and introduce automatic semantic annotation and progressive model refinement capability to our system.

An Efficient Authenticated Key Transfer Scheme in Client-Server Networks

NASA Astrophysics Data System (ADS)

Shi, Runhua; Zhang, Shun

2017-10-01

In this paper, we presented a novel authenticated key transfer scheme in client-server networks, which can achieve two secure goals of remote user authentication and the session key establishment between the remote user and the server. Especially, the proposed scheme can subtly provide two fully different authentications: identity-base authentication and anonymous authentication, while the remote user only holds a private key. Furthermore, our scheme only needs to transmit 1-round messages from the remote user to the server, thus it is very efficient in communication complexity. In addition, the most time-consuming computation in our scheme is elliptic curve scalar point multiplication, so it is also feasible even for mobile devices.

Experience with Adaptive Security Policies.

DTIC Science & Technology

1998-03-01

3.1 Introduction r: 3.2 Logical Groupings of audited permission checks 29 3.3 Auditing of system servers via microkernel snooping 31 3.4...performed by servers other than the microkernel . Since altering each server to audit events would complicate the integration of new servers, a...modification to the microkernel was implemented to allow the microkernel to audit the requests made of other servers. Both methods for enhancing audit

Interception and modification of network authentication packets with the purpose of allowing alternative authentication modes

DOEpatents

Kent, Alexander Dale [Los Alamos, NM

2008-09-02

Methods and systems in a data/computer network for authenticating identifying data transmitted from a client to a server through use of a gateway interface system which are communicately coupled to each other are disclosed. An authentication packet transmitted from a client to a server of the data network is intercepted by the interface, wherein the authentication packet is encrypted with a one-time password for transmission from the client to the server. The one-time password associated with the authentication packet can be verified utilizing a one-time password token system. The authentication packet can then be modified for acceptance by the server, wherein the response packet generated by the server is thereafter intercepted, verified and modified for transmission back to the client in a similar but reverse process.

Web Service Distributed Management Framework for Autonomic Server Virtualization

NASA Astrophysics Data System (ADS)

Solomon, Bogdan; Ionescu, Dan; Litoiu, Marin; Mihaescu, Mircea

Virtualization for the x86 platform has imposed itself recently as a new technology that can improve the usage of machines in data centers and decrease the cost and energy of running a high number of servers. Similar to virtualization, autonomic computing and more specifically self-optimization, aims to improve server farm usage through provisioning and deprovisioning of instances as needed by the system. Autonomic systems are able to determine the optimal number of server machines - real or virtual - to use at a given time, and add or remove servers from a cluster in order to achieve optimal usage. While provisioning and deprovisioning of servers is very important, the way the autonomic system is built is also very important, as a robust and open framework is needed. One such management framework is the Web Service Distributed Management (WSDM) system, which is an open standard of the Organization for the Advancement of Structured Information Standards (OASIS). This paper presents an open framework built on top of the WSDM specification, which aims to provide self-optimization for applications servers residing on virtual machines.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment.

PubMed

Harrigan, Robert L; Yvernault, Benjamin C; Boyd, Brian D; Damon, Stephen M; Gibney, Kyla David; Conrad, Benjamin N; Phillips, Nicholas S; Rogers, Baxter P; Gao, Yurui; Landman, Bennett A

2016-01-01

The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has developed a database built on XNAT housing over a quarter of a million scans. The database provides framework for (1) rapid prototyping, (2) large scale batch processing of images and (3) scalable project management. The system uses the web-based interfaces of XNAT and REDCap to allow for graphical interaction. A python middleware layer, the Distributed Automation for XNAT (DAX) package, distributes computation across the Vanderbilt Advanced Computing Center for Research and Education high performance computing center. All software are made available in open source for use in combining portable batch scripting (PBS) grids and XNAT servers. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid earthquake characterization using MEMS accelerometers and volunteer hosts following the M 7.2 Darfield, New Zealand, Earthquake

USGS Publications Warehouse

Lawrence, J. F.; Cochran, E.S.; Chung, A.; Kaiser, A.; Christensen, C. M.; Allen, R.; Baker, J.W.; Fry, B.; Heaton, T.; Kilb, Debi; Kohler, M.D.; Taufer, M.

2014-01-01

We test the feasibility of rapidly detecting and characterizing earthquakes with the Quake‐Catcher Network (QCN) that connects low‐cost microelectromechanical systems accelerometers to a network of volunteer‐owned, Internet‐connected computers. Following the 3 September 2010 M 7.2 Darfield, New Zealand, earthquake we installed over 180 QCN sensors in the Christchurch region to record the aftershock sequence. The sensors are monitored continuously by the host computer and send trigger reports to the central server. The central server correlates incoming triggers to detect when an earthquake has occurred. The location and magnitude are then rapidly estimated from a minimal set of received ground‐motion parameters. Full seismic time series are typically not retrieved for tens of minutes or even hours after an event. We benchmark the QCN real‐time detection performance against the GNS Science GeoNet earthquake catalog. Under normal network operations, QCN detects and characterizes earthquakes within 9.1 s of the earthquake rupture and determines the magnitude within 1 magnitude unit of that reported in the GNS catalog for 90% of the detections.

Computational algorithm to evaluate product disassembly cost index

NASA Astrophysics Data System (ADS)

Zeid, Ibrahim; Gupta, Surendra M.

2002-02-01

Environmentally conscious manufacturing is an important paradigm in today's engineering practice. Disassembly is a crucial factor in implementing this paradigm. Disassembly allows the reuse and recycling of parts and products that reach their death after their life cycle ends. There are many questions that must be answered before a disassembly decision can be reached. The most important question is economical. The cost of disassembly versus the cost of scrapping a product is always considered. This paper develops a computational tool that allows decision-makers to calculate the disassembly cost of a product. The tool makes it simple to perform 'what if' scenarios fairly quickly. The tool is Web based and has two main parts. The front-end part is a Web page and runs on the client side in a Web browser, while the back-end part is a disassembly engine (servlet) that has disassembly knowledge and costing algorithms and runs on the server side. The tool is based on the client/server model that is pervasively utilized throughout the World Wide Web. An example is used to demonstrate the implementation and capabilities of the tool.

Implications of the Java language on computer-based patient records.

PubMed

Pollard, D; Kucharz, E; Hammond, W E

1996-01-01

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

Automated Gene Ontology annotation for anonymous sequence data.

PubMed

Hennig, Steffen; Groth, Detlef; Lehrach, Hans

2003-07-01

Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for computer based classification methods. However, direct use of GO in small sequencing projects is not easy, especially for species not commonly represented in public databases. We present a software package (GOblet), which performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. The paper also addresses the reliability of automated GO annotations by using a reference set of more than 6000 human proteins. The GOblet server is accessible at http://goblet.molgen.mpg.de.

An efficient biometric and password-based remote user authentication using smart card for Telecare Medical Information Systems in multi-server environment.

PubMed

Maitra, Tanmoy; Giri, Debasis

2014-12-01

The medical organizations have introduced Telecare Medical Information System (TMIS) to provide a reliable facility by which a patient who is unable to go to a doctor in critical or urgent period, can communicate to a doctor through a medical server via internet from home. An authentication mechanism is needed in TMIS to hide the secret information of both parties, namely a server and a patient. Recent research includes patient's biometric information as well as password to design a remote user authentication scheme that enhances the security level. In a single server environment, one server is responsible for providing services to all the authorized remote patients. However, the problem arises if a patient wishes to access several branch servers, he/she needs to register to the branch servers individually. In 2014, Chuang and Chen proposed an remote user authentication scheme for multi-server environment. In this paper, we have shown that in their scheme, an non-register adversary can successfully logged-in into the system as a valid patient. To resist the weaknesses, we have proposed an authentication scheme for TMIS in multi-server environment where the patients can register to a root telecare server called registration center (RC) in one time to get services from all the telecare branch servers through their registered smart card. Security analysis and comparison shows that our proposed scheme provides better security with low computational and communication cost.

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Digital communications study

NASA Technical Reports Server (NTRS)

Boorstyn, R. R.

1973-01-01

Research is reported dealing with problems of digital data transmission and computer communications networks. The results of four individual studies are presented which include: (1) signal processing with finite state machines, (2) signal parameter estimation from discrete-time observations, (3) digital filtering for radar signal processing applications, and (4) multiple server queues where all servers are not identical.

EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles.

PubMed

Dittmar, W James; McIver, Lauren; Michalak, Pawel; Garner, Harold R; Valdez, Gregorio

2014-07-01

The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are likely to have co-evolved and be expressed in the same tissues and cells. Unfortunately, the expertise and computational resources required to compare tens of genomes and gene expression data sets make this type of analysis difficult for the average end-user. Here, we describe the implementation of a web server that predicts genes involved in affecting specific cellular processes together with a gene of interest. We termed the server 'EvoCor', to denote that it detects functional relationships among genes through evolutionary analysis and gene expression correlation. This web server integrates profiles of sequence divergence derived by a Hidden Markov Model (HMM) and tissue-wide gene expression patterns to determine putative functional linkages between pairs of genes. This server is easy to use and freely available at http://pilot-hmm.vbi.vt.edu/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Computational Prediction of the Immunomodulatory Potential of RNA Sequences.

PubMed

Nagpal, Gandharva; Chaudhary, Kumardeep; Dhanda, Sandeep Kumar; Raghava, Gajendra Pal Singh

2017-01-01

Advances in the knowledge of various roles played by non-coding RNAs have stimulated the application of RNA molecules as therapeutics. Among these molecules, miRNA, siRNA, and CRISPR-Cas9 associated gRNA have been identified as the most potent RNA molecule classes with diverse therapeutic applications. One of the major limitations of RNA-based therapeutics is immunotoxicity of RNA molecules as it may induce the innate immune system. In contrast, RNA molecules that are potent immunostimulators are strong candidates for use in vaccine adjuvants. Thus, it is important to understand the immunotoxic or immunostimulatory potential of these RNA molecules. The experimental techniques for determining immunostimulatory potential of siRNAs are time- and resource-consuming. To overcome this limitation, recently our group has developed a web-based server "imRNA" for predicting the immunomodulatory potential of RNA sequences. This server integrates a number of modules that allow users to perform various tasks including (1) generation of RNA analogs with reduced immunotoxicity, (2) identification of highly immunostimulatory regions in RNA sequence, and (3) virtual screening. This server may also assist users in the identification of minimum mutations required in a given RNA sequence to minimize its immunomodulatory potential that is required for designing RNA-based therapeutics. Besides, the server can be used for designing RNA-based vaccine adjuvants as it may assist users in the identification of mutations required for increasing immunomodulatory potential of a given RNA sequence. In summary, this chapter describes major applications of the "imRNA" server in designing RNA-based therapeutics and vaccine adjuvants (http://www.imtech.res.in/raghava/imrna/).

Bio-inspired diversity for increasing attacker workload

NASA Astrophysics Data System (ADS)

Kuhn, Stephen

2014-05-01

Much of the traffic in modern computer networks is conducted between clients and servers, rather than client-toclient. As a result, servers represent a high-value target for collection and analysis of network traffic. As they reside at a single network location (i.e. IP/MAC address) for long periods of time. Servers present a static target for surveillance, and a unique opportunity to observe the network traffic. Although servers present a heightened value for attackers, the security community as a whole has shifted more towards protecting clients in recent years leaving a gap in coverage. In addition, servers typically remain active on networks for years, potentially decades. This paper builds on previous work that demonstrated a proof of concept leveraging existing technology for increasing attacker workload. Here we present our clean slate approach to increasing attacker workload through a novel hypervisor and micro-kernel, utilizing next generation virtualization technology to create synthetic diversity of the server's presence including the hardware components.

QuakeSim Project Networking

NASA Astrophysics Data System (ADS)

Kong, D.; Donnellan, A.; Pierce, M. E.

2012-12-01

QuakeSim is an online computational framework focused on using remotely sensed geodetic imaging data to model and understand earthquakes. With the rise in online social networking over the last decade, many tools and concepts have been developed that are useful to research groups. In particular, QuakeSim is interested in the ability for researchers to post, share, and annotate files generated by modeling tools in order to facilitate collaboration. To accomplish this, features were added to the preexisting QuakeSim site that include single sign-on, automated saving of output from modeling tools, and a personal user space to manage sharing permissions on these saved files. These features implement OpenID and Lightweight Data Access Protocol (LDAP) technologies to manage files across several different servers, including a web server running Drupal and other servers hosting the computational tools themselves.

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria.

PubMed

Chanumolu, Sree Krishna; Rout, Chittaranjan; Chauhan, Rajinder S

2012-01-01

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed. A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein's critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed. The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets. UniDrug-Target is expected to accelerate pathogen-specific drug targets identification which will increase their success and durability as drugs developed against them have less chance to develop resistances and adverse impact on environment. The server is freely available at http://117.211.115.67/UDT/main.html. The standalone application (source codes) is available at http://www.bioinformatics.org/ftp/pub/bioinfojuit/UDT.rar.

A Real-Time High Performance Computation Architecture for Multiple Moving Target Tracking Based on Wide-Area Motion Imagery via Cloud and Graphic Processing Units

PubMed Central

Liu, Kui; Wei, Sixiao; Chen, Zhijiang; Jia, Bin; Chen, Genshe; Ling, Haibin; Sheaff, Carolyn; Blasch, Erik

2017-01-01

This paper presents the first attempt at combining Cloud with Graphic Processing Units (GPUs) in a complementary manner within the framework of a real-time high performance computation architecture for the application of detecting and tracking multiple moving targets based on Wide Area Motion Imagery (WAMI). More specifically, the GPU and Cloud Moving Target Tracking (GC-MTT) system applied a front-end web based server to perform the interaction with Hadoop and highly parallelized computation functions based on the Compute Unified Device Architecture (CUDA©). The introduced multiple moving target detection and tracking method can be extended to other applications such as pedestrian tracking, group tracking, and Patterns of Life (PoL) analysis. The cloud and GPUs based computing provides an efficient real-time target recognition and tracking approach as compared to methods when the work flow is applied using only central processing units (CPUs). The simultaneous tracking and recognition results demonstrate that a GC-MTT based approach provides drastically improved tracking with low frame rates over realistic conditions. PMID:28208684

A Real-Time High Performance Computation Architecture for Multiple Moving Target Tracking Based on Wide-Area Motion Imagery via Cloud and Graphic Processing Units.

PubMed

Liu, Kui; Wei, Sixiao; Chen, Zhijiang; Jia, Bin; Chen, Genshe; Ling, Haibin; Sheaff, Carolyn; Blasch, Erik

2017-02-12

This paper presents the first attempt at combining Cloud with Graphic Processing Units (GPUs) in a complementary manner within the framework of a real-time high performance computation architecture for the application of detecting and tracking multiple moving targets based on Wide Area Motion Imagery (WAMI). More specifically, the GPU and Cloud Moving Target Tracking (GC-MTT) system applied a front-end web based server to perform the interaction with Hadoop and highly parallelized computation functions based on the Compute Unified Device Architecture (CUDA©). The introduced multiple moving target detection and tracking method can be extended to other applications such as pedestrian tracking, group tracking, and Patterns of Life (PoL) analysis. The cloud and GPUs based computing provides an efficient real-time target recognition and tracking approach as compared to methods when the work flow is applied using only central processing units (CPUs). The simultaneous tracking and recognition results demonstrate that a GC-MTT based approach provides drastically improved tracking with low frame rates over realistic conditions.

SSL - THE SIMPLE SOCKETS LIBRARY

NASA Technical Reports Server (NTRS)

Campbell, C. E.

1994-01-01

The Simple Sockets Library (SSL) allows C programmers to develop systems of cooperating programs using Berkeley streaming Sockets running under the TCP/IP protocol over Ethernet. The SSL provides a simple way to move information between programs running on the same or different machines and does so with little overhead. The SSL can create three types of Sockets: namely a server, a client, and an accept Socket. The SSL's Sockets are designed to be used in a fashion reminiscent of the use of FILE pointers so that a C programmer who is familiar with reading and writing files will immediately feel comfortable with reading and writing with Sockets. The SSL consists of three parts: the library, PortMaster, and utilities. The user of the SSL accesses it by linking programs to the SSL library. The PortMaster initializes connections between clients and servers. The PortMaster also supports a "firewall" facility to keep out socket requests from unapproved machines. The "firewall" is a file which contains Internet addresses for all approved machines. There are three utilities provided with the SSL. SKTDBG can be used to debug programs that make use of the SSL. SPMTABLE lists the servers and port numbers on requested machine(s). SRMSRVR tells the PortMaster to forcibly remove a server name from its list. The package also includes two example programs: multiskt.c, which makes multiple accepts on one server, and sktpoll.c, which repeatedly attempts to connect a client to some server at one second intervals. SSL is a machine independent library written in the C-language for computers connected via Ethernet using the TCP/IP protocol. It has been successfully compiled and implemented on a variety of platforms, including Sun series computers running SunOS, DEC VAX series computers running VMS, SGI computers running IRIX, DECstations running ULTRIX, DEC alpha AXPs running OSF/1, IBM RS/6000 computers running AIX, IBM PC and compatibles running BSD/386 UNIX and HP Apollo 3000/4000/9000/400T computers running HP-UX. SSL requires 45K of RAM to run under SunOS and 80K of RAM to run under VMS. For use on IBM PC series computers and compatibles running DOS, SSL requires Microsoft C 6.0 and the Wollongong TCP/IP package. Source code for sample programs and debugging tools are provided. The documentation is available on the distribution medium in TeX and PostScript formats. The standard distribution medium for SSL is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format and a 5.25 inch 360K MS-DOS format diskette. The SSL was developed in 1992 and was updated in 1993.

[Development of a System to Use Patient's Information Which is Required at the Radiological Department].

PubMed

Satoh, Akihiro

2016-04-01

The purpose of this study is to develop a new system to get and share some data of a patient which are required for a radiological examination not using an electronic medical chart or a radiological information system (RIS), and also to demonstrate that this system is operated on cloud technology. I used Java Enterprise Edition (Java EE) as a programing language and MySQL as a server software, and I used two laptops as hardware for client computer and server computer. For cloud computing, I hired a server of Google App Engine for Java (GAE). As a result, I could get some data of the patient required at his/her examination instantly using this system. This system also helps to improve the efficiency of examination. For example, it has been useful when I want to decide radiographic condition or to create CT images such as multi-planar reconstruction (MPR) or volume rendering (VR). When it comes to cloud computing, the GAE was used experimentally due to some legal restrictions. From the above points it is clear that this system has played an important role in radiological examinations, but there has been still few things which I have to resolve for cloud computing.

The Scientific Uplink and User Support System for SIRTF

NASA Astrophysics Data System (ADS)

Heinrichsen, I.; Chavez, J.; Hartley, B.; Mei, Y.; Potts, S.; Roby, T.; Turek, G.; Valjavec, E.; Wu, X.

The Space Infrared Telescope Facility (SIRTF) is one of NASA's Great Observatory missions, scheduled for launch in 2001. As such its ground segment design is driven by the requirement to provide strong support for the entire astronomical community starting with the call for Legacy Proposals in early 2000. In this contribution, we present the astronomical user interface and the design of the server software that comprises the Scientific Uplink System for SIRTF. The software architecture is split into three major parts: A front-end Java application deployed to the astronomical community providing the capabilities to visualize and edit proposals and the associated lists of observations. This observer toolkit provides templates to define all parameters necessary to carry out the required observations. A specialized version of this software, based on the same overall architecture, is used internal to the SIRTF Science Center to prepare calibration and engineering observations. A Weblogic (TM) based middleware component brokers the transactions with the servers, astronomical image and catalog sources as well as the SIRTF operational databases. Several server systems perform the necessary computations, to obtain resource estimates, target visibilities and to access the instrument models for signal to noise calculations. The same server software is used internally at a later stage to derive the detailed command sequences needed by the SIRTF instruments and spacecraft to execute a given observation.

The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins

PubMed Central

Kozakov, Dima; Grove, Laurie E.; Hall, David R.; Bohnuud, Tanggis; Mottarella, Scott; Luo, Lingqi; Xia, Bing; Beglov, Dmitri; Vajda, Sandor

2016-01-01

FTMap is a computational mapping server that identifies binding hot spots of macromolecules, i.e., regions of the surface with major contributions to the ligand binding free energy. To use FTMap, users submit a protein, DNA, or RNA structure in PDB format. FTMap samples billions of positions of small organic molecules used as probes and scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots, in good agreement with experimental data. FTMap serves as basis for other servers, namely FTSite to predict ligand binding sites, FTFlex to account for side chain flexibility, FTMap/param to parameterize additional probes, and FTDyn to map ensembles of protein structures. Applications include determining druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures, and providing input for fragment based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and is much faster than the more recent approaches to protein mapping based on mixed molecular dynamics. Using 16 probe molecules, the FTMap server finds the hot spots of an average size protein in less than an hour. Since FTFlex performs mapping for all low energy conformers of side chains in the binding site, its completion time is proportionately longer. PMID:25855957

Modernization of the USGS Hawaiian Volcano Observatory Seismic Processing Infrastructure

NASA Astrophysics Data System (ADS)

Antolik, L.; Shiro, B.; Friberg, P. A.

2016-12-01

The USGS Hawaiian Volcano Observatory (HVO) operates a Tier 1 Advanced National Seismic System (ANSS) seismic network to monitor, characterize, and report on volcanic and earthquake activity in the State of Hawaii. Upgrades at the observatory since 2009 have improved the digital telemetry network, computing resources, and seismic data processing with the adoption of the ANSS Quake Management System (AQMS) system. HVO aims to build on these efforts by further modernizing its seismic processing infrastructure and strengthen its ability to meet ANSS performance standards. Most notably, this will also allow HVO to support redundant systems, both onsite and offsite, in order to provide better continuity of operation during intermittent power and network outages. We are in the process of implementing a number of upgrades and improvements on HVO's seismic processing infrastructure, including: 1) Virtualization of AQMS physical servers; 2) Migration of server operating systems from Solaris to Linux; 3) Consolidation of AQMS real-time and post-processing services to a single server; 4) Upgrading database from Oracle 10 to Oracle 12; and 5) Upgrading to the latest Earthworm and AQMS software. These improvements will make server administration more efficient, minimize hardware resources required by AQMS, simplify the Oracle replication setup, and provide better integration with HVO's existing state of health monitoring tools and backup system. Ultimately, it will provide HVO with the latest and most secure software available while making the software easier to deploy and support.

StarScan: a web server for scanning small RNA targets from degradome sequencing data.

PubMed

Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2015-07-01

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

Development of a Cloud Computing-Based Pier Type Port Structure Stability Evaluation Platform Using Fiber Bragg Grating Sensors.

PubMed

Jo, Byung Wan; Jo, Jun Ho; Khan, Rana Muhammad Asad; Kim, Jung Hoon; Lee, Yun Sung

2018-05-23

Structure Health Monitoring is a topic of great interest in port structures due to the ageing of structures and the limitations of evaluating structures. This paper presents a cloud computing-based stability evaluation platform for a pier type port structure using Fiber Bragg Grating (FBG) sensors in a system consisting of a FBG strain sensor, FBG displacement gauge, FBG angle meter, gateway, and cloud computing-based web server. The sensors were installed on core components of the structure and measurements were taken to evaluate the structures. The measurement values were transmitted to the web server via the gateway to analyze and visualize them. All data were analyzed and visualized in the web server to evaluate the structure based on the safety evaluation index (SEI). The stability evaluation platform for pier type port structures involves the efficient monitoring of the structures which can be carried out easily anytime and anywhere by converging new technologies such as cloud computing and FBG sensors. In addition, the platform has been successfully implemented at “Maryang Harbor” situated in Maryang-Meyon of Korea to test its durability.

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

View compensated compression of volume rendered images for remote visualization.

PubMed

Lalgudi, Hariharan G; Marcellin, Michael W; Bilgin, Ali; Oh, Han; Nadar, Mariappan S

2009-07-01

Remote visualization of volumetric images has gained importance over the past few years in medical and industrial applications. Volume visualization is a computationally intensive process, often requiring hardware acceleration to achieve a real time viewing experience. One remote visualization model that can accomplish this would transmit rendered images from a server, based on viewpoint requests from a client. For constrained server-client bandwidth, an efficient compression scheme is vital for transmitting high quality rendered images. In this paper, we present a new view compensation scheme that utilizes the geometric relationship between viewpoints to exploit the correlation between successive rendered images. The proposed method obviates motion estimation between rendered images, enabling significant reduction to the complexity of a compressor. Additionally, the view compensation scheme, in conjunction with JPEG2000 performs better than AVC, the state of the art video compression standard.

Evaluation of FPGA to PC feedback loop

NASA Astrophysics Data System (ADS)

Linczuk, Pawel; Zabolotny, Wojciech M.; Wojenski, Andrzej; Krawczyk, Rafal D.; Pozniak, Krzysztof T.; Chernyshova, Maryna; Czarski, Tomasz; Gaska, Michal; Kasprowicz, Grzegorz; Kowalska-Strzeciwilk, Ewa; Malinowski, Karol

2017-08-01

The paper presents the evaluation study of the performance of the data transmission subsystem which can be used in High Energy Physics (HEP) and other High-Performance Computing (HPC) systems. The test environment consisted of Xilinx Artix-7 FPGA and server-grade PC connected via the PCIe 4xGen2 bus. The DMA engine was based on the Xilinx DMA for PCI Express Subsystem1 controlled by the modified Xilinx XDMA kernel driver.2 The research is focused on the influence of the system configuration on achievable throughput and latency of data transfer.

Implementation of a filmless mini picture archiving and communication system in ultrasonography: experience after one year of use.

PubMed

Henri, C J; Cox, R D; Bret, P M

1997-08-01

This article details our experience in developing and operating an ultrasound mini-picture archiving and communication system (PACS). Using software developed in-house, low-end Macintosh computers (Apple Computer Co. Cupertino, CA) equipped with framegrabbers coordinate the entry of patient demographic information, image acquisition, and viewing on each ultrasound scanner. After each exam, the data are transmitted to a central archive server where they can be accessed from anywhere on the network. The archive server also provides web-based access to the data and manages pre-fetch and other requests for data that may no longer be on-line. Archival is fully automatic and is performed on recordable compact disk (CD) without compression. The system has been filmless now for over 18 months. In the meantime, one film processor has been eliminated and the position of one film clerk has been reallocated. Previously, nine ultrasound machines produced approximately 150 sheets of laser film per day (at 14 images per sheet). The same quantity of data are now archived without compression onto a single CD. Start-up costs were recovered within six months, and the project has been extended to include computed tomography (CT) and magnetic resonance imaging (MRI).

Static Memory Deduplication for Performance Optimization in Cloud Computing.

PubMed

Jia, Gangyong; Han, Guangjie; Wang, Hao; Yang, Xuan

2017-04-27

In a cloud computing environment, the number of virtual machines (VMs) on a single physical server and the number of applications running on each VM are continuously growing. This has led to an enormous increase in the demand of memory capacity and subsequent increase in the energy consumption in the cloud. Lack of enough memory has become a major bottleneck for scalability and performance of virtualization interfaces in cloud computing. To address this problem, memory deduplication techniques which reduce memory demand through page sharing are being adopted. However, such techniques suffer from overheads in terms of number of online comparisons required for the memory deduplication. In this paper, we propose a static memory deduplication (SMD) technique which can reduce memory capacity requirement and provide performance optimization in cloud computing. The main innovation of SMD is that the process of page detection is performed offline, thus potentially reducing the performance cost, especially in terms of response time. In SMD, page comparisons are restricted to the code segment, which has the highest shared content. Our experimental results show that SMD efficiently reduces memory capacity requirement and improves performance. We demonstrate that, compared to other approaches, the cost in terms of the response time is negligible.

Static Memory Deduplication for Performance Optimization in Cloud Computing

PubMed Central

Jia, Gangyong; Han, Guangjie; Wang, Hao; Yang, Xuan

2017-01-01

In a cloud computing environment, the number of virtual machines (VMs) on a single physical server and the number of applications running on each VM are continuously growing. This has led to an enormous increase in the demand of memory capacity and subsequent increase in the energy consumption in the cloud. Lack of enough memory has become a major bottleneck for scalability and performance of virtualization interfaces in cloud computing. To address this problem, memory deduplication techniques which reduce memory demand through page sharing are being adopted. However, such techniques suffer from overheads in terms of number of online comparisons required for the memory deduplication. In this paper, we propose a static memory deduplication (SMD) technique which can reduce memory capacity requirement and provide performance optimization in cloud computing. The main innovation of SMD is that the process of page detection is performed offline, thus potentially reducing the performance cost, especially in terms of response time. In SMD, page comparisons are restricted to the code segment, which has the highest shared content. Our experimental results show that SMD efficiently reduces memory capacity requirement and improves performance. We demonstrate that, compared to other approaches, the cost in terms of the response time is negligible. PMID:28448434

HPC in a HEP lab: lessons learned from setting up cost-effective HPC clusters

NASA Astrophysics Data System (ADS)

Husejko, Michal; Agtzidis, Ioannis; Baehler, Pierre; Dul, Tadeusz; Evans, John; Himyr, Nils; Meinhard, Helge

2015-12-01

In this paper we present our findings gathered during the evaluation and testing of Windows Server High-Performance Computing (Windows HPC) in view of potentially using it as a production HPC system for engineering applications. The Windows HPC package, an extension of Microsofts Windows Server product, provides all essential interfaces, utilities and management functionality for creating, operating and monitoring a Windows-based HPC cluster infrastructure. The evaluation and test phase was focused on verifying the functionalities of Windows HPC, its performance, support of commercial tools and the integration with the users work environment. We describe constraints imposed by the way the CERN Data Centre is operated, licensing for engineering tools and scalability and behaviour of the HPC engineering applications used at CERN. We will present an initial set of requirements, which were created based on the above constraints and requests from the CERN engineering user community. We will explain how we have configured Windows HPC clusters to provide job scheduling functionalities required to support the CERN engineering user community, quality of service, user- and project-based priorities, and fair access to limited resources. Finally, we will present several performance tests we carried out to verify Windows HPC performance and scalability.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Parida, Pritish R.

Systems and methods for cooling include one or more computing structure, an inter-structure liquid cooling system that includes valves configured to selectively provide liquid coolant to the one or more computing structures; a heat rejection system that includes one or more heat rejection units configured to cool liquid coolant; and one or more liquid-to-liquid heat exchangers that include valves configured to selectively transfer heat from liquid coolant in the inter-structure liquid cooling system to liquid coolant in the heat rejection system. Each computing structure further includes one or more liquid-cooled servers; and an intra-structure liquid cooling system that has valvesmore » configured to selectively provide liquid coolant to the one or more liquid-cooled servers.« less

Provisioning cooling elements for chillerless data centers

DOEpatents

Chainer, Timothy J.; Parida, Pritish R.

2016-12-13

Systems and methods for cooling include one or more computing structure, an inter-structure liquid cooling system that includes valves configured to selectively provide liquid coolant to the one or more computing structures; a heat rejection system that includes one or more heat rejection units configured to cool liquid coolant; and one or more liquid-to-liquid heat exchangers that include valves configured to selectively transfer heat from liquid coolant in the inter-structure liquid cooling system to liquid coolant in the heat rejection system. Each computing structure further includes one or more liquid-cooled servers; and an intra-structure liquid cooling system that has valves configured to selectively provide liquid coolant to the one or more liquid-cooled servers.

A Study on Secure Medical-Contents Strategies with DRM Based on Cloud Computing

PubMed Central

Měsíček, Libor; Choi, Jongsun

2018-01-01

Many hospitals and medical clinics have been using a wearable sensor in its health care system because the wearable sensor, which is able to measure the patients' biometric information, has been developed to analyze their patients remotely. The measured information is saved to a server in a medical center, and the server keeps the medical information, which also involves personal information, on a cloud system. The server and network devices are used by connecting each other, and sensitive medical records are dealt with remotely. However, these days, the attackers, who try to attack the server or the network systems, are increasing. In addition, the server and the network system have a weak protection and security policy against the attackers. In this paper, it is suggested that security compliance of medical contents should be followed to improve the level of security. As a result, the medical contents are kept safely. PMID:29796233

A Study on Secure Medical-Contents Strategies with DRM Based on Cloud Computing.

PubMed

Ko, Hoon; Měsíček, Libor; Choi, Jongsun; Hwang, Seogchan

2018-01-01

Many hospitals and medical clinics have been using a wearable sensor in its health care system because the wearable sensor, which is able to measure the patients' biometric information, has been developed to analyze their patients remotely. The measured information is saved to a server in a medical center, and the server keeps the medical information, which also involves personal information, on a cloud system. The server and network devices are used by connecting each other, and sensitive medical records are dealt with remotely. However, these days, the attackers, who try to attack the server or the network systems, are increasing. In addition, the server and the network system have a weak protection and security policy against the attackers. In this paper, it is suggested that security compliance of medical contents should be followed to improve the level of security. As a result, the medical contents are kept safely.

KFC Server: interactive forecasting of protein interaction hot spots.

PubMed

Darnell, Steven J; LeGault, Laura; Mitchell, Julie C

2008-07-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model-a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org.

KFC Server: interactive forecasting of protein interaction hot spots

PubMed Central

Darnell, Steven J.; LeGault, Laura; Mitchell, Julie C.

2008-01-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model—a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein–protein or protein–DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org. PMID:18539611

Computing and Communications Infrastructure for Network-Centric Warfare: Exploiting COTS, Assuring Performance

DTIC Science & Technology

2004-06-01

remote databases, has seen little vendor acceptance. Each database ( Oracle , DB2, MySQL , etc.) has its own client- server protocol. Therefore each...existing standards – SQL , X.500/LDAP, FTP, etc. • View information dissemination as selective replication – State-oriented vs . message-oriented...allowing the 8 application to start. The resource management system would serve as a broker to the resources, making sure that resources are not

An effective model for store and retrieve big health data in cloud computing.

PubMed

Goli-Malekabadi, Zohreh; Sargolzaei-Javan, Morteza; Akbari, Mohammad Kazem

2016-08-01

The volume of healthcare data including different and variable text types, sounds, and images is increasing day to day. Therefore, the storage and processing of these data is a necessary and challenging issue. Generally, relational databases are used for storing health data which are not able to handle the massive and diverse nature of them. This study aimed at presenting the model based on NoSQL databases for the storage of healthcare data. Despite different types of NoSQL databases, document-based DBs were selected by a survey on the nature of health data. The presented model was implemented in the Cloud environment for accessing to the distribution properties. Then, the data were distributed on the database by applying the Shard property. The efficiency of the model was evaluated in comparison with the previous data model, Relational Database, considering query time, data preparation, flexibility, and extensibility parameters. The results showed that the presented model approximately performed the same as SQL Server for "read" query while it acted more efficiently than SQL Server for "write" query. Also, the performance of the presented model was better than SQL Server in the case of flexibility, data preparation and extensibility. Based on these observations, the proposed model was more effective than Relational Databases for handling health data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Privacy-Preserving Authentication of Users with Smart Cards Using One-Time Credentials

NASA Astrophysics Data System (ADS)

Park, Jun-Cheol

User privacy preservation is critical to prevent many sophisticated attacks that are based on the user's server access patterns and ID-related information. We propose a password-based user authentication scheme that provides strong privacy protection using one-time credentials. It eliminates the possibility of tracing a user's authentication history and hides the user's ID and password even from servers. In addition, it is resistant against user impersonation even if both a server's verification database and a user's smart card storage are disclosed. We also provide a revocation scheme for a user to promptly invalidate the user's credentials on a server when the user's smart card is compromised. The schemes use lightweight operations only such as computing hashes and bitwise XORs.

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

TCP/IP Interface for the Satellite Orbit Analysis Program (SOAP)

NASA Technical Reports Server (NTRS)

Carnright, Robert; Stodden, David; Coggi, John

2009-01-01

The Transmission Control Protocol/ Internet protocol (TCP/IP) interface for the Satellite Orbit Analysis Program (SOAP) provides the means for the software to establish real-time interfaces with other software. Such interfaces can operate between two programs, either on the same computer or on different computers joined by a network. The SOAP TCP/IP module employs a client/server interface where SOAP is the server and other applications can be clients. Real-time interfaces between software offer a number of advantages over embedding all of the common functionality within a single program. One advantage is that they allow each program to divide the computation labor between processors or computers running the separate applications. Secondly, each program can be allowed to provide its own expertise domain with other programs able to use this expertise.

Mass Storage Systems.

ERIC Educational Resources Information Center

Ranade, Sanjay; Schraeder, Jeff

1991-01-01

Presents an overview of the mass storage market and discusses mass storage systems as part of computer networks. Systems for personal computers, workstations, minicomputers, and mainframe computers are described; file servers are explained; system integration issues are raised; and future possibilities are suggested. (LRW)

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

PubMed Central

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E.; Troein, Carl; Millar, Andrew J.; Goryanin, Igor; Gilmore, Stephen

2013-01-01

Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats. Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials. Contact: stg@inf.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23329415

Real-Time Robust Adaptive Modeling and Scheduling for an Electronic Commerce Server

NASA Astrophysics Data System (ADS)

Du, Bing; Ruan, Chun

With the increasing importance and pervasiveness of Internet services, it is becoming a challenge for the proliferation of electronic commerce services to provide performance guarantees under extreme overload. This paper describes a real-time optimization modeling and scheduling approach for performance guarantee of electronic commerce servers. We show that an electronic commerce server may be simulated as a multi-tank system. A robust adaptive server model is subject to unknown additive load disturbances and uncertain model matching. Overload control techniques are based on adaptive admission control to achieve timing guarantees. We evaluate the performance of the model using a complex simulation that is subjected to varying model parameters and massive overload.

Docker Container Manager: A Simple Toolkit for Isolated Work with Shared Computational, Storage, and Network Resources

NASA Astrophysics Data System (ADS)

Polyakov, S. P.; Kryukov, A. P.; Demichev, A. P.

2018-01-01

We present a simple set of command line interface tools called Docker Container Manager (DCM) that allow users to create and manage Docker containers with preconfigured SSH access while keeping the users isolated from each other and restricting their access to the Docker features that could potentially disrupt the work of the server. Users can access DCM server via SSH and are automatically redirected to DCM interface tool. From there, they can create new containers, stop, restart, pause, unpause, and remove containers and view the status of the existing containers. By default, the containers are also accessible via SSH using the same private key(s) but through different server ports. Additional publicly available ports can be mapped to the respective ports of a container, allowing for some network services to be run within it. The containers are started from read-only filesystem images. Some initial images must be provided by the DCM server administrators, and after containers are configured to meet one’s needs, the changes can be saved as new images. Users can see the available images and remove their own images. DCM server administrators are provided with commands to create and delete users. All commands were implemented as Python scripts. The tools allow to deploy and debug medium-sized distributed systems for simulation in different fields on one or several local computers.

Modular Mount Control System for Telescopes

NASA Astrophysics Data System (ADS)

Mooney, J.; Cleis, R.; Kyono, T.; Edwards, M.

The Space Observatory Control Kit (SpOCK) is the hardware, computers and software used to run small and large telescopes in the RDS division of the Air Force Research Laboratories (AFRL). The system is used to track earth satellites, celestial objects, terrestrial objects and aerial objects. The system will track general targets when provided with state vectors in one of five coordinate systems. Client-toserver and server-to-gimbals communication occurs via human-readable s-expressions that may be evaluated by the computer language called Racket. Software verification is achieved by scripts that exercise these expressions by sending them to the server, and receiving the expressions that the server evaluates. This paper describes the adaptation of a modular mount control system developed primarily for LEO satellite imaging on large and small portable AFRL telescopes with a goal of orbit determination and the generation of satellite metrics.

Experiences From NASA/Langley's DMSS Project

NASA Technical Reports Server (NTRS)

1996-01-01

There is a trend in institutions with high performance computing and data management requirements to explore mass storage systems with peripherals directly attached to a high speed network. The Distributed Mass Storage System (DMSS) Project at the NASA Langley Research Center (LaRC) has placed such a system into production use. This paper will present the experiences, both good and bad, we have had with this system since putting it into production usage. The system is comprised of: 1) National Storage Laboratory (NSL)/UniTree 2.1, 2) IBM 9570 HIPPI attached disk arrays (both RAID 3 and RAID 5), 3) IBM RS6000 server, 4) HIPPI/IPI3 third party transfers between the disk array systems and the supercomputer clients, a CRAY Y-MP and a CRAY 2, 5) a "warm spare" file server, 6) transition software to convert from CRAY's Data Migration Facility (DMF) based system to DMSS, 7) an NSC PS32 HIPPI switch, and 8) a STK 4490 robotic library accessed from the IBM RS6000 block mux interface. This paper will cover: the performance of the DMSS in the following areas: file transfer rates, migration and recall, and file manipulation (listing, deleting, etc.); the appropriateness of a workstation class of file server for NSL/UniTree with LaRC's present storage requirements in mind the role of the third party transfers between the supercomputers and the DMSS disk array systems in DMSS; a detailed comparison (both in performance and functionality) between the DMF and DMSS systems LaRC's enhancements to the NSL/UniTree system administration environment the mechanism for DMSS to provide file server redundancy the statistics on the availability of DMSS the design and experiences with the locally developed transparent transition software which allowed us to make over 1.5 million DMF files available to NSL/UniTree with minimal system outage

Comparing performance of many-core CPUs and GPUs for static and motion compensated reconstruction of C-arm CT data.

PubMed

Hofmann, Hannes G; Keck, Benjamin; Rohkohl, Christopher; Hornegger, Joachim

2011-01-01

Interventional reconstruction of 3-D volumetric data from C-arm CT projections is a computationally demanding task. Hardware optimization is not an option but mandatory for interventional image processing and, in particular, for image reconstruction due to the high demands on performance. Several groups have published fast analytical 3-D reconstruction on highly parallel hardware such as GPUs to mitigate this issue. The authors show that the performance of modern CPU-based systems is in the same order as current GPUs for static 3-D reconstruction and outperforms them for a recent motion compensated (3-D+time) image reconstruction algorithm. This work investigates two algorithms: Static 3-D reconstruction as well as a recent motion compensated algorithm. The evaluation was performed using a standardized reconstruction benchmark, RABBITCT, to get comparable results and two additional clinical data sets. The authors demonstrate for a parametric B-spline motion estimation scheme that the derivative computation, which requires many write operations to memory, performs poorly on the GPU and can highly benefit from modern CPU architectures with large caches. Moreover, on a 32-core Intel Xeon server system, the authors achieve linear scaling with the number of cores used and reconstruction times almost in the same range as current GPUs. Algorithmic innovations in the field of motion compensated image reconstruction may lead to a shift back to CPUs in the future. For analytical 3-D reconstruction, the authors show that the gap between GPUs and CPUs became smaller. It can be performed in less than 20 s (on-the-fly) using a 32-core server.

Continuous-variable quantum computing on encrypted data.

PubMed

Marshall, Kevin; Jacobsen, Christian S; Schäfermeier, Clemens; Gehring, Tobias; Weedbrook, Christian; Andersen, Ulrik L

2016-12-14

The ability to perform computations on encrypted data is a powerful tool for protecting a client's privacy, especially in today's era of cloud and distributed computing. In terms of privacy, the best solutions that classical techniques can achieve are unfortunately not unconditionally secure in the sense that they are dependent on a hacker's computational power. Here we theoretically investigate, and experimentally demonstrate with Gaussian displacement and squeezing operations, a quantum solution that achieves the security of a user's privacy using the practical technology of continuous variables. We demonstrate losses of up to 10 km both ways between the client and the server and show that security can still be achieved. Our approach offers a number of practical benefits (from a quantum perspective) that could one day allow the potential widespread adoption of this quantum technology in future cloud-based computing networks.

Verifiable Measurement-Only Blind Quantum Computing with Stabilizer Testing.

PubMed

Hayashi, Masahito; Morimae, Tomoyuki

2015-11-27

We introduce a simple protocol for verifiable measurement-only blind quantum computing. Alice, a client, can perform only single-qubit measurements, whereas Bob, a server, can generate and store entangled many-qubit states. Bob generates copies of a graph state, which is a universal resource state for measurement-based quantum computing, and sends Alice each qubit of them one by one. Alice adaptively measures each qubit according to her program. If Bob is honest, he generates the correct graph state, and, therefore, Alice can obtain the correct computation result. Regarding the security, whatever Bob does, Bob cannot get any information about Alice's computation because of the no-signaling principle. Furthermore, malicious Bob does not necessarily send the copies of the correct graph state, but Alice can check the correctness of Bob's state by directly verifying the stabilizers of some copies.

Continuous-variable quantum computing on encrypted data

PubMed Central

Marshall, Kevin; Jacobsen, Christian S.; Schäfermeier, Clemens; Gehring, Tobias; Weedbrook, Christian; Andersen, Ulrik L.

2016-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting a client's privacy, especially in today's era of cloud and distributed computing. In terms of privacy, the best solutions that classical techniques can achieve are unfortunately not unconditionally secure in the sense that they are dependent on a hacker's computational power. Here we theoretically investigate, and experimentally demonstrate with Gaussian displacement and squeezing operations, a quantum solution that achieves the security of a user's privacy using the practical technology of continuous variables. We demonstrate losses of up to 10 km both ways between the client and the server and show that security can still be achieved. Our approach offers a number of practical benefits (from a quantum perspective) that could one day allow the potential widespread adoption of this quantum technology in future cloud-based computing networks. PMID:27966528

Verifiable Measurement-Only Blind Quantum Computing with Stabilizer Testing

NASA Astrophysics Data System (ADS)

Hayashi, Masahito; Morimae, Tomoyuki

2015-11-01

We introduce a simple protocol for verifiable measurement-only blind quantum computing. Alice, a client, can perform only single-qubit measurements, whereas Bob, a server, can generate and store entangled many-qubit states. Bob generates copies of a graph state, which is a universal resource state for measurement-based quantum computing, and sends Alice each qubit of them one by one. Alice adaptively measures each qubit according to her program. If Bob is honest, he generates the correct graph state, and, therefore, Alice can obtain the correct computation result. Regarding the security, whatever Bob does, Bob cannot get any information about Alice's computation because of the no-signaling principle. Furthermore, malicious Bob does not necessarily send the copies of the correct graph state, but Alice can check the correctness of Bob's state by directly verifying the stabilizers of some copies.

Continuous-variable quantum computing on encrypted data

NASA Astrophysics Data System (ADS)

Marshall, Kevin; Jacobsen, Christian S.; Schäfermeier, Clemens; Gehring, Tobias; Weedbrook, Christian; Andersen, Ulrik L.

2016-12-01

The ability to perform computations on encrypted data is a powerful tool for protecting a client's privacy, especially in today's era of cloud and distributed computing. In terms of privacy, the best solutions that classical techniques can achieve are unfortunately not unconditionally secure in the sense that they are dependent on a hacker's computational power. Here we theoretically investigate, and experimentally demonstrate with Gaussian displacement and squeezing operations, a quantum solution that achieves the security of a user's privacy using the practical technology of continuous variables. We demonstrate losses of up to 10 km both ways between the client and the server and show that security can still be achieved. Our approach offers a number of practical benefits (from a quantum perspective) that could one day allow the potential widespread adoption of this quantum technology in future cloud-based computing networks.

Informatics in radiology (infoRAD): A complete continuous-availability PACS archive server.

PubMed

Liu, Brent J; Huang, H K; Cao, Fei; Zhou, Michael Z; Zhang, Jianguo; Mogel, Greg

2004-01-01

The operational reliability of the picture archiving and communication system (PACS) server in a filmless hospital environment is always a major concern because server failure could cripple the entire PACS operation. A simple, low-cost, continuous-availability (CA) PACS archive server was designed and developed. The server makes use of a triple modular redundancy (TMR) system with a simple majority voting logic that automatically identifies a faulty module and removes it from service. The remaining two modules continue normal operation with no adverse effects on data flow or system performance. In addition, the server is integrated with two external mass storage devices for short- and long-term storage. Evaluation and testing of the server were conducted with laboratory experiments in which hardware failures were simulated to observe recovery time and the resumption of normal data flow. The server provides maximum uptime (99.999%) for end users while ensuring the transactional integrity of all clinical PACS data. Hardware failure has only minimal impact on performance, with no interruption of clinical data flow or loss of data. As hospital PACS become more widespread, the need for CA PACS solutions will increase. A TMR CA PACS archive server can reliably help achieve CA in this setting. Copyright RSNA, 2004

A collaborative platform for consensus sessions in pathology over Internet.

PubMed

Zapletal, Eric; Le Bozec, Christel; Degoulet, Patrice; Jaulent, Marie-Christine

2003-01-01

The design of valid databases in pathology faces the problem of diagnostic disagreement between pathologists. Organizing consensus sessions between experts to reduce the variability is a difficult task. The TRIDEM platform addresses the issue to organize consensus sessions in pathology over the Internet. In this paper, we present the basis to achieve such collaborative platform. On the one hand, the platform integrates the functionalities of the IDEM consensus module that alleviates the consensus task by presenting to pathologists preliminary computed consensus through ergonomic interfaces (automatic step). On the other hand, a set of lightweight interaction tools such as vocal annotations are implemented to ease the communication between experts as they discuss a case (interactive step). The architecture of the TRIDEM platform is based on a Java-Server-Page web server that communicate with the ObjectStore PSE/PRO database used for the object storage. The HTML pages generated by the web server run Java applets to perform the different steps (automatic and interactive) of the consensus. The current limitations of the platform is to only handle a synchronous process. Moreover, improvements like re-writing the consensus workflow with a protocol such as BPML are already forecast.

Characterizing output bottlenecks in a supercomputer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Bing; Chase, Jeffrey; Dillow, David A

2012-01-01

Supercomputer I/O loads are often dominated by writes. HPC (High Performance Computing) file systems are designed to absorb these bursty outputs at high bandwidth through massive parallelism. However, the delivered write bandwidth often falls well below the peak. This paper characterizes the data absorption behavior of a center-wide shared Lustre parallel file system on the Jaguar supercomputer. We use a statistical methodology to address the challenges of accurately measuring a shared machine under production load and to obtain the distribution of bandwidth across samples of compute nodes, storage targets, and time intervals. We observe and quantify limitations from competing traffic,more » contention on storage servers and I/O routers, concurrency limitations in the client compute node operating systems, and the impact of variance (stragglers) on coupled output such as striping. We then examine the implications of our results for application performance and the design of I/O middleware systems on shared supercomputers.« less

WMS Server 2.0

NASA Technical Reports Server (NTRS)

Plesea, Lucian; Wood, James F.

2012-01-01

This software is a simple, yet flexible server of raster map products, compliant with the Open Geospatial Consortium (OGC) Web Map Service (WMS) 1.1.1 protocol. The server is a full implementation of the OGC WMS 1.1.1 as a fastCGI client and using Geospatial Data Abstraction Library (GDAL) for data access. The server can operate in a proxy mode, where all or part of the WMS requests are done on a back server. The server has explicit support for a colocated tiled WMS, including rapid response of black (no-data) requests. It generates JPEG and PNG images, including 16-bit PNG. The GDAL back-end support allows great flexibility on the data access. The server is a port to a Linux/GDAL platform from the original IRIX/IL platform. It is simpler to configure and use, and depending on the storage format used, it has better performance than other available implementations. The WMS server 2.0 is a high-performance WMS implementation due to the fastCGI architecture. The use of GDAL data back end allows for great flexibility. The configuration is relatively simple, based on a single XML file. It provides scaling and cropping, as well as blending of multiple layers based on layer transparency.

Cloud Based Educational Systems and Its Challenges and Opportunities and Issues

ERIC Educational Resources Information Center

Paul, Prantosh Kr.; Lata Dangwal, Kiran

2014-01-01

Cloud Computing (CC) is actually is a set of hardware, software, networks, storage, services an interface combines to deliver aspects of computing as a service. Cloud Computing (CC) actually uses the central remote servers to maintain data and applications. Practically Cloud Computing (CC) is extension of Grid computing with independency and…

Server-based Approach to Web Visualization of Integrated Three-dimensional Brain Imaging Data

PubMed Central

Poliakov, Andrew V.; Albright, Evan; Hinshaw, Kevin P.; Corina, David P.; Ojemann, George; Martin, Richard F.; Brinkley, James F.

2005-01-01

The authors describe a client-server approach to three-dimensional (3-D) visualization of neuroimaging data, which enables researchers to visualize, manipulate, and analyze large brain imaging datasets over the Internet. All computationally intensive tasks are done by a graphics server that loads and processes image volumes and 3-D models, renders 3-D scenes, and sends the renderings back to the client. The authors discuss the system architecture and implementation and give several examples of client applications that allow visualization and analysis of integrated language map data from single and multiple patients. PMID:15561787

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2012-01-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2011-12-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

Use of World Wide Web Server and Browser Software To Support a First-Year Medical Physiology Course.

ERIC Educational Resources Information Center

Davis, Michael J.; And Others

1997-01-01

Describes the use of a World Wide Web server to support a team-taught physiology course for first-year medical students. The students' evaluations indicate that computer use in class made lecture material more interesting, while the online documents helped reinforce lecture materials and textbooks. Lists factors which contribute to the…

High Performance Descriptive Semantic Analysis of Semantic Graph Databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Adolf, Robert D.; al-Saffar, Sinan

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to understand their inherent semantic structure, whether codified in explicit ontologies or not. Our group is researching novel methods for what we call descriptive semantic analysis of RDF triplestores, to serve purposes of analysis, interpretation, visualization, and optimization. But data size and computational complexity makes it increasingly necessary to bring high performance computational resources to bear on this task. Our research group built a novel high performance hybrid system comprisingmore » computational capability for semantic graph database processing utilizing the large multi-threaded architecture of the Cray XMT platform, conventional servers, and large data stores. In this paper we describe that architecture and our methods, and present the results of our analyses of basic properties, connected components, namespace interaction, and typed paths such for the Billion Triple Challenge 2010 dataset.« less

The growth of the UniTree mass storage system at the NASA Center for Computational Sciences

NASA Technical Reports Server (NTRS)

Tarshish, Adina; Salmon, Ellen

1993-01-01

In October 1992, the NASA Center for Computational Sciences made its Convex-based UniTree system generally available to users. The ensuing months saw the growth of near-online data from nil to nearly three terabytes, a doubling of the number of CPU's on the facility's Cray YMP (the primary data source for UniTree), and the necessity for an aggressive regimen for repacking sparse tapes and hierarchical 'vaulting' of old files to freestanding tape. Connectivity was enhanced as well with the addition of UltraNet HiPPI. This paper describes the increasing demands placed on the storage system's performance and throughput that resulted from the significant augmentation of compute-server processor power and network speed.

The software-defined fast post-processing for GEM soft x-ray diagnostics in the Tungsten Environment in Steady-state Tokamak thermal fusion reactor

NASA Astrophysics Data System (ADS)

Krawczyk, Rafał Dominik; Czarski, Tomasz; Linczuk, Paweł; Wojeński, Andrzej; Kolasiński, Piotr; GÄ ska, Michał; Chernyshova, Maryna; Mazon, Didier; Jardin, Axel; Malard, Philippe; Poźniak, Krzysztof; Kasprowicz, Grzegorz; Zabołotny, Wojciech; Kowalska-Strzeciwilk, Ewa; Malinowski, Karol

2018-06-01

This article presents a novel software-defined server-based solutions that were introduced in the fast, real-time computation systems for soft X-ray diagnostics for the WEST (Tungsten Environment in Steady-state Tokamak) reactor in Cadarache, France. The objective of the research was to provide a fast processing of data at high throughput and with low latencies for investigating the interplay between the particle transport and magnetohydrodynamic activity. The long-term objective is to implement in the future a fast feedback signal in the reactor control mechanisms to sustain the fusion reaction. The implemented electronic measurement device is anticipated to be deployed in the WEST. A standalone software-defined computation engine was designed to handle data collected at high rates in the server back-end of the system. Signals are obtained from the front-end field-programmable gate array mezzanine cards that acquire and perform a selection from the gas electron multiplier detector. A fast, authorial library for plasma diagnostics was written in C++. It originated from reference offline MATLAB implementations. They were redesigned for runtime analysis during the experiment in the novel online modes of operation. The implementation allowed the benchmarking, evaluation, and optimization of plasma processing algorithms with the possibility to check the consistency with reference computations written in MATLAB. The back-end software and hardware architecture are presented with data evaluation mechanisms. The online modes of operation for the WEST are discussed. The results concerning the performance of the processing and the introduced functionality are presented.

An MPA-IO interface to HPSS

NASA Technical Reports Server (NTRS)

Jones, Terry; Mark, Richard; Martin, Jeanne; May, John; Pierce, Elsie; Stanberry, Linda

1996-01-01

This paper describes an implementation of the proposed MPI-IO (Message Passing Interface - Input/Output) standard for parallel I/O. Our system uses third-party transfer to move data over an external network between the processors where it is used and the I/O devices where it resides. Data travels directly from source to destination, without the need for shuffling it among processors or funneling it through a central node. Our distributed server model lets multiple compute nodes share the burden of coordinating data transfers. The system is built on the High Performance Storage System (HPSS), and a prototype version runs on a Meiko CS-2 parallel computer.

Provisioning cooling elements for chillerless data centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Parida, Pritish R.

Systems and methods for cooling include one or more computing structure, an inter-structure liquid cooling system that includes valves configured to selectively provide liquid coolant to the one or more computing structures; a heat rejection system that includes one or more heat rejection units configured to cool liquid coolant; and one or more liquid-to-liquid heat exchangers that include valves configured to selectively transfer heat from liquid coolant in the inter-structure liquid cooling system to liquid coolant in the heat rejection system. Each computing structure further includes one or more liquid-cooled servers; and an intra-structure liquid cooling system that has valvesmore » configured to selectively provide liquid coolant to the one or more liquid-cooled servers.« less

Maintaining the Database for Information Object Analysis, Intent, Dissemination and Enhancement (IOAIDE) and the US Army Research Laboratory Campus Sensor Network (ARL CSN)

DTIC Science & Technology

2017-01-01

CII-B 2800 Powder Mill Road Adelphi, MD 20783-1138 8. PERFORMING ORGANIZATION REPORT NUMBER ARL-TR-7921 9. SPONSORING/MONITORING AGENCY NAME(S...server database, structured query language, information objects, instructions, maintenance , cursor on target events, unattended ground sensors...unlimited. iii Contents List of Figures iv 1. Introduction 1 2. Computer and Software Development Tools Requirements 1 3. Database Maintenance 2 3.1

Photo-z-SQL: Photometric redshift estimation framework

NASA Astrophysics Data System (ADS)

Beck, Róbert; Dobos, László; Budavári, Tamás; Szalay, Alexander S.; Csabai, István

2017-04-01

Photo-z-SQL is a flexible template-based photometric redshift estimation framework that can be seamlessly integrated into a SQL database (or DB) server and executed on demand in SQL. The DB integration eliminates the need to move large photometric datasets outside a database for redshift estimation, and uses the computational capabilities of DB hardware. Photo-z-SQL performs both maximum likelihood and Bayesian estimation and handles inputs of variable photometric filter sets and corresponding broad-band magnitudes.

A distributed parallel storage architecture and its potential application within EOSDIS

NASA Technical Reports Server (NTRS)

Johnston, William E.; Tierney, Brian; Feuquay, Jay; Butzer, Tony

1994-01-01

We describe the architecture, implementation, use of a scalable, high performance, distributed-parallel data storage system developed in the ARPA funded MAGIC gigabit testbed. A collection of wide area distributed disk servers operate in parallel to provide logical block level access to large data sets. Operated primarily as a network-based cache, the architecture supports cooperation among independently owned resources to provide fast, large-scale, on-demand storage to support data handling, simulation, and computation.

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments

PubMed Central

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Koo, JaeHyung; Kim, Min-Soo

2016-01-01

Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com. PMID:27154272

MetaboAnalyst 3.0--making metabolomics more meaningful.

PubMed

Xia, Jianguo; Sinelnikov, Igor V; Han, Beomsoo; Wishart, David S

2015-07-01

MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Closeout Report ARRA supplement to DE-FG02-08ER41546, 03/15/2010 to 03/14/2011 - Advanced Transfer Map Methods for the Description of Particle Beam Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berz, Martin; Makino, Kyoko

The ARRA funds were utilized to acquire a cluster of high performance computers, consisting of one Altus 2804 Server based on a Quad AMD Opteron 6174 12C with 4 2.2 GHz nodes of 12 cores each, resulting in 48 directly usable cores; as well as a Relion 1751 Server using an Intel Xeon X5677 consisting of 4 3.46 GHz cores supporting 8 threads. Both systems run the Unix flavor CentOS, which is designed for use without need of updates, which greatly enhances their reliability. The systems are used to operate our COSY INFINITY environment which supports MPI parallelization. The unitsmore » arrived at MSU in September 2010, and were taken into operation shortly thereafter.« less

Cloud-ECG for real time ECG monitoring and analysis.

PubMed

Xia, Henian; Asif, Irfan; Zhao, Xiaopeng

2013-06-01

Recent advances in mobile technology and cloud computing have inspired numerous designs of cloud-based health care services and devices. Within the cloud system, medical data can be collected and transmitted automatically to medical professionals from anywhere and feedback can be returned to patients through the network. In this article, we developed a cloud-based system for clients with mobile devices or web browsers. Specially, we aim to address the issues regarding the usefulness of the ECG data collected from patients themselves. Algorithms for ECG enhancement, ECG quality evaluation and ECG parameters extraction were implemented in the system. The system was demonstrated by a use case, in which ECG data was uploaded to the web server from a mobile phone at a certain frequency and analysis was performed in real time using the server. The system has been proven to be functional, accurate and efficient. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Autonomous mission planning and scheduling: Innovative, integrated, responsive

NASA Technical Reports Server (NTRS)

Sary, Charisse; Liu, Simon; Hull, Larry; Davis, Randy

1994-01-01

Autonomous mission scheduling, a new concept for NASA ground data systems, is a decentralized and distributed approach to scientific spacecraft planning, scheduling, and command management. Systems and services are provided that enable investigators to operate their own instruments. In autonomous mission scheduling, separate nodes exist for each instrument and one or more operations nodes exist for the spacecraft. Each node is responsible for its own operations which include planning, scheduling, and commanding; and for resolving conflicts with other nodes. One or more database servers accessible to all nodes enable each to share mission and science planning, scheduling, and commanding information. The architecture for autonomous mission scheduling is based upon a realistic mix of state-of-the-art and emerging technology and services, e.g., high performance individual workstations, high speed communications, client-server computing, and relational databases. The concept is particularly suited to the smaller, less complex missions of the future.

A Practical Approach to Spatiotemporal Data Compression

NASA Astrophysics Data System (ADS)

Prudden, Rachel; Robinson, Niall; Arribas, Alberto

2017-04-01

Datasets representing the world around us are becoming ever more unwieldy as data volumes grow. This is largely due to increased measurement and modelling resolution, but the problem is often exacerbated when data are stored at spuriously high precisions. In an effort to facilitate analysis of these datasets, computationally intensive calculations are increasingly being performed on specialised remote servers before the reduced data are transferred to the consumer. Due to bandwidth limitations, this often means data are displayed as simple 2D data visualisations, such as scatter plots or images. We present here a novel way to efficiently encode and transmit 4D data fields on-demand so that they can be locally visualised and interrogated. This nascent "4D video" format allows us to more flexibly move the boundary between data server and consumer client. However, it has applications beyond purely scientific visualisation, in the transmission of data to virtual and augmented reality.

Development of stable Grid service at the next generation system of KEKCC

NASA Astrophysics Data System (ADS)

Nakamura, T.; Iwai, G.; Matsunaga, H.; Murakami, K.; Sasaki, T.; Suzuki, S.; Takase, W.

2017-10-01

A lot of experiments in the field of accelerator based science are actively running at High Energy Accelerator Research Organization (KEK) by using SuperKEKB and J-PARC accelerator in Japan. In these days at KEK, the computing demand from the various experiments for the data processing, analysis, and MC simulation is monotonically increasing. It is not only for the case with high-energy experiments, the computing requirement from the hadron and neutrino experiments and some projects of astro-particle physics is also rapidly increasing due to the very high precision measurement. Under this situation, several projects, Belle II, T2K, ILC and KAGRA experiments supported by KEK are going to utilize Grid computing infrastructure as the main computing resource. The Grid system and services in KEK, which is already in production, are upgraded for the further stable operation at the same time of whole scale hardware replacement of KEK Central Computer System (KEKCC). The next generation system of KEKCC starts the operation from the beginning of September 2016. The basic Grid services e.g. BDII, VOMS, LFC, CREAM computing element and StoRM storage element are made by the more robust hardware configuration. Since the raw data transfer is one of the most important tasks for the KEKCC, two redundant GridFTP servers are adapted to the StoRM service instances with 40 Gbps network bandwidth on the LHCONE routing. These are dedicated to the Belle II raw data transfer to the other sites apart from the servers for the data transfer usage of the other VOs. Additionally, we prepare the redundant configuration for the database oriented services like LFC and AMGA by using LifeKeeper. The LFC servers are made by two read/write servers and two read-only servers for the Belle II experiment, and all of them have an individual database for the purpose of load balancing. The FTS3 service is newly deployed as a service for the Belle II data distribution. The service of CVMFS stratum-0 is started for the Belle II software repository, and stratum-1 service is prepared for the other VOs. In this way, there are a lot of upgrade for the real production service of Grid infrastructure at KEK Computing Research Center. In this paper, we would like to introduce the detailed configuration of the hardware for Grid instance, and several mechanisms to construct the robust Grid system in the next generation system of KEKCC.

A WPS Based Architecture for Climate Data Analytic Services (CDAS) at NASA

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; McInerney, M.; Duffy, D.; Carriere, L.; Potter, G. L.; Doutriaux, C.

2015-12-01

Faced with unprecedented growth in the Big Data domain of climate science, NASA has developed the Climate Data Analytic Services (CDAS) framework. This framework enables scientists to execute trusted and tested analysis operations in a high performance environment close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using trusted climate data analysis tools (ESMF, CDAT, NCO, etc.). The framework is structured as a set of interacting modules allowing maximal flexibility in deployment choices. The current set of module managers include: Staging Manager: Runs the computation locally on the WPS server or remotely using tools such as celery or SLURM. Compute Engine Manager: Runs the computation serially or distributed over nodes using a parallelization framework such as celery or spark. Decomposition Manger: Manages strategies for distributing the data over nodes. Data Manager: Handles the import of domain data from long term storage and manages the in-memory and disk-based caching architectures. Kernel manager: A kernel is an encapsulated computational unit which executes a processor's compute task. Each kernel is implemented in python exploiting existing analysis packages (e.g. CDAT) and is compatible with all CDAS compute engines and decompositions. CDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be executed using either direct web service calls, a python script or application, or a javascript-based web application. Client packages in python or javascript contain everything needed to make CDAS requests. The CDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service permits decision makers to investigate climate changes around the globe, inspect model trends, compare multiple reanalysis datasets, and variability.

Performance Modeling of the ADA Rendezvous

DTIC Science & Technology

1991-10-01

queueing network of figure 2, SERVERTASK can complete only one rendezvous at a time. Thus, the rate that the rendezvous requests are processed at the... Network 1, SERVERTASK competes with the traffic tasks of Server Processor. Each time SERVERTASK gains access to the processor, SERVERTASK completes...Client Processor Server Processor Software Server Nek Netork2 Figure 10. A conceptualization of the algorithm. The SERVERTASK software server of Network 2

CIS4/403: Design and Implementation of an Intranet-based system for Real-Time Tele-Consultation in Oncology

PubMed Central

Eccher, C; Berloffa, F; Demichelis, F; Larcher, B; Galvagni, M; Sboner, A; Graiff, A; Forti, S

1999-01-01

Introduction This study describes a tele-consultation system (TCS) developed to provide a computing environment over a Wide Area Network (WAN) in North Italy (Province of Trento), that can be used by two or more physicians to share medical data and to work co-operatively on medical records. A pilot study has been carried out in oncology to assess the effectiveness of the system. The aim of this project is to facilitate the management of oncology patients by improving communication among the specialists of central and district hospitals. Methods and Results The TCS is an Intranet-based solution. The Intranet is based on a PC WAN with Windows NT Server, Microsoft SQL Server, and Internet Information Server. TCS is composed of native and custom applications developed in the Microsoft Windows (9x and NT) environment. The basic component of the system is the multimedia digital medical record, structured as a collection of HTML and ASP pages. A distributed relational database will allow users to store and retrieve medical records, accessed by a dedicated Web browser via the Web Server. The medical data to be stored and the presentation architecture of the clinical record had been determined in close collaboration with the clinicians involved in the project. TCS will allow a multi-point tele-consultation (TC) among two or more participants on remote computers, providing synchronized surfing through the clinical report. A set of collaborative and personal tools, whiteboard with drawing tools, point-to-point digital audio-conference, chat, local notepad, e-mail service, are integrated in the system to provide an user friendly environment. TCS has been developed as a client-server architecture. The client part of the system is based on the Microsoft Web Browser control and provides the user interface and the tools described above. The server part, running all the time on a dedicated computer, accepts connection requests and manages the connections among the participants in a TC, allowing multiple TC to run simultaneously. TCS has been developed in Visual C++ environment using MFC library and COM technology; ActiveX controls have been written in Visual Basic to perform dedicated tasks from the inside of the HTML clinical report. Before deploying the system in the hospital departments involved in the project, TCS has been tested in our laboratory by clinicians involved in the project to evaluate the usability of the system. Discussion TCS has the potential to support a "multi-disciplinary distributed virtual oncological meeting". The specialists of different departments and of different hospitals can attend "virtual meetings" and interactively discuss on medical data. An expected benefit of the "virtual meeting" should be the possibility to provide expert remote advice from oncologists to peripheral cancer units in formulating treatment plans, conducting follow-up sessions and supporting clinical research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strohmaier, Erich; Meuer, Hans W.; Dongarra, Jack

20th Edition of TOP500 List of World's Fastest Supercomputers Released MANNHEIM, Germany; KNOXVILLE, Tenn.;&BERKELEY, Calif. In what has become a much-anticipated event in the world of high-performance computing, the 20th edition of the TOP500 list of the world's fastest supercomputers was released today (November 15, 2002). The Earth Simulator supercomputer installed earlier this year at the Earth Simulator Center in Yokohama, Japan, is with its Linpack benchmark performance of 35.86 Tflop/s (trillions of calculations per second) retains the number one position. The No.2 and No.3 positions are held by two new, identical ASCI Q systems at Los Alamos National Laboratorymore » (7.73Tflop/s each). These systems are built by Hewlett-Packard and based on the Alpha Server SC computer system.« less

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

Federal Emergency Management Information System (FEMIS) system administration guide, version 1.4.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arp, J.A.; Burnett, R.A.; Carter, R.J.

The Federal Emergency Management Information Systems (FEMIS) is an emergency management planning and response tool that was developed by the Pacific Northwest National Laboratory (PNNL) under the direction of the US Army Chemical Biological Defense Command. The FEMIS System Administration Guide provides information necessary for the system administrator to maintain the FEMIS system. The FEMIS system is designed for a single Chemical Stockpile Emergency Preparedness Program (CSEPP) site that has multiple Emergency Operations Centers (EOCs). Each EOC has personal computers (PCs) that emergency planners and operations personnel use to do their jobs. These PCs are connected via a local areamore » network (LAN) to servers that provide EOC-wide services. Each EOC is interconnected to other EOCs via a Wide Area Network (WAN). Thus, FEMIS is an integrated software product that resides on client/server computer architecture. The main body of FEMIS software, referred to as the FEMIS Application Software, resides on the PC client(s) and is directly accessible to emergency management personnel. The remainder of the FEMIS software, referred to as the FEMIS Support Software, resides on the UNIX server. The Support Software provides the communication, data distribution, and notification functionality necessary to operate FEMIS in a networked, client/server environment. The UNIX server provides an Oracle relational database management system (RDBMS) services, ARC/INFO GIS (optional) capabilities, and basic file management services. PNNL developed utilities that reside on the server include the Notification Service, the Command Service that executes the evacuation model, and AutoRecovery. To operate FEMIS, the Application Software must have access to a site specific FEMIS emergency management database. Data that pertains to an individual EOC`s jurisdiction is stored on the EOC`s local server. Information that needs to be accessible to all EOCs is automatically distributed by the FEMIS database to the other EOCs at the site.« less

Design and development of a mobile system for supporting emergency triage.

PubMed

Michalowski, W; Slowinski, R; Wilk, S; Farion, K J; Pike, J; Rubin, S

2005-01-01

Our objective was to design and develop a mobile clinical decision support system for emergency triage of different acute pain presentations. The system should interact with existing hospital information systems, run on mobile computing devices (handheld computers) and be suitable for operation in weak-connectivity conditions (with unstable connections between mobile clients and a server). The MET (Mobile Emergency Triage) system was designed following an extended client-server architecture. The client component, responsible for triage decision support, is built as a knowledge-based system, with domain ontology separated from generic problem solving methods and used for the automatic creation of a user interface. The MET system is well suited for operation in the Emergency Department of a hospital. The system's external interactions are managed by the server, while the MET clients, running on handheld computers are used by clinicians for collecting clinical data and supporting triage at the bedside. The functionality of the MET client is distributed into specialized modules, responsible for triaging specific types of acute pain presentations. The modules are stored on the server, and on request they can be transferred and executed on the mobile clients. The modular design provides for easy extension of the system's functionality. A clinical trial of the MET system validated the appropriateness of the system's design, and proved the usefulness and acceptance of the system in clinical practice. The MET system captures the necessary hospital data, allows for entry of patient information, and provides triage support. By operating on handheld computers, it fits into the regular emergency department workflow without introducing any hindrances or disruptions. It supports triage anytime and anywhere, directly at the point of care, and also can be used as an electronic patient chart, facilitating structured data collection.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

NASA Astrophysics Data System (ADS)

Dykstra, D.; Bockelman, B.; Blomer, J.; Herner, K.; Levshina, T.; Slyz, M.

2015-12-01

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliary data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called "alien cache" to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dykstra, D.; Bockelman, B.; Blomer, J.

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliarymore » data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called 'alien cache' to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.« less

Astronomy Education using the Web and a Computer Algebra System

NASA Astrophysics Data System (ADS)

Flurchick, K. M.; Culver, Roger B.; Griego, Ben

2013-04-01

The combination of a web server and a Computer Algebra System to provide students the ability to explore and investigate astronomical concepts presented in a class can help student understanding. This combination of technologies provides a framework to extend the classroom experience with independent student exploration. In this presentation we report on the developmen of this web based material and some initial results of students making use of the computational tools using webMathematica^TM. The material developed allow the student toanalyze and investigate a variety of astronomical phenomena, including topics such as the Runge-Lenz vector, descriptions of the orbits of some of the exo-planets, Bode' law and other topics related to celestial mechanics. The server based Computer Algebra System system allows for computations without installing software on the student's computer but provides a powerful environment to explore the various concepts. The current system is installed at North Carolina A&T State University and has been used in several undergraduate classes.

Association of Small Computer Users in Education (ASCUE) Summer Conference. Proceedings (27th, North Myrtle Beach, South Carolina, June 12-16, 1994).

ERIC Educational Resources Information Center

Huston, Rick, Ed.; Armel, Donald, Ed.

Topics addressed by 40 papers from a conference on microcomputers include: developing a campus wide computer ethics policy; integrating new technologies into professional education; campus computer networks; computer assisted instruction; client/server architecture; competencies for entry-level computing positions; auditing and professional…

Node Resource Manager: A Distributed Computing Software Framework Used for Solving Geophysical Problems

NASA Astrophysics Data System (ADS)

Lawry, B. J.; Encarnacao, A.; Hipp, J. R.; Chang, M.; Young, C. J.

2011-12-01

With the rapid growth of multi-core computing hardware, it is now possible for scientific researchers to run complex, computationally intensive software on affordable, in-house commodity hardware. Multi-core CPUs (Central Processing Unit) and GPUs (Graphics Processing Unit) are now commonplace in desktops and servers. Developers today have access to extremely powerful hardware that enables the execution of software that could previously only be run on expensive, massively-parallel systems. It is no longer cost-prohibitive for an institution to build a parallel computing cluster consisting of commodity multi-core servers. In recent years, our research team has developed a distributed, multi-core computing system and used it to construct global 3D earth models using seismic tomography. Traditionally, computational limitations forced certain assumptions and shortcuts in the calculation of tomographic models; however, with the recent rapid growth in computational hardware including faster CPU's, increased RAM, and the development of multi-core computers, we are now able to perform seismic tomography, 3D ray tracing and seismic event location using distributed parallel algorithms running on commodity hardware, thereby eliminating the need for many of these shortcuts. We describe Node Resource Manager (NRM), a system we developed that leverages the capabilities of a parallel computing cluster. NRM is a software-based parallel computing management framework that works in tandem with the Java Parallel Processing Framework (JPPF, http://www.jppf.org/), a third party library that provides a flexible and innovative way to take advantage of modern multi-core hardware. NRM enables multiple applications to use and share a common set of networked computers, regardless of their hardware platform or operating system. Using NRM, algorithms can be parallelized to run on multiple processing cores of a distributed computing cluster of servers and desktops, which results in a dramatic speedup in execution time. NRM is sufficiently generic to support applications in any domain, as long as the application is parallelizable (i.e., can be subdivided into multiple individual processing tasks). At present, NRM has been effective in decreasing the overall runtime of several algorithms: 1) the generation of a global 3D model of the compressional velocity distribution in the Earth using tomographic inversion, 2) the calculation of the model resolution matrix, model covariance matrix, and travel time uncertainty for the aforementioned velocity model, and 3) the correlation of waveforms with archival data on a massive scale for seismic event detection. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Android application and REST server system for quasar spectrum presentation and analysis

NASA Astrophysics Data System (ADS)

Wasiewicz, P.; Pietralik, K.; Hryniewicz, K.

2017-08-01

This paper describes the implementation of a system consisting of a mobile application and RESTful architecture server intended for the analysis and presentation of quasars' spectrum. It also depicts the quasar's characteristics and significance to the scientific community, the source for acquiring astronomical objects' spectral data, used software solutions as well as presents the aspect of Cloud Computing and various possible deployment configurations.

Distributed control system for demand response by servers

NASA Astrophysics Data System (ADS)

Hall, Joseph Edward

Within the broad topical designation of smart grid, research in demand response, or demand-side management, focuses on investigating possibilities for electrically powered devices to adapt their power consumption patterns to better match generation and more efficiently integrate intermittent renewable energy sources, especially wind. Devices such as battery chargers, heating and cooling systems, and computers can be controlled to change the time, duration, and magnitude of their power consumption while still meeting workload constraints such as deadlines and rate of throughput. This thesis presents a system by which a computer server, or multiple servers in a data center, can estimate the power imbalance on the electrical grid and use that information to dynamically change the power consumption as a service to the grid. Implementation on a testbed demonstrates the system with a hypothetical but realistic usage case scenario of an online video streaming service in which there are workloads with deadlines (high-priority) and workloads without deadlines (low-priority). The testbed is implemented with real servers, estimates the power imbalance from the grid frequency with real-time measurements of the live outlet, and uses a distributed, real-time algorithm to dynamically adjust the power consumption of the servers based on the frequency estimate and the throughput of video transcoder workloads. Analysis of the system explains and justifies multiple design choices, compares the significance of the system in relation to similar publications in the literature, and explores the potential impact of the system.

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

PubMed

van der Schot, Gijs; Bonvin, Alexandre M J J

2015-08-01

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

Addressing Small Computers in the First OS Course

ERIC Educational Resources Information Center

Nutt, Gary

2006-01-01

Small computers are emerging as important components of the contemporary computing scene. Their operating systems vary from specialized software for an embedded system to the same style of OS used on a generic desktop or server computer. This article describes a course in which systems are classified by their hardware capability and the…

Performance characteristics of a batch service queueing system with functioning server failure and multiple vacations

NASA Astrophysics Data System (ADS)

Niranjan, S. P.; Chandrasekaran, V. M.; Indhira, K.

2018-04-01

This paper examines bulk arrival and batch service queueing system with functioning server failure and multiple vacations. Customers are arriving into the system in bulk according to Poisson process with rate λ. Arriving customers are served in batches with minimum of ‘a’ and maximum of ‘b’ number of customers according to general bulk service rule. In the service completion epoch if the queue length is less than ‘a’ then the server leaves for vacation (secondary job) of random length. After a vacation completion, if the queue length is still less than ‘a’ then the server leaves for another vacation. The server keeps on going vacation until the queue length reaches the value ‘a’. The server is not stable at all the times. Sometimes it may fails during functioning of customers. Though the server fails service process will not be interrupted.It will be continued for the current batch of customers with lower service rate than the regular service rate. The server will be repaired after the service completion with lower service rate. The probability generating function of the queue size at an arbitrary time epoch will be obtained for the modelled queueing system by using supplementary variable technique. Moreover various performance characteristics will also be derived with suitable numerical illustrations.

Practical experience with graphical user interfaces and object-oriented design in the clinical laboratory.

PubMed

Wells, I G; Cartwright, R Y; Farnan, L P

1993-12-15

The computing strategy in our laboratories evolved from research in Artificial Intelligence, and is based on powerful software tools running on high performance desktop computers with a graphical user interface. This allows most tasks to be regarded as design problems rather than implementation projects, and both rapid prototyping and an object-oriented approach to be employed during the in-house development and enhancement of the laboratory information systems. The practical application of this strategy is discussed, with particular reference to the system designer, the laboratory user and the laboratory customer. Routine operation covers five departments, and the systems are stable, flexible and well accepted by the users. Client-server computing, currently undergoing final trials, is seen as the key to further development, and this approach to Pathology computing has considerable potential for the future.

The data storage grid: the next generation of fault-tolerant storage for backup and disaster recovery of clinical images

NASA Astrophysics Data System (ADS)

King, Nelson E.; Liu, Brent; Zhou, Zheng; Documet, Jorge; Huang, H. K.

2005-04-01

Grid Computing represents the latest and most exciting technology to evolve from the familiar realm of parallel, peer-to-peer and client-server models that can address the problem of fault-tolerant storage for backup and recovery of clinical images. We have researched and developed a novel Data Grid testbed involving several federated PAC systems based on grid architecture. By integrating a grid computing architecture to the DICOM environment, a failed PACS archive can recover its image data from others in the federation in a timely and seamless fashion. The design reflects the five-layer architecture of grid computing: Fabric, Resource, Connectivity, Collective, and Application Layers. The testbed Data Grid architecture representing three federated PAC systems, the Fault-Tolerant PACS archive server at the Image Processing and Informatics Laboratory, Marina del Rey, the clinical PACS at Saint John's Health Center, Santa Monica, and the clinical PACS at the Healthcare Consultation Center II, USC Health Science Campus, will be presented. The successful demonstration of the Data Grid in the testbed will provide an understanding of the Data Grid concept in clinical image data backup as well as establishment of benchmarks for performance from future grid technology improvements and serve as a road map for expanded research into large enterprise and federation level data grids to guarantee 99.999 % up time.

Striped Data Server for Scalable Parallel Data Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Jin; Gutsche, Oliver; Mandrichenko, Igor

A columnar data representation is known to be an efficient way for data storage, specifically in cases when the analysis is often done based only on a small fragment of the available data structures. A data representation like Apache Parquet is a step forward from a columnar representation, which splits data horizontally to allow for easy parallelization of data analysis. Based on the general idea of columnar data storage, working on the [LDRD Project], we have developed a striped data representation, which, we believe, is better suited to the needs of High Energy Physics data analysis. A traditional columnar approachmore » allows for efficient data analysis of complex structures. While keeping all the benefits of columnar data representations, the striped mechanism goes further by enabling easy parallelization of computations without requiring special hardware. We will present an implementation and some performance characteristics of such a data representation mechanism using a distributed no-SQL database or a local file system, unified under the same API and data representation model. The representation is efficient and at the same time simple so that it allows for a common data model and APIs for wide range of underlying storage mechanisms such as distributed no-SQL databases and local file systems. Striped storage adopts Numpy arrays as its basic data representation format, which makes it easy and efficient to use in Python applications. The Striped Data Server is a web service, which allows to hide the server implementation details from the end user, easily exposes data to WAN users, and allows to utilize well known and developed data caching solutions to further increase data access efficiency. We are considering the Striped Data Server as the core of an enterprise scale data analysis platform for High Energy Physics and similar areas of data processing. We have been testing this architecture with a 2TB dataset from a CMS dark matter search and plan to expand it to multiple 100 TB or even PB scale. We will present the striped format, Striped Data Server architecture and performance test results.« less

Optimization of analytical laboratory work using computer networking and databasing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Upp, D.L.; Metcalf, R.A.

1996-06-01

The Health Physics Analysis Laboratory (HPAL) performs around 600,000 analyses for radioactive nuclides each year at Los Alamos National Laboratory (LANL). Analysis matrices vary from nasal swipes, air filters, work area swipes, liquids, to the bottoms of shoes and cat litter. HPAL uses 8 liquid scintillation counters, 8 gas proportional counters, and 9 high purity germanium detectors in 5 laboratories to perform these analyses. HPAL has developed a computer network between the labs and software to produce analysis results. The software and hardware package includes barcode sample tracking, log-in, chain of custody, analysis calculations, analysis result printing, and utility programs.more » All data are written to a database, mirrored on a central server, and eventually written to CD-ROM to provide for online historical results. This system has greatly reduced the work required to provide for analysis results as well as improving the quality of the work performed.« less

75 FR 32915 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-10

... used to authenticate authorized desktop and laptop computer users. Computer servers are scanned monthly... data is also used for management and statistical reports and studies. Routine uses of records... duties. The computer files are password protected with access restricted to authorized users. Records are...

Passive Detection of Misbehaving Name Servers

DTIC Science & Technology

2013-10-01

Passive Detection of Misbehaving Name Servers Leigh B. Metcalf Jonathan M. Spring October 2013 TECHNICAL REPORT CMU/SEI-2013-TR-010 ESC-TR...Detection of Misbehaving Name Servers 5. FUNDING NUMBERS FA8721-05-C-0003 6. AUTHOR(S) Leigh B. Metcalf and Jonathan M. Spring 7. PERFORMING

Simulating Hydrologic Flow and Reactive Transport with PFLOTRAN and PETSc on Emerging Fine-Grained Parallel Computer Architectures

NASA Astrophysics Data System (ADS)

Mills, R. T.; Rupp, K.; Smith, B. F.; Brown, J.; Knepley, M.; Zhang, H.; Adams, M.; Hammond, G. E.

2017-12-01

As the high-performance computing community pushes towards the exascale horizon, power and heat considerations have driven the increasing importance and prevalence of fine-grained parallelism in new computer architectures. High-performance computing centers have become increasingly reliant on GPGPU accelerators and "manycore" processors such as the Intel Xeon Phi line, and 512-bit SIMD registers have even been introduced in the latest generation of Intel's mainstream Xeon server processors. The high degree of fine-grained parallelism and more complicated memory hierarchy considerations of such "manycore" processors present several challenges to existing scientific software. Here, we consider how the massively parallel, open-source hydrologic flow and reactive transport code PFLOTRAN - and the underlying Portable, Extensible Toolkit for Scientific Computation (PETSc) library on which it is built - can best take advantage of such architectures. We will discuss some key features of these novel architectures and our code optimizations and algorithmic developments targeted at them, and present experiences drawn from working with a wide range of PFLOTRAN benchmark problems on these architectures.

Unidata Cyberinfrastructure in the Cloud

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.; Young, J. W.

2016-12-01

Data services, software, and user support are critical components of geosciences cyber-infrastructure to help researchers to advance science. With the maturity of and significant advances in cloud computing, it has recently emerged as an alternative new paradigm for developing and delivering a broad array of services over the Internet. Cloud computing is now mature enough in usability in many areas of science and education, bringing the benefits of virtualized and elastic remote services to infrastructure, software, computation, and data. Cloud environments reduce the amount of time and money spent to procure, install, and maintain new hardware and software, and reduce costs through resource pooling and shared infrastructure. Given the enormous potential of cloud-based services, Unidata has been moving to augment its software, services, data delivery mechanisms to align with the cloud-computing paradigm. To realize the above vision, Unidata has worked toward: * Providing access to many types of data from a cloud (e.g., via the THREDDS Data Server, RAMADDA and EDEX servers); * Deploying data-proximate tools to easily process, analyze, and visualize those data in a cloud environment cloud for consumption by any one, by any device, from anywhere, at any time; * Developing and providing a range of pre-configured and well-integrated tools and services that can be deployed by any university in their own private or public cloud settings. Specifically, Unidata has developed Docker for "containerized applications", making them easy to deploy. Docker helps to create "disposable" installs and eliminates many configuration challenges. Containerized applications include tools for data transport, access, analysis, and visualization: THREDDS Data Server, Integrated Data Viewer, GEMPAK, Local Data Manager, RAMADDA Data Server, and Python tools; * Leveraging Jupyter as a central platform and hub with its powerful set of interlinking tools to connect interactively data servers, Python scientific libraries, scripts, and workflows; * Exploring end-to-end modeling and prediction capabilities in the cloud; * Partnering with NOAA and public cloud vendors (e.g., Amazon and OCC) on the NOAA Big Data Project to harness their capabilities and resources for the benefit of the academic community.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

NASA Astrophysics Data System (ADS)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

Real-time, interactive animation of deformable two- and three-dimensional objects

DOEpatents

Desbrun, Mathieu; Schroeder, Peter; Meyer, Mark; Barr, Alan H.

2003-06-03

A method of updating in real-time the locations and velocities of mass points of a two- or three-dimensional object represented by a mass-spring system. A modified implicit Euler integration scheme is employed to determine the updated locations and velocities. In an optional post-integration step, the updated locations are corrected to preserve angular momentum. A processor readable medium and a network server each tangibly embodying the method are also provided. A system comprising a processor in combination with the medium, and a system comprising the server in combination with a client for accessing the server over a computer network, are also provided.

OPserver: opacities and radiative accelerations on demand

NASA Astrophysics Data System (ADS)

Mendoza, C.; González, J.; Seaton, M. J.; Buerger, P.; Bellorín, A.; Meléndez, M.; Rodríguez, L. S.; Delahaye, F.; Zeippen, C. J.; Palacios, E.; Pradhan, A. K.

2009-05-01

We report on developments carried out within the Opacity Project (OP) to upgrade atomic database services to comply with e-infrastructure requirements. We give a detailed description of an interactive, online server for astrophysical opacities, referred to as OPserver, to be used in sophisticated stellar modelling where Rosseland mean opacities and radiative accelerations are computed at every depth point and each evolution cycle. This is crucial, for instance, in chemically peculiar stars and in the exploitation of the new asteroseismological data. OPserver, downloadable with the new OPCD_3.0 release from the Centre de Données Astronomiques de Strasbourg, France, computes mean opacities and radiative data for arbitrary chemical mixtures from the OP monochromatic opacities. It is essentially a client-server network restructuring and optimization of the suite of codes included in the earlier OPCD_2.0 release. The server can be installed locally or, alternatively, accessed remotely from the Ohio Supercomputer Center, Columbus, Ohio, USA. The client is an interactive web page or a subroutine library that can be linked to the user code. The suitability of this scheme in grid computing environments is emphasized, and its extension to other atomic database services for astrophysical purposes is discussed.

The HydroServer Platform for Sharing Hydrologic Data

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Schreuders, K.; Maidment, D. R.; Zaslavsky, I.; Valentine, D. W.

2010-12-01

The CUAHSI Hydrologic Information System (HIS) is an internet based system that supports sharing of hydrologic data. HIS consists of databases connected using the Internet through Web services, as well as software for data discovery, access, and publication. The HIS system architecture is comprised of servers for publishing and sharing data, a centralized catalog to support cross server data discovery and a desktop client to access and analyze data. This paper focuses on HydroServer, the component developed for sharing and publishing space-time hydrologic datasets. A HydroServer is a computer server that contains a collection of databases, web services, tools, and software applications that allow data producers to store, publish, and manage the data from an experimental watershed or project site. HydroServer is designed to permit publication of data as part of a distributed national/international system, while still locally managing access to the data. We describe the HydroServer architecture and software stack, including tools for managing and publishing time series data for fixed point monitoring sites as well as spatially distributed, GIS datasets that describe a particular study area, watershed, or region. HydroServer adopts a standards based approach to data publication, relying on accepted and emerging standards for data storage and transfer. CUAHSI developed HydroServer code is free with community code development managed through the codeplex open source code repository and development system. There is some reliance on widely used commercial software for general purpose and standard data publication capability. The sharing of data in a common format is one way to stimulate interdisciplinary research and collaboration. It is anticipated that the growing, distributed network of HydroServers will facilitate cross-site comparisons and large scale studies that synthesize information from diverse settings, making the network as a whole greater than the sum of its parts in advancing hydrologic research. Details of the CUAHSI HIS can be found at http://his.cuahsi.org, and HydroServer codeplex site http://hydroserver.codeplex.com.

Computational resources for ribosome profiling: from database to Web server and software.

PubMed

Wang, Hongwei; Wang, Yan; Xie, Zhi

2017-08-14

Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation. This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. At present, however, a comprehensive review on these resources is still lacking. Here, we survey the recent computational advances guided by ribosome profiling, with a focus on databases, Web servers and software tools for storing, visualizing and analyzing ribosome profiling data. This review is intended to provide experimental and computational biologists with a reference to make appropriate choices among existing resources for the question at hand. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Semiquantum key distribution with secure delegated quantum computation

PubMed Central

Li, Qin; Chan, Wai Hong; Zhang, Shengyu

2016-01-01

Semiquantum key distribution allows a quantum party to share a random key with a “classical” party who only can prepare and measure qubits in the computational basis or reorder some qubits when he has access to a quantum channel. In this work, we present a protocol where a secret key can be established between a quantum user and an almost classical user who only needs the quantum ability to access quantum channels, by securely delegating quantum computation to a quantum server. We show the proposed protocol is robust even when the delegated quantum server is a powerful adversary, and is experimentally feasible with current technology. As one party of our protocol is the most quantum-resource efficient, it can be more practical and significantly widen the applicability scope of quantum key distribution. PMID:26813384

Experimental parametric study of servers cooling management in data centers buildings

NASA Astrophysics Data System (ADS)

Nada, S. A.; Elfeky, K. E.; Attia, Ali M. A.; Alshaer, W. G.

2017-06-01

A parametric study of air flow and cooling management of data centers servers is experimentally conducted for different design conditions. A physical scale model of data center accommodating one rack of four servers was designed and constructed for testing purposes. Front and rear rack and server's temperatures distributions and supply/return heat indices (SHI/RHI) are used to evaluate data center thermal performance. Experiments were conducted to parametrically study the effects of perforated tiles opening ratio, servers power load variation and rack power density. The results showed that (1) perforated tile of 25% opening ratio provides the best results among the other opening ratios, (2) optimum benefit of cold air in servers cooling is obtained at uniformly power loading of servers (3) increasing power density decrease air re-circulation but increase air bypass and servers temperature. The present results are compared with previous experimental and CFD results and fair agreement was found.

Planning and management of cloud computing networks

NASA Astrophysics Data System (ADS)

Larumbe, Federico

The evolution of the Internet has a great impact on a big part of the population. People use it to communicate, query information, receive news, work, and as entertainment. Its extraordinary usefulness as a communication media made the number of applications and technological resources explode. However, that network expansion comes at the cost of an important power consumption. If the power consumption of telecommunication networks and data centers is considered as the power consumption of a country, it would rank at the 5 th place in the world. Furthermore, the number of servers in the world is expected to grow by a factor of 10 between 2013 and 2020. This context motivates us to study techniques and methods to allocate cloud computing resources in an optimal way with respect to cost, quality of service (QoS), power consumption, and environmental impact. The results we obtained from our test cases show that besides minimizing capital expenditures (CAPEX) and operational expenditures (OPEX), the response time can be reduced up to 6 times, power consumption by 30%, and CO2 emissions by a factor of 60. Cloud computing provides dynamic access to IT resources as a service. In this paradigm, programs are executed in servers connected to the Internet that users access from their computers and mobile devices. The first advantage of this architecture is to reduce the time of application deployment and interoperability, because a new user only needs a web browser and does not need to install software on local computers with specific operating systems. Second, applications and information are available from everywhere and with any device with an Internet access. Also, servers and IT resources can be dynamically allocated depending on the number of users and workload, a feature called elasticity. This thesis studies the resource management of cloud computing networks and is divided in three main stages. We start by analyzing the planning of cloud computing networks to get a comprehensive vision. The first question to be solved is what are the optimal data center locations. We found that the location of each data center has a big impact on cost, QoS, power consumption, and greenhouse gas emissions. An optimization problem with a multi-criteria objective function is proposed to decide jointly the optimal location of data centers and software components, link capacities, and information routing. Once the network planning has been analyzed, the problem of dynamic resource provisioning in real time is addressed. In this context, virtualization is a key technique in cloud computing because each server can be shared by multiple Virtual Machines (VMs) and the total power consumption can be reduced. In the same line of location problems, we propose a Green Cloud Broker that optimizes VM placement across multiple data centers. In fact, when multiple data centers are considered, response time can be reduced by placing VMs close to users, cost can be minimized, power consumption can be optimized by using energy efficient data centers, and CO2 emissions can be decreased by choosing data centers provided with renewable energy sources. The third stage of the analysis is the short-term management of a cloud data center. In particular, a method is proposed to assign VMs to servers by considering communication traffic among VMs. Cloud data centers receive new applications over time and these applications need on-demand resource provisioning. Each application is composed of multiple types of VMs that interact among themselves. A program called scheduler must place each new VM in a server and that impacts the QoS and power consumption. Our method places VMs that communicate among themselves in servers that are close to each other in the network topology, thus reducing communication delay and increasing the throughput available among VMs. Furthermore, the power consumption of each type of server is considered and the most efficient ones are chosen to place the VMs. The number of VMs of each application can be dynamically changed to match the workload and servers not needed in a particular period can be suspended to save energy. The methodology developed is based on Mixed Integer Programming (MIP) models to formalize the problems and use state of the art optimization solvers. Then, heuristics are developed to solve cases with more than 1,000 potential data center locations for the planning problem, 1,000 nodes for the cloud broker, and 128,000 servers for the VM placement problem. Solutions with very short optimality gaps, between 0% and 1.95%, are obtained, and execution time in the order of minutes for the planning problem and less than a second for real time cases. We consider that this thesis on resource provisioning of cloud computing networks includes important contributions on this research area, and innovative commercial applications based on the proposed methods have promising future.

NASA/University JOint VEnture (JOVE) Program. VIXEN(tm): Object-Oriented, Technology-Adaptive, Virtual Information Exchange Environment

NASA Technical Reports Server (NTRS)

Anyiwo, Joshua C.

2000-01-01

Vixen is a collection of enabling technologies for uninhibited distributed object computing. In the Spring of 1995 when Vixen was proposed, it was an innovative idea very much ahead of its time. But today the technologies proposed in Vixen have become standard technologies for Enterprise Computing. Sun Microsystems J2EE/EJB specifications, among others, are independently proposed technologies of the Vixen type. I have brought Vixen completely under the J2EE standard in order to maximize interoperability and compatibility with other computing industry efforts. Vixen and the Enterprise JavaBean (EJB) Server technologies are now practically identical; OIL, another Vixen technology, and the Java Messaging System (JMS) are practically identical; and so on. There is no longer anything novel or patentable in the Vixen work performed under this grant. The above discussion, notwithstanding, my independent development of Vixen has significantly helped me, my university, my students and the local community. The undergraduate students who worked with me in developing Vixen have enhanced their expertise in what has become the cutting edge technology of their industry and are therefore well positioned for lucrative employment opportunities in the industry. My academic department has gained a new course: "Multi-media System Development", which provides a highly desirable expertise to our students for employment in any enterprise today. The many Outreach Programs that I conducted during this grant period have exposed local Middle School students to the contributions that NASA is making in our society as well as awakened desires in many such students for careers in Science and Technology. I have applied Vixen to the development of two software packages: (a) JAS: Joshua Application Server - which allows a user to configure an EJB Server to serve a J2EE compliant application over the world wide web; (b) PCM: Professor Course Manager: a J2EE compliant application for configuring a course for distance learning. These types of applications are, however, generally available in the industry today.

How to maintain blood supply during computer network breakdown: a manual backup system.

PubMed

Zeiler, T; Slonka, J; Bürgi, H R; Kretschmer, V

2000-12-01

Electronic data management systems using computer network systems and client/server architecture are increasingly used in laboratories and transfusion services. Severe problems arise if there is no network access to the database server and critical functions are not available. We describe a manual backup system (MBS) developed to maintain the delivery of blood products to patients in a hospital transfusion service in case of a computer network breakdown. All data are kept on a central SQL database connected to peripheral workstations in a local area network (LAN). Request entry from wards is performed via machine-readable request forms containing self-adhesive specimen labels with barcodes for test tubes. Data entry occurs on-line by bidirectional automated systems or off-line manually. One of the workstations in the laboratory contains a second SQL database which is frequently and incrementally updated. This workstation is run as a stand-alone, read-only database if the central SQL database is not available. In case of a network breakdown, the time-graded MBS is launched. Patient data, requesting ward and ordered tests/requests, are photocopied through a template from the request forms on special MBS worksheets serving as laboratory journal for manual processing and result report (a copy is left in the laboratory). As soon as the network is running again the data from the off-line period are entered into the primary SQL server. The MBS was successfully used at several occasions. The documentation of a 90-min breakdown period is presented in detail. Additional work resulted from the copy work and the belated manual data entry after restoration of the system. There was no delay in issue of blood products or result reporting. The backup system described has been proven to be simple, quick and safe to maintain urgent blood supply and distribution of laboratory results in case of unexpected network breakdown.

CASTp 3.0: computed atlas of surface topography of proteins.

PubMed

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Earthquake Early Warning Management based on Client-Server using Primary Wave data from Vibrating Sensor

NASA Astrophysics Data System (ADS)

Laumal, F. E.; Nope, K. B. N.; Peli, Y. S.

2018-01-01

Early warning is a warning mechanism before an actual incident occurs, can be implemented on natural events such as tsunamis or earthquakes. Earthquakes are classified in tectonic and volcanic types depend on the source and nature. The tremor in the form of energy propagates in all directions as Primary and Secondary waves. Primary wave as initial earthquake vibrations propagates longitudinally, while the secondary wave propagates like as a sinusoidal wave after Primary, destructive and as a real earthquake. To process the primary vibration data captured by the earthquake sensor, a network management required client computer to receives primary data from sensors, authenticate and forward to a server computer to set up an early warning system. With the water propagation concept, a method of early warning system has been determined in which some sensors are located on the same line, sending initial vibrations as primary data on the same scale and the server recommended to the alarm sound as an early warning.

Design and implementation of a cloud based lithography illumination pupil processing application

NASA Astrophysics Data System (ADS)

Zhang, Youbao; Ma, Xinghua; Zhu, Jing; Zhang, Fang; Huang, Huijie

2017-02-01

Pupil parameters are important parameters to evaluate the quality of lithography illumination system. In this paper, a cloud based full-featured pupil processing application is implemented. A web browser is used for the UI (User Interface), the websocket protocol and JSON format are used for the communication between the client and the server, and the computing part is implemented in the server side, where the application integrated a variety of high quality professional libraries, such as image processing libraries libvips and ImageMagic, automatic reporting system latex, etc., to support the program. The cloud based framework takes advantage of server's superior computing power and rich software collections, and the program could run anywhere there is a modern browser due to its web UI design. Compared to the traditional way of software operation model: purchased, licensed, shipped, downloaded, installed, maintained, and upgraded, the new cloud based approach, which is no installation, easy to use and maintenance, opens up a new way. Cloud based application probably is the future of the software development.

12 CFR 1235.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., or stored by electronic means. E-mail means a document created or received on a computer network for... conduct of the business of a regulated entity or the Office of Finance (which business, in the case of the... is stored or located, including network servers, desktop or laptop computers and handheld computers...

12 CFR 1235.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., or stored by electronic means. E-mail means a document created or received on a computer network for... conduct of the business of a regulated entity or the Office of Finance (which business, in the case of the... is stored or located, including network servers, desktop or laptop computers and handheld computers...

76 FR 61717 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-05

... computer science based technology that may provide the capability of detecting untoward events such as... is comprised of a dedicated computer server that executes specially designed software with input data... computer assisted clinical ordering. J Biomed Inform. 2003 Feb-Apr;36(1-2):4-22. [PMID 14552843...

Federal Emergency Management Information System (FEMIS) System Administration Guide for FEMIS Version 1.4.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arp, J.A.; Bower, J.C.; Burnett, R.A.

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and response tool that was developed by the Pacific Northwest National Laboratory (PNNL) under the direction of the U.S. Army Chemical Biological Defense Command. The FEMIS System Administration Guide provides information necessary for the system administrator to maintain the FEMIS system. The FEMIS system is designed for a single Chemical Stockpile Emergency Preparedness Program (CSEPP) site that has multiple Emergency Operations Centers (EOCs). Each EOC has personal computers (PCs) that emergency planners and operations personnel use to do their jobs. These PCs are corrected via a local areamore » network (LAN) to servers that provide EOC-wide services. Each EOC is interconnected to other EOCs via a Wide Area Network (WAN). Thus, FEMIS is an integrated software product that resides on client/server computer architecture. The main body of FEMIS software, referred to as the FEMIS Application Software, resides on the PC client(s) and is directly accessible to emergency management personnel. The remainder of the FEMIS software, referred to as the FEMIS Support Software, resides on the UNIX server. The Support Software provides the communication data distribution and notification functionality necessary to operate FEMIS in a networked, client/server environment.« less

Federal Emergency Management Information System (FEMIS), Installation Guide for FEMIS 1.4.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arp, J.A.; Burnett, R.A.; Carter, R.J.

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and response tool that was developed by the Pacific Northwest National Laboratory (PNNL) under the direction of the U.S. Army Chemical Biological Defense Command. The FEMIS System Administration Guide provides information necessary for the system administrator to maintain the FEMIS system. The FEMIS system is designed for a single Chemical Stockpile Emergency Preparedness Program (CSEPP) site that has multiple Emergency Operations Centers (EOCs). Each EOC has personal computers (PCs) that emergency planners and operations personnel use to do their jobs. These PCs are corrected via a local areamore » network (LAN) to servers that provide EOC-wide services. Each EOC is interconnected to other EOCs via a Wide Area Network (WAN). Thus, FEMIS is an integrated software product that resides on client/server computer architecture. The main body of FEMIS software, referred to as the FEMIS Application Software, resides on the PC client(s) and is directly accessible to emergency management personnel. The remainder of the FEMIS software, referred to as the FEMIS Support Software, resides on the UNIX server. The Support Software provides the communication data distribution and notification functionality necessary to operate FEMIS in a networked, client/server environment.« less

Federal Emergency Management Information System (FEMIS) Data Management Guide for FEMIS Version 1.4.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angel, L.K.; Bower, J.C.; Burnett, R.A.

1999-06-29

The Federal Emergency Management Information System (FEMIS) is an emergency management planning and response tool that was developed by the Pacific Northwest National Laboratory (PNNL) under the direction of the U.S. Army Chemical Biological Defense Command. The FEMIS System Administration Guide provides information necessary for the system administrator to maintain the FEMIS system. The FEMIS system is designed for a single Chemical Stockpile Emergency Preparedness Program (CSEPP) site that has multiple Emergency Operations Centers (EOCs). Each EOC has personal computers (PCs) that emergency planners and operations personnel use to do their jobs. These PCs are corrected via a local areamore » network (LAN) to servers that provide EOC-wide services. Each EOC is interconnected to other EOCs via a Wide Area Network (WAN). Thus, FEMIS is an integrated software product that resides on client/server computer architecture. The main body of FEMIS software, referred to as the FEMIS Application Software, resides on the PC client(s) and is directly accessible to emergency management personnel. The remainder of the FEMIS software, referred to as the FEMIS Support Software, resides on the UNIX server. The Support Software provides the communication data distribution and notification functionality necessary to operate FEMIS in a networked, client/server environment.« less

An Improvement to a Multi-Client Searchable Encryption Scheme for Boolean Queries.

PubMed

Jiang, Han; Li, Xue; Xu, Qiuliang

2016-12-01

The migration of e-health systems to the cloud computing brings huge benefits, as same as some security risks. Searchable Encryption(SE) is a cryptography encryption scheme that can protect the confidentiality of data and utilize the encrypted data at the same time. The SE scheme proposed by Cash et al. in Crypto2013 and its follow-up work in CCS2013 are most practical SE Scheme that support Boolean queries at present. In their scheme, the data user has to generate the search tokens by the counter number one by one and interact with server repeatedly, until he meets the correct one, or goes through plenty of tokens to illustrate that there is no search result. In this paper, we make an improvement to their scheme. We allow server to send back some information and help the user to generate exact search token in the search phase. In our scheme, there are only two round interaction between server and user, and the search token has [Formula: see text] elements, where n is the keywords number in query expression, and [Formula: see text] is the minimum documents number that contains one of keyword in query expression, and the computation cost of server is [Formula: see text] modular exponentiation operation.

Towards ubiquitous access of computer-assisted surgery systems.

PubMed

Liu, Hui; Lufei, Hanping; Shi, Weishong; Chaudhary, Vipin

2006-01-01

Traditional stand-alone computer-assisted surgery (CAS) systems impede the ubiquitous and simultaneous access by multiple users. With advances in computing and networking technologies, ubiquitous access to CAS systems becomes possible and promising. Based on our preliminary work, CASMIL, a stand-alone CAS server developed at Wayne State University, we propose a novel mobile CAS system, UbiCAS, which allows surgeons to retrieve, review and interpret multimodal medical images, and to perform some critical neurosurgical procedures on heterogeneous devices from anywhere at anytime. Furthermore, various optimization techniques, including caching, prefetching, pseudo-streaming-model, and compression, are used to guarantee the QoS of the UbiCAS system. UbiCAS enables doctors at remote locations to actively participate remote surgeries, share patient information in real time before, during, and after the surgery.

Energy 101: Energy Efficient Data Centers

ScienceCinema

None

2018-04-16

Data centers provide mission-critical computing functions vital to the daily operation of top U.S. economic, scientific, and technological organizations. These data centers consume large amounts of energy to run and maintain their computer systems, servers, and associated high-performance components—up to 3% of all U.S. electricity powers data centers. And as more information comes online, data centers will consume even more energy. Data centers can become more energy efficient by incorporating features like power-saving "stand-by" modes, energy monitoring software, and efficient cooling systems instead of energy-intensive air conditioners. These and other efficiency improvements to data centers can produce significant energy savings, reduce the load on the electric grid, and help protect the nation by increasing the reliability of critical computer operations.

Certification of Completion of Level-2 Milestone 464: Complete Phase 1 Integration of Site-Wide Global Parallel File System (SWGPFS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heidelberg, S T; Fitzgerald, K J; Richmond, G H

2006-01-24

There has been substantial development of the Lustre parallel filesystem prior to the configuration described below for this milestone. The initial Lustre filesystems that were deployed were directly connected to the cluster interconnect, i.e. Quadrics Elan3. That is, the clients (OSSes) and Meta-data Servers (MDS) were all directly connected to the cluster's internal high speed interconnect. This configuration serves a single cluster very well, but does not provide sharing of the filesystem among clusters. LLNL funded the development of high-efficiency ''portals router'' code by CFS (the company that develops Lustre) to enable us to move the Lustre servers to amore » GigE-connected network configuration, thus making it possible to connect to the servers from several clusters. With portals routing available, here is what changes: (1) another storage-only cluster is deployed to front the Lustre storage devices (these become the Lustre OSSes and MDS), (2) this ''Lustre cluster'' is attached via GigE connections to a large GigE switch/router cloud, (3) a small number of compute-cluster nodes are designated as ''gateway'' or ''portal router'' nodes, and (4) the portals router nodes are GigE-connected to the switch/router cloud. The Lustre configuration is then changed to reflect the new network paths. A typical example of this is a compute cluster and a related visualization cluster: the compute cluster produces the data (writes it to the Lustre filesystem), and the visualization cluster consumes some of the data (reads it from the Lustre filesystem). This process can be expanded by aggregating several collections of Lustre backend storage resources into one or more ''centralized'' Lustre filesystems, and then arranging to have several ''client'' clusters mount these centralized filesystems. The ''client clusters'' can be any combination of compute, visualization, archiving, or other types of cluster. This milestone demonstrates the operation and performance of a scaled-down version of such a large, centralized, shared Lustre filesystem concept.« less

Environmental Monitoring Using Sensor Networks

NASA Astrophysics Data System (ADS)

Yang, J.; Zhang, C.; Li, X.; Huang, Y.; Fu, S.; Acevedo, M. F.

2008-12-01

Environmental observatories, consisting of a variety of sensor systems, computational resources and informatics, are important for us to observe, model, predict, and ultimately help preserve the health of the nature. The commoditization and proliferation of coin-to-palm sized wireless sensors will allow environmental monitoring with unprecedented fine spatial and temporal resolution. Once scattered around, these sensors can identify themselves, locate their positions, describe their functions, and self-organize into a network. They communicate through wireless channel with nearby sensors and transmit data through multi-hop protocols to a gateway, which can forward information to a remote data server. In this project, we describe an environmental observatory called Texas Environmental Observatory (TEO) that incorporates a sensor network system with intertwined wired and wireless sensors. We are enhancing and expanding the existing wired weather stations to include wireless sensor networks (WSNs) and telemetry using solar-powered cellular modems. The new WSNs will monitor soil moisture and support long-term hydrologic modeling. Hydrologic models are helpful in predicting how changes in land cover translate into changes in the stream flow regime. These models require inputs that are difficult to measure over large areas, especially variables related to storm events, such as soil moisture antecedent conditions and rainfall amount and intensity. This will also contribute to improve rainfall estimations from meteorological radar data and enhance hydrological forecasts. Sensor data are transmitted from monitoring site to a Central Data Collection (CDC) Server. We incorporate a GPRS modem for wireless telemetry, a single-board computer (SBC) as Remote Field Gateway (RFG) Server, and a WSN for distributed soil moisture monitoring. The RFG provides effective control, management, and coordination of two independent sensor systems, i.e., a traditional datalogger-based wired sensor system and the WSN-based wireless sensor system. The RFG also supports remote manipulation of the devices in the field such as the SBC, datalogger, and WSN. Sensor data collected from the distributed monitoring stations are stored in a database (DB) Server. The CDC Server acts as an intermediate component to hide the heterogeneity of different devices and support data validation required by the DB Server. Daemon programs running on the CDC Server pre-process the data before it is inserted into the database, and periodically perform synchronization tasks. A SWE-compliant data repository is installed to enable data exchange, accepting data from both internal DB Server and external sources through the OGC web services. The web portal, i.e. TEO Online, serves as a user-friendly interface for data visualization, analysis, synthesis, modeling, and K-12 educational outreach activities. It also provides useful capabilities for system developers and operators to remotely monitor system status and remotely update software and system configuration, which greatly simplifies the system debugging and maintenance tasks. We also implement Sensor Observation Services (SOS) at this layer, conforming to the SWE standard to facilitate data exchange. The standard SensorML/O&M data representation makes it easy to integrate our sensor data into the existing Geographic Information Systems (GIS) web services and exchange the data with other organizations.

An Evaluation of Alternative Designs for a Grid Information Service

NASA Technical Reports Server (NTRS)

Smith, Warren; Waheed, Abdul; Meyers, David; Yan, Jerry; Kwak, Dochan (Technical Monitor)

2001-01-01

The Globus information service wasn't working well. There were many updates of data from Globus daemons which saturated the single server and users couldn't retrieve information. We created a second server for NASA and Alliance. Things were great on that server, but a bit slow on the other server. We needed to know exactly how the information service was being used. What were the best servers and configurations? This viewgraph presentation gives an overview of the evaluation of alternative designs for a Grid Information Service. Details are given on the workload characterization, methodology used, and the performance evaluation.

Java RMI Software Technology for the Payload Planning System of the International Space Station

NASA Technical Reports Server (NTRS)

Bryant, Barrett R.

1999-01-01

The Payload Planning System is for experiment planning on the International Space Station. The planning process has a number of different aspects which need to be stored in a database which is then used to generate reports on the planning process in a variety of formats. This process is currently structured as a 3-tier client/server software architecture comprised of a Java applet at the front end, a Java server in the middle, and an Oracle database in the third tier. This system presently uses CGI, the Common Gateway Interface, to communicate between the user-interface and server tiers and Active Data Objects (ADO) to communicate between the server and database tiers. This project investigated other methods and tools for performing the communications between the three tiers of the current system so that both the system performance and software development time could be improved. We specifically found that for the hardware and software platforms that PPS is required to run on, the best solution is to use Java Remote Method Invocation (RMI) for communication between the client and server and SQLJ (Structured Query Language for Java) for server interaction with the database. Prototype implementations showed that RMI combined with SQLJ significantly improved performance and also greatly facilitated construction of the communication software.

I/O performance evaluation of a Linux-based network-attached storage device

NASA Astrophysics Data System (ADS)

Sun, Zhaoyan; Dong, Yonggui; Wu, Jinglian; Jia, Huibo; Feng, Guanping

2002-09-01

In a Local Area Network (LAN), clients are permitted to access the files on high-density optical disks via a network server. But the quality of read service offered by the conventional server is not satisfied because of the multiple functions on the server and the overmuch caller. This paper develops a Linux-based Network-Attached Storage (NAS) server. The Operation System (OS), composed of an optimized kernel and a miniaturized file system, is stored in a flash memory. After initialization, the NAS device is connected into the LAN. The administrator and users could configure the access the server through the web page respectively. In order to enhance the quality of access, the management of buffer cache in file system is optimized. Some benchmark programs are peformed to evaluate the I/O performance of the NAS device. Since data recorded in optical disks are usually for reading accesses, our attention is focused on the reading throughput of the device. The experimental results indicate that the I/O performance of our NAS device is excellent.

A medical application integrating remote 3D visualization tools to access picture archiving and communication system on mobile devices.

PubMed

He, Longjun; Ming, Xing; Liu, Qian

2014-04-01

With computing capability and display size growing, the mobile device has been used as a tool to help clinicians view patient information and medical images anywhere and anytime. However, for direct interactive 3D visualization, which plays an important role in radiological diagnosis, the mobile device cannot provide a satisfactory quality of experience for radiologists. This paper developed a medical system that can get medical images from the picture archiving and communication system on the mobile device over the wireless network. In the proposed application, the mobile device got patient information and medical images through a proxy server connecting to the PACS server. Meanwhile, the proxy server integrated a range of 3D visualization techniques, including maximum intensity projection, multi-planar reconstruction and direct volume rendering, to providing shape, brightness, depth and location information generated from the original sectional images for radiologists. Furthermore, an algorithm that changes remote render parameters automatically to adapt to the network status was employed to improve the quality of experience. Finally, performance issues regarding the remote 3D visualization of the medical images over the wireless network of the proposed application were also discussed. The results demonstrated that this proposed medical application could provide a smooth interactive experience in the WLAN and 3G networks.

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

PubMed

Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

2012-07-01

The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes.

PubMed

Seo, Sangjae; Kim, Moon Ki

2012-07-01

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences

PubMed Central

Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

2016-01-01

Abstract In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

Universal Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Fitzsimons, Joseph; Kashefi, Elham

2012-02-01

Blind Quantum Computing (BQC) allows a client to have a server carry out a quantum computation for them such that the client's inputs, outputs and computation remain private. Recently we proposed a universal unconditionally secure BQC scheme, based on the conceptual framework of the measurement-based quantum computing model, where the client only needs to be able to prepare single qubits in separable states randomly chosen from a finite set and send them to the server, who has the balance of the required quantum computational resources. Here we present a refinement of the scheme which vastly expands the class of quantum circuits which can be directly implemented as a blind computation, by introducing a new class of resource states which we term dotted-complete graph states and expanding the set of single qubit states the client is required to prepare. These two modifications significantly simplify the overall protocol and remove the previously present restriction that only nearest-neighbor circuits could be implemented as blind computations directly. As an added benefit, the refined protocol admits a substantially more intuitive and simplified verification mechanism, allowing the correctness of a blind computation to be verified with arbitrarily small probability of error.

Enhancement web proxy cache performance using Wrapper Feature Selection methods with NB and J48

NASA Astrophysics Data System (ADS)

Mahmoud Al-Qudah, Dua'a.; Funke Olanrewaju, Rashidah; Wong Azman, Amelia

2017-11-01

Web proxy cache technique reduces response time by storing a copy of pages between client and server sides. If requested pages are cached in the proxy, there is no need to access the server. Due to the limited size and excessive cost of cache compared to the other storages, cache replacement algorithm is used to determine evict page when the cache is full. On the other hand, the conventional algorithms for replacement such as Least Recently Use (LRU), First in First Out (FIFO), Least Frequently Use (LFU), Randomized Policy etc. may discard important pages just before use. Furthermore, using conventional algorithm cannot be well optimized since it requires some decision to intelligently evict a page before replacement. Hence, most researchers propose an integration among intelligent classifiers and replacement algorithm to improves replacement algorithms performance. This research proposes using automated wrapper feature selection methods to choose the best subset of features that are relevant and influence classifiers prediction accuracy. The result present that using wrapper feature selection methods namely: Best First (BFS), Incremental Wrapper subset selection(IWSS)embedded NB and particle swarm optimization(PSO)reduce number of features and have a good impact on reducing computation time. Using PSO enhance NB classifier accuracy by 1.1%, 0.43% and 0.22% over using NB with all features, using BFS and using IWSS embedded NB respectively. PSO rises J48 accuracy by 0.03%, 1.91 and 0.04% over using J48 classifier with all features, using IWSS-embedded NB and using BFS respectively. While using IWSS embedded NB fastest NB and J48 classifiers much more than BFS and PSO. However, it reduces computation time of NB by 0.1383 and reduce computation time of J48 by 2.998.

Development of a Multi-Centre Clinical Trial Data Archiving and Analysis Platform for Functional Imaging

NASA Astrophysics Data System (ADS)

Driscoll, Brandon; Jaffray, David; Coolens, Catherine

2014-03-01

Purpose: To provide clinicians & researchers participating in multi-centre clinical trials with a central repository for large volume dynamic imaging data as well as a set of tools for providing end-to-end testing and image analysis standards of practice. Methods: There are three main pieces to the data archiving and analysis system; the PACS server, the data analysis computer(s) and the high-speed networks that connect them. Each clinical trial is anonymized using a customizable anonymizer and is stored on a PACS only accessible by AE title access control. The remote analysis station consists of a single virtual machine per trial running on a powerful PC supporting multiple simultaneous instances. Imaging data management and analysis is performed within ClearCanvas Workstation® using custom designed plug-ins for kinetic modelling (The DCE-Tool®), quality assurance (The DCE-QA Tool) and RECIST. Results: A framework has been set up currently serving seven clinical trials spanning five hospitals with three more trials to be added over the next six months. After initial rapid image transfer (+ 2 MB/s), all data analysis is done server side making it robust and rapid. This has provided the ability to perform computationally expensive operations such as voxel-wise kinetic modelling on very large data archives (+20 GB/50k images/patient) remotely with minimal end-user hardware. Conclusions: This system is currently in its proof of concept stage but has been used successfully to send and analyze data from remote hospitals. Next steps will involve scaling up the system with a more powerful PACS and multiple high powered analysis machines as well as adding real-time review capabilities.

Information resources assessment of a healthcare integrated delivery system.

PubMed Central

Gadd, C. S.; Friedman, C. P.; Douglas, G.; Miller, D. J.

1999-01-01

While clinical healthcare systems may have lagged behind computer applications in other fields in the shift from mainframes to client-server architectures, the rapid deployment of newer applications is closing that gap. Organizations considering the transition to client-server must identify and position themselves to provide the resources necessary to implement and support the infrastructure requirements of client-server architectures and to manage the accelerated complexity at the desktop, including hardware and software deployment, training, and maintenance needs. This paper describes an information resources assessment of the recently aligned Pennsylvania regional Veterans Administration Stars and Stripes Health Network (VISN4), in anticipation of the shift from a predominantly mainframe to a client-server information systems architecture in its well-established VistA clinical information system. The multimethod assessment study is described here to demonstrate this approach and its value to regional healthcare networks undergoing organizational integration and/or significant information technology transformations. PMID:10566414

Paying for Express Checkout: Competition and Price Discrimination in Multi-Server Queuing Systems

PubMed Central

Deck, Cary; Kimbrough, Erik O.; Mongrain, Steeve

2014-01-01

We model competition between two firms selling identical goods to customers who arrive in the market stochastically. Shoppers choose where to purchase based upon both price and the time cost associated with waiting for service. One seller provides two separate queues, each with its own server, while the other seller has a single queue and server. We explore the market impact of the multi-server seller engaging in waiting cost-based-price discrimination by charging a premium for express checkout. Specifically, we analyze this situation computationally and through the use of controlled laboratory experiments. We find that this form of price discrimination is harmful to sellers and beneficial to consumers. When the two-queue seller offers express checkout for impatient customers, the single queue seller focuses on the patient shoppers thereby driving down prices and profits while increasing consumer surplus. PMID:24667809

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

PubMed

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/.

Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank.

PubMed

Collier, James H; Lesk, Arthur M; Garcia de la Banda, Maria; Konagurthu, Arun S

2012-07-01

Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80,500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from: http://lcb.infotech.monash.edu.au/super.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis

PubMed Central

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/ PMID:26571275

Paying for express checkout: competition and price discrimination in multi-server queuing systems.

PubMed

Deck, Cary; Kimbrough, Erik O; Mongrain, Steeve

2014-01-01

We model competition between two firms selling identical goods to customers who arrive in the market stochastically. Shoppers choose where to purchase based upon both price and the time cost associated with waiting for service. One seller provides two separate queues, each with its own server, while the other seller has a single queue and server. We explore the market impact of the multi-server seller engaging in waiting cost-based-price discrimination by charging a premium for express checkout. Specifically, we analyze this situation computationally and through the use of controlled laboratory experiments. We find that this form of price discrimination is harmful to sellers and beneficial to consumers. When the two-queue seller offers express checkout for impatient customers, the single queue seller focuses on the patient shoppers thereby driving down prices and profits while increasing consumer surplus.

Three-Dimensional Audio Client Library

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.

2005-01-01

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

XenoSite server: a web-available site of metabolism prediction tool.

PubMed

Matlock, Matthew K; Hughes, Tyler B; Swamidass, S Joshua

2015-04-01

Cytochrome P450 enzymes (P450s) are metabolic enzymes that process the majority of FDA-approved, small-molecule drugs. Understanding how these enzymes modify molecule structure is key to the development of safe, effective drugs. XenoSite server is an online implementation of the XenoSite, a recently published computational model for P450 metabolism. XenoSite predicts which atomic sites of a molecule--sites of metabolism (SOMs)--are modified by P450s. XenoSite server accepts input in common chemical file formats including SDF and SMILES and provides tools for visualizing the likelihood that each atomic site is a site of metabolism for a variety of important P450s, as well as a flat file download of SOM predictions. XenoSite server is available at http://swami.wustl.edu/xenosite. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Method for a dummy CD mirror server based on NAS

NASA Astrophysics Data System (ADS)

Tang, Muna; Pei, Jing

2002-09-01

With the development of computer network, information sharing is becoming the necessity in human life. The rapid development of CD-ROM and CD-ROM driver techniques makes it possible to issue large database online. After comparing many designs of dummy CD mirror database, which are the embodiment of a main product in CD-ROM database now and in near future, we proposed and realized a new PC based scheme. Our system has the following merits, such as, supporting all kinds of CD format; supporting many network protocol; the independence of mirror network server and the main server; low price, super large capacity, without the need of any special hardware. Preliminarily experiments have verified the validity of the proposed scheme. Encouraged by the promising application future, we are now preparing to put it into market. This paper discusses the design and implement of the CD-ROM server detailedly.

miRNAFold: a web server for fast miRNA precursor prediction in genomes.

PubMed

Tav, Christophe; Tempel, Sébastien; Poligny, Laurent; Tahi, Fariza

2016-07-08

Computational methods are required for prediction of non-coding RNAs (ncRNAs), which are involved in many biological processes, especially at post-transcriptional level. Among these ncRNAs, miRNAs have been largely studied and biologists need efficient and fast tools for their identification. In particular, ab initio methods are usually required when predicting novel miRNAs. Here we present a web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high sensitivity. miRNAFold is implemented as a web server with an intuitive and user-friendly interface, as well as a standalone version. The web server is freely available at: http://EvryRNA.ibisc.univ-evry.fr/miRNAFold. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

PubMed

Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

2016-07-08

Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Modular multiple sensors information management for computer-integrated surgery.

PubMed

Vaccarella, Alberto; Enquobahrie, Andinet; Ferrigno, Giancarlo; Momi, Elena De

2012-09-01

In the past 20 years, technological advancements have modified the concept of modern operating rooms (ORs) with the introduction of computer-integrated surgery (CIS) systems, which promise to enhance the outcomes, safety and standardization of surgical procedures. With CIS, different types of sensor (mainly position-sensing devices, force sensors and intra-operative imaging devices) are widely used. Recently, the need for a combined use of different sensors raised issues related to synchronization and spatial consistency of data from different sources of information. In this study, we propose a centralized, multi-sensor management software architecture for a distributed CIS system, which addresses sensor information consistency in both space and time. The software was developed as a data server module in a client-server architecture, using two open-source software libraries: Image-Guided Surgery Toolkit (IGSTK) and OpenCV. The ROBOCAST project (FP7 ICT 215190), which aims at integrating robotic and navigation devices and technologies in order to improve the outcome of the surgical intervention, was used as the benchmark. An experimental protocol was designed in order to prove the feasibility of a centralized module for data acquisition and to test the application latency when dealing with optical and electromagnetic tracking systems and ultrasound (US) imaging devices. Our results show that a centralized approach is suitable for minimizing synchronization errors; latency in the client-server communication was estimated to be 2 ms (median value) for tracking systems and 40 ms (median value) for US images. The proposed centralized approach proved to be adequate for neurosurgery requirements. Latency introduced by the proposed architecture does not affect tracking system performance in terms of frame rate and limits US images frame rate at 25 fps, which is acceptable for providing visual feedback to the surgeon in the OR. Copyright © 2012 John Wiley & Sons, Ltd.

Development of a high-performance image server using ATM technology

NASA Astrophysics Data System (ADS)

Do Van, Minh; Humphrey, Louis M.; Ravin, Carl E.

1996-05-01

The ability to display digital radiographs to a radiologist in a reasonable time has long been the goal of many PACS. Intelligent routing, or pre-fetching images, has become a solution whereby a system uses a set of rules to route the images to a pre-determined destination. Images would then be stored locally on a workstation for faster display times. Some PACS use a large, centralized storage approach and workstations retrieve images over high bandwidth connections. Another approach to image management is to provide a high performance, clustered storage system. This has the advantage of eliminating the complexity of pre-fetching and allows for rapid image display from anywhere within the hospital. We discuss the development of such a storage device, which provides extremely fast access to images across a local area network. Among the requirements for development of the image server were high performance, DICOM 3.0 compliance, and the use of industry standard components. The completed image server provides performance more than sufficient for use in clinical practice. Setting up modalities to send images to the image server is simple due to the adherence to the DICOM 3.0 specification. Using only off-the-shelf components allows us to keep the cost of the server relatively inexpensive and allows for easy upgrades as technology becomes more advanced. These factors make the image server ideal for use as a clustered storage system in a radiology department.

12 CFR 1732.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... home computer systems of an employee; or (4) Whether the information is active or inactive. (k) Record... (e.g., e-mail, databases, spreadsheets, PowerPoint presentations, electronic reporting systems... information is stored or located, including network servers, desktop or laptop computers and handheld...

The University of Michigan's Computer-Aided Engineering Network.

ERIC Educational Resources Information Center

Atkins, D. E.; Olsen, Leslie A.

1986-01-01

Presents an overview of the Computer-Aided Engineering Network (CAEN) of the University of Michigan. Describes its arrangement of workstations, communication networks, and servers. Outlines the factors considered in hardware and software decision making. Reviews the program's impact on students. (ML)

Integration and Exposure of Large Scale Computational Resources Across the Earth System Grid Federation (ESGF)

NASA Astrophysics Data System (ADS)

Duffy, D.; Maxwell, T. P.; Doutriaux, C.; Williams, D. N.; Chaudhary, A.; Ames, S.

2015-12-01

As the size of remote sensing observations and model output data grows, the volume of the data has become overwhelming, even to many scientific experts. As societies are forced to better understand, mitigate, and adapt to climate changes, the combination of Earth observation data and global climate model projects is crucial to not only scientists but to policy makers, downstream applications, and even the public. Scientific progress on understanding climate is critically dependent on the availability of a reliable infrastructure that promotes data access, management, and provenance. The Earth System Grid Federation (ESGF) has created such an environment for the Intergovernmental Panel on Climate Change (IPCC). ESGF provides a federated global cyber infrastructure for data access and management of model outputs generated for the IPCC Assessment Reports (AR). The current generation of the ESGF federated grid allows consumers of the data to find and download data with limited capabilities for server-side processing. Since the amount of data for future AR is expected to grow dramatically, ESGF is working on integrating server-side analytics throughout the federation. The ESGF Compute Working Team (CWT) has created a Web Processing Service (WPS) Application Programming Interface (API) to enable access scalable computational resources. The API is the exposure point to high performance computing resources across the federation. Specifically, the API allows users to execute simple operations, such as maximum, minimum, average, and anomalies, on ESGF data without having to download the data. These operations are executed at the ESGF data node site with access to large amounts of parallel computing capabilities. This presentation will highlight the WPS API, its capabilities, provide implementation details, and discuss future developments.

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.

PubMed

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Koo, JaeHyung; Kim, Min-Soo

2016-07-08

Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Performance Analysis of Ivshmem for High-Performance Computing in Virtual Machines

NASA Astrophysics Data System (ADS)

Ivanovic, Pavle; Richter, Harald

2018-01-01

High-Performance computing (HPC) is rarely accomplished via virtual machines (VMs). In this paper, we present a remake of ivshmem which can change this. Ivshmem was a shared memory (SHM) between virtual machines on the same server, with SHM-access synchronization included, until about 5 years ago when newer versions of Linux and its virtualization library libvirt evolved. We restored that SHM-access synchronization feature because it is indispensable for HPC and made ivshmem runnable with contemporary versions of Linux, libvirt, KVM, QEMU and especially MPICH, which is an implementation of MPI - the standard HPC communication library. Additionally, MPICH was transparently modified by us to get ivshmem included, resulting in a three to ten times performance improvement compared to TCP/IP. Furthermore, we have transparently replaced MPI_PUT, a single-side MPICH communication mechanism, by an own MPI_PUT wrapper. As a result, our ivshmem even surpasses non-virtualized SHM data transfers for block lengths greater than 512 KBytes, showing the benefits of virtualization. All improvements were possible without using SR-IOV.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Process Integrated Mechanism for Human-Computer Collaboration and Coordination

DTIC Science & Technology

2012-09-12

system we implemented the TAFLib library that provides the communication with TAF . The data received from the TAF server is collected in a data structure...send new commands and flight plans for the UAVs to the TAF server. Test scenarios Several scenarios have been implemented to test and prove our...areas. Shooting Enemies The basic scenario proved the successful integration of PIM and the TAF simulation environment. Subsequently we improved the CP

A web-based computer aided system for liver surgery planning: initial implementation on RayPlus

NASA Astrophysics Data System (ADS)

Luo, Ming; Yuan, Rong; Sun, Zhi; Li, Tianhong; Xie, Qingguo

2016-03-01

At present, computer aided systems for liver surgery design and risk evaluation are widely used in clinical all over the world. However, most systems are local applications that run on high-performance workstations, and the images have to processed offline. Compared with local applications, a web-based system is accessible anywhere and for a range of regardless of relative processing power or operating system. RayPlus (http://rayplus.life.hust.edu.cn), a B/S platform for medical image processing, was developed to give a jump start on web-based medical image processing. In this paper, we implement a computer aided system for liver surgery planning on the architecture of RayPlus. The system consists of a series of processing to CT images including filtering, segmentation, visualization and analyzing. Each processing is packaged into an executable program and runs on the server side. CT images in DICOM format are processed step by to interactive modeling on browser with zero-installation and server-side computing. The system supports users to semi-automatically segment the liver, intrahepatic vessel and tumor from the pre-processed images. Then, surface and volume models are built to analyze the vessel structure and the relative position between adjacent organs. The results show that the initial implementation meets satisfactorily its first-order objectives and provide an accurate 3D delineation of the liver anatomy. Vessel labeling and resection simulation are planned to add in the future. The system is available on Internet at the link mentioned above and an open username for testing is offered.