Implementationof a modular software system for multiphysical processes in porous media

NASA Astrophysics Data System (ADS)

Naumov, Dmitri; Watanabe, Norihiro; Bilke, Lars; Fischer, Thomas; Lehmann, Christoph; Rink, Karsten; Walther, Marc; Wang, Wenqing; Kolditz, Olaf

2016-04-01

Subsurface georeservoirs are a candidate technology for large scale energy storage required as part of the transition to renewable energy sources. The increased use of the subsurface results in competing interests and possible impacts on protected entities. To optimize and plan the use of the subsurface in large scale scenario analyses,powerful numerical frameworks are required that aid process understanding and can capture the coupled thermal (T), hydraulic (H), mechanical (M), and chemical (C) processes with high computational efficiency. Due to having a multitude of different couplings between basic T, H, M, or C processes and the necessity to implement new numerical schemes the development focus has moved to software's modularity. The decreased coupling between the components results in two major advantages: easier addition of specialized processes and improvement of the code's testability and therefore its quality. The idea of modularization is implemented on several levels, in addition to library based separation of the previous code version, by using generalized algorithms available in the Standard Template Library and the Boost library, relying on efficient implementations of liner algebra solvers, using concepts when designing new types, and localization of frequently accessed data structures. This procedure shows certain benefits for a flexible high-performance framework applied to the analysis of multipurpose georeservoirs.

Biomathematical Description of Synthetic Peptide Libraries

PubMed Central

Trepel, Martin

2015-01-01

Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries. PMID:26042419

A high-speed linear algebra library with automatic parallelism

NASA Technical Reports Server (NTRS)

Boucher, Michael L.

1994-01-01

Parallel or distributed processing is key to getting highest performance workstations. However, designing and implementing efficient parallel algorithms is difficult and error-prone. It is even more difficult to write code that is both portable to and efficient on many different computers. Finally, it is harder still to satisfy the above requirements and include the reliability and ease of use required of commercial software intended for use in a production environment. As a result, the application of parallel processing technology to commercial software has been extremely small even though there are numerous computationally demanding programs that would significantly benefit from application of parallel processing. This paper describes DSSLIB, which is a library of subroutines that perform many of the time-consuming computations in engineering and scientific software. DSSLIB combines the high efficiency and speed of parallel computation with a serial programming model that eliminates many undesirable side-effects of typical parallel code. The result is a simple way to incorporate the power of parallel processing into commercial software without compromising maintainability, reliability, or ease of use. This gives significant advantages over less powerful non-parallel entries in the market.

rpe v5: an emulator for reduced floating-point precision in large numerical simulations

NASA Astrophysics Data System (ADS)

Dawson, Andrew; Düben, Peter D.

2017-06-01

This paper describes the rpe (reduced-precision emulator) library which has the capability to emulate the use of arbitrary reduced floating-point precision within large numerical models written in Fortran. The rpe software allows model developers to test how reduced floating-point precision affects the result of their simulations without having to make extensive code changes or port the model onto specialized hardware. The software can be used to identify parts of a program that are problematic for numerical precision and to guide changes to the program to allow a stronger reduction in precision.The development of rpe was motivated by the strong demand for more computing power. If numerical precision can be reduced for an application under consideration while still achieving results of acceptable quality, computational cost can be reduced, since a reduction in numerical precision may allow an increase in performance or a reduction in power consumption. For simulations with weather and climate models, savings due to a reduction in precision could be reinvested to allow model simulations at higher spatial resolution or complexity, or to increase the number of ensemble members to improve predictions. rpe was developed with a particular focus on the community of weather and climate modelling, but the software could be used with numerical simulations from other domains.

Library and Classroom Use of Copyrighted Videotapes and Computer Software.

ERIC Educational Resources Information Center

Reed, Mary Hutchings; Stanek, Debra

1986-01-01

This pullout guide addresses issues regarding library use of copyrighted videotapes and computer software. Guidelines for videotapes cover in-classroom use, in-library use in public library, loan, and duplication. Guidelines for computer software cover purchase conditions, avoiding license restrictions, loaning, archival copies, and in-library and…

Library-Specific Microcomputer Software.

ERIC Educational Resources Information Center

Levert, Virginia M.

1985-01-01

Discusses number and type of microcomputer software programs useful to libraries and types of hardware on which they run, as identified by Nolan Information Management Services. Highlights include general application programs, applications designed to support library technical processes, producers of library software, and choosing among options.…

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2012 CFR

2012-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2013 CFR

2013-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2011 CFR

2011-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2010 CFR

2010-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2014 CFR

2014-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights U.S... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

Ideas for the rapid development of the structural models in mechanical engineering

NASA Astrophysics Data System (ADS)

Oanta, E.; Raicu, A.; Panait, C.

2017-08-01

Conceiving computer based instruments is a long run concern of the authors. Some of the original solutions are: optimal processing of the large matrices, interfaces between the programming languages, approximation theory using spline functions, numerical programming increased accuracy based on the extended arbitrary precision libraries. For the rapid development of the models we identified the following directions: atomization, ‘librarization’, parameterization, automatization and integration. Each of these directions has some particular aspects if we approach mechanical design problems or software development. Atomization means a thorough top-down decomposition analysis which offers an insight regarding the basic features of the phenomenon. Creation of libraries of reusable mechanical parts and libraries of programs (data types, functions) save time, cost and effort when a new model must be conceived. Parameterization leads to flexible definition of the mechanical parts, the values of the parameters being changed either using a dimensioning program or in accord to other parts belonging to the same assembly. The resulting templates may be also included in libraries. Original software applications are useful for the model’s input data generation, to input the data into CAD/FEA commercial applications and for the data integration of the various types of studies included in the same project.

Application Reuse Library for Software, Requirements, and Guidelines

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Thronesbery, Carroll

1994-01-01

Better designs are needed for expert systems and other operations automation software, for more reliable, usable and effective human support. A prototype computer-aided Application Reuse Library shows feasibility of supporting concurrent development and improvement of advanced software by users, analysts, software developers, and human-computer interaction experts. Such a library expedites development of quality software, by providing working, documented examples, which support understanding, modification and reuse of requirements as well as code. It explicitly documents and implicitly embodies design guidelines, standards and conventions. The Application Reuse Library provides application modules with Demo-and-Tester elements. Developers and users can evaluate applicability of a library module and test modifications, by running it interactively. Sub-modules provide application code and displays and controls. The library supports software modification and reuse, by providing alternative versions of application and display functionality. Information about human support and display requirements is provided, so that modifications will conform to guidelines. The library supports entry of new application modules from developers throughout an organization. Example library modules include a timer, some buttons and special fonts, and a real-time data interface program. The library prototype is implemented in the object-oriented G2 environment for developing real-time expert systems.

Analyzing Dynamics of Cooperating Spacecraft

NASA Technical Reports Server (NTRS)

Hughes, Stephen P.; Folta, David C.; Conway, Darrel J.

2004-01-01

A software library has been developed to enable high-fidelity computational simulation of the dynamics of multiple spacecraft distributed over a region of outer space and acting with a common purpose. All of the modeling capabilities afforded by this software are available independently in other, separate software systems, but have not previously been brought together in a single system. A user can choose among several dynamical models, many high-fidelity environment models, and several numerical-integration schemes. The user can select whether to use models that assume weak coupling between spacecraft, or strong coupling in the case of feedback control or tethering of spacecraft to each other. For weak coupling, spacecraft orbits are propagated independently, and are synchronized in time by controlling the step size of the integration. For strong coupling, the orbits are integrated simultaneously. Among the integration schemes that the user can choose are Runge-Kutta Verner, Prince-Dormand, Adams-Bashforth-Moulton, and Bulirsh- Stoer. Comparisons of performance are included for both the weak- and strongcoupling dynamical models for all of the numerical integrators.

Computer Software: Copyright and Licensing Considerations for Schools and Libraries. ERIC Digest.

ERIC Educational Resources Information Center

Reed, Mary Hutchings

This digest notes that the terms and conditions of computer software package license agreements control the use of software in schools and libraries, and examines the implications of computer software license agreements for classroom use and for library lending policies. Guidelines are provided for interpreting the Copyright Act, and insuring the…

Award ER25750: Coordinated Infrastructure for Fault Tolerance Systems Indiana University Final Report

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

Lumsdaine, Andrew

2013-03-08

The main purpose of the Coordinated Infrastructure for Fault Tolerance in Systems initiative has been to conduct research with a goal of providing end-to-end fault tolerance on a systemwide basis for applications and other system software. While fault tolerance has been an integral part of most high-performance computing (HPC) system software developed over the past decade, it has been treated mostly as a collection of isolated stovepipes. Visibility and response to faults has typically been limited to the particular hardware and software subsystems in which they are initially observed. Little fault information is shared across subsystems, allowing little flexibility ormore » control on a system-wide basis, making it practically impossible to provide cohesive end-to-end fault tolerance in support of scientific applications. As an example, consider faults such as communication link failures that can be seen by a network library but are not directly visible to the job scheduler, or consider faults related to node failures that can be detected by system monitoring software but are not inherently visible to the resource manager. If information about such faults could be shared by the network libraries or monitoring software, then other system software, such as a resource manager or job scheduler, could ensure that failed nodes or failed network links were excluded from further job allocations and that further diagnosis could be performed. As a founding member and one of the lead developers of the Open MPI project, our efforts over the course of this project have been focused on making Open MPI more robust to failures by supporting various fault tolerance techniques, and using fault information exchange and coordination between MPI and the HPC system software stack from the application, numeric libraries, and programming language runtime to other common system components such as jobs schedulers, resource managers, and monitoring tools.« less

Microcomputer Software Packages--Choose with Caution.

ERIC Educational Resources Information Center

Naumer, Janet Noll

1983-01-01

Briefly discusses types of software available for library and media center operations and library instruction, suggests three sources of software reviews, and describes almost 50 specific application programs available for bibliographic management, cataloging, circulation, inventory and purchasing, readability, and teaching library skills in…

High-performance computing — an overview

NASA Astrophysics Data System (ADS)

Marksteiner, Peter

1996-08-01

An overview of high-performance computing (HPC) is given. Different types of computer architectures used in HPC are discussed: vector supercomputers, high-performance RISC processors, various parallel computers like symmetric multiprocessors, workstation clusters, massively parallel processors. Software tools and programming techniques used in HPC are reviewed: vectorizing compilers, optimization and vector tuning, optimization for RISC processors; parallel programming techniques like shared-memory parallelism, message passing and data parallelism; and numerical libraries.

Electronic Resources Evaluation Central: Using Off-the-Shelf Software, Web 2.0 Tools, and LibGuides to Manage an Electronic Resources Evaluation Process

ERIC Educational Resources Information Center

England, Lenore; Fu, Li

2011-01-01

A critical part of electronic resources management, the electronic resources evaluation process is multi-faceted and includes a seemingly endless range of resources and tools involving numerous library staff. A solution is to build a Web site to bring all of the components together that can be implemented quickly and result in an organizational…

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

Clinedinst, Winston C.; Slominski, Christopher J.; Dickson, Richard W.; Wolverton, David A.

1993-01-01

The individual software processes used in the flight computers on-board the Advanced Transport Operating System (ATOPS) aircraft have many common functional elements. A library of commonly used software modules was created for general uses among the processes. The library includes modules for mathematical computations, data formatting, system database interfacing, and condition handling. The modules available in the library and their associated calling requirements are described.

Proposal for a CLIPS software library

NASA Technical Reports Server (NTRS)

Porter, Ken

1991-01-01

This paper is a proposal to create a software library for the C Language Integrated Production System (CLIPS) expert system shell developed by NASA. Many innovative ideas for extending CLIPS were presented at the First CLIPS Users Conference, including useful user and database interfaces. CLIPS developers would benefit from a software library of reusable code. The CLIPS Users Group should establish a software library-- a course of action to make that happen is proposed. Open discussion to revise this library concept is essential, since only a group effort is likely to succeed. A response form intended to solicit opinions and support from the CLIPS community is included.

Selecting Software for Libraries.

ERIC Educational Resources Information Center

Beiser, Karl

1993-01-01

Discusses resources and strategies that libraries can use to evaluate competing database management software for purchase. Needs assessments, types of software available, features of good software, evaluation aids, shareware, and marketing and product trends are covered. (KRN)

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

Preparation of cherry-picked combinatorial libraries by string synthesis.

PubMed

Furka, Arpád; Dibó, Gábor; Gombosuren, Naran

2005-03-01

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.

libdrdc: software standards library

NASA Astrophysics Data System (ADS)

Erickson, David; Peng, Tie

2008-04-01

This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

Yurkovich, James T; Yurkovich, Benjamin J; Dräger, Andreas; Palsson, Bernhard O; King, Zachary A

2017-11-22

With the rapid adoption of computational tools in the life sciences, scientists are taking on the challenge of developing their own software libraries and releasing them for public use. This trend is being accelerated by popular technologies and platforms, such as GitHub, Jupyter, R/Shiny, that make it easier to develop scientific software and by open-source licenses that make it easier to release software. But how do you build a software library that people will use? And what characteristics do the best libraries have that make them enduringly popular? Here, we provide a reference guide, based on our own experiences, for developing software libraries along with real-world examples to help provide context for scientists who are learning about these concepts for the first time. While we can only scratch the surface of these topics, we hope that this article will act as a guide for scientists who want to write great software that is built to last. Copyright © 2017 Elsevier Inc. All rights reserved.

The Vendors' Corner: Biblio-Techniques' Library and Information System (BLIS).

ERIC Educational Resources Information Center

Library Software Review, 1984

1984-01-01

Describes online catalog and integrated library computer system designed to enhance Washington Library Network's software. Highlights include system components; implementation options; system features (integrated library functions, database design, system management facilities); support services (installation and training, software maintenance and…

Comet Gas and Dust Dynamics Modeling

NASA Technical Reports Server (NTRS)

Von Allmen, Paul A.; Lee, Seungwon

2010-01-01

This software models the gas and dust dynamics of comet coma (the head region of a comet) in order to support the Microwave Instrument for Rosetta Orbiter (MIRO) project. MIRO will study the evolution of the comet 67P/Churyumov-Gerasimenko's coma system. The instrument will measure surface temperature, gas-production rates and relative abundances, and velocity and excitation temperatures of each species along with their spatial temporal variability. This software will use these measurements to improve the understanding of coma dynamics. The modeling tool solves the equation of motion of a dust particle, the energy balance equation of the dust particle, the continuity equation for the dust and gas flow, and the dust and gas mixture energy equation. By solving these equations numerically, the software calculates the temperature and velocity of gas and dust as a function of time for a given initial gas and dust production rate, and a dust characteristic parameter that measures the ability of a dust particle to adjust its velocity to the local gas velocity. The software is written in a modular manner, thereby allowing the addition of more dynamics equations as needed. All of the numerical algorithms are added in-house and no third-party libraries are used.

Connecting the Library's Patron Database to Campus Administrative Software: Simplifying the Library's Accounts Receivable Process

ERIC Educational Resources Information Center

Oliver, Astrid; Dahlquist, Janet; Tankersley, Jan; Emrich, Beth

2010-01-01

This article discusses the processes that occurred when the Library, Controller's Office, and Information Technology Department agreed to create an interface between the Library's Innovative Interfaces patron database and campus administrative software, Banner, using file transfer protocol, in an effort to streamline the Library's accounts…

Evaluation of Incremental Releases of ECS User Interfaces and the Development of HDF/HDF-EOS Tutorials

NASA Technical Reports Server (NTRS)

Emmitt, G. D.; Greco, S.

2001-01-01

During the reporting period, the PI has continued to serve on numerous review panels, task forces, and committees with the goal of providing input and guidance for the Earth Observing System Data and Information System (EOSDIS) program at NASA Headquarters and NASA Goddard Space Flight Center (GSFC). In addition, the PI has worked together with personnel at Simpson Weather Associates (SWA) to help create an on-line HDF/HDF-EOS tutorial for beginning and non-expert users of both the Hierarchical Data Format (HDF) and HDF-EOS data format and software libraries. Finally, the PI has worked together with personnel at SWA and the Information Technology and Systems Center (ITSC) at the University of Alabama in Huntsville (UAH) on a feasibility study regarding the use of data mining software to ascertain features from the gridded output from numerical meteorological forecast models. A summary of these activities is provided.

Astronomy education and the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Nemiroff, Robert J.

2016-01-01

The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one's own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others' codes.

Flight Software Math Library

NASA Technical Reports Server (NTRS)

McComas, David

2013-01-01

The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

TiConverter: A training image converting tool for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Fadlelmula F., Mohamed M.; Killough, John; Fraim, Michael

2016-11-01

TiConverter is a tool developed to ease the application of multiple-point geostatistics whether by the open source Stanford Geostatistical Modeling Software (SGeMS) or other available commercial software. TiConverter has a user-friendly interface and it allows the conversion of 2D training images into numerical representations in four different file formats without the need for additional code writing. These are the ASCII (.txt), the geostatistical software library (GSLIB) (.txt), the Isatis (.dat), and the VTK formats. It performs the conversion based on the RGB color system. In addition, TiConverter offers several useful tools including image resizing, smoothing, and segmenting tools. The purpose of this study is to introduce the TiConverter, and to demonstrate its application and advantages with several examples from the literature.

Integrated Online Software for Libraries: An Overview of Today's Best-Selling IOLS. Options from the U.S. Perspective.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Profiles the top-selling IOLS (integrated online library systems) software for libraries based on sales figures reported in the 1996 "Library Journal" annual survey of the library automation marketplace. Highlights include microcomputer-based systems and minicomputer-based systems, system components, MARC formats, and market sectors.…

Mining Software Usage with the Automatic Library Tracking Database (ALTD)

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

Hadri, Bilel; Fahey, Mark R

2013-01-01

Tracking software usage is important for HPC centers, computer vendors, code developers and funding agencies to provide more efficient and targeted software support, and to forecast needs and guide HPC software effort towards the Exascale era. However, accurately tracking software usage on HPC systems has been a challenging task. In this paper, we present a tool called Automatic Library Tracking Database (ALTD) that has been developed and put in production on several Cray systems. The ALTD infrastructure prototype automatically and transparently stores information about libraries linked into an application at compilation time and also the executables launched in a batchmore » job. We will illustrate the usage of libraries, compilers and third party software applications on a system managed by the National Institute for Computational Sciences.« less

A Computerized Cataloging System for an Outdoor Program Library or Resource Center.

ERIC Educational Resources Information Center

Watters, Ron

The Outdoor Resource Library Cataloging System is a computer software program designed primarily for outdoor programs with small to medium-sized resource centers. The software is free to nonprofit organizations and is available from the Idaho State University Outdoor Program. The software is used to construct a database of library materials, which…

Demographic Variables as Factors Influencing Accessibility and Utilisation of Library Software by Undergraduates in Two Private Universities in Nigeria

ERIC Educational Resources Information Center

Tolulope, Akano

2017-01-01

Libraries before the 21st century carried out daily routine library task such as cataloguing and classification, acquisition, reference services etc using manual procedures only but the advent of Information Technology as transformed these routine task that libraries can now automate their activities by deploying the use of library software in…

CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

PubMed

Duffy, Fergal J; Verniere, Mélanie; Devocelle, Marc; Bernard, Elise; Shields, Denis C; Chubb, Anthony J

2011-04-25

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Nuclear Data Online Services at Peking University

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

Fan, T.S.; Guo, Z.Y.; Ye, W.G.

2005-05-24

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

Fan, T. S.; Guo, Z. Y.; Ye, W. G.; Liu, W. L.; Liu, T. J.; Liu, C. X.; Chen, J. X.; Tang, G. Y.; Shi, Z. M.; Huang, X. L.; Chen, J. E.

2005-05-01

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Software Defined GPS API: Development and Implementation of GPS Correlator Architectures Using MATLAB with Focus on SDR Implementations

DTIC Science & Technology

2014-05-18

intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques...with the intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved...intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques to

Toward performance portability of the Albany finite element analysis code using the Kokkos library

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

Demeshko, Irina; Watkins, Jerry; Tezaur, Irina K.

Performance portability on heterogeneous high-performance computing (HPC) systems is a major challenge faced today by code developers: parallel code needs to be executed correctly as well as with high performance on machines with different architectures, operating systems, and software libraries. The finite element method (FEM) is a popular and flexible method for discretizing partial differential equations arising in a wide variety of scientific, engineering, and industrial applications that require HPC. This paper presents some preliminary results pertaining to our development of a performance portable implementation of the FEM-based Albany code. Performance portability is achieved using the Kokkos library. We presentmore » performance results for the Aeras global atmosphere dynamical core module in Albany. Finally, numerical experiments show that our single code implementation gives reasonable performance across three multicore/many-core architectures: NVIDIA General Processing Units (GPU’s), Intel Xeon Phis, and multicore CPUs.« less

Toward performance portability of the Albany finite element analysis code using the Kokkos library

DOE PAGES

Demeshko, Irina; Watkins, Jerry; Tezaur, Irina K.; ...

2018-02-05

Performance portability on heterogeneous high-performance computing (HPC) systems is a major challenge faced today by code developers: parallel code needs to be executed correctly as well as with high performance on machines with different architectures, operating systems, and software libraries. The finite element method (FEM) is a popular and flexible method for discretizing partial differential equations arising in a wide variety of scientific, engineering, and industrial applications that require HPC. This paper presents some preliminary results pertaining to our development of a performance portable implementation of the FEM-based Albany code. Performance portability is achieved using the Kokkos library. We presentmore » performance results for the Aeras global atmosphere dynamical core module in Albany. Finally, numerical experiments show that our single code implementation gives reasonable performance across three multicore/many-core architectures: NVIDIA General Processing Units (GPU’s), Intel Xeon Phis, and multicore CPUs.« less

Structured grid technology to enable flow simulation in an integrated system environment

NASA Astrophysics Data System (ADS)

Remotigue, Michael Gerard

An application-driven Computational Fluid Dynamics (CFD) environment needs flexible and general tools to effectively solve complex problems in a timely manner. In addition, reusable, portable, and maintainable specialized libraries will aid in rapidly developing integrated systems or procedures. The presented structured grid technology enables the flow simulation for complex geometries by addressing grid generation, grid decomposition/solver setup, solution, and interpretation. Grid generation is accomplished with the graphical, arbitrarily-connected, multi-block structured grid generation software system (GUM-B) developed and presented here. GUM-B is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a solid-modeling data structure that utilizes a structured grid generation library and a geometric library based on Non-Uniform Rational B-Splines (NURBS). A presented modification of the solid-modeling data structure provides the capability for arbitrarily-connected regions between the grid blocks. The presented grid generation library provides algorithms that are reliable and accurate. GUM-B has been utilized to generate numerous structured grids for complex geometries in hydrodynamics, propulsors, and aerodynamics. The versatility of the libraries that compose GUM-B is also displayed in a prototype to automatically regenerate a grid for a free-surface solution. Grid decomposition and solver setup is accomplished with the graphical grid manipulation and repartition software system (GUMBO) developed and presented here. GUMBO is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a structured grid-tools library. The described functions within the grid-tools library reduce the possibility of human error during decomposition and setup for the numerical solver by accounting for boundary conditions and connectivity. GUMBO is linked with a flow solver interface, to the parallel UNCLE code, to provide load balancing tools and solver setup. Weeks of boundary condition and connectivity specification and validation has been reduced to hours. The UNCLE flow solver is utilized for the solution of the flow field. To accelerate convergence toward a quick engineering answer, a full multigrid (FMG) approach coupled with UNCLE, which is a full approximation scheme (FAS), is presented. The prolongation operators used in the FMG-FAS method are compared. The procedure is demonstrated on a marine propeller in incompressible flow. Interpretation of the solution is accomplished by vortex feature detection. Regions of "Intrinsic Swirl" are located by interrogating the velocity gradient tensor for complex eigenvalues. The "Intrinsic Swirl" parameter is visualized on a solution of a marine propeller to determine if any vortical features are captured. The libraries and the structured grid technology presented herein are flexible and general enough to tackle a variety of complex applications. This technology has significantly enabled the capability of the ERC personnel to effectively calculate solutions for complex geometries.

Making it Easy to Construct Accurate Hydrological Models that Exploit High Performance Computers (Invited)

NASA Astrophysics Data System (ADS)

Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.

2013-12-01

This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.

Emerge - A Python environment for the modeling of subsurface transfers

NASA Astrophysics Data System (ADS)

Lopez, S.; Smai, F.; Sochala, P.

2014-12-01

The simulation of subsurface mass and energy transfers often relies on specific codes that were mainly developed using compiled languages which usually ensure computational efficiency at the expense of relatively long development times and relatively rigid software. Even if a very detailed, possibly graphical, user-interface is developed the core numerical aspects are rarely accessible and the smallest modification will always need a compilation step. Thus, user-defined physical laws or alternative numerical schemes may be relatively difficult to use. Over the last decade, Python has emerged as a popular and widely used language in the scientific community. There already exist several libraries for the pre and post-treatment of input and output files for reservoir simulators (e.g. pytough). Development times in Python are considerably reduced compared to compiled languages, and programs can be easily interfaced with libraries written in compiled languages with several comprehensive numerical libraries that provide sequential and parallel solvers (e.g. PETSc, Trilinos…). The core objective of the Emerge project is to explore the possibility to develop a modeling environment in full Python. Consequently, we are developing an open python package with the classes/objects necessary to express, discretize and solve the physical problems encountered in the modeling of subsurface transfers. We heavily relied on Python to have a convenient and concise way of manipulating potentially complex concepts with a few lines of code and a high level of abstraction. Our result aims to be a friendly numerical environment targeting both numerical engineers and physicist or geoscientists with the possibility to quickly specify and handle geometries, arbitrary meshes, spatially or temporally varying properties, PDE formulations, boundary conditions…

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

Software Quality Assurance and Verification for the MPACT Library Generation Process

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

Liu, Yuxuan; Williams, Mark L.; Wiarda, Dorothea

This report fulfills the requirements for the Consortium for the Advanced Simulation of Light-Water Reactors (CASL) milestone L2:RTM.P14.02, “SQA and Verification for MPACT Library Generation,” by documenting the current status of the software quality, verification, and acceptance testing of nuclear data libraries for MPACT. It provides a brief overview of the library generation process, from general-purpose evaluated nuclear data files (ENDF/B) to a problem-dependent cross section library for modeling of light-water reactors (LWRs). The software quality assurance (SQA) programs associated with each of the software used to generate the nuclear data libraries are discussed; specific tests within the SCALE/AMPX andmore » VERA/XSTools repositories are described. The methods and associated tests to verify the quality of the library during the generation process are described in detail. The library generation process has been automated to a degree to (1) ensure that it can be run without user intervention and (2) to ensure that the library can be reproduced. Finally, the acceptance testing process that will be performed by representatives from the Radiation Transport Methods (RTM) Focus Area prior to the production library’s release is described in detail.« less

Update on PISCES

NASA Technical Reports Server (NTRS)

Pearson, Don; Hamm, Dustin; Kubena, Brian; Weaver, Jonathan K.

2010-01-01

An updated version of the Platform Independent Software Components for the Exploration of Space (PISCES) software library is available. A previous version was reported in Library for Developing Spacecraft-Mission-Planning Software (MSC-22983), NASA Tech Briefs, Vol. 25, No. 7 (July 2001), page 52. To recapitulate: This software provides for Web-based, collaborative development of computer programs for planning trajectories and trajectory- related aspects of spacecraft-mission design. The library was built using state-of-the-art object-oriented concepts and software-development methodologies. The components of PISCES include Java-language application programs arranged in a hierarchy of classes that facilitates the reuse of the components. As its full name suggests, the PISCES library affords platform-independence: The Java language makes it possible to use the classes and application programs with a Java virtual machine, which is available in most Web-browser programs. Another advantage is expandability: Object orientation facilitates expansion of the library through creation of a new class. Improvements in the library since the previous version include development of orbital-maneuver- planning and rendezvous-launch-window application programs, enhancement of capabilities for propagation of orbits, and development of a desktop user interface.

GNU Data Language (GDL) - a free and open-source implementation of IDL

NASA Astrophysics Data System (ADS)

Arabas, Sylwester; Schellens, Marc; Coulais, Alain; Gales, Joel; Messmer, Peter

2010-05-01

GNU Data Language (GDL) is developed with the aim of providing an open-source drop-in replacement for the ITTVIS's Interactive Data Language (IDL). It is free software developed by an international team of volunteers led by Marc Schellens - the project's founder (a list of contributors is available on the project's website). The development is hosted on SourceForge where GDL continuously ranks in the 99th percentile of most active projects. GDL with its library routines is designed as a tool for numerical data analysis and visualisation. As its proprietary counterparts (IDL and PV-WAVE), GDL is used particularly in geosciences and astronomy. GDL is dynamically-typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, interaction with host OS and data input/output. GDL supports several data formats such as netCDF, HDF4, HDF5, GRIB, PNG, TIFF, DICOM, etc. Graphical output is handled by X11, PostScript, SVG or z-buffer terminals, the last one allowing output to be saved in a variety of raster graphics formats. GDL is an incremental compiler with integrated debugging facilities. It is written in C++ using the ANTLR language-recognition framework. Most of the library routines are implemented as interfaces to open-source packages such as GNU Scientific Library, PLPlot, FFTW, ImageMagick, and others. GDL features a Python bridge (Python code can be called from GDL; GDL can be compiled as a Python module). Extensions to GDL can be written in C++, GDL, and Python. A number of open software libraries written in IDL, such as the NASA Astronomy Library, MPFIT, CMSVLIB and TeXtoIDL are fully or partially functional under GDL. Packaged versions of GDL are available for several Linux distributions and Mac OS X. The source code compiles on some other UNIX systems, including BSD and OpenSolaris. The presentation will cover the current status of the project, the key accomplishments, and the weaknesses - areas where contributions and users' feedback are welcome! While still being in beta-stage of development, GDL proved to be a useful tool for classroom work on data analysis. Its usage for teaching meteorological-data processing at the University of Warsaw will serve as an example.

NA-42 TI Shared Software Component Library FY2011 Final Report

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

Knudson, Christa K.; Rutz, Frederick C.; Dorow, Kevin E.

The NA-42 TI program initiated an effort in FY2010 to standardize its software development efforts with the long term goal of migrating toward a software management approach that will allow for the sharing and reuse of code developed within the TI program, improve integration, ensure a level of software documentation, and reduce development costs. The Pacific Northwest National Laboratory (PNNL) has been tasked with two activities that support this mission. PNNL has been tasked with the identification, selection, and implementation of a Shared Software Component Library. The intent of the library is to provide a common repository that is accessiblemore » by all authorized NA-42 software development teams. The repository facilitates software reuse through a searchable and easy to use web based interface. As software is submitted to the repository, the component registration process captures meta-data and provides version control for compiled libraries, documentation, and source code. This meta-data is then available for retrieval and review as part of library search results. In FY2010, PNNL and staff from the Remote Sensing Laboratory (RSL) teamed up to develop a software application with the goal of replacing the aging Aerial Measuring System (AMS). The application under development includes an Advanced Visualization and Integration of Data (AVID) framework and associated AMS modules. Throughout development, PNNL and RSL have utilized a common AMS code repository for collaborative code development. The AMS repository is hosted by PNNL, is restricted to the project development team, is accessed via two different geographic locations and continues to be used. The knowledge gained from the collaboration and hosting of this repository in conjunction with PNNL software development and systems engineering capabilities were used in the selection of a package to be used in the implementation of the software component library on behalf of NA-42 TI. The second task managed by PNNL is the development and continued maintenance of the NA-42 TI Software Development Questionnaire. This questionnaire is intended to help software development teams working under NA-42 TI in documenting their development activities. When sufficiently completed, the questionnaire illustrates that the software development activities recorded incorporate significant aspects of the software engineering lifecycle. The questionnaire template is updated as comments are received from NA-42 and/or its development teams and revised versions distributed to those using the questionnaire. PNNL also maintains a list of questionnaire recipients. The blank questionnaire template, the AVID and AMS software being developed, and the completed AVID AMS specific questionnaire are being used as the initial content to be established in the TI Component Library. This report summarizes the approach taken to identify requirements, search for and evaluate technologies, and the approach taken for installation of the software needed to host the component library. Additionally, it defines the process by which users request access for the contribution and retrieval of library content.« less

Microcomputer Software for Libraries: A Survey.

ERIC Educational Resources Information Center

Nolan, Jeanne M.

1983-01-01

Reports on findings of research done by Nolan Information Management Services concerning availability of microcomputer software for libraries. Highlights include software categories (specific, generic-database management programs, original); number of programs available in 1982 for 12 applications; projections for 1983; and future software…

Utilizing Visual Effects Software for Efficient and Flexible Isostatic Adjustment Modelling

NASA Astrophysics Data System (ADS)

Meldgaard, A.; Nielsen, L.; Iaffaldano, G.

2017-12-01

The isostatic adjustment signal generated by transient ice sheet loading is an important indicator of past ice sheet extent and the rheological constitution of the interior of the Earth. Finite element modelling has proved to be a very useful tool in these studies. We present a simple numerical model for 3D visco elastic Earth deformation and a new approach to the design of such models utilizing visual effects software designed for the film and game industry. The software package Houdini offers an assortment of optimized tools and libraries which greatly facilitate the creation of efficient numerical algorithms. In particular, we make use of Houdini's procedural work flow, the SIMD programming language VEX, Houdini's sparse matrix creation and inversion libraries, an inbuilt tetrahedralizer for grid creation, and the user interface, which facilitates effortless manipulation of 3D geometry. We mitigate many of the time consuming steps associated with the authoring of efficient algorithms from scratch while still keeping the flexibility that may be lost with the use of commercial dedicated finite element programs. We test the efficiency of the algorithm by comparing simulation times with off-the-shelf solutions from the Abaqus software package. The algorithm is tailored for the study of local isostatic adjustment patterns, in close vicinity to present ice sheet margins. In particular, we wish to examine possible causes for the considerable spatial differences in the uplift magnitude which are apparent from field observations in these areas. Such features, with spatial scales of tens of kilometres, are not resolvable with current global isostatic adjustment models, and may require the inclusion of local topographic features. We use the presented algorithm to study a near field area where field observations are abundant, namely, Disko Bay in West Greenland with the intention of constraining Earth parameters and ice thickness. In addition, we assess how local topographic features may influence the differential isostatic uplift in the area.

Evolving the Reuse Process at the Flight Dynamics Division (FDD) Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Condon, S.; Seaman, C.; Basili, Victor; Kraft, S.; Kontio, J.; Kim, Y.

1996-01-01

This paper presents the interim results from the Software Engineering Laboratory's (SEL) Reuse Study. The team conducting this study has, over the past few months, been studying the Generalized Support Software (GSS) domain asset library and architecture, and the various processes associated with it. In particular, we have characterized the process used to configure GSS-based attitude ground support systems (AGSS) to support satellite missions at NASA's Goddard Space Flight Center. To do this, we built detailed models of the tasks involved, the people who perform these tasks, and the interdependencies and information flows among these people. These models were based on information gleaned from numerous interviews with people involved in this process at various levels. We also analyzed effort data in order to determine the cost savings in moving from actual development of AGSSs to support each mission (which was necessary before GSS was available) to configuring AGSS software from the domain asset library. While characterizing the GSS process, we became aware of several interesting factors which affect the successful continued use of GSS. Many of these issues fall under the subject of evolving technologies, which were not available at the inception of GSS, but are now. Some of these technologies could be incorporated into the GSS process, thus making the whole asset library more usable. Other technologies are being considered as an alternative to the GSS process altogether. In this paper, we outline some of issues we will be considering in our continued study of GSS and the impact of evolving technologies.

Development of the TACOM (Tank Automotive Command) Thermal Imaging Model (TTIM). Volume 1. Technical Guide and User’s Manual.

DTIC Science & Technology

1984-12-01

BLOCK DATA Default values for variables input by menus. LIBR Interface with frame I/O routines. SNSR Interface with sensor routines. ATMOS Interface with...Routines Included in Frame I/O Interface Routine Description LIBR Selects options for input or output to a data library. FRREAD Reads frame from file and/or...Layer", Journal of Applied Meteorology 20, pp. 242-249, March 1981. 15 L.J. Harding, Numerical Analysis and Applications Software Abstracts, Computing

Programming biological models in Python using PySB.

PubMed

Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

2013-01-01

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

Programming biological models in Python using PySB

PubMed Central

Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

2013-01-01

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis. PMID:23423320

A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Lou, John Z.; Norton, Charles D.; Cwik, Thomas A.

1999-01-01

The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.

Copyright: Know Your Electronic Rights!

ERIC Educational Resources Information Center

Valauskas, Edward J.

1992-01-01

Defines copyright and examines the interests of computer software publishers. Issues related to the rights of libraries in the circulation of software are discussed, including the fair use principle, software vendors' licensing agreements, and cooperation between libraries and vendors. An inset describes procedures for internal auditing of…

Teaching Reprint File Management: Basic Principles and Software Programs.

ERIC Educational Resources Information Center

Wood, Elizabeth H.

1989-01-01

Describes a workshop for teaching library users how to manage reprint files which was developed at the University of Southern California Norris Medical Library. Software programs designed for this purpose are suggested, and a sidebar lists software features to consider. (eight references) (MES)

Apples in the Apple Library--How One Library Took a Byte.

ERIC Educational Resources Information Center

Ertel, Monica

1983-01-01

Summarizes automation of a specialized library at Apple Computer, Inc., describing software packages chosen for the following functions: word processing/text editing; cataloging and circulation; reference; and in-house databases. Examples of each function and additional sources of information on software and equipment mentioned in the article are…

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

Describes the development of Bookshelf, a multi-user microcomputer system for small libraries that uses an integrated software package. The discussion covers the design parameters of the package, which were based on a survey of seven small libraries, and some characteristics of the software. (three notes with references) (CLB)

Advanced Data Format (ADF) Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Smith, Matthew; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial. Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: 1) The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its 1/0 software, which handles the actual reading and writing of data from and to external storage media; 2) The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; 3) The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and 4) The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The ADF is a generic database manager with minimal intrinsic capability. It was written for the purpose of storing large numerical datasets in an efficient, platform independent manner. To be effective, it must be used in conjunction with external agreements on how the data will be organized within the ADF database such defined by the SIDS. There are currently 34 user callable functions that comprise the ADF Core library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Building Interactive Simulations in Web Pages without Programming.

PubMed

Mailen Kootsey, J; McAuley, Grant; Bernal, Julie

2005-01-01

A software system is described for building interactive simulations and other numerical calculations in Web pages. The system is based on a new Java-based software architecture named NumberLinX (NLX) that isolates each function required to build the simulation so that a library of reusable objects could be assembled. The NLX objects are integrated into a commercial Web design program for coding-free page construction. The model description is entered through a wizard-like utility program that also functions as a model editor. The complete system permits very rapid construction of interactive simulations without coding. A wide range of applications are possible with the system beyond interactive calculations, including remote data collection and processing and collaboration over a network.

One library's experience with review and selection of chat software for reference.

PubMed

Behm, Leslie M

2003-01-01

When Michigan State University (MSU) Libraries decided to make the foray into virtual reference, the first thing that needed to be done was to decide on the software to use. This article discusses the process used including the items considered essential (deal-breakers) for software to make the first cut, what other features needed to be included, and what features would be useful but were not critical. A literature review of some useful current articles on virtual reference is included. The vendor and software ultimately selected was not one of the original vendors; how MSU Libraries was able to evaluate and select Docutek is presented. A matrix for software comparison is included in the appendix.

Public Access to Digital Material; A Call to Researchers: Digital Libraries Need Collaboration across Disciplines; Greenstone: Open-Source Digital Library Software; Retrieval Issues for the Colorado Digitization Project's Heritage Database; Report on the 5th European Conference on Digital Libraries, ECDL 2001; Report on the First Joint Conference on Digital Libraries.

ERIC Educational Resources Information Center

Kahle, Brewster; Prelinger, Rick; Jackson, Mary E.; Boyack, Kevin W.; Wylie, Brian N.; Davidson, George S.; Witten, Ian H.; Bainbridge, David; Boddie, Stefan J.; Garrison, William A.; Cunningham, Sally Jo; Borgman, Christine L.; Hessel, Heather

2001-01-01

These six articles discuss various issues relating to digital libraries. Highlights include public access to digital materials; intellectual property concerns; the need for collaboration across disciplines; Greenstone software for construction and presentation of digital information collections; the Colorado Digitization Project; and conferences…

GeoTess: A generalized Earth model software utility

DOE PAGES

Ballard, Sanford; Hipp, James; Kraus, Brian; ...

2016-03-23

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

U.S. Tsunami Information technology (TIM) Modernization:Developing a Maintainable and Extensible Open Source Earthquake and Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Lisowski, S.; Baker, B.; Hagerty, M.; Lomax, A.; Leifer, J. M.; Thies, D. A.; Schnackenberg, A.; Barrows, J.

2015-12-01

Tsunami Information technology Modernization (TIM) is a National Oceanic and Atmospheric Administration (NOAA) project to update and standardize the earthquake and tsunami monitoring systems currently employed at the U.S. Tsunami Warning Centers in Ewa Beach, Hawaii (PTWC) and Palmer, Alaska (NTWC). While this project was funded by NOAA to solve a specific problem, the requirements that the delivered system be both open source and easily maintainable have resulted in the creation of a variety of open source (OS) software packages. The open source software is now complete and this is a presentation of the OS Software that has been funded by NOAA for benefit of the entire seismic community. The design architecture comprises three distinct components: (1) The user interface, (2) The real-time data acquisition and processing system and (3) The scientific algorithm library. The system follows a modular design with loose coupling between components. We now identify the major project constituents. The user interface, CAVE, is written in Java and is compatible with the existing National Weather Service (NWS) open source graphical system AWIPS. The selected real-time seismic acquisition and processing system is open source SeisComp3 (sc3). The seismic library (libseismic) contains numerous custom written and wrapped open source seismic algorithms (e.g., ML/mb/Ms/Mwp, mantle magnitude (Mm), w-phase moment tensor, bodywave moment tensor, finite-fault inversion, array processing). The seismic library is organized in a way (function naming and usage) that will be familiar to users of Matlab. The seismic library extends sc3 so that it can be called by the real-time system, but it can also be driven and tested outside of sc3, for example, by ObsPy or Earthworm. To unify the three principal components we have developed a flexible and lightweight communication layer called SeismoEdex.

Designing a Decision Support System (DSS) for Academic Library Managers Using Preprogrammed Application Software on a Microcomputer.

ERIC Educational Resources Information Center

McDonald, Joseph

1986-01-01

Focusing on management decisions in academic libraries, this article compares management information systems (MIS) with decision support systems (DSS) and discusses the decision-making process, information needs of library managers, sources of data, reasons for choosing microcomputer, preprogrammed application software, prototyping a system, and…

Digital Preservation in Open-Source Digital Library Software

ERIC Educational Resources Information Center

Madalli, Devika P.; Barve, Sunita; Amin, Saiful

2012-01-01

Digital archives and digital library projects are being initiated all over the world for materials of different formats and domains. To organize, store, and retrieve digital content, many libraries as well as archiving centers are using either proprietary or open-source software. While it is accepted that print media can survive for centuries with…

The Elusive Cost of Library Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Software pricing is not a straightforward issue, since each procurement involves a special business arrangement between a library and its chosen vendor. The author thinks that it is reasonable to scale the cost of a product to such factors as the size of the library, the complexity of the installation, the number of simultaneous users, or the…

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

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

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

Tiger LDRD final report

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

Steich, D J; Brugger, S T; Kallman, J S

2000-02-01

This final report describes our efforts on the Three-Dimensional Massively Parallel CEM Technologies LDRD project (97-ERD-009). Significant need exists for more advanced time domain computational electromagnetics modeling. Bookkeeping details and modifying inflexible software constitute a vast majority of the effort required to address such needs. The required effort escalates rapidly as problem complexity increases. For example, hybrid meshes requiring hybrid numerics on massively parallel platforms (MPPs). This project attempts to alleviate the above limitations by investigating flexible abstractions for these numerical algorithms on MPPs using object-oriented methods, providing a programming environment insulating physics from bookkeeping. The three major design iterationsmore » during the project, known as TIGER-I to TIGER-III, are discussed. Each version of TIGER is briefly discussed along with lessons learned during the development and implementation. An Application Programming Interface (API) of the object-oriented interface for Tiger-III is included in three appendices. The three appendices contain the Utilities, Entity-Attribute, and Mesh libraries developed during the project. The API libraries represent a snapshot of our latest attempt at insulated the physics from the bookkeeping.« less

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

CADNA: a library for estimating round-off error propagation

NASA Astrophysics Data System (ADS)

Jézéquel, Fabienne; Chesneaux, Jean-Marie

2008-06-01

The CADNA library enables one to estimate round-off error propagation using a probabilistic approach. With CADNA the numerical quality of any simulation program can be controlled. Furthermore by detecting all the instabilities which may occur at run time, a numerical debugging of the user code can be performed. CADNA provides new numerical types on which round-off errors can be estimated. Slight modifications are required to control a code with CADNA, mainly changes in variable declarations, input and output. This paper describes the features of the CADNA library and shows how to interpret the information it provides concerning round-off error propagation in a code. Program summaryProgram title:CADNA Catalogue identifier:AEAT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAT_v1_0.html Program obtainable from:CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:53 420 No. of bytes in distributed program, including test data, etc.:566 495 Distribution format:tar.gz Programming language:Fortran Computer:PC running LINUX with an i686 or an ia64 processor, UNIX workstations including SUN, IBM Operating system:LINUX, UNIX Classification:4.14, 6.5, 20 Nature of problem:A simulation program which uses floating-point arithmetic generates round-off errors, due to the rounding performed at each assignment and at each arithmetic operation. Round-off error propagation may invalidate the result of a program. The CADNA library enables one to estimate round-off error propagation in any simulation program and to detect all numerical instabilities that may occur at run time. Solution method:The CADNA library [1] implements Discrete Stochastic Arithmetic [2-4] which is based on a probabilistic model of round-off errors. The program is run several times with a random rounding mode generating different results each time. From this set of results, CADNA estimates the number of exact significant digits in the result that would have been computed with standard floating-point arithmetic. Restrictions:CADNA requires a Fortran 90 (or newer) compiler. In the program to be linked with the CADNA library, round-off errors on complex variables cannot be estimated. Furthermore array functions such as product or sum must not be used. Only the arithmetic operators and the abs, min, max and sqrt functions can be used for arrays. Running time:The version of a code which uses CADNA runs at least three times slower than its floating-point version. This cost depends on the computer architecture and can be higher if the detection of numerical instabilities is enabled. In this case, the cost may be related to the number of instabilities detected. References:The CADNA library, URL address: http://www.lip6.fr/cadna. J.-M. Chesneaux, L'arithmétique Stochastique et le Logiciel CADNA, Habilitation á diriger des recherches, Université Pierre et Marie Curie, Paris, 1995. J. Vignes, A stochastic arithmetic for reliable scientific computation, Math. Comput. Simulation 35 (1993) 233-261. J. Vignes, Discrete stochastic arithmetic for validating results of numerical software, Numer. Algorithms 37 (2004) 377-390.

DOCLIB: a software library for document processing

NASA Astrophysics Data System (ADS)

Jaeger, Stefan; Zhu, Guangyu; Doermann, David; Chen, Kevin; Sampat, Summit

2006-01-01

Most researchers would agree that research in the field of document processing can benefit tremendously from a common software library through which institutions are able to develop and share research-related software and applications across academic, business, and government domains. However, despite several attempts in the past, the research community still lacks a widely-accepted standard software library for document processing. This paper describes a new library called DOCLIB, which tries to overcome the drawbacks of earlier approaches. Many of DOCLIB's features are unique either in themselves or in their combination with others, e.g. the factory concept for support of different image types, the juxtaposition of image data and metadata, or the add-on mechanism. We cherish the hope that DOCLIB serves the needs of researchers better than previous approaches and will readily be accepted by a larger group of scientists.

The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

NASA Astrophysics Data System (ADS)

Oliveira, Micael

The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

Component Technology for High-Performance Scientific Simulation Software

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

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

INTERIM -- Starlink Software Environment

NASA Astrophysics Data System (ADS)

Pearce, Dave; Pavelin, Cliff; Lawden, M. D.

Early versions of this paper were based on a number of other papers produced at a very early stage of the Starlink project. They contained a description of a specific implementation of a subroutine library, speculations on the desirable attributes of a software environment, and future development plans. They reflected the experimental nature of the Starlink software environment at that time. Since then, the situation has changed. The implemented subroutine library, INTERIM_DIR:INTERIM.OLB, is now a well established and widely used piece of software. A completely new Starlink software environment (ADAM) has been developed and distributed. Thus the library released in 1980 as `STARLINK' and now called `INTERIM' has reached the end of its development cycle and is now frozen in its current state, apart from bug corrections. This paper has, therefore, been completely rewritten and restructured to reflect the new situation. Its aim is to describe the facilities of the INTERIM subroutine library as clearly and concisely as possible. It avoids speculation, discussion of design decisions, and announcements of future plans.

Software Library for Bruker TopSpin NMR Data Files

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

A software library for parsing and manipulating frequency-domain data files that have been processed using the Bruker TopSpin NMR software package. In the context of NMR, the term "processed" indicates that the end-user of the Bruker TopSpin NMR software package has (a) Fourier transformed the raw, time-domain data (the Free Induction Decay) into the frequency-domain and (b) has extracted the list of NMR peaks.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Student project of optical system analysis API-library development

NASA Astrophysics Data System (ADS)

Ivanova, Tatiana; Zhukova, Tatiana; Dantcaranov, Ruslan; Romanova, Maria; Zhadin, Alexander; Ivanov, Vyacheslav; Kalinkina, Olga

2017-08-01

In the paper API-library software developed by students of Applied and Computer Optics Department (ITMO University) for optical system design is presented. The library performs paraxial and real ray tracing, calculates 3d order (Seidel) aberration and real ray aberration of axis and non-axis beams (wave, lateral, longitudinal, coma, distortion etc.) and finally, approximate wave aberration by Zernike polynomials. Real aperture can be calculated by considering of real rays tracing failure on each surface. So far we assume optical system is centered, with spherical or 2d order aspherical surfaces. Optical glasses can be set directly by refraction index or by dispersion coefficients. The library can be used for education or research purposes in optical system design area. It provides ready to use software functions for optical system simulation and analysis that developer can simply plug into their software development for different purposes, for example for some specific synthesis tasks or investigation of new optimization modes. In the paper we present an example of using the library for development of cemented doublet synthesis software based on Slusarev's methodology. The library is used in optical system optimization recipes course for deep studying of optimization model and its application for optical system design. Development of such software is an excellent experience for students and help to understanding optical image modeling and quality analysis. This development is organized as student group joint project. We try to organize it as a group in real research and development project, so each student has his own role in the project and then use whole library functionality in his own master or bachelor thesis. Working in such group gives students useful experience and opportunity to work as research and development engineer of scientific software in the future.

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

TIGER: A graphically interactive grid system for turbomachinery applications

NASA Technical Reports Server (NTRS)

Shih, Ming-Hsin; Soni, Bharat K.

1992-01-01

Numerical grid generation algorithm associated with the flow field about turbomachinery geometries is presented. Graphical user interface is developed with FORMS Library to create an interactive, user-friendly working environment. This customized algorithm reduces the man-hours required to generate a grid associated with turbomachinery geometry, as compared to the use of general-purpose grid generation softwares. Bezier curves are utilized both interactively and automatically to accomplish grid line smoothness and orthogonality. Graphical User Interactions are provided in the algorithm, allowing the user to design and manipulate the grid lines with a mouse.

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.

PubMed

Koelmel, Jeremy P; Kroeger, Nicholas M; Ulmer, Candice Z; Bowden, John A; Patterson, Rainey E; Cochran, Jason A; Beecher, Christopher W W; Garrett, Timothy J; Yost, Richard A

2017-07-10

Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode. LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules.

Automation and Networking of Public Libraries in India Using the E-Granthalaya Software from the National Informatics Centre

ERIC Educational Resources Information Center

Matoria, Ram Kumar; Upadhyay, P. K.; Moni, Madaswamy

2007-01-01

Purpose: To describe the development of the library management system, e-Granthalaya, for public libraries in India. This is an initiative of the Indian government's National Informatics Centre (NIC). The paper outlines the challenges and the potential of a full-scale deployment of this software at a national level. Design/methodology/approach:…

A user's guide to Sandia's latin hypercube sampling software : LHS UNIX library/standalone version.

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

Swiler, Laura Painton; Wyss, Gregory Dane

2004-07-01

This document is a reference guide for the UNIX Library/Standalone version of the Latin Hypercube Sampling Software. This software has been developed to generate Latin hypercube multivariate samples. This version runs on Linux or UNIX platforms. This manual covers the use of the LHS code in a UNIX environment, run either as a standalone program or as a callable library. The underlying code in the UNIX Library/Standalone version of LHS is almost identical to the updated Windows version of LHS released in 1998 (SAND98-0210). However, some modifications were made to customize it for a UNIX environment and as a librarymore » that is called from the DAKOTA environment. This manual covers the use of the LHS code as a library and in the standalone mode under UNIX.« less

Space Missions: Long Term Preservation of IDL-based Software using GDL

NASA Astrophysics Data System (ADS)

Coulais, A.; Schellens, M.; Arabas, S.; Lenoir, M.; Noreskal, L.; Erard, S.

2012-09-01

GNU Data Language (GDL) is a free software clone of IDL, an interactive language widely used in Astronomy and space missions since decades. Proprietary status, license restrictions, price, sustainability and continuity of support for particular platforms are recurrent concerns in the Astronomy community, especially concerning space missions, which require long-term support. In this paper, we describe the key features of GDL and the main achievements from recent development work. We illustrate the maturity of GDL by presenting two examples of application: reading spectral cubes in PDS format and use of the HEALPix library. These examples support the main argument of the paper: that GDL has reached a level of maturity and usability ensuring long term preservation of analysis capabilities for numerous ground experiments and spaces missions based on IDL.

A Language for Specifying Compiler Optimizations for Generic Software

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

Willcock, Jeremiah J.

2007-01-01

Compiler optimization is important to software performance, and modern processor architectures make optimization even more critical. However, many modern software applications use libraries providing high levels of abstraction. Such libraries often hinder effective optimization — the libraries are difficult to analyze using current compiler technology. For example, high-level libraries often use dynamic memory allocation and indirectly expressed control structures, such as iteratorbased loops. Programs using these libraries often cannot achieve an optimal level of performance. On the other hand, software libraries have also been recognized as potentially aiding in program optimization. One proposed implementation of library-based optimization is to allowmore » the library author, or a library user, to define custom analyses and optimizations. Only limited systems have been created to take advantage of this potential, however. One problem in creating a framework for defining new optimizations and analyses is how users are to specify them: implementing them by hand inside a compiler is difficult and prone to errors. Thus, a domain-specific language for librarybased compiler optimizations would be beneficial. Many optimization specification languages have appeared in the literature, but they tend to be either limited in power or unnecessarily difficult to use. Therefore, I have designed, implemented, and evaluated the Pavilion language for specifying program analyses and optimizations, designed for library authors and users. These analyses and optimizations can be based on the implementation of a particular library, its use in a specific program, or on the properties of a broad range of types, expressed through concepts. The new system is intended to provide a high level of expressiveness, even though the intended users are unlikely to be compiler experts.« less

Building a Library Web Server on a Budget.

ERIC Educational Resources Information Center

Orr, Giles

1998-01-01

Presents a method for libraries with limited budgets to create reliable Web servers with existing hardware and free software available via the Internet. Discusses staff, hardware and software requirements, and security; outlines the assembly process. (PEN)

Software Framework for Development of Web-GIS Systems for Analysis of Georeferenced Geophysical Data

NASA Astrophysics Data System (ADS)

Okladnikov, I.; Gordov, E. P.; Titov, A. G.

2011-12-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, remote sensing products, etc.) are currently actively used in numerous applications including modeling, interpretation and forecast of climatic and ecosystem changes for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset at present studies in the area of climate and environmental change require a special software support. A dedicated software framework for rapid development of providing such support information-computational systems based on Web-GIS technologies has been created. The software framework consists of 3 basic parts: computational kernel developed using ITTVIS Interactive Data Language (IDL), a set of PHP-controllers run within specialized web portal, and JavaScript class library for development of typical components of web mapping application graphical user interface (GUI) based on AJAX technology. Computational kernel comprise of number of modules for datasets access, mathematical and statistical data analysis and visualization of results. Specialized web-portal consists of web-server Apache, complying OGC standards Geoserver software which is used as a base for presenting cartographical information over the Web, and a set of PHP-controllers implementing web-mapping application logic and governing computational kernel. JavaScript library aiming at graphical user interface development is based on GeoExt library combining ExtJS Framework and OpenLayers software. Based on the software framework an information-computational system for complex analysis of large georeferenced data archives was developed. Structured environmental datasets available for processing now include two editions of NCEP/NCAR Reanalysis, JMA/CRIEPI JRA-25 Reanalysis, ECMWF ERA-40 Reanalysis, ECMWF ERA Interim Reanalysis, MRI/JMA APHRODITE's Water Resources Project Reanalysis, meteorological observational data for the territory of the former USSR for the 20th century, and others. Current version of the system is already involved into a scientific research process. Particularly, recently the system was successfully used for analysis of Siberia climate changes and its impact in the region. The software framework presented allows rapid development of Web-GIS systems for geophysical data analysis thus providing specialists involved into multidisciplinary research projects with reliable and practical instruments for complex analysis of climate and ecosystems changes on global and regional scales. This work is partially supported by RFBR grants #10-07-00547, #11-05-01190, and SB RAS projects 4.31.1.5, 4.31.2.7, 4, 8, 9, 50 and 66.

Numerical ‘health check’ for scientific codes: the CADNA approach

NASA Astrophysics Data System (ADS)

Scott, N. S.; Jézéquel, F.; Denis, C.; Chesneaux, J.-M.

2007-04-01

Scientific computation has unavoidable approximations built into its very fabric. One important source of error that is difficult to detect and control is round-off error propagation which originates from the use of finite precision arithmetic. We propose that there is a need to perform regular numerical 'health checks' on scientific codes in order to detect the cancerous effect of round-off error propagation. This is particularly important in scientific codes that are built on legacy software. We advocate the use of the CADNA library as a suitable numerical screening tool. We present a case study to illustrate the practical use of CADNA in scientific codes that are of interest to the Computer Physics Communications readership. In doing so we hope to stimulate a greater awareness of round-off error propagation and present a practical means by which it can be analyzed and managed.

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

Ballard, Sanford; Hipp, James; Kraus, Brian

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

A review of some problems in global-local stress analysis

NASA Technical Reports Server (NTRS)

Nelson, Richard B.

1989-01-01

The various types of local-global finite-element problems point out the need to develop a new generation of software. First, this new software needs to have a complete analysis capability, encompassing linear and nonlinear analysis of 1-, 2-, and 3-dimensional finite-element models, as well as mixed dimensional models. The software must be capable of treating static and dynamic (vibration and transient response) problems, including the stability effects of initial stress, and the software should be able to treat both elastic and elasto-plastic materials. The software should carry a set of optional diagnostics to assist the program user during model generation in order to help avoid obvious structural modeling errors. In addition, the program software should be well documented so the user has a complete technical reference for each type of element contained in the program library, including information on such topics as the type of numerical integration, use of underintegration, and inclusion of incompatible modes, etc. Some packaged information should also be available to assist the user in building mixed-dimensional models. An important advancement in finite-element software should be in the development of program modularity, so that the user can select from a menu various basic operations in matrix structural analysis.

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2015-09-30

libraries. Many levels of library interfaces—where some libraries are dynamically linked and some are provided in binary form only—significantly limit...software at build time. The opportunity: Our objective in this project is to substantially improve the performance, size, and robustness of binary ...executables by using static and dynamic binary program analysis techniques to perform whole-program optimization directly on compiled programs

National Software Reference Library (NSRL)

National Institute of Standards and Technology Data Gateway

National Software Reference Library (NSRL) (PC database for purchase)   A collaboration of the National Institute of Standards and Technology (NIST), the National Institute of Justice (NIJ), the Federal Bureau of Investigation (FBI), the Defense Computer Forensics Laboratory (DCFL),the U.S. Customs Service, software vendors, and state and local law enforement organizations, the NSRL is a tool to assist in fighting crime involving computers.

Moving Reference to the Web.

ERIC Educational Resources Information Center

McGlamery, Susan; Coffman, Steve

2000-01-01

Explores the possibility of using Web contact center software to offer reference assistance to remote users. Discusses a project by the Metropolitan Cooperative Library System/Santiago Library System consortium to test contact center software and to develop a virtual reference network. (Author/LRW)

Flightspeed Integral Image Analysis Toolkit

NASA Technical Reports Server (NTRS)

Thompson, David R.

2009-01-01

The Flightspeed Integral Image Analysis Toolkit (FIIAT) is a C library that provides image analysis functions in a single, portable package. It provides basic low-level filtering, texture analysis, and subwindow descriptor for applications dealing with image interpretation and object recognition. Designed with spaceflight in mind, it addresses: Ease of integration (minimal external dependencies) Fast, real-time operation using integer arithmetic where possible (useful for platforms lacking a dedicated floatingpoint processor) Written entirely in C (easily modified) Mostly static memory allocation 8-bit image data The basic goal of the FIIAT library is to compute meaningful numerical descriptors for images or rectangular image regions. These n-vectors can then be used directly for novelty detection or pattern recognition, or as a feature space for higher-level pattern recognition tasks. The library provides routines for leveraging training data to derive descriptors that are most useful for a specific data set. Its runtime algorithms exploit a structure known as the "integral image." This is a caching method that permits fast summation of values within rectangular regions of an image. This integral frame facilitates a wide range of fast image-processing functions. This toolkit has applicability to a wide range of autonomous image analysis tasks in the space-flight domain, including novelty detection, object and scene classification, target detection for autonomous instrument placement, and science analysis of geomorphology. It makes real-time texture and pattern recognition possible for platforms with severe computational restraints. The software provides an order of magnitude speed increase over alternative software libraries currently in use by the research community. FIIAT can commercially support intelligent video cameras used in intelligent surveillance. It is also useful for object recognition by robots or other autonomous vehicles

Libraries for Software Use on Peregrine | High-Performance Computing | NREL

Science.gov Websites

-specific libraries. Libraries List Name Description BLAS Basic Linear Algebra Subroutines, libraries only managing hierarchically structured data. LAPACK Standard Netlib offering for computational linear algebra

The U. S. Geological Survey, Digital Spectral Library: Version 1 (0.2 to 3.0um)

USGS Publications Warehouse

Clark, Roger N.; Swayze, Gregg A.; Gallagher, Andrea J.; King, Trude V.V.; Calvin, Wendy M.

1993-01-01

We have developed a digital reflectance spectral library, with management and spectral analysis software. The library includes 498 spectra of 444 samples (some samples include a series of grain sizes) measured from approximately 0.2 to 3.0 um . The spectral resolution (Full Width Half Maximum) of the reflectance data is <= 4 nm in the visible (0.2-0.8 um) and <= 10 nm in the NIR (0.8-2.35 um). All spectra were corrected to absolute reflectance using an NIST Halon standard. Library management software lets users search on parameters (e.g. chemical formulae, chemical analyses, purity of samples, mineral groups, etc.) as well as spectral features. Minerals from borate, carbonate, chloride, element, halide, hydroxide, nitrate, oxide, phosphate, sulfate, sulfide, sulfosalt, and the silicate (cyclosilicate, inosilicate, nesosilicate, phyllosilicate, sorosilicate, and tectosilicate) classes are represented. X-Ray and chemical analyses are tabulated for many of the entries, and all samples have been evaluated for spectral purity. The library also contains end and intermediate members for the olivine, garnet, scapolite, montmorillonite, muscovite, jarosite, and alunite solid-solution series. We have included representative spectra of H2O ice, kerogen, ammonium-bearing minerals, rare-earth oxides, desert varnish coatings, kaolinite crystallinity series, kaolinite-smectite series, zeolite series, and an extensive evaporite series. Because of the importance of vegetation to climate-change studies we have include 17 spectra of tree leaves, bushes, and grasses. The library and software are available as a series of U.S.G.S. Open File reports. PC user software is available to convert the binary data to ascii files (a separate U.S.G.S. open file report). Additionally, a binary data files are on line at the U.S.G.S. in Denver for anonymous ftp to users on the Internet. The library search software enables a user to search on documentation parameters as well as spectral features. The analysis system includes general spectral analysis routines, plotting packages, radiative transfer software for computing intimate mixtures, routines to derive optical constants from reflectance spectra, tools to analyze spectral features, and the capability to access imaging spectrometer data cubes for spectral analysis. Users may build customized libraries (at specific wavelengths and spectral resolution) for their own instruments using the library software. We are currently extending spectral coverage to 150 um. The libraries (original and convolved) will be made available in the future on a CD-ROM.

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Numeric Data Products and Services. SPEC Kit.

ERIC Educational Resources Information Center

Cook, Michael N., Comp.; Hernandez, John J., Comp.; Nicholson, Shawn, Comp.

2001-01-01

This SPEC (Systems and Procedures Exchange Center) Kit presents the results of a survey of Association of Research Libraries (ARL) member libraries. The survey addressed the following questions about numeric data (i.e., any information resource, print or non-print, with considerable numeric content) in academic libraries: (1) What relationships…

Towards a high performance geometry library for particle-detector simulations

DOE PAGES

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.; ...

2015-05-22

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Towards a high performance geometry library for particle-detector simulations

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

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Electronic Library: A TERI Experiment.

ERIC Educational Resources Information Center

Kar, Debal C.; Deb, Subrata; Kumar, Satish

2003-01-01

Discusses the development of Electronic Library at TERI (The Energy and Resources Institute, New Delhi). Highlights include: hardware and software used; the digital library/Virtual Electronic Library; directory of Internet journals; virtual reference resources; electronic collection/Physical Electronic Library; downloaded online full-length…

Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat.

PubMed

Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

2017-01-01

Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic. Here, we present Leaf-GP (Growth Phenotypes), an easy-to-use and open software application that can be executed on different computing platforms. To facilitate diverse scientific communities, we provide three software versions, including a graphic user interface (GUI) for personal computer (PC) users, a command-line interface for high-performance computer (HPC) users, and a well-commented interactive Jupyter Notebook (also known as the iPython Notebook) for computational biologists and computer scientists. The software is capable of extracting multiple growth traits automatically from large image datasets. We have utilised it in Arabidopsis thaliana and wheat ( Triticum aestivum ) growth studies at the Norwich Research Park (NRP, UK). By quantifying a number of growth phenotypes over time, we have identified diverse plant growth patterns between different genotypes under several experimental conditions. As Leaf-GP has been evaluated with noisy image series acquired by different imaging devices (e.g. smartphones and digital cameras) and still produced reliable biological outputs, we therefore believe that our automated analysis workflow and customised computer vision based feature extraction software implementation can facilitate a broader plant research community for their growth and development studies. Furthermore, because we implemented Leaf-GP based on open Python-based computer vision, image analysis and machine learning libraries, we believe that our software not only can contribute to biological research, but also demonstrates how to utilise existing open numeric and scientific libraries (e.g. Scikit-image, OpenCV, SciPy and Scikit-learn) to build sound plant phenomics analytic solutions, in a efficient and effective way. Leaf-GP is a sophisticated software application that provides three approaches to quantify growth phenotypes from large image series. We demonstrate its usefulness and high accuracy based on two biological applications: (1) the quantification of growth traits for Arabidopsis genotypes under two temperature conditions; and (2) measuring wheat growth in the glasshouse over time. The software is easy-to-use and cross-platform, which can be executed on Mac OS, Windows and HPC, with open Python-based scientific libraries preinstalled. Our work presents the advancement of how to integrate computer vision, image analysis, machine learning and software engineering in plant phenomics software implementation. To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases.

Monitoring of the orbital position of geostationary satellite by spatially separated reception of signals of digital satellite television

NASA Astrophysics Data System (ADS)

Kaliuzhnyi, M. P.; Bushuev, F. I.; Sibiriakova, Ye. S.; Shulga, O. V.; Shakun, L. S.; Bezrukovs, V.; Kulishenko, V. F.; Moskalenko, S. S.; Malynovsky, Ye. V.; Balagura, O. A.

2017-02-01

The results of the determination of the geostationary satellite "Eutelsat-13B" orbital position obtained during 2015-2016 years using European stations' network for reception of DVB-S signals from the satellite are presented. The network consists of five stations located in Ukraine and Latvia. The stations are equipped with a radio engineering complex developed by the RI "MAO". The measured parameter is a time difference of arrival (TDOA) of the DVB-S signals to the stations of the network. The errors of TDOA determination and satellite coordinates, obtained using a numerical model of satellite motion, are equal ±2.6 m and ±35 m respectively. Software implementation of the numerical model is taken from the free space dynamics library OREKIT.

Library Computing.

ERIC Educational Resources Information Center

Goodgion, Laurel; And Others

1986-01-01

Eight articles in special supplement to "Library Journal" and "School Library Journal" cover a computer program called "Byte into Books"; microcomputers and the small library; creating databases with students; online searching with a microcomputer; quality automation software; Meckler Publishing Company's…

Library Computing

ERIC Educational Resources Information Center

Library Computing, 1985

1985-01-01

Special supplement to "Library Journal" and "School Library Journal" covers topics of interest to school, public, academic, and special libraries planning for automation: microcomputer use, readings in automation, online searching, databases of microcomputer software, public access to microcomputers, circulation, creating a…

Managing Automation: A Process, Not a Project.

ERIC Educational Resources Information Center

Hoffmann, Ellen

1988-01-01

Discussion of issues in management of library automation includes: (1) hardware, including systems growth and contracts; (2) software changes, vendor relations, local systems, and microcomputer software; (3) item and authority databases; (4) automation and library staff, organizational structure, and managing change; and (5) environmental issues,…

ENCOMPASS: A SAGA based environment for the compositon of programs and specifications, appendix A

NASA Technical Reports Server (NTRS)

Terwilliger, Robert B.; Campbell, Roy H.

1985-01-01

ENCOMPASS is an example integrated software engineering environment being constructed by the SAGA project. ENCOMPASS supports the specification, design, construction and maintenance of efficient, validated, and verified programs in a modular programming language. The life cycle paradigm, schema of software configurations, and hierarchical library structure used by ENCOMPASS is presented. In ENCOMPASS, the software life cycle is viewed as a sequence of developments, each of which reuses components from the previous ones. Each development proceeds through the phases planning, requirements definition, validation, design, implementation, and system integration. The components in a software system are modeled as entities which have relationships between them. An entity may have different versions and different views of the same project are allowed. The simple entities supported by ENCOMPASS may be combined into modules which may be collected into projects. ENCOMPASS supports multiple programmers and projects using a hierarchical library system containing a workspace for each programmer; a project library for each project, and a global library common to all projects.

libmpdata++ 1.0: a library of parallel MPDATA solvers for systems of generalised transport equations

NASA Astrophysics Data System (ADS)

Jaruga, A.; Arabas, S.; Jarecka, D.; Pawlowska, H.; Smolarkiewicz, P. K.; Waruszewski, M.

2015-04-01

This paper accompanies the first release of libmpdata++, a C++ library implementing the multi-dimensional positive-definite advection transport algorithm (MPDATA) on regular structured grid. The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; a shallow-water system compared with analytical solution (originally derived for a 2-D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The design, based on the principle of separation of concerns, prioritises the user and developer productivity. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensional array containers, and is released as free/libre and open-source software.

libmpdata++ 0.1: a library of parallel MPDATA solvers for systems of generalised transport equations

NASA Astrophysics Data System (ADS)

Jaruga, A.; Arabas, S.; Jarecka, D.; Pawlowska, H.; Smolarkiewicz, P. K.; Waruszewski, M.

2014-11-01

This paper accompanies first release of libmpdata++, a C++ library implementing the Multidimensional Positive-Definite Advection Transport Algorithm (MPDATA). The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include: homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; shallow-water system compared with analytical solution (originally derived for a 2-D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The design, based on the principle of separation of concerns, prioritises the user and developer productivity. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensional array containers, and is released as free/libre and open-source software.

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectropscopy using IFEFFIT

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

Ravel, B.; Newville, M.; UC)

2010-07-20

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demandsmore » of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.« less

High-performance computing on GPUs for resistivity logging of oil and gas wells

NASA Astrophysics Data System (ADS)

Glinskikh, V.; Dudaev, A.; Nechaev, O.; Surodina, I.

2017-10-01

We developed and implemented into software an algorithm for high-performance simulation of electrical logs from oil and gas wells using high-performance heterogeneous computing. The numerical solution of the 2D forward problem is based on the finite-element method and the Cholesky decomposition for solving a system of linear algebraic equations (SLAE). Software implementations of the algorithm used the NVIDIA CUDA technology and computing libraries are made, allowing us to perform decomposition of SLAE and find its solution on central processor unit (CPU) and graphics processor unit (GPU). The calculation time is analyzed depending on the matrix size and number of its non-zero elements. We estimated the computing speed on CPU and GPU, including high-performance heterogeneous CPU-GPU computing. Using the developed algorithm, we simulated resistivity data in realistic models.

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

PubMed

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

2005-04-01

We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

JDiffraction: A GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields

NASA Astrophysics Data System (ADS)

Piedrahita-Quintero, Pablo; Trujillo, Carlos; Garcia-Sucerquia, Jorge

2017-05-01

JDiffraction, a GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields, is presented. Angular spectrum, Fresnel transform, and Fresnel-Bluestein transform are the numerical algorithms implemented in the methods and functions of the library to compute the scalar propagation of the complex wavefield. The functionality of the library is tested with the modeling of easy to forecast numerical experiments and also with the numerical reconstruction of a digitally recorded hologram. The performance of JDiffraction is contrasted with a library written for C++, showing great competitiveness in the apparently less complex environment of JAVA language. JDiffraction also includes JAVA easy-to-use methods and functions that take advantage of the computation power of the graphic processing units to accelerate the processing times of 2048×2048 pixel images up to 74 frames per second.

Resolution of singularities for multi-loop integrals

NASA Astrophysics Data System (ADS)

Bogner, Christian; Weinzierl, Stefan

2008-04-01

We report on a program for the numerical evaluation of divergent multi-loop integrals. The program is based on iterated sector decomposition. We improve the original algorithm of Binoth and Heinrich such that the program is guaranteed to terminate. The program can be used to compute numerically the Laurent expansion of divergent multi-loop integrals regulated by dimensional regularisation. The symbolic and the numerical steps of the algorithm are combined into one program. Program summaryProgram title: sector_decomposition Catalogue identifier: AEAG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 47 506 No. of bytes in distributed program, including test data, etc.: 328 485 Distribution format: tar.gz Programming language: C++ Computer: all Operating system: Unix RAM: Depending on the complexity of the problem Classification: 4.4 External routines: GiNaC, available from http://www.ginac.de, GNU scientific library, available from http://www.gnu.org/software/gsl Nature of problem: Computation of divergent multi-loop integrals. Solution method: Sector decomposition. Restrictions: Only limited by the available memory and CPU time. Running time: Depending on the complexity of the problem.

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

libFLASM: a software library for fixed-length approximate string matching.

PubMed

Ayad, Lorraine A K; Pissis, Solon P P; Retha, Ahmad

2016-11-10

Approximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time [Formula: see text] and space [Formula: see text] under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere. We present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds. Fixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei (OA)

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This presentation describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this presentation is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture.

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

PubMed

Yu, Jen-Shiang K; Yu, Chin-Hui

2002-01-01

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

Climbing the Mountain: The Americans with Disabilities Act and Libraries.

ERIC Educational Resources Information Center

Lenn, Katy

1993-01-01

Provides suggestions for academic libraries to comply with the Americans with Disabilities Act. Topics addressed are planning, including patron surveys; physical access to buildings; signage; library security systems; furniture; library services; staff development; telephone access; library acquisitions; and equipment and software. A sidebar lists…

Phantom-GRAPE: Numerical software library to accelerate collisionless N-body simulation with SIMD instruction set on x86 architecture

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru; Yoshikawa, Kohji; Nitadori, Keigo; Okamoto, Takashi

2013-02-01

We have developed a numerical software library for collisionless N-body simulations named "Phantom-GRAPE" which highly accelerates force calculations among particles by use of a new SIMD instruction set extension to the x86 architecture, Advanced Vector eXtensions (AVX), an enhanced version of the Streaming SIMD Extensions (SSE). In our library, not only the Newton's forces, but also central forces with an arbitrary shape f(r), which has a finite cutoff radius rcut (i.e. f(r)=0 at r>rcut), can be quickly computed. In computing such central forces with an arbitrary force shape f(r), we refer to a pre-calculated look-up table. We also present a new scheme to create the look-up table whose binning is optimal to keep good accuracy in computing forces and whose size is small enough to avoid cache misses. Using an Intel Core i7-2600 processor, we measure the performance of our library for both of the Newton's forces and the arbitrarily shaped central forces. In the case of Newton's forces, we achieve 2×109 interactions per second with one processor core (or 75 GFLOPS if we count 38 operations per interaction), which is 20 times higher than the performance of an implementation without any explicit use of SIMD instructions, and 2 times than that with the SSE instructions. With four processor cores, we obtain the performance of 8×109 interactions per second (or 300 GFLOPS). In the case of the arbitrarily shaped central forces, we can calculate 1×109 and 4×109 interactions per second with one and four processor cores, respectively. The performance with one processor core is 6 times and 2 times higher than those of the implementations without any use of SIMD instructions and with the SSE instructions. These performances depend only weakly on the number of particles, irrespective of the force shape. It is good contrast with the fact that the performance of force calculations accelerated by graphics processing units (GPUs) depends strongly on the number of particles. Substantially weak dependence of the performance on the number of particles is suitable to collisionless N-body simulations, since these simulations are usually performed with sophisticated N-body solvers such as Tree- and TreePM-methods combined with an individual timestep scheme. We conclude that collisionless N-body simulations accelerated with our library have significant advantage over those accelerated by GPUs, especially on massively parallel environments.

GLCF: Library

Science.gov Websites

Global Land Cover Facility About GLCF Research Publications Data & Products Gallery Library Services Contact Site Map Go Library Documents Proposal Reports Publications FAQ Display Materials Release News Archive Library * Display Materials * Documents * News Archive * Software e-link 4321

Software, Copyright, and Site-License Agreements: Publishers' Perspective of Library Practice.

ERIC Educational Resources Information Center

Happer, Stephanie K.

Thirty-one academic publishers of stand-alone software and book/disk packages were surveyed to determine whether publishers have addressed the copyright issues inherent in circulating these packages within the library environment. Twenty-two questionnaires were returned, providing a 71% return rate. There were 18 usable questionnaires. Publishers…

Copyright Handbook for Videotapes and Microcomputer Software.

ERIC Educational Resources Information Center

Ensign, David; And Others

Developed to help library media personnel, administrators, and educators understand and work with the copyright law as it applies to videotape and microcomputer software, this handbook provides: (1) an overview of copyright, including rights granted to copyright holders and libraries and court interpretation of the copyright law; (2) suggestions…

User’s Manual for the Modular Analysis-Package Libraries ANAPAC and TRANL

DTIC Science & Technology

1977-09-01

number) Computer software Fourier transforms Computer software library Interpolation software Digitized data...disregarded to give the user a simplified plot. (b) The last digit of ISPACE determines the type of line to be drawn, provided KODE is not...negative. If the last digit of ISPACE is 0 a solid line is drawn 1 a dashed line is drawn - - - 2 a dotted line is drawn .... 3 a dash-dot line is

Libraries Online!: Microsoft Partnering with American Library Association (ALA).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Describes Libraries Online, a pilot project created by Microsoft and the American Library Association to develop ways to provide access to information technologies to underserved populations. Presents the nine public libraries that will receive cash grants, staff training, computer hardware and software, and technical support to help support local…

Wyoming: Open Range for Library Technology.

ERIC Educational Resources Information Center

Maul, Helen Meadors

1996-01-01

Describes the development of library technology and the need for telecommunications in a state with a lack of population density. Topics include the state library's role; shared library resources and library networks; government information; the Wyoming State Home Page on the World Wide Web; Ariel software; network coordinating; and central…

Introduction to Minicomputers in Federal Libraries.

ERIC Educational Resources Information Center

Young, Micki Jo; And Others

This book for library administrators and Federal library staff covers the application of minicomputers in Federal libraries and offers a review of minicomputer technology. A brief overview of automation explains computer technology, hardware, and software. The role of computers in libraries is examined in terms of the history of computers and…

Sex, Kids, and the Public Library.

ERIC Educational Resources Information Center

Mason, Marilyn Gell

1997-01-01

Considers issues relating to children's access to information on the Internet in public libraries. Topics include censorship versus selection; First Amendment rights; the American Library Association's challenge to the Communications Decency Act; filtering software; and the role of the public library. (LRW)

The National Transport Code Collaboration Module Library

NASA Astrophysics Data System (ADS)

Kritz, A. H.; Bateman, G.; Kinsey, J.; Pankin, A.; Onjun, T.; Redd, A.; McCune, D.; Ludescher, C.; Pletzer, A.; Andre, R.; Zakharov, L.; Lodestro, L.; Pearlstein, L. D.; Jong, R.; Houlberg, W.; Strand, P.; Wiley, J.; Valanju, P.; John, H. St.; Waltz, R.; Mandrekas, J.; Mau, T. K.; Carlsson, J.; Braams, B.

2004-12-01

This paper reports on the progress in developing a library of code modules under the auspices of the National Transport Code Collaboration (NTCC). Code modules are high quality, fully documented software packages with a clearly defined interface. The modules provide a variety of functions, such as implementing numerical physics models; performing ancillary functions such as I/O or graphics; or providing tools for dealing with common issues in scientific programming such as portability of Fortran codes. Researchers in the plasma community submit code modules, and a review procedure is followed to insure adherence to programming and documentation standards. The review process is designed to provide added confidence with regard to the use of the modules and to allow users and independent reviews to validate the claims of the modules' authors. All modules include source code; clear instructions for compilation of binaries on a variety of target architectures; and test cases with well-documented input and output. All the NTCC modules and ancillary information, such as current standards and documentation, are available from the NTCC Module Library Website http://w3.pppl.gov/NTCC. The goal of the project is to develop a resource of value to builders of integrated modeling codes and to plasma physics researchers generally. Currently, there are more than 40 modules in the module library.

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.

High-Performance Design Patterns for Modern Fortran

DOE PAGES

Haveraaen, Magne; Morris, Karla; Rouson, Damian; ...

2015-01-01

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented thesemore » patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow.« less

Documentation Library Application (DLA) Version 2.0.0.1, User Guide

DTIC Science & Technology

2013-05-08

document DIScard chotnoes and undo <ht:dc-oot. View AN Library ~IR8librMY ~ooc~~.tiOn Llbt~ry View W AA Library View ~MI Libr -ary...Windows XP and access to the DLA SQL Server database. To install the DLA, navigate to N:\\Dept 161\\3 - PRODUCTS\\ Software Installation...Health Research Center. You should see the DLA menu item listed under the NHRC programs there. Contact the DLA software POC if you encounter any

Development of an Ada package library

NASA Technical Reports Server (NTRS)

Burton, Bruce; Broido, Michael

1986-01-01

A usable prototype Ada package library was developed and is currently being evaluated for use in large software development efforts. The library system is comprised of an Ada-oriented design language used to facilitate the collection of reuse information, a relational data base to store reuse information, a set of reusable Ada components and tools, and a set of guidelines governing the system's use. The prototyping exercise is discussed and the lessons learned from it have led to the definition of a comprehensive tool set to facilitate software reuse.

The Social Ties That Bind. Online Treasures

ERIC Educational Resources Information Center

Balas, Janet L.

2006-01-01

This article discusses how, in the new world of the information age, libraries must seek to bring relevant services to their technically savvy patrons. This includes designing a library that can serve not only the geographic community, but also the virtual online community. Software used to create online communities is known as social software and…

Using Web Metric Software to Drive: Mobile Website Development

ERIC Educational Resources Information Center

Tidal, Junior

2011-01-01

Many libraries have developed mobile versions of their websites. In order to understand their users, web developers have conducted both usability tests and focus groups, yet analytical software and web server logs can also be used to better understand users. Using data collected from these tools, the Ursula C. Schwerin Library has made informed…

Linux Adventures on a Laptop. Computers in Small Libraries

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

Securing PCs and Data in Libraries and Schools: A Handbook with Menuing, Anti-Virus, and Other Protective Software.

ERIC Educational Resources Information Center

Benson, Allen C.

This handbook is designed to help readers identify and eliminate security risks, with sound recommendations and library-tested security software. Chapter 1 "Managing Your Facilities and Assessing Your Risks" addresses fundamental management responsibilities including planning for a secure system, organizing computer-related information, assessing…

A Survey on the Use of Microcomputers in Special Libraries.

ERIC Educational Resources Information Center

Krieger, Tillie

1986-01-01

Describes a survey on the use of microcomputers in special libraries. The discussion of the findings includes types of hardware and software in use; applications in public services, technical processes, and administrative tasks; data back-up techniques; training received; evaluation of software; and future plans for microcomputer applications. (1…

After Losing Users in Catalogs, Libraries Find Better Search Software

ERIC Educational Resources Information Center

Parry, Marc

2010-01-01

Traditional online library catalogs do not tend to order search results by ranked relevance, and they can befuddle users with clunky interfaces. However, that's changing because of two technology trends. First, a growing number of universities are shelling out serious money for sophisticated software that makes exploring their collections more…

Real Time with the Librarian: Using Web Conferencing Software to Connect to Distance Students

ERIC Educational Resources Information Center

Riedel, Tom; Betty, Paul

2013-01-01

A pilot program to provide real-time library webcasts to Regis University distance students using Adobe Connect software was initiated in fall of 2011. Previously, most interaction between librarians and online students had been accomplished by asynchronous discussion threads in the Learning Management System. Library webcasts were offered in…

ALSC 2011 Notable Videos, Recordings & Interactive Software

ERIC Educational Resources Information Center

School Library Journal, 2011

2011-01-01

This article presents the Notable Children's Videos, Recordings, and Interactive Software for Kids lists which are compiled annually by committees of the Association for Library Service to children (ALSC), a division of the American Library Association (ALA). These lists were released in January 2011 at the ALA Midwinter meeting in San Diego,…

PVM Wrapper

NASA Technical Reports Server (NTRS)

Katz, Daniel

2004-01-01

PVM Wrapper is a software library that makes it possible for code that utilizes the Parallel Virtual Machine (PVM) software library to run using the message-passing interface (MPI) software library, without needing to rewrite the entire code. PVM and MPI are the two most common software libraries used for applications that involve passing of messages among parallel computers. Since about 1996, MPI has been the de facto standard. Codes written when PVM was popular often feature patterns of {"initsend," "pack," "send"} and {"receive," "unpack"} calls. In many cases, these calls are not contiguous and one set of calls may even exist over multiple subroutines. These characteristics make it difficult to obtain equivalent functionality via a single MPI "send" call. Because PVM Wrapper is written to run with MPI- 1.2, some PVM functions are not permitted and must be replaced - a task that requires some programming expertise. The "pvm_spawn" and "pvm_parent" function calls are not replaced, but a programmer can use "mpirun" and knowledge of the ranks of parent and child tasks with supplied macroinstructions to enable execution of codes that use "pvm_spawn" and "pvm_parent."

Automated toxicological screening reports of modified Agilent MSD Chemstation combined with Microsoft Visual Basic application programs.

PubMed

Choe, Sanggil; Kim, Suncheun; Choi, Hyeyoung; Choi, Hwakyoung; Chung, Heesun; Hwang, Bangyeon

2010-06-15

Agilent GC-MS MSD Chemstation offers automated library search report for toxicological screening using total ion chromatogram (TIC) and mass spectroscopy in normal mode. Numerous peaks appear in the chromatogram of biological specimen such as blood or urine and often large migrating peaks obscure small target peaks, in addition, any target peaks of low abundance regularly give wrong library search result or low matching score. As a result, retention time and mass spectrum of all the peaks in the chromatogram have to be checked to see if they are relevant. These repeated actions are very tedious and time-consuming to toxicologists. MSD Chemstation software operates using a number of macro files which give commands and instructions on how to work on and extract data from the chromatogram and spectroscopy. These macro files are developed by the own compiler of the software. All the original macro files can be modified and new macro files can be added to the original software by users. To get more accurate results with more convenient method and to save time for data analysis, we developed new macro files for reports generation and inserted new menus in the Enhanced Data Analysis program. Toxicological screening reports generated by these new macro files are in text mode or graphic mode and these reports can be generated with three different automated subtraction options. Text reports have Brief mode and Full mode and graphic reports have the option with or without mass spectrum mode. Matched mass spectrum and matching score for detected compounds are printed in reports by modified library searching modules. We have also developed an independent application program named DrugMan. This program manages drug groups, lists and parameters that are in use in MSD Chemstation. The incorporation of DrugMan with modified macro modules provides a powerful tool for toxicological screening and save a lot of valuable time on toxicological work. (c) 2010 Elsevier Ireland Ltd. All rights reserved.

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

Parallel Processing of Numerical Tsunami Simulations on a High Performance Cluster based on the GDAL Library

NASA Astrophysics Data System (ADS)

Schroeder, Matthias; Jankowski, Cedric; Hammitzsch, Martin; Wächter, Joachim

2014-05-01

Thousands of numerical tsunami simulations allow the computation of inundation and run-up along the coast for vulnerable areas over the time. A so-called Matching Scenario Database (MSDB) [1] contains this large number of simulations in text file format. In order to visualize these wave propagations the scenarios have to be reprocessed automatically. In the TRIDEC project funded by the seventh Framework Programme of the European Union a Virtual Scenario Database (VSDB) and a Matching Scenario Database (MSDB) were established amongst others by the working group of the University of Bologna (UniBo) [1]. One part of TRIDEC was the developing of a new generation of a Decision Support System (DSS) for tsunami Early Warning Systems (TEWS) [2]. A working group of the GFZ German Research Centre for Geosciences was responsible for developing the Command and Control User Interface (CCUI) as central software application which support operator activities, incident management and message disseminations. For the integration and visualization in the CCUI, the numerical tsunami simulations from MSDB must be converted into the shapefiles format. The usage of shapefiles enables a much easier integration into standard Geographic Information Systems (GIS). Since also the CCUI is based on two widely used open source products (GeoTools library and uDig), whereby the integration of shapefiles is provided by these libraries a priori. In this case, for an example area around the Western Iberian margin several thousand tsunami variations were processed. Due to the mass of data only a program-controlled process was conceivable. In order to optimize the computing efforts and operating time the use of an existing GFZ High Performance Computing Cluster (HPC) had been chosen. Thus, a geospatial software was sought after that is capable for parallel processing. The FOSS tool Geospatial Data Abstraction Library (GDAL/OGR) was used to match the coordinates with the wave heights and generates the different shapefiles for certain time steps. The shapefiles contain afterwards lines for visualizing the isochrones of the wave propagation and moreover, data about the maximum wave height and the Estimated Time of Arrival (ETA) at the coast. Our contribution shows the entire workflow and the visualizing results of the-processing for the example region Western Iberian ocean margin. [1] Armigliato A., Pagnoni G., Zaniboni F, Tinti S. (2013), Database of tsunami scenario simulations for Western Iberia: a tool for the TRIDEC Project Decision Support System for tsunami early warning, Vol. 15, EGU2013-5567, EGU General Assembly 2013, Vienna (Austria). [2] Löwe, P., Wächter, J., Hammitzsch, M., Lendholt, M., Häner, R. (2013): The Evolution of Service-oriented Disaster Early Warning Systems in the TRIDEC Project, 23rd International Ocean and Polar Engineering Conference - ISOPE-2013, Anchorage (USA).

How Much Security Does Your Library Need?

ERIC Educational Resources Information Center

Banerjee, Kyle

2003-01-01

Explains how to keep library systems healthy and functioning by taking sensible security measures. Examines why hackers would target library systems and how library systems are compromised. Describes tools that can help, including: firewalls; antivirus software; alarms; network analysis tools; and encryption. Identifies several strategies for…

Construction of Hierarchical Models for Fluid Dynamics in Earth and Planetary Sciences : DCMODEL project

NASA Astrophysics Data System (ADS)

Takahashi, Y. O.; Takehiro, S.; Sugiyama, K.; Odaka, M.; Ishiwatari, M.; Sasaki, Y.; Nishizawa, S.; Ishioka, K.; Nakajima, K.; Hayashi, Y.

2012-12-01

Toward the understanding of fluid motions of planetary atmospheres and planetary interiors by performing multiple numerical experiments with multiple models, we are now proceeding ``dcmodel project'', where a series of hierarchical numerical models with various complexity is developed and maintained. In ``dcmodel project'', a series of the numerical models are developed taking care of the following points: 1) a common ``style'' of program codes assuring readability of the software, 2) open source codes of the models to the public, 3) scalability of the models assuring execution on various scales of computational resources, 4) stressing the importance of documentation and presenting a method for writing reference manuals. The lineup of the models and utility programs of the project is as follows: Gtool5, ISPACK/SPML, SPMODEL, Deepconv, Dcpam, and Rdoc-f95. In the followings, features of each component are briefly described. Gtool5 (Ishiwatari et al., 2012) is a Fortran90 library, which provides data input/output interfaces and various utilities commonly used in the models of dcmodel project. A self-descriptive data format netCDF is adopted as a IO format of Gtool5. The interfaces of gtool5 library can reduce the number of operation steps for the data IO in the program code of the models compared with the interfaces of the raw netCDF library. Further, by use of gtool5 library, procedures for data IO and addition of metadata for post-processing can be easily implemented in the program codes in a consolidated form independent of the size and complexity of the models. ``ISPACK'' is the spectral transformation library and ``SPML (SPMODEL library)'' (Takehiro et al., 2006) is its wrapper library. Most prominent feature of SPML is a series of array-handling functions with systematic function naming rules, and this enables us to write codes with a form which is easily deduced from the mathematical expressions of the governing equations. ``SPMODEL'' (Takehiro et al., 2006) is a collection of various sample programs using ``SPML''. These sample programs provide the basekit for simple numerical experiments of geophysical fluid dynamics. For example, SPMODEL includes 1-dimensional KdV equation model, 2-dimensional barotropic, shallow water, Boussinesq models, 3-dimensional MHD dynamo models in rotating spherical shells. These models are written in the common style in harmony with SPML functions. ``Deepconv'' (Sugiyama et al., 2010) and ``Dcpam'' are a cloud resolving model and a general circulation model for the purpose of applications to the planetary atmospheres, respectively. ``Deepconv'' includes several physical processes appropriate for simulations of Jupiter and Mars atmospheres, while ``Dcpam'' does for simulations of Earth, Mars, and Venus-like atmospheres. ``Rdoc-f95'' is a automatic generator of reference manuals of Fortran90/95 programs, which is an extension of ruby documentation tool kit ``rdoc''. It analyzes dependency of modules, functions, and subroutines in the multiple program source codes. At the same time, it can list up the namelist variables in the programs.

Advances in Software Tools for Pre-processing and Post-processing of Overset Grid Computations

NASA Technical Reports Server (NTRS)

Chan, William M.

2004-01-01

Recent developments in three pieces of software for performing pre-processing and post-processing work on numerical computations using overset grids are presented. The first is the OVERGRID graphical interface which provides a unified environment for the visualization, manipulation, generation and diagnostics of geometry and grids. Modules are also available for automatic boundary conditions detection, flow solver input preparation, multiple component dynamics input preparation and dynamics animation, simple solution viewing for moving components, and debris trajectory analysis input preparation. The second is a grid generation script library that enables rapid creation of grid generation scripts. A sample of recent applications will be described. The third is the OVERPLOT graphical interface for displaying and analyzing history files generated by the flow solver. Data displayed include residuals, component forces and moments, number of supersonic and reverse flow points, and various dynamics parameters.

Features in simulation of crystal growth using the hyperbolic PFC equation and the dependence of the numerical solution on the parameters of the computational grid

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

Starodumov, Ilya; Kropotin, Nikolai

2016-08-10

We investigate the three-dimensional mathematical model of crystal growth called PFC (Phase Field Crystal) in a hyperbolic modification. This model is also called the modified model PFC (originally PFC model is formulated in parabolic form) and allows to describe both slow and rapid crystallization processes on atomic length scales and on diffusive time scales. Modified PFC model is described by the differential equation in partial derivatives of the sixth order in space and second order in time. The solution of this equation is possible only by numerical methods. Previously, authors created the software package for the solution of the Phasemore » Field Crystal problem, based on the method of isogeometric analysis (IGA) and PetIGA program library. During further investigation it was found that the quality of the solution can strongly depends on the discretization parameters of a numerical method. In this report, we show the features that should be taken into account during constructing the computational grid for the numerical simulation.« less

Technology for Libraries.

ERIC Educational Resources Information Center

Phenix, Katharine; And Others

1990-01-01

Five articles discuss information technology in libraries: (1) "Software for Libraries" (Katharine Phenix); (2) "Online Update: European Online Services" (Martin Kesselman); (3) "Connect Time: Online Pricing Breakthroughs" (Barbara Quint); (4) "Microcomputing: Micro Biology Computer Viruses" (James LaRue);…

Information Technology in Libraries. A Pakistani Perspective.

ERIC Educational Resources Information Center

Mahmood, Khalid

This book presents an overview of the present status of the use of library automation hardware and software in Pakistan. The following 20 articles are included: (1) "The Status of Library Automation in Pakistan"; (2) "Promoting Information Technology in Pakistan: the Netherlands Library Development Project"; (3) "Library…

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

The primary objective of the proposed Earth Science Markup Language (ESML) research is to transition from design to application. The resulting schema and prototype software will foster community acceptance for the "define once, use anywhere" concept central to ESML. Supporting goals include: 1. Refinement of the ESML schema and software libraries in cooperation with the user community. 2. Application of the ESML schema and software libraries to a variety of Earth science data sets and analysis tools. 3. Development of supporting prototype software for enhanced ease of use. 4. Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate. 5. Widespread publication of the ESML approach, schema, and software.

The simulation library of the Belle II software system

NASA Astrophysics Data System (ADS)

Kim, D. Y.; Ritter, M.; Bilka, T.; Bobrov, A.; Casarosa, G.; Chilikin, K.; Ferber, T.; Godang, R.; Jaegle, I.; Kandra, J.; Kodys, P.; Kuhr, T.; Kvasnicka, P.; Nakayama, H.; Piilonen, L.; Pulvermacher, C.; Santelj, L.; Schwenker, B.; Sibidanov, A.; Soloviev, Y.; Starič, M.; Uglov, T.

2017-10-01

SuperKEKB, the next generation B factory, has been constructed in Japan as an upgrade of KEKB. This brand new e+ e- collider is expected to deliver a very large data set for the Belle II experiment, which will be 50 times larger than the previous Belle sample. Both the triggered physics event rate and the background event rate will be increased by at least 10 times than the previous ones, and will create a challenging data taking environment for the Belle II detector. The software system of the Belle II experiment is designed to execute this ambitious plan. A full detector simulation library, which is a part of the Belle II software system, is created based on Geant4 and has been tested thoroughly. Recently the library has been upgraded with Geant4 version 10.1. The library is behaving as expected and it is utilized actively in producing Monte Carlo data sets for various studies. In this paper, we will explain the structure of the simulation library and the various interfaces to other packages including geometry and beam background simulation.

Evaluating Open Source Software for Use in Library Initiatives: A Case Study Involving Electronic Publishing

ERIC Educational Resources Information Center

Samuels, Ruth Gallegos; Griffy, Henry

2012-01-01

This article discusses best practices for evaluating open source software for use in library projects, based on the authors' experience evaluating electronic publishing solutions. First, it presents a brief review of the literature, emphasizing the need to evaluate open source solutions carefully in order to minimize Total Cost of Ownership. Next,…

Hammond Workforce 2000: A Three-Year Project. October 1989 to September 1992.

ERIC Educational Resources Information Center

Meyers, Arthur S.; Somerville, Deborah J.

A 3-year Library Services and Construction Act grant project from 1989-1992 provided for adult learning centers, equipped with Apple IIGS computers and software at each location of the Hammond Public Library (Indiana). User-friendly, job-based software to strengthen reading, writing, mathematics, spelling, and grammar skills, as well as video and…

Library iTour: Introducing the iPod Generation to the Academic Library

ERIC Educational Resources Information Center

Cairns, Virginia; Dean, Toni C.

2009-01-01

Purpose: For many years, the Lupton Library offered a traditional library introduction class to first year students participating in the Freshman Seminar Program at the University of Tennessee at Chattanooga. In 2007, the library applied for and received a campus grant to purchase thirty iPod Touches, along with accompanying hardware and software.…

Small but Pristine--Lessons for Small Library Automation.

ERIC Educational Resources Information Center

Clement, Russell; Robertson, Dane

1990-01-01

Compares the more positive library automation experiences of a small public library with those of a large research library. Topics addressed include collection size; computer size and the need for outside control of a data processing center; staff size; selection process for hardware and software; and accountability. (LRW)

The Generalized Support Software (GSS) Domain Engineering Process: An Object-Oriented Implementation and Reuse Success at Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Condon, Steven; Hendrick, Robert; Stark, Michael E.; Steger, Warren

1997-01-01

The Flight Dynamics Division (FDD) of NASA's Goddard Space Flight Center (GSFC) recently embarked on a far-reaching revision of its process for developing and maintaining satellite support software. The new process relies on an object-oriented software development method supported by a domain specific library of generalized components. This Generalized Support Software (GSS) Domain Engineering Process is currently in use at the NASA GSFC Software Engineering Laboratory (SEL). The key facets of the GSS process are (1) an architecture for rapid deployment of FDD applications, (2) a reuse asset library for FDD classes, and (3) a paradigm shift from developing software to configuring software for mission support. This paper describes the GSS architecture and process, results of fielding the first applications, lessons learned, and future directions

Microcomputers in Libraries.

ERIC Educational Resources Information Center

Ertel, Monica M.

1984-01-01

This discussion of current microcomputer technologies available to libraries focuses on software applications in four major classifications: communications (online database searching); word processing; administration; and database management systems. Specific examples of library applications are given and six references are cited. (EJS)

3D Voronoi grid dedicated software for modeling gas migration in deep layered sedimentary formations with TOUGH2-TMGAS

NASA Astrophysics Data System (ADS)

Bonduà, Stefano; Battistelli, Alfredo; Berry, Paolo; Bortolotti, Villiam; Consonni, Alberto; Cormio, Carlo; Geloni, Claudio; Vasini, Ester Maria

2017-11-01

As is known, a full three-dimensional (3D) unstructured grid permits a great degree of flexibility when performing accurate numerical reservoir simulations. However, when the Integral Finite Difference Method (IFDM) is used for spatial discretization, constraints (arising from the required orthogonality between the segment connecting the blocks nodes and the interface area between blocks) pose difficulties in the creation of grids with irregular shaped blocks. The full 3D Voronoi approach guarantees the respect of IFDM constraints and allows generation of grids conforming to geological formations and structural objects and at the same time higher grid resolution in volumes of interest. In this work, we present dedicated pre- and post-processing gridding software tools for the TOUGH family of numerical reservoir simulators, developed by the Geothermal Research Group of the DICAM Department, University of Bologna. VORO2MESH is a new software coded in C++, based on the voro++ library, allowing computation of the 3D Voronoi tessellation for a given domain and the creation of a ready to use TOUGH2 MESH file. If a set of geological surfaces is available, the software can directly generate the set of Voronoi seed points used for tessellation. In order to reduce the number of connections and so to decrease computation time, VORO2MESH can produce a mixed grid with regular blocks (orthogonal prisms) and irregular blocks (polyhedron Voronoi blocks) at the point of contact between different geological formations. In order to visualize 3D Voronoi grids together with the results of numerical simulations, the functionality of the TOUGH2Viewer post-processor has been extended. We describe an application of VORO2MESH and TOUGH2Viewer to validate the two tools. The case study deals with the simulation of the migration of gases in deep layered sedimentary formations at basin scale using TOUGH2-TMGAS. A comparison between the simulation performances of unstructured and structured grids is presented.

Expanding roles in a library-based bioinformatics service program: a case study

PubMed Central

Li, Meng; Chen, Yi-Bu; Clintworth, William A

2013-01-01

Question: How can a library-based bioinformatics support program be implemented and expanded to continuously support the growing and changing needs of the research community? Setting: A program at a health sciences library serving a large academic medical center with a strong research focus is described. Methods: The bioinformatics service program was established at the Norris Medical Library in 2005. As part of program development, the library assessed users' bioinformatics needs, acquired additional funds, established and expanded service offerings, and explored additional roles in promoting on-campus collaboration. Results: Personnel and software have increased along with the number of registered software users and use of the provided services. Conclusion: With strategic efforts and persistent advocacy within the broader university environment, library-based bioinformatics service programs can become a key part of an institution's comprehensive solution to researchers' ever-increasing bioinformatics needs. PMID:24163602

The Extensibility of an Interpreted Language Using Plugin Libraries

NASA Astrophysics Data System (ADS)

Herceg, Dorde; Radaković, Davorka

2011-09-01

Dynamic geometry software (DGS) are computer programs that allow one to create and manipulate geometrical drawings. They are mostly used in teaching and studying geometry. However, DGS can also be used to develop interactive drawings not directly related to geometry. Examples include teaching materials for numerical mathematics at secondary school and university levels, or interactive mathematical games for elementary school children. Such applications often surpass the intended purposes of the DGS and may require complicated programming on behalf of the user. In this paper we present a simple plug-in model which enables easy development and deployment of interactive GUI components for "Geometrijica", a DGS we are developing on Silverlight.

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

PubMed

Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

2012-01-01

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

PubMed Central

Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.; Beerli, Peter; Holder, Mark T.; Lewis, Paul O.; Huelsenbeck, John P.; Ronquist, Fredrik; Swofford, David L.; Cummings, Michael P.; Rambaut, Andrew; Suchard, Marc A.

2012-01-01

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. PMID:21963610

Random learning units using WIRIS quizzes in Moodle

NASA Astrophysics Data System (ADS)

Mora, Ángel; Mérida, Enrique; Eixarch, Ramon

2011-09-01

Moodle is an extended learning management system for developing learning units, including mathematically-based subjects. A wide variety of material can be developed in Moodle which contains facilities for forums, questionnaires, lessons, tasks, wikis, glossaries and chats. Therefore, the Moodle platform provides a meeting point for those working in a mathematics course. Mathematics requires special materials and activities: The material must include mathematical objects and the activities included in the virtual course must be able to do mathematical computations. WIRIS is a powerful software for educational environments. It has libraries for calculus, algebra, geometry and much more. In this article, examples showing the use of WIRIS in numerical methods and examples of using a new tool, WIRIS quizzes, are illustrated. By enhancing Moodle with WIRIS, we can add random learning questions to modules. Moodle has a simpler version of this capability, but WIRIS extends the method in which the random material is presented to the students. Random objects can appear in a question, in a variable of a question, in a plot or in the definition of a mathematical object. This article illustrates material prepared for numerical methods using a WIRIS library integrated in WIRIS quizzes. As a result, WIRIS in Moodle can be considered as a global solution for mathematics education.

NIFTY - Numerical Information Field Theory. A versatile PYTHON library for signal inference

NASA Astrophysics Data System (ADS)

Selig, M.; Bell, M. R.; Junklewitz, H.; Oppermann, N.; Reinecke, M.; Greiner, M.; Pachajoa, C.; Enßlin, T. A.

2013-06-01

NIFTy (Numerical Information Field Theory) is a software package designed to enable the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTy offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically without concerning the user. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and then apply the developed code in higher-dimensional settings of real world problems. The set of spaces on which NIFTy operates comprises point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those. The functionality and diversity of the package is demonstrated by a Wiener filter code example that successfully runs without modification regardless of the space on which the inference problem is defined. NIFTy homepage http://www.mpa-garching.mpg.de/ift/nifty/; Excerpts of this paper are part of the NIFTy source code and documentation.

SU-G-BRB-02: An Open-Source Software Analysis Library for Linear Accelerator Quality Assurance

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

Kerns, J; Yaldo, D

Purpose: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. Methods: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence. The analysis library was built using the general programming language Python. Each test was analyzed with the library algorithms and compared to manual measurements taken at the timemore » of acquisition. Results: VMAT QA results agreed within 0.1% between the library and manual measurements. Machine logs (dynalogs & trajectory logs) were successfully parsed; mechanical axis positions were verified for accuracy and MLC fluence agreed well with EPID measurements. CBCT QA measurements were within 10 HU and 0.2mm where applicable. Winston Lutz isocenter size measurements were within 0.2mm of TrueBeam’s Machine Performance Check. Starshot analysis was within 0.2mm of the Winston Lutz results for the same conditions. Picket fence images with and without a known error showed that the library was capable of detecting MLC offsets within 0.02mm. Conclusion: A new routine QA software library has been benchmarked and is available for use by the community. The library is open-source and extensible for use in larger systems.« less

The Weakest Link: Library Catalogs.

ERIC Educational Resources Information Center

Young, Terrence E., Jr.

2002-01-01

Describes methods of correcting MARC records in online public access catalogs in school libraries. Highlights include in-house methods; professional resources; conforming to library cataloging standards; vendor services, including Web-based services; software specifically developed for record cleanup; and outsourcing. (LRW)

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

Bowen, Benjamin; Ruebel, Oliver; Fischer, Curt Fischer R.

BASTet is an advanced software library written in Python. BASTet serves as the analysis and storage library for the OpenMSI project. BASTet is an integrate framework for: i) storage of spectral imaging data, ii) storage of derived analysis data, iii) provenance of analyses, iv) integration and execution of analyses via complex workflows. BASTet implements the API for the HDF5 storage format used by OpenMSI. Analyses that are developed using BASTet benefit from direct integration with storage format, automatic tracking of provenance, and direct integration with command-line and workflow execution tools. BASTet also defines interfaces to enable developers to directly integratemore » their analysis with OpenMSI's web-based viewing infrastruture without having to know OpenMSI. BASTet also provides numerous helper classes and tools to assist with the conversion of data files, ease parallel implementation of analysis algorithms, ease interaction with web-based functions, description methods for data reduction. BASTet also includes detailed developer documentation, user tutorials, iPython notebooks, and other supporting documents.« less

DSPSR: Digital Signal Processing Software for Pulsar Astronomy

NASA Astrophysics Data System (ADS)

van Straten, W.; Bailes, M.

2010-10-01

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

Enhancements to the EPANET-RTX (Real-Time Analytics) ...

EPA Pesticide Factsheets

Technical brief and software The U.S. Environmental Protection Agency (EPA) developed EPANET-RTX as a collection of object-oriented software libraries comprising the core data access, data transformation, and data synthesis (real-time analytics) components of a real-time hydraulic and water quality modeling system. While EPANET-RTX uses the hydraulic and water quality solvers of EPANET, the object libraries are a self-contained set of building blocks for software developers. “Real-time EPANET” promises to change the way water utilities, commercial vendors, engineers, and the water community think about modeling.

Monitoring Object Library Usage and Changes

NASA Technical Reports Server (NTRS)

Owen, R. K.; Craw, James M. (Technical Monitor)

1995-01-01

The NASA Ames Numerical Aerodynamic Simulation program Aeronautics Consolidated Supercomputing Facility (NAS/ACSF) supercomputing center services over 1600 users, and has numerous analysts with root access. Several tools have been developed to monitor object library usage and changes. Some of the tools do "noninvasive" monitoring and other tools implement run-time logging even for object-only libraries. The run-time logging identifies who, when, and what is being used. The benefits are that real usage can be measured, unused libraries can be discontinued, training and optimization efforts can be focused at those numerical methods that are actually used. An overview of the tools will be given and the results will be discussed.

Wrapping Python around MODFLOW/MT3DMS based groundwater models

NASA Astrophysics Data System (ADS)

Post, V.

2008-12-01

Numerical models that simulate groundwater flow and solute transport require a great amount of input data that is often organized into different files. A large proportion of the input data consists of spatially-distributed model parameters. The model output consists of a variety data such as heads, fluxes and concentrations. Typically all files have different formats. Consequently, preparing input and managing output is a complex and error-prone task. Proprietary software tools are available that facilitate the preparation of input files and analysis of model outcomes. The use of such software may be limited if it does not support all the features of the groundwater model or when the costs of such tools are prohibitive. Therefore a Python library was developed that contains routines to generate input files and process output files of MODFLOW/MT3DMS based models. The library is freely available and has an open structure so that the routines can be customized and linked into other scripts and libraries. The current set of functions supports the generation of input files for MODFLOW and MT3DMS, including the capability to read spatially-distributed input parameters (e.g. hydraulic conductivity) from PNG files. Both ASCII and binary output files can be read efficiently allowing for visualization of, for example, solute concentration patterns in contour plots with superimposed flow vectors using matplotlib. Series of contour plots are then easily saved as an animation. The subroutines can also be used within scripts to calculate derived quantities such as the mass of a solute within a particular region of the model domain. Using Python as a wrapper around groundwater models provides an efficient and flexible way of processing input and output data, which is not constrained by limitations of third-party products.

An object-oriented class library for medical software development.

PubMed

O'Kane, K C; McColligan, E E

1996-12-01

The objective of this research is the development of a Medical Object Library (MOL) consisting of reusable, inheritable, portable, extendable C++ classes that facilitate rapid development of medical software at reduced cost and increased functionality. The result of this research is a library of class objects that range in function from string and hierarchical file handling entities to high level, procedural agents that perform increasingly complex, integrated tasks. A system built upon these classes is compatible with any other system similarly constructed with respect to data definitions, semantics, data organization and storage. As new objects are built, they can be added to the class library for subsequent use. The MOL is a toolkit of software objects intended to support a common file access methodology, a unified medical record structure, consistent message processing, standard graphical display facilities and uniform data collection procedures. This work emphasizes the relationship that potentially exists between the structure of a hierarchical medical record and procedural language components by means of a hierarchical class library and tree structured file access facility. In doing so, it attempts to establish interest in and demonstrate the practicality of the hierarchical medical record model in the modern context of object oriented programming.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

The Australian Bibliographic Network--An Introduction.

ERIC Educational Resources Information Center

Hannan, Chris

1982-01-01

Focuses on the centralized, online, shared-cataloging facility of the Australian Bibliographic Network operated by the National Library of Australia. Existing automated library systems in Australia, selection and implementation of Washington Library Network software, comparison of Australian and U.S. automation, and projections for future…

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients.

PubMed

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F; Long, Daniel J; Bolch, Wesley E; Liu, Bob; Xu, X George

2015-07-21

This paper describes the development and testing of VirtualDose--a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the 'software as a service (SaaS)' delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose's functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT-two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

From LAMP to Koha: Case Study of the Pakistan Legislative Assembly Libraries

ERIC Educational Resources Information Center

Shafi-Ullah, Farasat; Qutab, Saima

2012-01-01

Purpose: This paper aims to elaborate the library data migration process from LAMP (Library Automation Management Program) to the open source software Koha's (2.2.8 Windows based) Pakistani flavour PakLAG-Koha in six legislative assembly libraries of Pakistan. Design/methodology/approach: The paper explains different steps of the data migration…

Using the Intel Math Kernel Library on Peregrine | High-Performance

Science.gov Websites

Computing | NREL the Intel Math Kernel Library on Peregrine Using the Intel Math Kernel Library on Peregrine Learn how to use the Intel Math Kernel Library (MKL) with Peregrine system software. MKL architectures. Core math functions in MKL include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier

Perceptions of Personnel at Selected Texas Community Colleges Regarding the Impact of Technology on Their Libraries

ERIC Educational Resources Information Center

Kenan, Sharon K.

2012-01-01

Technological innovations have transformed all areas of community college libraries. Automated library systems, office software, and Internet access have altered work processes for library personnel and have changed research methodologies for students and faculty. The purpose of this bounded multiple case study was to explore how the adoption of…

Automated software development workstation

NASA Technical Reports Server (NTRS)

Prouty, Dale A.; Klahr, Philip

1988-01-01

A workstation is being developed that provides a computational environment for all NASA engineers across application boundaries, which automates reuse of existing NASA software and designs, and efficiently and effectively allows new programs and/or designs to be developed, catalogued, and reused. The generic workstation is made domain specific by specialization of the user interface, capturing engineering design expertise for the domain, and by constructing/using a library of pertinent information. The incorporation of software reusability principles and expert system technology into this workstation provide the obvious benefits of increased productivity, improved software use and design reliability, and enhanced engineering quality by bringing engineering to higher levels of abstraction based on a well tested and classified library.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Software to Go--And It Goes!

ERIC Educational Resources Information Center

Abrams, Mary; Kurlychek, Ken

1989-01-01

This article describes the Software Evaluation Clearinghouse for Educators of the Hearing Impaired at Gallaudet University (Washington, DC). Software compatible with Apple and IBM hardware is collected, rated by clearinghouse members, and described in a printed catalog. Tips on starting a software lending library are offered. (PB)

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

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

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

DOE PAGES

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina; ...

2017-03-01

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

An Online Library Catalogue.

ERIC Educational Resources Information Center

Alloro, Giovanna; Ugolini, Donatella

1992-01-01

Describes the implementation of an online catalog in the library of the National Institute for Cancer Research and the Clinical and Experimental Oncology Institute of the University of Genoa. Topics addressed include automation of various library functions, software features, database management, training, and user response. (10 references) (MES)

Hagerstown-Jefferson Township Public Library Internet Web Site.

ERIC Educational Resources Information Center

Albertson, Marie

1997-01-01

Describes the development of the Hagerstown (Indiana) public library's Web site. Highlights include writing successful grant proposals for funding; software from Microsoft; community support; free community access to the Internet from home computers as well as at the library; problems encountered; and future plans. (LRW)

Continuous quality improvement using intelligent infusion pump data analysis.

PubMed

Breland, Burnis D

2010-09-01

The use of continuous quality-improvement (CQI) processes in the implementation of intelligent infusion pumps in a community teaching hospital is described. After the decision was made to implement intelligent i.v. infusion pumps in a 413-bed, community teaching hospital, drug libraries for use in the safety software had to be created. Before drug libraries could be created, it was necessary to determine the epidemiology of medication use in various clinical care areas. Standardization of medication administration was performed through the CQI process, using practical knowledge of clinicians at the bedside and evidence-based drug safety parameters in the scientific literature. Post-implementation, CQI allowed refinement of clinically important safety limits while minimizing inappropriate, meaningless soft limit alerts on a few select agents. Assigning individual clinical care areas (CCAs) to individual patient care units facilitated customization of drug libraries and identification of specific CCA compliance concerns. Between June 2007 and June 2008, there were seven library updates. These involved drug additions and deletions, customization of individual CCAs, and alterations of limits. Overall compliance with safety software use rose over time, from 33% in November 2006 to over 98% in December 2009. Many potentially clinically significant dosing errors were intercepted by the safety software, prompting edits by end users. Only 4-6% of soft limit alerts resulted in edits. Compliance rates for use of infusion pump safety software varied among CCAs over time. Education, auditing, and refinement of drug libraries led to improved compliance in most CCAs.

The Making of "The Transfer Agreement": A Library Odyssey.

ERIC Educational Resources Information Center

Black, Edwin

1984-01-01

Describes author's use of numerous library resources in preparation for writing untold story of secret pact between the Third Reich and Jewish Palestine. Library of Congress, Asher Library (Chicago), Zionist Library (New York City), Klau Library (Cincinnati, Ohio), public libraries (Chicago, Boston, New York), availability of materials, and…

Rehabilitation and Prosthetic Services

MedlinePlus

... VA Learning University (VALU) SimLearn Libraries (VALNET) VA Software Documentation Library (VDL) About VHA Learn about VHA Forms & ... & Sensory Aids Service (PSAS) Our Mission The mission of the Prosthetic & ...

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

Stereo Vision Inside Tire

DTIC Science & Technology

2015-08-21

using the Open Computer Vision ( OpenCV ) libraries [6] for computer vision and the Qt library [7] for the user interface. The software has the...depth. The software application calibrates the cameras using the plane based calibration model from the OpenCV calib3D module and allows the...6] OpenCV . 2015. OpenCV Open Source Computer Vision. [Online]. Available at: opencv.org [Accessed]: 09/01/2015. [7] Qt. 2015. Qt Project home

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

High-Performance Java Codes for Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

Algorithms and Libraries

NASA Technical Reports Server (NTRS)

Dongarra, Jack

1998-01-01

This exploratory study initiated our inquiry into algorithms and applications that would benefit by latency tolerant approach to algorithm building, including the construction of new algorithms where appropriate. In a multithreaded execution, when a processor reaches a point where remote memory access is necessary, the request is sent out on the network and a context--switch occurs to a new thread of computation. This effectively masks a long and unpredictable latency due to remote loads, thereby providing tolerance to remote access latency. We began to develop standards to profile various algorithm and application parameters, such as the degree of parallelism, granularity, precision, instruction set mix, interprocessor communication, latency etc. These tools will continue to develop and evolve as the Information Power Grid environment matures. To provide a richer context for this research, the project also focused on issues of fault-tolerance and computation migration of numerical algorithms and software. During the initial phase we tried to increase our understanding of the bottlenecks in single processor performance. Our work began by developing an approach for the automatic generation and optimization of numerical software for processors with deep memory hierarchies and pipelined functional units. Based on the results we achieved in this study we are planning to study other architectures of interest, including development of cost models, and developing code generators appropriate to these architectures.

Finding the Right Educational Software for Your Child.

ERIC Educational Resources Information Center

Moore, Jack

1990-01-01

Ideas are presented for identifying, evaluating, and selecting instructional software for children with special needs. The article notes several library research tools as sources of information and lists specific questions to consider when evaluating software. (JDD)

International Inventory of Software Packages in the Information Field.

ERIC Educational Resources Information Center

Keren, Carl, Ed.; Sered, Irina, Ed.

Designed to provide guidance in selecting appropriate software for library automation, information storage and retrieval, or management of bibliographic databases, this inventory describes 188 computer software packages. The information was obtained through a questionnaire survey of 600 software suppliers and developers who were asked to describe…

Cataloging and Organizing Microcomputer Software--Where Do We Go from First Base?

ERIC Educational Resources Information Center

Choi, Susan E.

This position paper addresses general topics to be considered when organizing library software collections. Tasks involved in organizing and cataloging educational software collections are discussed, including arrangement/classification; the type of catalog; descriptions of the software; the general materials designator; storage requirements; and…

A real-time MPEG software decoder using a portable message-passing library

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

Kwong, Man Kam; Tang, P.T. Peter; Lin, Biquan

1995-12-31

We present a real-time MPEG software decoder that uses message-passing libraries such as MPL, p4 and MPI. The parallel MPEG decoder currently runs on the IBM SP system but can be easil ported to other parallel machines. This paper discusses our parallel MPEG decoding algorithm as well as the parallel programming environment under which it uses. Several technical issues are discussed, including balancing of decoding speed, memory limitation, 1/0 capacities, and optimization of MPEG decoding components. This project shows that a real-time portable software MPEG decoder is feasible in a general-purpose parallel machine.

Logic Model Checking of Time-Periodic Real-Time Systems

NASA Technical Reports Server (NTRS)

Florian, Mihai; Gamble, Ed; Holzmann, Gerard

2012-01-01

In this paper we report on the work we performed to extend the logic model checker SPIN with built-in support for the verification of periodic, real-time embedded software systems, as commonly used in aircraft, automobiles, and spacecraft. We first extended the SPIN verification algorithms to model priority based scheduling policies. Next, we added a library to support the modeling of periodic tasks. This library was used in a recent application of the SPIN model checker to verify the engine control software of an automobile, to study the feasibility of software triggers for unintended acceleration events.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Laliberte, D.; Render, H.; Sum, R.; Smith, W.; Terwilliger, R.

1987-01-01

The Software Automation, Generation and Administration (SAGA) project is investigating the design and construction of practical software engineering environments for developing and maintaining aerospace systems and applications software. The research includes the practical organization of the software lifecycle, configuration management, software requirements specifications, executable specifications, design methodologies, programming, verification, validation and testing, version control, maintenance, the reuse of software, software libraries, documentation, and automated management.

Integration of the NRL Digital Library.

ERIC Educational Resources Information Center

King, James

2001-01-01

The Naval Research Laboratory (NRL) Library has identified six primary areas that need improvement: infrastructure, InfoWeb, TORPEDO Ultra, journal data management, classified data, and linking software. It is rebuilding InfoWeb and TORPEDO Ultra as database-driven Web applications, upgrading the STILAS library catalog, and creating other support…

Library Programming with LEGO MINDSTORMS, Scratch, and PicoCricket: Analysis of Best Practices for Public Libraries

ERIC Educational Resources Information Center

Romero, Juan Suarez

2010-01-01

Public libraries are redefining their roles in order to stay relevant to the needs of the communities they serve. Today, libraries are places where reading meets hands-on learning and where quietness coexists with voices and music. The latest advances in technology for children and teens, specifically, robotics sets and media-rich software, are…

Migration of Data from One Library Management System to Another: A Case Study in India

ERIC Educational Resources Information Center

Matoria, Ram Kumar; Upadhyay, P. K.

2005-01-01

Purpose: To share the experiences gained during the migration of library data from one library management system (LibSys[TM]) to another (e-Granthalaya[TM]). Design/methodology/approach: The paper describes the step-by-step approach taken to migrate the existing library data to the new software. The paper also discusses the peculiarities of the…

The New York City Subways: The First Ten Years. A Library Research Exercise Using a Computer.

ERIC Educational Resources Information Center

Machalow, Robert

This document presents a library research exercise developed at York College which uses the Apple IIe microcomputer and word processing software--the Applewriter--to teach library research skills. Unlike some other library research exercises on disk, this program allows the student to decide on alternative approaches to solving the given problem:…

Salvus: A flexible open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, M.; Boehm, C.; van Driel, M.; Krischer, L.; May, D.; Rietmann, M.; Fichtner, A.

2016-12-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Based on a high order finite (spectral) element discretization, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

Salvus: A flexible high-performance and open-source package for waveform modelling and inversion from laboratory to global scales

NASA Astrophysics Data System (ADS)

Afanasiev, Michael; Boehm, Christian; van Driel, Martin; Krischer, Lion; May, Dave; Rietmann, Max; Fichtner, Andreas

2017-04-01

Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Currently based on an abstract implementation of high order finite (spectral) elements, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. viscoelastic, coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ template mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and discuss some of the extensible design points.

LEGION: Lightweight Expandable Group of Independently Operating Nodes

NASA Technical Reports Server (NTRS)

Burl, Michael C.

2012-01-01

LEGION is a lightweight C-language software library that enables distributed asynchronous data processing with a loosely coupled set of compute nodes. Loosely coupled means that a node can offer itself in service to a larger task at any time and can withdraw itself from service at any time, provided it is not actively engaged in an assignment. The main program, i.e., the one attempting to solve the larger task, does not need to know up front which nodes will be available, how many nodes will be available, or at what times the nodes will be available, which is normally the case in a "volunteer computing" framework. The LEGION software accomplishes its goals by providing message-based, inter-process communication similar to MPI (message passing interface), but without the tight coupling requirements. The software is lightweight and easy to install as it is written in standard C with no exotic library dependencies. LEGION has been demonstrated in a challenging planetary science application in which a machine learning system is used in closed-loop fashion to efficiently explore the input parameter space of a complex numerical simulation. The machine learning system decides which jobs to run through the simulator; then, through LEGION calls, the system farms those jobs out to a collection of compute nodes, retrieves the job results as they become available, and updates a predictive model of how the simulator maps inputs to outputs. The machine learning system decides which new set of jobs would be most informative to run given the results so far; this basic loop is repeated until sufficient insight into the physical system modeled by the simulator is obtained.

Library Operations Policies and Procedures, Volume 2. Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-02-28

improvements. Pare 10 ka•- V •DkI U Release Manager The Release Manager provides franchisees with media copies of existing libraries, as needed. Security...implementors, and potential library franchisees . Security Team The Security Team assists the Security Officer with security analysis. Team members are...and Franchisees . A Potential User is an individual who requests a Library Account. A User Recruit has been sent a CARDS Library Account Registration

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages

PubMed Central

Nunez-Iglesias, Juan; Kennedy, Ryan; Plaza, Stephen M.; Chakraborty, Anirban; Katz, William T.

2014-01-01

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. PMID:24772079

Using component technology to facilitate external software reuse in ground-based planning systems

NASA Technical Reports Server (NTRS)

Chase, A.

2003-01-01

APGEN (Activity Plan GENerator - 314), a multi-mission planning tool, must interface with external software to vest serve its users. AP-GEN's original method for incorporating external software, the User-Defined library mechanism, has been very successful in allowing APGEN users access to external software functionality.

The tensor network theory library

NASA Astrophysics Data System (ADS)

Al-Assam, S.; Clark, S. R.; Jaksch, D.

2017-09-01

In this technical paper we introduce the tensor network theory (TNT) library—an open-source software project aimed at providing a platform for rapidly developing robust, easy to use and highly optimised code for TNT calculations. The objectives of this paper are (i) to give an overview of the structure of TNT library, and (ii) to help scientists decide whether to use the TNT library in their research. We show how to employ the TNT routines by giving examples of ground-state and dynamical calculations of one-dimensional bosonic lattice system. We also discuss different options for gaining access to the software available at www.tensornetworktheory.org.

A Security-façade Library for Virtual-observatory Software

NASA Astrophysics Data System (ADS)

Rixon, G.

2009-09-01

The security-façade library implements, for Java, IVOA's security standards. It supports the authentication mechanisms for SOAP and REST web-services, the sign-on mechanisms (with MyProxy, AstroGrid Accounts protocol or local credential-caches), the delegation protocol, and RFC3820-enabled HTTPS for Apache Tomcat. Using the façade, a developer who is not a security specialist can easily add access control to a virtual-observatory service and call secured services from an application. The library has been an internal part of AstroGrid software for some time and it is now offered for use by other developers.

The Microcomputer in the Library: VI. Implementation and Future Development.

ERIC Educational Resources Information Center

Leggate, Peter; Dyer, Hilary

1986-01-01

This sixth article in a series discusses planning for the installation and implementation of automated systems in the library, workstation design and location, scheduling of software implementation, security, data input, staff and reader training, job design, impact of automation on library procedures, evaluation of system performance, and future…

101 Computer Projects for Libraries. 101 Micro Series.

ERIC Educational Resources Information Center

Dewey, Patrick R.

The projects collected in this book represent a wide cross section of the way microcomputers are used in libraries. Each project description includes organization and contact information, hardware and software used, cost and project length estimates, and Web or print references when available. Projects come from academic and public libraries,…

Library Users: How They Adapt to Changing Roles.

ERIC Educational Resources Information Center

Miido, Helis

Traditional library tasks, for example database searching, are increasingly performed by library users, forcing both the librarian and the user to assume at times dichotomous roles of teacher and student. Modern librarians install new software and guide organizations in multimedia applications. Librarians need to be cognizant of the human factor,…

Opening up Library Automation Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Throughout the history of library automation, the author has seen a steady advancement toward more open systems. In the early days of library automation, when proprietary systems dominated, the need for standards was paramount since other means of inter-operability and data exchange weren't possible. Today's focus on Application Programming…

An Integrated Library System from Existing Microcomputer Programs.

ERIC Educational Resources Information Center

Kuntz, Lynda S.

1988-01-01

Demonstrates how three commercial microcomputer software packages--PC-Talk III, Wordstar, and dBase III--were combined to produce an integrated library system at the U.S. Army Concepts Analysis Agency library. The retrospective conversion process is discussed, and the four modules of the system are described: acquisitions/cataloging; online…

Mini-Micro CDS/ISIS in the Thailand Development Research Institute Library.

ERIC Educational Resources Information Center

Wongkoltoot, Poonsin; Indee, Somsak

1992-01-01

Describes the Thailand Development Research Institute Library's development of an integrated bibliographic system using UNESCO's Micro-ISIS software. Linkages between databases were made using an in-house application (TIBIS) written in CDS/ISIS Pascal. The library system is available on a local area network (LAN). (three references) (EA)

Washington Public Libraries Online: Collaborating in Cyberspace.

ERIC Educational Resources Information Center

Wildin, Nancy

1997-01-01

Discussion of public libraries, the Internet, and the World Wide Web focuses on development of a Web site in Washington. Highlights include access to the Internet through online public access catalogs; partnerships between various types of libraries; hardware and software; HTML training; content design; graphics design; marketing; evaluation; and…

CONTENTdm Digital Collection Management Software and End-User Efficacy

ERIC Educational Resources Information Center

Dickson, Maggie

2008-01-01

Digital libraries and collections are a growing facet of today's traditional library. Digital library technologies have become increasingly more sophisticated in the effort to provide more and better access to the collections they contain. The evaluation of the usability of these technologies has not kept pace with technological developments,…

Software To Go: A Catalog of Software Available for Loan.

ERIC Educational Resources Information Center

Kurlychek, Ken, Comp.

This catalog lists the holdings of the Software To Go software lending library and clearinghouse for programs and agencies serving students or clients who are deaf or hard of hearing. An introduction describes the clearinghouse and its collection of software, much of it commercial and copyrighted material, for Apple, Macintosh, and IBM (MS-DOS)…

A conceptual model for megaprogramming

NASA Technical Reports Server (NTRS)

Tracz, Will

1990-01-01

Megaprogramming is component-based software engineering and life-cycle management. Magaprogramming and its relationship to other research initiatives (common prototyping system/common prototyping language, domain specific software architectures, and software understanding) are analyzed. The desirable attributes of megaprogramming software components are identified and a software development model and resulting prototype megaprogramming system (library interconnection language extended by annotated Ada) are described.

Maintenance of Automated Library Systems.

ERIC Educational Resources Information Center

Epstein, Susan Baerg

1983-01-01

Discussion of the maintenance of both the software and hardware in an automated library system highlights maintenance by the vendor, contracts and costs, the maintenance log, downtime, and planning for trouble. (EJS)

ODIN-object-oriented development interface for NMR.

PubMed

Jochimsen, Thies H; von Mengershausen, Michael

2004-09-01

A cross-platform development environment for nuclear magnetic resonance (NMR) experiments is presented. It allows rapid prototyping of new pulse sequences and provides a common programming interface for different system types. With this object-oriented interface implemented in C++, the programmer is capable of writing applications to control an experiment that can be executed on different measurement devices, even from different manufacturers, without the need to modify the source code. Due to the clear design of the software, new pulse sequences can be created, tested, and executed within a short time. To post-process the acquired data, an interface to well-known numerical libraries is part of the framework. This allows a transparent integration of the data processing instructions into the measurement module. The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments. To demonstrate the capabilities of the framework, results of the same experiment, carried out on two NMR imaging systems from different manufacturers are shown and compared with the results of a simulation.

Collision of Physics and Software in the Monte Carlo Application Toolkit (MCATK)

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

Sweezy, Jeremy Ed

2016-01-21

The topic is presented in a series of slides organized as follows: MCATK overview, development strategy, available algorithms, problem modeling (sources, geometry, data, tallies), parallelism, miscellaneous tools/features, example MCATK application, recent areas of research, and summary and future work. MCATK is a C++ component-based Monte Carlo neutron-gamma transport software library with continuous energy neutron and photon transport. Designed to build specialized applications and to provide new functionality in existing general-purpose Monte Carlo codes like MCNP, it reads ACE formatted nuclear data generated by NJOY. The motivation behind MCATK was to reduce costs. MCATK physics involves continuous energy neutron & gammamore » transport with multi-temperature treatment, static eigenvalue (k eff and α) algorithms, time-dependent algorithm, and fission chain algorithms. MCATK geometry includes mesh geometries and solid body geometries. MCATK provides verified, unit-test Monte Carlo components, flexibility in Monte Carlo application development, and numerous tools such as geometry and cross section plotters.« less

An application of machine learning to the organization of institutional software repositories

NASA Technical Reports Server (NTRS)

Bailin, Sidney; Henderson, Scott; Truszkowski, Walt

1993-01-01

Software reuse has become a major goal in the development of space systems, as a recent NASA-wide workshop on the subject made clear. The Data Systems Technology Division of Goddard Space Flight Center has been working on tools and techniques for promoting reuse, in particular in the development of satellite ground support software. One of these tools is the Experiment in Libraries via Incremental Schemata and Cobweb (ElvisC). ElvisC applies machine learning to the problem of organizing a reusable software component library for efficient and reliable retrieval. In this paper we describe the background factors that have motivated this work, present the design of the system, and evaluate the results of its application.

Automated Reuse of Scientific Subroutine Libraries through Deductive Synthesis

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Pressburger, Thomas; VanBaalen, Jeffrey; Roach, Steven

1997-01-01

Systematic software construction offers the potential of elevating software engineering from an art-form to an engineering discipline. The desired result is more predictable software development leading to better quality and more maintainable software. However, the overhead costs associated with the formalisms, mathematics, and methods of systematic software construction have largely precluded their adoption in real-world software development. In fact, many mainstream software development organizations, such as Microsoft, still maintain a predominantly oral culture for software development projects; which is far removed from a formalism-based culture for software development. An exception is the limited domain of safety-critical software, where the high-assuiance inherent in systematic software construction justifies the additional cost. We believe that systematic software construction will only be adopted by mainstream software development organization when the overhead costs have been greatly reduced. Two approaches to cost mitigation are reuse (amortizing costs over many applications) and automation. For the last four years, NASA Ames has funded the Amphion project, whose objective is to automate software reuse through techniques from systematic software construction. In particular, deductive program synthesis (i.e., program extraction from proofs) is used to derive a composition of software components (e.g., subroutines) that correctly implements a specification. The construction of reuse libraries of software components is the standard software engineering solution for improving software development productivity and quality.

BASKET on-board software library

NASA Astrophysics Data System (ADS)

Luntzer, Armin; Ottensamer, Roland; Kerschbaum, Franz

2014-07-01

The University of Vienna is a provider of on-board data processing software with focus on data compression, such as used on board the highly successful Herschel/PACS instrument, as well as in the small BRITE-Constellation fleet of cube-sats. Current contributions are made to CHEOPS, SAFARI and PLATO. The effort was taken to review the various functions developed for Herschel and provide a consolidated software library to facilitate the work for future missions. This library is a shopping basket of algorithms. Its contents are separated into four classes: auxiliary functions (e.g. circular buffers), preprocessing functions (e.g. for calibration), lossless data compression (arithmetic or Rice coding) and lossy reduction steps (ramp fitting etc.). The "BASKET" has all functionality that is needed to create an on-board data processing chain. All sources are written in C, supplemented by optimized versions in assembly, targeting popular CPU architectures for space applications. BASKET is open source and constantly growing

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

Mr.CAS-A minimalistic (pure) Ruby CAS for fast prototyping and code generation

NASA Astrophysics Data System (ADS)

Ragni, Matteo

There are Computer Algebra System (CAS) systems on the market with complete solutions for manipulation of analytical models. But exporting a model that implements specific algorithms on specific platforms, for target languages or for particular numerical library, is often a rigid procedure that requires manual post-processing. This work presents a Ruby library that exposes core CAS capabilities, i.e. simplification, substitution, evaluation, etc. The library aims at programmers that need to rapidly prototype and generate numerical code for different target languages, while keeping separated mathematical expression from the code generation rules, where best practices for numerical conditioning are implemented. The library is written in pure Ruby language and is compatible with most Ruby interpreters.

Shoestring Digital Library: If Existing Digital Library Software Doesn't Suit Your Needs, Create Your Own

ERIC Educational Resources Information Center

Weber, Jonathan

2006-01-01

Creating a digital library might seem like a task best left to a large research collection with a vast staff and generous budget. However, tools for successfully creating digital libraries are getting easier to use all the time. The explosion of people creating content for the web has led to the availability of many high-quality applications and…

Preliminary Specifications (Hardware and Software) for a Center for Information Services. Final Report on Mechanized Information Services in the University Library, Phase I - Planning. Part 10.

ERIC Educational Resources Information Center

California Univ., Los Angeles. Inst. of Library Research.

The general conclusions of the planning study on Mechanized Information Services in the University Library are that such services represent a desirable, even necessary, extension of the library's traditional functions. Preliminary specifications for such a library-based "Center for Information Services" (CIS) are presented in this report. Covered…

Parallel computation and the Basis system

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

Smith, G.R.

1992-12-16

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to-use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communication costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis and Parallelmore » Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

Parallel computation and the basis system

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

Smith, G.R.

1993-05-01

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communications costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis andmore » Parallel Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

The Electronic Hermit: Trends in Library Automation.

ERIC Educational Resources Information Center

LaRue, James

1988-01-01

Reviews trends in library software development including: (1) microcomputer applications; (2) CD-ROM; (3) desktop publishing; (4) public access microcomputers; (5) artificial intelligence; (6) mainframes and minicomputers; and (7) automated catalogs. (MES)

Development of the FITS tools package for multiple software environments

NASA Technical Reports Server (NTRS)

Pence, W. D.; Blackburn, J. K.

1992-01-01

The HEASARC is developing a package of general purpose software for analyzing data files in FITS format. This paper describes the design philosophy which makes the software both machine-independent (it runs on VAXs, Suns, and DEC-stations) and software environment-independent. Currently the software can be compiled and linked to produce IRAF tasks, or alternatively, the same source code can be used to generate stand-alone tasks using one of two implementations of a user-parameter interface library. The machine independence of the software is achieved by writing the source code in ANSI standard Fortran or C, using the machine-independent FITSIO subroutine interface for all data file I/O, and using a standard user-parameter subroutine interface for all user I/O. The latter interface is based on the Fortran IRAF Parameter File interface developed at STScI. The IRAF tasks are built by linking to the IRAF implementation of this parameter interface library. Two other implementations of this parameter interface library, which have no IRAF dependencies, are now available which can be used to generate stand-alone executable tasks. These stand-alone tasks can simply be executed from the machine operating system prompt either by supplying all the task parameters on the command line or by entering the task name after which the user will be prompted for any required parameters. A first release of this FTOOLS package is now publicly available. The currently available tasks are described, along with instructions on how to obtain a copy of the software.

The Organization of a Computer Software Collection Using an Information Storage and Retrieval Software Package.

ERIC Educational Resources Information Center

Davies, Denise M.

1985-01-01

Discusses design, development, and use of a database to provide organization and access to a computer software collection at the University of Hawaii School of Library Studies. Field specifications, samples of report forms, and a description of the physical organization of the software collection are included. (MBR)

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients

NASA Astrophysics Data System (ADS)

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F.; Long, Daniel J.; Bolch, Wesley E.; Liu, Bob; Xu, X. George

2015-07-01

This paper describes the development and testing of VirtualDose—a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the ‘software as a service (SaaS)’ delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose’s functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT—two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

Observation Scheduling System

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel Q.; Rabideau, Gregg R.; Schaffer, Steven R.

2011-01-01

Software has been designed to schedule remote sensing with the Earth Observing One spacecraft. The software attempts to satisfy as many observation requests as possible considering each against spacecraft operation constraints such as data volume, thermal, pointing maneuvers, and others. More complex constraints such as temperature are approximated to enable efficient reasoning while keeping the spacecraft within safe limits. Other constraints are checked using an external software library. For example, an attitude control library is used to determine the feasibility of maneuvering between pairs of observations. This innovation can deal with a wide range of spacecraft constraints and solve large scale scheduling problems like hundreds of observations and thousands of combinations of observation sequences.

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that contains tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Frameworkmore » components from domain-relevant data.« less

Advanced data acquisition and display techniques for laser velocimetry

NASA Technical Reports Server (NTRS)

Kjelgaard, Scott O.; Weston, Robert P.

1991-01-01

The Basic Aerodynamics Research Tunnel (BART) has been equipped with state-of-the-art instrumentation for acquiring the data needed for code validation. This paper describes the three-component LDV and the workstation-based data-acquisition system (DAS) which has been developed for the BART. The DAS allows the use of automation and the quick integration of advanced instrumentation, while minimizing the software development time required between investigations. The paper also includes a description of a graphics software library developed to support the windowing environment of the DAS. The real-time displays generated using the graphics library help the researcher ensure the test is proceeding properly. The graphics library also supports the requirements of posttest data analysis. The use of the DAS and graphics libraries is illustrated by presenting examples of the real-time and postprocessing display graphics for LDV investigations.

The Use of BookshelF in Teaching Students of Information and Library Management.

ERIC Educational Resources Information Center

Rowley, Jenny E.; Fisher, Shelagh

1992-01-01

Describes how BookshelF software, a library management system, has been integrated into the library and information management curriculum at Manchester Polytechnic (England), and discusses the learning objectives that have been achieved. The use of BookshelF modules for ordering, circulation control, cataloging, OPAC (online public access…

Introduction of Electronic Book Ordering with EDIFACT in a Special Library: A Case Study.

ERIC Educational Resources Information Center

Stadler, Peter; Thomas, Martin; Mernke, Ernst

1999-01-01

Describes book ordering procedures at a German pharmaceutical library using the Electronic Data Interchange for Administration, Commerce and Transport (EDIFACT) guidelines developed by the United Nations. Topics include advantages for libraries and for the book trade, changes needed in software, productivity gains, and EDIFACT versus the Internet.…

A Survey of Popular R Packages for Cluster Analysis

ERIC Educational Resources Information Center

Flynt, Abby; Dean, Nema

2016-01-01

Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring data sets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans, and hclust functions; the mclust library; the poLCA…

Automation Challenges of the 80's: What to Do until Your Integrated Library System Arrives.

ERIC Educational Resources Information Center

Allan, Ferne C.; Shields, Joyce M.

1986-01-01

A medium-sized aerospace library has developed interim solutions to automation needs by using software and equipment that were available in-house in preparation for an expected integrated library system. Automated processes include authors' file of items authored by employees, journal routing (including routing slips), statistics, journal…

Library Information System Time-Sharing (LISTS) Project. Final Report.

ERIC Educational Resources Information Center

Black, Donald V.

The Library Information System Time-Sharing (LISTS) experiment was based on three innovations in data processing technology: (1) the advent of computer time-sharing on third-generation machines, (2) the development of general-purpose file-management software and (3) the introduction of large, library-oriented data bases. The main body of the…

Two Ways to Set Up Wireless Hotspot: Comparing Apples and Oranges

ERIC Educational Resources Information Center

Mutch, Andrew; Ventura, Karen

2006-01-01

Every place has it--coffee shops, bookstores, universities ... and now libraries are offering wireless Internet access too. At the Waterford Township Public Library (Waterford, Michigan), Andrew Mutch created a wide-open wireless network using Public IP open source software. About 20 miles away, at the Novi Public Library (Novi, Michigan), Karen…

A Tour of the Stacks--HyperCard for Libraries.

ERIC Educational Resources Information Center

Ertel, Monica; Oros, Jane

1989-01-01

Description of HyperCard, a software package that runs on Macintosh microcomputers, focuses on its use in the Apple Computer, Inc., Library as a user guide to the library. Examples of screen displays are given, and a list of resources is included to help use and understand HyperCard more completely. (LRW)

The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

ERIC Educational Resources Information Center

DeBardeleben, Marian Z.; And Others

1983-01-01

Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

Surviving the First Three Months as a Community College Library Director

ERIC Educational Resources Information Center

Kelly, Robert E., IV

2003-01-01

The experiences of a first-time community college library director during the initial three months on the job are detailed. The process of automation software migration is used as a vehicle for demonstrating activities performed to improve knowledge. Marketing, customer service, and identification of core library supporters are addressed. Concern…

The UNIX Operating System in Libraries: Advantages of LAN's and Bulletin Board Systems in Your Library.

ERIC Educational Resources Information Center

Rose, Phillip E.

1988-01-01

Describes the experiences of the AT&T Technical Library in installing a local area network (LAN) and bulletin board using the UNIX operating system. Reasons why a LAN was needed, how the system works, and hardware and software used are discussed. (1 reference) (MES)

Library and Classroom Use of Copyrighted Videotapes and Computer Software.

ERIC Educational Resources Information Center

Reed, Mary Hutchings; Stanek, Debra

Designed to provide guidance for librarians, this publication expresses the opinion of the legal counsel of the American Library Association (ALA) regarding library and classroom use of copyrighted videotapes and computer programs. A discussion of videotapes considers the impact of the Copyright Revision Act of 1976 on in-classroom use, in-library…

Visual programming for next-generation sequencing data analytics.

PubMed

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Novaresio, Valerio; García-Camprubí, María; Izquierdo, Salvador; Asinari, Pietro; Fueyo, Norberto

2012-01-01

The generation of direct current electricity using solid oxide fuel cells (SOFCs) involves several interplaying transport phenomena. Their simulation is crucial for the design and optimization of reliable and competitive equipment, and for the eventual market deployment of this technology. An open-source library for the computational modeling of mass-transport phenomena in SOFCs is presented in this article. It includes several multicomponent mass-transport models ( i.e. Fickian, Stefan-Maxwell and Dusty Gas Model), which can be applied both within porous media and in porosity-free domains, and several diffusivity models for gases. The library has been developed for its use with OpenFOAM ®, a widespread open-source code for fluid and continuum mechanics. The library can be used to model any fluid flow configuration involving multicomponent transport phenomena and it is validated in this paper against the analytical solution of one-dimensional test cases. In addition, it is applied for the simulation of a real SOFC and further validated using experimental data. Program summaryProgram title: multiSpeciesTransportModels Catalogue identifier: AEKB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 18 140 No. of bytes in distributed program, including test data, etc.: 64 285 Distribution format: tar.gz Programming language:: C++ Computer: Any x86 (the instructions reported in the paper consider only the 64 bit case for the sake of simplicity) Operating system: Generic Linux (the instructions reported in the paper consider only the open-source Ubuntu distribution for the sake of simplicity) Classification: 12 External routines: OpenFOAM® (version 1.6-ext) ( http://www.extend-project.de) Nature of problem: This software provides a library of models for the simulation of the steady state mass and momentum transport in a multi-species gas mixture, possibly in a porous medium. The software is particularly designed to be used as the mass-transport library for the modeling of solid oxide fuel cells (SOFC). When supplemented with other sub-models, such as thermal and charge-transport ones, it allows the prediction of the cell polarization curve and hence the cell performance. Solution method: Standard finite volume method (FVM) is used for solving all the conservation equations. The pressure-velocity coupling is solved using the SIMPLE algorithm (possibly adding a porous drag term if required). The mass transport can be calculated using different alternative models, namely Fick, Maxwell-Stefan or dusty gas model. The code adopts a segregated method to solve the resulting linear system of equations. The different regions of the SOFC, namely gas channels, electrodes and electrolyte, are solved independently, and coupled through boundary conditions. Restrictions: When extremely large species fluxes are considered, current implementation of the Neumann and Robin boundary conditions do not avoid negative values of molar and/or mass fractions, which finally end up with numerical instability. However this never happened in the documented runs. Eventually these boundary conditions could be reformulated to become more robust. Running time: From seconds to hours depending on the mesh size and number of species. For example, on a 64 bit machine with Intel Core Duo T8300 and 3 GBytes of RAM, the provided test run requires less than 1 second.

Performance testing of 3D point cloud software

NASA Astrophysics Data System (ADS)

Varela-González, M.; González-Jorge, H.; Riveiro, B.; Arias, P.

2013-10-01

LiDAR systems are being used widely in recent years for many applications in the engineering field: civil engineering, cultural heritage, mining, industry and environmental engineering. One of the most important limitations of this technology is the large computational requirements involved in data processing, especially for large mobile LiDAR datasets. Several software solutions for data managing are available in the market, including open source suites, however, users often unknown methodologies to verify their performance properly. In this work a methodology for LiDAR software performance testing is presented and four different suites are studied: QT Modeler, VR Mesh, AutoCAD 3D Civil and the Point Cloud Library running in software developed at the University of Vigo (SITEGI). The software based on the Point Cloud Library shows better results in the loading time of the point clouds and CPU usage. However, it is not as strong as commercial suites in working set and commit size tests.

A design for a reusable Ada library

NASA Technical Reports Server (NTRS)

Litke, John D.

1986-01-01

A goal of the Ada language standardization effort is to promote reuse of software, implying the existence of substantial software libraries and the storage/retrieval mechanisms to support them. A searching/cataloging mechanism is proposed that permits full or partial distribution of the database, adapts to a variety of searching mechanisms, permits a changine taxonomy with minimal disruption, and minimizes the requirement of specialized cataloger/indexer skills. The important observation is that key words serve not only as indexing mechanism, but also as an identification mechanism, especially via concatenation and as support for a searching mechanism. By deliberately separating these multiple uses, the modifiability and ease of growth that current libraries require, is achieved.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Putting the Library at Students' Fingertips

ERIC Educational Resources Information Center

Foley, Marianne

2012-01-01

The absence of a well-defined space for library resources within course-management systems has been well documented in library literature. Academic libraries have sought to remedy this deficiency in numerous ways. This article describes how a "library nugget," or module, was added to the Buffalo State College course-management system,…

IRISpy: Analyzing IRIS Data in Python

NASA Astrophysics Data System (ADS)

Ryan, Daniel; Christe, Steven; Mumford, Stuart; Baruah, Ankit; Timothy, Shelbe; Pereira, Tiago; De Pontieu, Bart

2017-08-01

IRISpy is a new community-developed open-source software library for analysing IRIS level 2 data. It is written in Python, a free, cross-platform, general-purpose, high-level programming language. A wide array of scientific computing software packages have already been developed in Python, from numerical computation (NumPy, SciPy, etc.), to visualization and plotting (matplotlib), to solar-physics-specific data analysis (SunPy). IRISpy is currently under development as a SunPy-affiliated package which means it depends on the SunPy library, follows similar standards and conventions, and is developed with the support of of the SunPy development team. IRISpy’s has two primary data objects, one for analyzing slit-jaw imager data and another for analyzing spectrograph data. Both objects contain basic slicing, indexing, plotting, and animating functionality to allow users to easily inspect, reduce and analyze the data. As part of this functionality the objects can output SunPy Maps, TimeSeries, Spectra, etc. of relevant data slices for easier inspection and analysis. Work is also ongoing to provide additional data analysis functionality including derivation of systematic measurement errors (e.g. readout noise), exposure time correction, residual wavelength calibration, radiometric calibration, and fine scale pointing corrections. IRISpy’s code base is publicly available through github.com and can be contributed to by anyone. In this poster we demonstrate IRISpy’s functionality and future goals of the project. We also encourage interested users to become involved in further developing IRISpy.

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

Brief descriptions are provided of general-purpose mathematical and statistical software, including 27 "stand-alone" programs, three subroutine systems, and two nationally recognized statistical packages, which are available in the Air Force Human Resources Laboratory (AFHRL) software library. This index was created to enable researchers…

Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

PubMed

Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

2013-06-01

Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert; LeCompte, Tom

2015-10-29

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

Clinical data miner: an electronic case report form system with integrated data preprocessing and machine-learning libraries supporting clinical diagnostic model research.

PubMed

Installé, Arnaud Jf; Van den Bosch, Thierry; De Moor, Bart; Timmerman, Dirk

2014-10-20

Using machine-learning techniques, clinical diagnostic model research extracts diagnostic models from patient data. Traditionally, patient data are often collected using electronic Case Report Form (eCRF) systems, while mathematical software is used for analyzing these data using machine-learning techniques. Due to the lack of integration between eCRF systems and mathematical software, extracting diagnostic models is a complex, error-prone process. Moreover, due to the complexity of this process, it is usually only performed once, after a predetermined number of data points have been collected, without insight into the predictive performance of the resulting models. The objective of the study of Clinical Data Miner (CDM) software framework is to offer an eCRF system with integrated data preprocessing and machine-learning libraries, improving efficiency of the clinical diagnostic model research workflow, and to enable optimization of patient inclusion numbers through study performance monitoring. The CDM software framework was developed using a test-driven development (TDD) approach, to ensure high software quality. Architecturally, CDM's design is split over a number of modules, to ensure future extendability. The TDD approach has enabled us to deliver high software quality. CDM's eCRF Web interface is in active use by the studies of the International Endometrial Tumor Analysis consortium, with over 4000 enrolled patients, and more studies planned. Additionally, a derived user interface has been used in six separate interrater agreement studies. CDM's integrated data preprocessing and machine-learning libraries simplify some otherwise manual and error-prone steps in the clinical diagnostic model research workflow. Furthermore, CDM's libraries provide study coordinators with a method to monitor a study's predictive performance as patient inclusions increase. To our knowledge, CDM is the only eCRF system integrating data preprocessing and machine-learning libraries. This integration improves the efficiency of the clinical diagnostic model research workflow. Moreover, by simplifying the generation of learning curves, CDM enables study coordinators to assess more accurately when data collection can be terminated, resulting in better models or lower patient recruitment costs.

ROSE Version 1.0

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

Quinlan, D.; Yi, Q.; Buduc, R.

2005-02-17

ROSE is an object-oriented software infrastructure for source-to-source translation that provides an interface for programmers to write their own specialized translators for optimizing scientific applications. ROSE is a part of current research on telescoping languages, which provides optimizations of the use of libraries in scientific applications. ROSE defines approaches to extend the optimization techniques, common in well defined languages, to the optimization of scientific applications using well defined libraries. ROSE includes a rich set of tools for generating customized transformations to support optimization of applications codes. We currently support full C and C++ (including template instantiation etc.), with Fortran 90more » support under development as part of a collaboration and contract with Rice to use their version of the open source Open64 F90 front-end. ROSE represents an attempt to define an open compiler infrastructure to handle the full complexity of full scale DOE applications codes using the languages common to scientific computing within DOE. We expect that such an infrastructure will also be useful for the development of numerous tools that may then realistically expect to work on DOE full scale applications.« less

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

von Laszewski, G.; Foster, I.; Gawor, J.

In this paper we report on the features of the Java Commodity Grid Kit. The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus protocols, allowing the Java CoG Kit to communicate also with the C Globus reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well as numerous additional libraries and frameworks developed by the Java community tomore » enable network, Internet, enterprise, and peer-to peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus software. In this paper we also report on the efforts to develop server side Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Globus jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

PRATHAM: Parallel Thermal Hydraulics Simulations using Advanced Mesoscopic Methods

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

Joshi, Abhijit S; Jain, Prashant K; Mudrich, Jaime A

2012-01-01

At the Oak Ridge National Laboratory, efforts are under way to develop a 3D, parallel LBM code called PRATHAM (PaRAllel Thermal Hydraulic simulations using Advanced Mesoscopic Methods) to demonstrate the accuracy and scalability of LBM for turbulent flow simulations in nuclear applications. The code has been developed using FORTRAN-90, and parallelized using the message passing interface MPI library. Silo library is used to compact and write the data files, and VisIt visualization software is used to post-process the simulation data in parallel. Both the single relaxation time (SRT) and multi relaxation time (MRT) LBM schemes have been implemented in PRATHAM.more » To capture turbulence without prohibitively increasing the grid resolution requirements, an LES approach [5] is adopted allowing large scale eddies to be numerically resolved while modeling the smaller (subgrid) eddies. In this work, a Smagorinsky model has been used, which modifies the fluid viscosity by an additional eddy viscosity depending on the magnitude of the rate-of-strain tensor. In LBM, this is achieved by locally varying the relaxation time of the fluid.« less

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

An open-source java platform for automated reaction mapping.

PubMed

Crabtree, John D; Mehta, Dinesh P; Kouri, Tina M

2010-09-27

This article presents software applications that have been built upon a modular, open-source, reaction mapping library that can be used in both cheminformatics and bioinformatics research. We first describe the theoretical underpinnings and modular architecture of the core software library. We then describe two applications that have been built upon that core. The first is a generic reaction viewer and mapper, and the second classifies reactions according to rules that can be modified by end users with little or no programming skills.

NRL Hyperspectral Imagery Trafficability Tool (HITT): Software andSpectral-Geotechnical Look-up Tables for Estimation and Mapping of Soil Bearing Strength from Hyperspectral Imagery

DTIC Science & Technology

2012-09-28

spectral-geotechnical libraries and models developed during remote sensing and calibration/ validation campaigns conducted by NRL and collaborating...geotechnical libraries and models developed during remote sensing and calibration/ validation campaigns conducted by NRL and collaborating institutions in four...2010; Bachmann, Fry, et al, 2012a). The NRL HITT tool is a model for how we develop and validate software, and the future development of tools by

YAP Version 4.0

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

Nelson, Eric M.

2004-05-20

The YAP software library computes (1) electromagnetic modes, (2) electrostatic fields, (3) magnetostatic fields and (4) particle trajectories in 2d and 3d models. The code employs finite element methods on unstructured grids of tetrahedral, hexahedral, prism and pyramid elements, with linear through cubic element shapes and basis functions to provide high accuracy. The novel particle tracker is robust, accurate and efficient, even on unstructured grids with discontinuous fields. This software library is a component of the MICHELLE 3d finite element gun code.

Image analysis library software development

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr.; Bryant, J.

1977-01-01

The Image Analysis Library consists of a collection of general purpose mathematical/statistical routines and special purpose data analysis/pattern recognition routines basic to the development of image analysis techniques for support of current and future Earth Resources Programs. Work was done to provide a collection of computer routines and associated documentation which form a part of the Image Analysis Library.

Two Years on: Koha 3.0 in Use at the CAMLIS Library, Royal London Homoeopathic Hospital

ERIC Educational Resources Information Center

Bissels, Gerhard; Chandler, Andrea

2010-01-01

Purpose: The purpose of this paper is to describe the further development of the Koha 3.0 library management system (LMS) and the involvement of external software consultants at the Complementary and Alternative Medicine Library and Information Service (CAMLIS), Royal London Homoeopathic Hospital. Design/methodology/approach: The paper takes the…

Expert Systems for Libraries at SCIL [Small Computers in Libraries]'88.

ERIC Educational Resources Information Center

Kochtanek, Thomas R.; And Others

1988-01-01

Six brief papers on expert systems for libraries cover (1) a knowledge-based approach to database design; (2) getting started in expert systems; (3) using public domain software to develop a business reference system; (4) a music cataloging inquiry system; (5) linguistic analysis of reference transactions; and (6) a model of a reference librarian.…

Who Moved My Intranet? The Human Side of Introducing Collaborative Technologies to Library Staff

ERIC Educational Resources Information Center

Jeffery, Keven; Dworak, Ellie

2010-01-01

Intranets can be crucial tools in fostering communication within an academic library. This article describes the successful implementation of an intranet wiki at the San Diego State University Library & Information Access. The steps involved with implementing, marketing, and supporting the MediaWiki software are described, and the results of a…

Do We Really Have an Internet Problem? Statistics, Credibility and Issues Concerning Public Internet Access in Academic Libraries.

ERIC Educational Resources Information Center

Cubbage, Charlotte

2002-01-01

Discusses problems with patron Internet access in academic libraries and describes a study conducted at Northwestern University (Illinois) that used Internet tracking software to assess user Internet behavior. Topics include Internet use policies; pornography; and loss of control over library services and information content that is provided. (LRW)

Competencies for Librarians. Proceedings from the 1985 Spring Meeting of the Nebraska Library Association: College and University Section (Omaha, Nebraska, April 26, 1985).

ERIC Educational Resources Information Center

Krzywkowski, Valerie I., Ed.

Based on the conference theme, "Competencies for Librarians," papers presented at the 1985 meeting of the association include: (1) "Planning a Library-Based Public Access Microcomputer Facility" (Suzanne Kehm); (2) "Processing and Circulating Microcomputer Software in the Academic Library: A Sharing Session" (Jan…

Experiences Using an Open Source Software Library to Teach Computer Vision Subjects

ERIC Educational Resources Information Center

Cazorla, Miguel; Viejo, Diego

2015-01-01

Machine vision is an important subject in computer science and engineering degrees. For laboratory experimentation, it is desirable to have a complete and easy-to-use tool. In this work we present a Java library, oriented to teaching computer vision. We have designed and built the library from the scratch with emphasis on readability and…

Special Features of the Advanced Loans Module of the ABCD Integrated Library System

ERIC Educational Resources Information Center

de Smet, Egbert

2011-01-01

Purpose: The "advanced loans" module of the relatively new library software, ABCD, is an addition to the normal loans module and it offers a "generic transaction decision-making engine" functionality. The module requires extra installation effort and parameterisation, so this article aims to explain to the many potentially interested libraries,…

Assessing Homegrown Library Collections: Using Google Analytics to Track Use of Screencasts and Flash-Based Learning Objects

ERIC Educational Resources Information Center

Betty, Paul

2009-01-01

Increasing use of screencast and Flash authoring software within libraries is resulting in "homegrown" library collections of digital learning objects and multimedia presentations. The author explores the use of Google Analytics to track usage statistics for interactive Shockwave Flash (.swf) files, the common file output for screencast and Flash…

Upgrading a ColdFusion-Based Academic Medical Library Staff Intranet

ERIC Educational Resources Information Center

Vander Hart, Robert; Ingrassia, Barbara; Mayotte, Kerry; Palmer, Lisa A.; Powell, Julia

2010-01-01

This article details the process of upgrading and expanding an existing academic medical library intranet to include a wiki, blog, discussion forum, and photo collection manager. The first version of the library's intranet from early 2002 was powered by ColdFusion software and existed primarily to allow staff members to author and store minutes of…

Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA

PubMed Central

Kekenes-Huskey, P. M.; Gillette, A.; Hake, J.; McCammon, J. A.

2012-01-01

We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca2+-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca2+ ATPase (SERCA). We find that a combination of diffusional encounter and internal ‘buried channel’ descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude. PMID:23293662

Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.

PubMed

Kekenes-Huskey, P M; Gillette, A; Hake, J; McCammon, J A

2012-10-31

We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca(2+) ATPase (SERCA). We find that a combination of diffusional encounter and internal 'buried channel' descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude.

Finite-element estimation of protein-ligand association rates with post-encounter effects: applications to calcium binding in troponin C and SERCA

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A.; Hake, J.; McCammon, J. A.

2012-01-01

We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca2+-binding proteins: troponin C and the sarcoplasmic reticulum Ca2+ ATPase. We find that a combination of diffusional encounter and internal ‘buried channel’ descriptions provides superior descriptions of association rates, improving estimates by orders of magnitude.

A Performance Evaluation of the Cray X1 for Scientific Applications

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Borrill, Julian; Canning, Andrew; Carter, Jonathan; Djomehri, M. Jahed; Shan, Hongzhang; Skinner, David

2004-01-01

The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end capability and cost effectiveness. However, the recent development of massively parallel vector systems is having a significant effect on the supercomputing landscape. In this paper, we compare the performance of the recently released Cray X1 vector system with that of the cacheless NEC SX-6 vector machine, and the superscalar cache-based IBM Power3 and Power4 architectures for scientific applications. Overall results demonstrate that the X1 is quite promising, but performance improvements are expected as the hardware, systems software, and numerical libraries mature. Code reengineering to effectively utilize the complex architecture may also lead to significant efficiency enhancements.

Open Source Software and the Intellectual Commons.

ERIC Educational Resources Information Center

Dorman, David

2002-01-01

Discusses the Open Source Software method of software development and its relationship to control over information content. Topics include digital library resources; reference services; preservation; the legal and economic status of information; technical standards; access to digital data; control of information use; and copyright and patent laws.…

CGNS Mid-Level Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Poirier, Diane; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: - The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media; - The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; - The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and - The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The CGNS Mid-level Library was designed to ease the implementation of CGNS by providing developers with a collection of handy I/O functions. Since knowledge of the ADF core is not required to use this library, it will greatly facilitate the task of interfacing with CGNS. There are currently 48 user callable functions that comprise the Mid-level library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Video Discs in Libraries.

ERIC Educational Resources Information Center

Barker, Philip

1986-01-01

Discussion of developments in information storage technology likely to have significant impact upon library utilization focuses on hardware (videodisc technology) and software developments (knowledge databases; computer networks; database management systems; interactive video, computer, and multimedia user interfaces). Three generic computer-based…

Perl Extension to the Bproc Library

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

Grunau, Daryl W.

2004-06-07

The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less

Extended precision data types for the development of the original computer aided engineering applications

NASA Astrophysics Data System (ADS)

Pescaru, A.; Oanta, E.; Axinte, T.; Dascalescu, A.-D.

2015-11-01

Computer aided engineering is based on models of the phenomena which are expressed as algorithms. The implementations of the algorithms are usually software applications which are processing a large volume of numerical data, regardless the size of the input data. In this way, the finite element method applications used to have an input data generator which was creating the entire volume of geometrical data, starting from the initial geometrical information and the parameters stored in the input data file. Moreover, there were several data processing stages, such as: renumbering of the nodes meant to minimize the size of the band length of the system of equations to be solved, computation of the equivalent nodal forces, computation of the element stiffness matrix, assemblation of system of equations, solving the system of equations, computation of the secondary variables. The modern software application use pre-processing and post-processing programs to easily handle the information. Beside this example, CAE applications use various stages of complex computation, being very interesting the accuracy of the final results. Along time, the development of CAE applications was a constant concern of the authors and the accuracy of the results was a very important target. The paper presents the various computing techniques which were imagined and implemented in the resulting applications: finite element method programs, finite difference element method programs, applied general numerical methods applications, data generators, graphical applications, experimental data reduction programs. In this context, the use of the extended precision data types was one of the solutions, the limitations being imposed by the size of the memory which may be allocated. To avoid the memory-related problems the data was stored in files. To minimize the execution time, part of the file was accessed using the dynamic memory allocation facilities. One of the most important consequences of the paper is the design of a library which includes the optimized solutions previously tested, that may be used for the easily development of original CAE cross-platform applications. Last but not least, beside the generality of the data type solutions, there is targeted the development of a software library which may be used for the easily development of node-based CAE applications, each node having several known or unknown parameters, the system of equations being automatically generated and solved.

Academic Libraries and High-Impact Practices for Student Retention: Library Deans' Perspectives

ERIC Educational Resources Information Center

Murray, Adam

2015-01-01

Numerous studies on retention have highlighted the role of student engagement in influencing students' withdrawal decisions. This study seeks to address how academic libraries affect student retention by examining the perception of academic library deans or directors on the alignment between library services and resources with ten nationally…

QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

PubMed

García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

2014-07-05

The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. Copyright © 2014 Wiley Periodicals, Inc.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.

PubMed

Trümbach, Dietrich; Pfeiffer, Susanne; Poppe, Manuel; Scherb, Hagen; Doll, Sebastian; Wurst, Wolfgang; Schick, Joel A

2017-11-25

As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import. We demonstrate the capabilities of ENCoRE to interrogate results from a pooled CRISPR cellular viability screen following Tumor Necrosis Factor-alpha challenge. The results not only identified stereotypical players in extrinsic apoptotic signaling but two as yet uncharacterized members of the extrinsic apoptotic cascade, Smg7 and Ces2a. We further validated and characterized cell lines containing mutations in these genes against a panel of cell death stimuli and involvement in p53 signaling. In summary, this software enables bench scientists with sensitive data or without access to informatic cores to rapidly interpret results from large scale experiments resulting from pooled CRISPR/Cas9 library screens.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

Software for Teaching Physiology and Biophysics.

ERIC Educational Resources Information Center

Weiss, Thomas F.; And Others

1992-01-01

Describes a software library developed to teach biophysics and physiology undergraduates that includes software on (1) the Hodgkin-Huxley model for excitation of action potentials in electrically excitable cells; (2) a random-walk model of diffusion; (3) single voltage-gated ion channels; (4) steady-state chemically mediated transport; and (5)…

A Public Domain Software Library for Reading and Language Arts.

ERIC Educational Resources Information Center

Balajthy, Ernest

A three-year project carried out by the Microcomputers and Reading Committee of the New Jersey Reading Association involved the collection, improvement, and distribution of free microcomputer software (public domain programs) designed to deal with reading and writing skills. Acknowledging that this free software is not without limitations (poor…

Microcomputers in Libraries: The Quiet Revolution.

ERIC Educational Resources Information Center

Boss, Richard

1985-01-01

This article defines three separate categories of microcomputers--personal, desk-top, multi-user devices--and relates storage capabilities (expandability, floppy disks) to library applications. Highlghts include de facto standards, operating systems, database management systems, applications software, circulation control systems, dumb and…

Zooming In on Copyright with Integrated Library Software Services

ERIC Educational Resources Information Center

Oye, Karen

2007-01-01

Over the last decade, many of Kelvin Smith Library's (KSL) content delivery services have gone digital, and some, such as enhanced course reserves products, are new to the market. The best digital library services have given KSL options and integrated solutions that allow it to do more than it thought possible just a few years ago. As with many…

Largenet2: an object-oriented programming library for simulating large adaptive networks.

PubMed

Zschaler, Gerd; Gross, Thilo

2013-01-15

The largenet2 C++ library provides an infrastructure for the simulation of large dynamic and adaptive networks with discrete node and link states. The library is released as free software. It is available at http://biond.github.com/largenet2. Largenet2 is licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License. gerd@biond.org

Effective e-Training: Using a Course Management System and e-Learning Tools to Train Library Employees

ERIC Educational Resources Information Center

See, Andrew; Teetor, Travis Stephen

2014-01-01

In the summer of 2012, the University of Arizona Libraries implemented an online training program to effectively train Access Services staff and student employees at a large academic research library. This article discusses the program, which was built using a course management system (D2L) and various e-Learning software applications (Articulate…

Computers in Libraries, 2000: Proceedings (15th, Washington, D.C., March 15-17, 2000).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Burmood, Jennifer, Comp.

Topics of the Proceedings of the 15th Annual Computers in Libraries Conference (March 15-17, 2000) include: Linux and open source software in an academic library; a Master Trainer Program; what educators need to know about multimedia and copyright; how super searchers find business information online; managing print costs; new technologies in wide…

Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

DTIC Science & Technology

2012-06-14

implemented a prototype DFT simulation software using two different open source Finite Element (FE) libraries: DEALII and FENICS . These two libraries have been...ATK. In the first part of this Phase I project we investigated two different candidate finite element libraries, DEAL II and FENICS . Although both...element libraries, Deal.II and FEniCS /dolfin, for use as back-ends to a finite element DFT in ATK, Quantum Insight and QuantumWise A/S, October 2011.

On the tradeoffs of programming language choice for numerical modelling in geoscience. A case study comparing modern Fortran, C++/Blitz++ and Python/NumPy.

NASA Astrophysics Data System (ADS)

Jarecka, D.; Arabas, S.; Fijalkowski, M.; Gaynor, A.

2012-04-01

The language of choice for numerical modelling in geoscience has long been Fortran. A choice of a particular language and coding paradigm comes with different set of tradeoffs such as that between performance, ease of use (and ease of abuse), code clarity, maintainability and reusability, availability of open source compilers, debugging tools, adequate external libraries and parallelisation mechanisms. The availability of trained personnel and the scale and activeness of the developer community is of importance as well. We present a short comparison study aimed at identification and quantification of these tradeoffs for a particular example of an object oriented implementation of a parallel 2D-advection-equation solver in Python/NumPy, C++/Blitz++ and modern Fortran. The main angles of comparison will be complexity of implementation, performance of various compilers or interpreters and characterisation of the "added value" gained by a particular choice of the language. The choice of the numerical problem is dictated by the aim to make the comparison useful and meaningful to geoscientists. Python is chosen as a language that traditionally is associated with ease of use, elegant syntax but limited performance. C++ is chosen for its traditional association with high performance but even higher complexity and syntax obscurity. Fortran is included in the comparison for its widespread use in geoscience often attributed to its performance. We confront the validity of these traditional views. We point out how the usability of a particular language in geoscience depends on the characteristics of the language itself and the availability of pre-existing software libraries (e.g. NumPy, SciPy, PyNGL, PyNIO, MPI4Py for Python and Blitz++, Boost.Units, Boost.MPI for C++). Having in mind the limited complexity of the considered numerical problem, we present a tentative comparison of performance of the three implementations with different open source compilers including CPython and PyPy, Clang++ and GNU g++, and GNU gfortran.

NDL-v2.0: A new version of the numerical differentiation library for parallel architectures

NASA Astrophysics Data System (ADS)

Hadjidoukas, P. E.; Angelikopoulos, P.; Voglis, C.; Papageorgiou, D. G.; Lagaris, I. E.

2014-07-01

We present a new version of the numerical differentiation library (NDL) used for the numerical estimation of first and second order partial derivatives of a function by finite differencing. In this version we have restructured the serial implementation of the code so as to achieve optimal task-based parallelization. The pure shared-memory parallelization of the library has been based on the lightweight OpenMP tasking model allowing for the full extraction of the available parallelism and efficient scheduling of multiple concurrent library calls. On multicore clusters, parallelism is exploited by means of TORC, an MPI-based multi-threaded tasking library. The new MPI implementation of NDL provides optimal performance in terms of function calls and, furthermore, supports asynchronous execution of multiple library calls within legacy MPI programs. In addition, a Python interface has been implemented for all cases, exporting the functionality of our library to sequential Python codes. Catalog identifier: AEDG_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 63036 No. of bytes in distributed program, including test data, etc.: 801872 Distribution format: tar.gz Programming language: ANSI Fortran-77, ANSI C, Python. Computer: Distributed systems (clusters), shared memory systems. Operating system: Linux, Unix. Has the code been vectorized or parallelized?: Yes. RAM: The library uses O(N) internal storage, N being the dimension of the problem. It can use up to O(N2) internal storage for Hessian calculations, if a task throttling factor has not been set by the user. Classification: 4.9, 4.14, 6.5. Catalog identifier of previous version: AEDG_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180(2009)1404 Does the new version supersede the previous version?: Yes Nature of problem: The numerical estimation of derivatives at several accuracy levels is a common requirement in many computational tasks, such as optimization, solution of nonlinear systems, and sensitivity analysis. For a large number of scientific and engineering applications, the underlying functions correspond to simulation codes for which analytical estimation of derivatives is difficult or almost impossible. A parallel implementation that exploits systems with multiple CPUs is very important for large scale and computationally expensive problems. Solution method: Finite differencing is used with a carefully chosen step that minimizes the sum of the truncation and round-off errors. The parallel versions employ both OpenMP and MPI libraries. Reasons for new version: The updated version was motivated by our endeavors to extend a parallel Bayesian uncertainty quantification framework [1], by incorporating higher order derivative information as in most state-of-the-art stochastic simulation methods such as Stochastic Newton MCMC [2] and Riemannian Manifold Hamiltonian MC [3]. The function evaluations are simulations with significant time-to-solution, which also varies with the input parameters such as in [1, 4]. The runtime of the N-body-type of problem changes considerably with the introduction of a longer cut-off between the bodies. In the first version of the library, the OpenMP-parallel subroutines spawn a new team of threads and distribute the function evaluations with a PARALLEL DO directive. This limits the functionality of the library as multiple concurrent calls require nested parallelism support from the OpenMP environment. Therefore, either their function evaluations will be serialized or processor oversubscription is likely to occur due to the increased number of OpenMP threads. In addition, the Hessian calculations include two explicit parallel regions that compute first the diagonal and then the off-diagonal elements of the array. Due to the barrier between the two regions, the parallelism of the calculations is not fully exploited. These issues have been addressed in the new version by first restructuring the serial code and then running the function evaluations in parallel using OpenMP tasks. Although the MPI-parallel implementation of the first version is capable of fully exploiting the task parallelism of the PNDL routines, it does not utilize the caching mechanism of the serial code and, therefore, performs some redundant function evaluations in the Hessian and Jacobian calculations. This can lead to: (a) higher execution times if the number of available processors is lower than the total number of tasks, and (b) significant energy consumption due to wasted processor cycles. Overcoming these drawbacks, which become critical as the time of a single function evaluation increases, was the primary goal of this new version. Due to the code restructure, the MPI-parallel implementation (and the OpenMP-parallel in accordance) avoids redundant calls, providing optimal performance in terms of the number of function evaluations. Another limitation of the library was that the library subroutines were collective and synchronous calls. In the new version, each MPI process can issue any number of subroutines for asynchronous execution. We introduce two library calls that provide global and local task synchronizations, similarly to the BARRIER and TASKWAIT directives of OpenMP. The new MPI-implementation is based on TORC, a new tasking library for multicore clusters [5-7]. TORC improves the portability of the software, as it relies exclusively on the POSIX-Threads and MPI programming interfaces. It allows MPI processes to utilize multiple worker threads, offering a hybrid programming and execution environment similar to MPI+OpenMP, in a completely transparent way. Finally, to further improve the usability of our software, a Python interface has been implemented on top of both the OpenMP and MPI versions of the library. This allows sequential Python codes to exploit shared and distributed memory systems. Summary of revisions: The revised code improves the performance of both parallel (OpenMP and MPI) implementations. The functionality and the user-interface of the MPI-parallel version have been extended to support the asynchronous execution of multiple PNDL calls, issued by one or multiple MPI processes. A new underlying tasking library increases portability and allows MPI processes to have multiple worker threads. For both implementations, an interface to the Python programming language has been added. Restrictions: The library uses only double precision arithmetic. The MPI implementation assumes the homogeneity of the execution environment provided by the operating system. Specifically, the processes of a single MPI application must have identical address space and a user function resides at the same virtual address. In addition, address space layout randomization should not be used for the application. Unusual features: The software takes into account bound constraints, in the sense that only feasible points are used to evaluate the derivatives, and given the level of the desired accuracy, the proper formula is automatically employed. Running time: Running time depends on the function's complexity. The test run took 23 ms for the serial distribution, 25 ms for the OpenMP with 2 threads, 53 ms and 1.01 s for the MPI parallel distribution using 2 threads and 2 processes respectively and yield-time for idle workers equal to 10 ms. References: [1] P. Angelikopoulos, C. Paradimitriou, P. Koumoutsakos, Bayesian uncertainty quantification and propagation in molecular dynamics simulations: a high performance computing framework, J. Chem. Phys 137 (14). [2] H.P. Flath, L.C. Wilcox, V. Akcelik, J. Hill, B. van Bloemen Waanders, O. Ghattas, Fast algorithms for Bayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial Hessian approximations, SIAM J. Sci. Comput. 33 (1) (2011) 407-432. [3] M. Girolami, B. Calderhead, Riemann manifold Langevin and Hamiltonian Monte Carlo methods, J. R. Stat. Soc. Ser. B (Stat. Methodol.) 73 (2) (2011) 123-214. [4] P. Angelikopoulos, C. Paradimitriou, P. Koumoutsakos, Data driven, predictive molecular dynamics for nanoscale flow simulations under uncertainty, J. Phys. Chem. B 117 (47) (2013) 14808-14816. [5] P.E. Hadjidoukas, E. Lappas, V.V. Dimakopoulos, A runtime library for platform-independent task parallelism, in: PDP, IEEE, 2012, pp. 229-236. [6] C. Voglis, P.E. Hadjidoukas, D.G. Papageorgiou, I. Lagaris, A parallel hybrid optimization algorithm for fitting interatomic potentials, Appl. Soft Comput. 13 (12) (2013) 4481-4492. [7] P.E. Hadjidoukas, C. Voglis, V.V. Dimakopoulos, I. Lagaris, D.G. Papageorgiou, Supporting adaptive and irregular parallelism for non-linear numerical optimization, Appl. Math. Comput. 231 (2014) 544-559.

SCIL Executive Summaries.

ERIC Educational Resources Information Center

Samuels, Alan R.; And Others

1987-01-01

These five papers by speakers at the Small Computers in Libraries 1987 conference include: "Acquiring and Using Shareware in Building Small Scale Automated Information systems" (Samuels); "A Software Lending Collection" (Talab); "Providing Subject Access to Microcomputer Software" (Mitchell); "Interfacing Vendor…

Computers and Library Management.

ERIC Educational Resources Information Center

Cooke, Deborah M.; And Others

1985-01-01

This five-article section discusses changes in the management of the school library resulting from use of the computer. Topics covered include data management programs (record keeping, word processing, and bibliographies); practical applications of a database; evaluation of "Circulation Plus" software; ergonomics and computers; and…

Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions

EPA Science Inventory

Cheminformatics-based software tools can predict the molecular structure of transformation products using a library of transformation reaction schemes. This paper presents the development of such a library for abiotic hydrolysis of organic chemicals under environmentally relevant...

The Electronic Library Workstation--Today.

ERIC Educational Resources Information Center

Nolte, James

1990-01-01

Describes the components--hardware, software and applications, CD-ROM and online reference resources, and telecommunications links--of an electronic library workstation in use at Clarkson University (Potsdam, New York). Data manipulation, a hypothetical research scenario, and recommended workstation capabilities are also discussed. (MES)

DiffPy-CMI-Python libraries for Complex Modeling Initiative

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

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Videotex--The Library of the Future.

ERIC Educational Resources Information Center

Mischo, Lare; Hegarty, Kevin

1982-01-01

Discusses a presentation prepared by Boeing Computer Services in cooperation with the Tacoma Public Library staff, which demonstrates the potential of interactive cable systems based on the Canadian Telidon system. Features of this videotex system, software, and equipment, including microcomputers, are noted. (EJS)

PMD2HD--a web tool aligning a PubMed search results page with the local German Cancer Research Centre library collection.

PubMed

Bohne-Lang, Andreas; Lang, Elke; Taube, Anke

2005-06-27

Web-based searching is the accepted contemporary mode of retrieving relevant literature, and retrieving as many full text articles as possible is a typical prerequisite for research success. In most cases only a proportion of references will be directly accessible as digital reprints through displayed links. A large number of references, however, have to be verified in library catalogues and, depending on their availability, are accessible as print holdings or by interlibrary loan request. The problem of verifying local print holdings from an initial retrieval set of citations can be solved using Z39.50, an ANSI protocol for interactively querying library information systems. Numerous systems include Z39.50 interfaces and therefore can process Z39.50 interactive requests. However, the programmed query interaction command structure is non-intuitive and inaccessible to the average biomedical researcher. For the typical user, it is necessary to implement the protocol within a tool that hides and handles Z39.50 syntax, presenting a comfortable user interface. PMD2HD is a web tool implementing Z39.50 to provide an appropriately functional and usable interface to integrate into the typical workflow that follows an initial PubMed literature search, providing users with an immediate asset to assist in the most tedious step in literature retrieval, checking for subscription holdings against a local online catalogue. PMD2HD can facilitate literature access considerably with respect to the time and cost of manual comparisons of search results with local catalogue holdings. The example presented in this article is related to the library system and collections of the German Cancer Research Centre. However, the PMD2HD software architecture and use of common Z39.50 protocol commands allow for transfer to a broad range of scientific libraries using Z39.50-compatible library information systems.

Geospatial Data Stream Processing in Python Using FOSS4G Components

NASA Astrophysics Data System (ADS)

McFerren, G.; van Zyl, T.

2016-06-01

One viewpoint of current and future IT systems holds that there is an increase in the scale and velocity at which data are acquired and analysed from heterogeneous, dynamic sources. In the earth observation and geoinformatics domains, this process is driven by the increase in number and types of devices that report location and the proliferation of assorted sensors, from satellite constellations to oceanic buoy arrays. Much of these data will be encountered as self-contained messages on data streams - continuous, infinite flows of data. Spatial analytics over data streams concerns the search for spatial and spatio-temporal relationships within and amongst data "on the move". In spatial databases, queries can assess a store of data to unpack spatial relationships; this is not the case on streams, where spatial relationships need to be established with the incomplete data available. Methods for spatially-based indexing, filtering, joining and transforming of streaming data need to be established and implemented in software components. This article describes the usage patterns and performance metrics of a number of well known FOSS4G Python software libraries within the data stream processing paradigm. In particular, we consider the RTree library for spatial indexing, the Shapely library for geometric processing and transformation and the PyProj library for projection and geodesic calculations over streams of geospatial data. We introduce a message oriented Python-based geospatial data streaming framework called Swordfish, which provides data stream processing primitives, functions, transports and a common data model for describing messages, based on the Open Geospatial Consortium Observations and Measurements (O&M) and Unidata Common Data Model (CDM) standards. We illustrate how the geospatial software components are integrated with the Swordfish framework. Furthermore, we describe the tight temporal constraints under which geospatial functionality can be invoked when processing high velocity, potentially infinite geospatial data streams. The article discusses the performance of these libraries under simulated streaming loads (size, complexity and volume of messages) and how they can be deployed and utilised with Swordfish under real load scenarios, illustrated by a set of Vessel Automatic Identification System (AIS) use cases. We conclude that the described software libraries are able to perform adequately under geospatial data stream processing scenarios - many real application use cases will be handled sufficiently by the software.

An Overview of Public Access Computer Software Management Tools for Libraries

ERIC Educational Resources Information Center

Wayne, Richard

2004-01-01

An IT decision maker gives an overview of public access PC software that's useful in controlling session length and scheduling, Internet access, print output, security, and the latest headaches: spyware and adware. In this article, the author describes a representative sample of software tools in several important categories such as setup…

Surgical pathology report in the era of desktop publishing.

PubMed

Pillarisetti, S G

1993-01-01

Since it is believed that "a picture is worth a thousand words," incorporation of computer-generated line art was used as a adjunct to gross description in surgical pathology reporting in selected cases. The lack of an integrated software program was overcome by using commercially available graphic and word processing software. A library of drawings was developed over the last few years. Most time-consuming is the development of templates and the graphic library. With some effort it is possible to integrate graphics of high quality into surgical pathology reports.

AstroBus On-Board Software

NASA Astrophysics Data System (ADS)

Biscarros, D.; Cantenot, C.; Séronie-Vivien, J.; Schmidt, G.

AstroBus on-board software is a customisable software for ERC32 based avionics implementing standard ESA Packet Utilization Standard functions. Its architecture based on generic design templates and relying on a library providing standard PUS TC, TM and event services enhances its reusability on various programs. Finally, AstroBus on-board software development and validation environment is based on last generation tools providing an optimised customisation environment.

Adaptive Integration of Nonsmooth Dynamical Systems

DTIC Science & Technology

2017-10-11

controlled time stepping method to interactively design running robots. [1] John Shepherd, Samuel Zapolsky, and Evan M. Drumwright, “Fast multi-body...software like this to test software running on my robots. Started working in simulation after attempting to use software like this to test software... running on my robots. The libraries that produce these beautiful results have failed at simulating robotic manipulation. Postulate: It is easier to

Airland Battlefield Environment (ALBE) Tactical Decision Aid (TDA) Demonstration Program,

DTIC Science & Technology

1987-11-12

Management System (DBMS) software, GKS graphics libraries, and user interface software. These components of the ATB system software architecture will be... knowlede base ano auqent the decision mak:n• process by providing infocr-mation useful in the formulation and execution of battlefield strategies...Topographic Laboratories as an Engineer. Ms. Capps is managing the software development of the AirLand Battlefield Environment (ALBE) geographic

TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks

NASA Astrophysics Data System (ADS)

Kazantsev, Daniil; Pickalov, Valery; Nagella, Srikanth; Pasca, Edoardo; Withers, Philip J.

2018-01-01

In the field of computerized tomographic imaging, many novel reconstruction techniques are routinely tested using simplistic numerical phantoms, e.g. the well-known Shepp-Logan phantom. These phantoms cannot sufficiently cover the broad spectrum of applications in CT imaging where, for instance, smooth or piecewise-smooth 3D objects are common. TomoPhantom provides quick access to an external library of modular analytical 2D/3D phantoms with temporal extensions. In TomoPhantom, quite complex phantoms can be built using additive combinations of geometrical objects, such as, Gaussians, parabolas, cones, ellipses, rectangles and volumetric extensions of them. Newly designed phantoms are better suited for benchmarking and testing of different image processing techniques. Specifically, tomographic reconstruction algorithms which employ 2D and 3D scanning geometries, can be rigorously analyzed using the software. TomoPhantom also provides a capability of obtaining analytical tomographic projections which further extends the applicability of software towards more realistic, free from the "inverse crime" testing. All core modules of the package are written in the C-OpenMP language and wrappers for Python and MATLAB are provided to enable easy access. Due to C-based multi-threaded implementation, volumetric phantoms of high spatial resolution can be obtained with computational efficiency.

An Object-Oriented Network-Centric Software Architecture for Physical Computing

NASA Astrophysics Data System (ADS)

Palmer, Richard

1997-08-01

Recent developments in object-oriented computer languages and infrastructure such as the Internet, Web browsers, and the like provide an opportunity to define a more productive computational environment for scientific programming that is based more closely on the underlying mathematics describing physics than traditional programming languages such as FORTRAN or C++. In this talk I describe an object-oriented software architecture for representing physical problems that includes classes for such common mathematical objects as geometry, boundary conditions, partial differential and integral equations, discretization and numerical solution methods, etc. In practice, a scientific program written using this architecture looks remarkably like the mathematics used to understand the problem, is typically an order of magnitude smaller than traditional FORTRAN or C++ codes, and hence easier to understand, debug, describe, etc. All objects in this architecture are ``network-enabled,'' which means that components of a software solution to a physical problem can be transparently loaded from anywhere on the Internet or other global network. The architecture is expressed as an ``API,'' or application programmers interface specification, with reference embeddings in Java, Python, and C++. A C++ class library for an early version of this API has been implemented for machines ranging from PC's to the IBM SP2, meaning that phidentical codes run on all architectures.

Using Modern Design Tools for Digital Avionics Development

NASA Technical Reports Server (NTRS)

Hyde, David W.; Lakin, David R., II; Asquith, Thomas E.

2000-01-01

Using Modem Design Tools for Digital Avionics Development Shrinking development time and increased complexity of new avionics forces the designer to use modem tools and methods during hardware development. Engineers at the Marshall Space Flight Center have successfully upgraded their design flow and used it to develop a Mongoose V based radiation tolerant processor board for the International Space Station's Water Recovery System. The design flow, based on hardware description languages, simulation, synthesis, hardware models, and full functional software model libraries, allowed designers to fully simulate the processor board from reset, through initialization before any boards were built. The fidelity of a digital simulation is limited to the accuracy of the models used and how realistically the designer drives the circuit's inputs during simulation. By using the actual silicon during simulation, device modeling errors are reduced. Numerous design flaws were discovered early in the design phase when they could be easily fixed. The use of hardware models and actual MIPS software loaded into full functional memory models also provided checkout of the software development environment. This paper will describe the design flow used to develop the processor board and give examples of errors that were found using the tools. An overview of the processor board firmware will also be covered.

Assessing the accuracy of software predictions of mammalian and microbial metabolites

EPA Science Inventory

New chemical development and hazard assessments benefit from accurate predictions of mammalian and microbial metabolites. Fourteen biotransformation libraries encoded in eight software packages that predict metabolite structures were assessed for their sensitivity (proportion of ...

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

Below the Surface: New Tools--And Savvy Librarians--Are Turning the ILS into a Gold Mine for Making More Informed Decisions

ERIC Educational Resources Information Center

Cummins, Caroline

2006-01-01

In this article, the author discusses the benefits offered by integrated library systems (ILS) for making more informed decisions. Library software vendors, realizing ILS products can reveal business intelligence, have begun to offer tools like Director's Station to help library managers get more out of their data, and librarians are taking…

Characterizing and Modeling the Cost of Rework in a Library of Reusable Software Components

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Condon, Steven E.; ElEmam, Khaled; Hendrick, Robert B.; Melo, Walcelio

1997-01-01

In this paper we characterize and model the cost of rework in a Component Factory (CF) organization. A CF is responsible for developing and packaging reusable software components. Data was collected on corrective maintenance activities for the Generalized Support Software reuse asset library located at the Flight Dynamics Division of NASA's GSFC. We then constructed a predictive model of the cost of rework using the C4.5 system for generating a logical classification model. The predictor variables for the model are measures of internal software product attributes. The model demonstrates good prediction accuracy, and can be used by managers to allocate resources for corrective maintenance activities. Furthermore, we used the model to generate proscriptive coding guidelines to improve programming, practices so that the cost of rework can be reduced in the future. The general approach we have used is applicable to other environments.

The Advent of Portals.

ERIC Educational Resources Information Center

Jackson, Mary E.

2002-01-01

Explains portals as tools that gather a variety of electronic information resources, including local library resources, into a single Web page. Highlights include cross-database searching; integration with university portals and course management software; the ARL (Association of Research Libraries) Scholars Portal Initiative; and selected vendors…

Technology and Microcomputers for an Information Centre/Special Library.

ERIC Educational Resources Information Center

Daehn, Ralph M.

1984-01-01

Discusses use of microcomputer hardware and software, telecommunications methods, and advanced library methods to create a specialized information center's database of literature relating to farm machinery and food processing. Systems and services (electronic messaging, serials control, database creation, cataloging, collections, circulation,…

The Virginia Tech Library System (VTLS).

ERIC Educational Resources Information Center

McGrath, Deborah Hall; Lee, Carl R.

1989-01-01

Discusses topics relating to the Virginia Tech Library System: the company (VTLS, Inc.); the software; data structure; cataloging, status, and authority control; circulation; serials control and acquisitions; the online catalog; management reporting; networking; and the operating environment. Sidebars discuss the Vanilla Network; LINNEA--a network…

75 FR 32692 - Schools and Libraries Universal Service Support Mechanism

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-09

..., wireless Internet access applications, and web hosting. We propose to revise the Commission's rules to.../anti-spam software, scheduling services, wireless Internet access applications, and web hosting should... schools and libraries may receive discounts for eligible telecommunications services, Internet access, and...

HONEI: A collection of libraries for numerical computations targeting multiple processor architectures

NASA Astrophysics Data System (ADS)

van Dyk, Danny; Geveler, Markus; Mallach, Sven; Ribbrock, Dirk; Göddeke, Dominik; Gutwenger, Carsten

2009-12-01

We present HONEI, an open-source collection of libraries offering a hardware oriented approach to numerical calculations. HONEI abstracts the hardware, and applications written on top of HONEI can be executed on a wide range of computer architectures such as CPUs, GPUs and the Cell processor. We demonstrate the flexibility and performance of our approach with two test applications, a Finite Element multigrid solver for the Poisson problem and a robust and fast simulation of shallow water waves. By linking against HONEI's libraries, we achieve a two-fold speedup over straight forward C++ code using HONEI's SSE backend, and additional 3-4 and 4-16 times faster execution on the Cell and a GPU. A second important aspect of our approach is that the full performance capabilities of the hardware under consideration can be exploited by adding optimised application-specific operations to the HONEI libraries. HONEI provides all necessary infrastructure for development and evaluation of such kernels, significantly simplifying their development. Program summaryProgram title: HONEI Catalogue identifier: AEDW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 No. of lines in distributed program, including test data, etc.: 216 180 No. of bytes in distributed program, including test data, etc.: 1 270 140 Distribution format: tar.gz Programming language: C++ Computer: x86, x86_64, NVIDIA CUDA GPUs, Cell blades and PlayStation 3 Operating system: Linux RAM: at least 500 MB free Classification: 4.8, 4.3, 6.1 External routines: SSE: none; [1] for GPU, [2] for Cell backend Nature of problem: Computational science in general and numerical simulation in particular have reached a turning point. The revolution developers are facing is not primarily driven by a change in (problem-specific) methodology, but rather by the fundamental paradigm shift of the underlying hardware towards heterogeneity and parallelism. This is particularly relevant for data-intensive problems stemming from discretisations with local support, such as finite differences, volumes and elements. Solution method: To address these issues, we present a hardware aware collection of libraries combining the advantages of modern software techniques and hardware oriented programming. Applications built on top of these libraries can be configured trivially to execute on CPUs, GPUs or the Cell processor. In order to evaluate the performance and accuracy of our approach, we provide two domain specific applications; a multigrid solver for the Poisson problem and a fully explicit solver for 2D shallow water equations. Restrictions: HONEI is actively being developed, and its feature list is continuously expanded. Not all combinations of operations and architectures might be supported in earlier versions of the code. Obtaining snapshots from http://www.honei.org is recommended. Unusual features: The considered applications as well as all library operations can be run on NVIDIA GPUs and the Cell BE. Running time: Depending on the application, and the input sizes. The Poisson solver executes in few seconds, while the SWE solver requires up to 5 minutes for large spatial discretisations or small timesteps. References:http://www.nvidia.com/cuda. http://www.ibm.com/developerworks/power/cell.

Implementing the HDF-EOS5 software library for data products in the UNAVCO InSAR archive

NASA Astrophysics Data System (ADS)

Baker, Scott; Meertens, Charles; Crosby, Christopher

2017-04-01

UNAVCO is a non-profit university-governed consortium that operates the U.S. National Science Foundation (NSF) Geodesy Advancing Geosciences and EarthScope (GAGE) facility and provides operational support to the Western North America InSAR Consortium (WInSAR). The seamless synthetic aperture radar archive (SSARA) is a seamless distributed access system for SAR data and higher-level data products. Under the NASA-funded SSARA project, a user-contributed InSAR archive for interferograms, time series, and other derived data products was developed at UNAVCO. The InSAR archive development has led to the adoption of the HDF-EOS5 data model, file format, and library. The HDF-EOS software library was designed to support NASA Earth Observation System (EOS) science data products and provides data structures for radar geometry (Swath) and geocoded (Grid) data based on the HDF5 data model and file format provided by the HDF Group. HDF-EOS5 inherits the benefits of HDF5 (open-source software support, internal compression, portability, support for structural data, self-describing file metadata enhanced performance, and xml support) and provides a way to standardize InSAR data products. Instrument- and datatype-independent services, such as subsetting, can be applied to files across a wide variety of data products through the same library interface. The library allows integration with GIS software packages such as ArcGIS and GDAL, conversion to other data formats like NetCDF and GeoTIFF, and is extensible with new data structures to support future requirements. UNAVCO maintains a GitHub repository that provides example software for creating data products from popular InSAR processing software packages like GMT5SAR and ISCE as well as examples for reading and converting the data products into other formats. Digital object identifiers (DOI) have been incorporated into the InSAR archive allowing users to assign a permanent location for their processed result and easily reference the final data products. A metadata attribute is added to the HDF-EOS5 file when a DOI is minted for a data product. These data products are searchable through the SSARA federated query providing access to processed data for both expert and non-expert InSAR users. The archive facilitates timely distribution of processed data with particular importance for geohazards and event response.

Level 1 Processing of MODIS Direct Broadcast Data From Terra

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Smith, Peter; Shotland, Larry; El-Ghazawi, Tarek; Zhu, Ming

2000-01-01

In February 2000, an effort was begun to adapt the Moderate Resolution Imaging Spectroradiometer (MODIS) Level 1 production software to process direct broadcast data. Three Level 1 algorithms have been adapted and packaged for release: Level 1A converts raw (level 0) data into Hierarchical Data Format (HDF), unpacking packets into scans; Geolocation computes geographic information for the data points in the Level 1A; and the Level 1B computes geolocated, calibrated radiances from the Level 1A and Geolocation products. One useful aspect of adapting the production software is the ability to incorporate enhancements contributed by the MODIS Science Team. We have therefore tried to limit changes to the software. However, in order to process the data immediately on receipt, we have taken advantage of a branch in the geolocation software that reads orbit and altitude information from the packets themselves, rather than external ancillary files used in standard production. We have also verified that the algorithms can be run with smaller time increments (2.5 minutes) than the five-minute increments used in production. To make the code easier to build and run, we have simplified directories and build scripts. Also, dependencies on a commercial numerics library have been replaced by public domain software. A version of the adapted code has been released for Silicon Graphics machines running lrix. Perhaps owing to its origin in production, the software is rather CPU-intensive. Consequently, a port to Linux is underway, followed by a version to run on PC clusters, with an eventual goal of running in near-real-time (i.e., process a ten-minute pass in ten minutes).

SLUG - stochastically lighting up galaxies - III. A suite of tools for simulated photometry, spectroscopy, and Bayesian inference with stochastic stellar populations

NASA Astrophysics Data System (ADS)

Krumholz, Mark R.; Fumagalli, Michele; da Silva, Robert L.; Rendahl, Theodore; Parra, Jonathan

2015-09-01

Stellar population synthesis techniques for predicting the observable light emitted by a stellar population have extensive applications in numerous areas of astronomy. However, accurate predictions for small populations of young stars, such as those found in individual star clusters, star-forming dwarf galaxies, and small segments of spiral galaxies, require that the population be treated stochastically. Conversely, accurate deductions of the properties of such objects also require consideration of stochasticity. Here we describe a comprehensive suite of modular, open-source software tools for tackling these related problems. These include the following: a greatly-enhanced version of the SLUG code introduced by da Silva et al., which computes spectra and photometry for stochastically or deterministically sampled stellar populations with nearly arbitrary star formation histories, clustering properties, and initial mass functions; CLOUDY_SLUG, a tool that automatically couples SLUG-computed spectra with the CLOUDY radiative transfer code in order to predict stochastic nebular emission; BAYESPHOT, a general-purpose tool for performing Bayesian inference on the physical properties of stellar systems based on unresolved photometry; and CLUSTER_SLUG and SFR_SLUG, a pair of tools that use BAYESPHOT on a library of SLUG models to compute the mass, age, and extinction of mono-age star clusters, and the star formation rate of galaxies, respectively. The latter two tools make use of an extensive library of pre-computed stellar population models, which are included in the software. The complete package is available at http://www.slugsps.com.

Translation table for DOE/OSTI - COSATI bibliographic records to MARC format records

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

Gursky, K.; Holtkamp, I.; Landenberger, S.

1985-11-01

This report contains the recommendations of the committee for the conversion of data in OSTI fields to MARC fields. It is intended as a tool for OSTI to use in developing software that would enable DOE libraries to download OSTI records into MARC-based systems. Goal is to transfer as complete a set of data for each record as possible. No attempt was made to incorporate changes in the use of numerical tags that OSTI has made over the years. In addition, there are a few OSTI fields generated for internal OSTI use only, or that cannot be transferred into anymore » MARC field in the Books format; these OSTI fields have been designated as ''not converted'' in the table.« less

A Performance Evaluation of the Cray X1 for Scientific Applications

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Borrill, Julian; Canning, Andrew; Carter, Jonathan; Djomehri, M. Jahed; Shan, Hongzhang; Skinner, David

2003-01-01

The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end capability and capacity computers because of their generality, scalability, and cost effectiveness. However, the recent development of massively parallel vector systems is having a significant effect on the supercomputing landscape. In this paper, we compare the performance of the recently-released Cray X1 vector system with that of the cacheless NEC SX-6 vector machine, and the superscalar cache-based IBM Power3 and Power4 architectures for scientific applications. Overall results demonstrate that the X1 is quite promising, but performance improvements are expected as the hardware, systems software, and numerical libraries mature. Code reengineering to effectively utilize the complex architecture may also lead to significant efficiency enhancements.

Release of RANKERN 16A

NASA Astrophysics Data System (ADS)

Bird, Adam; Murphy, Christophe; Dobson, Geoff

2017-09-01

RANKERN 16 is the latest version of the point-kernel gamma radiation transport Monte Carlo code from AMEC Foster Wheeler's ANSWERS Software Service. RANKERN is well established in the UK shielding community for radiation shielding and dosimetry assessments. Many important developments have been made available to users in this latest release of RANKERN. The existing general 3D geometry capability has been extended to include import of CAD files in the IGES format providing efficient full CAD modelling capability without geometric approximation. Import of tetrahedral mesh and polygon surface formats has also been provided. An efficient voxel geometry type has been added suitable for representing CT data. There have been numerous input syntax enhancements and an extended actinide gamma source library. This paper describes some of the new features and compares the performance of the new geometry capabilities.

Why Students Should Use Multimedia.

ERIC Educational Resources Information Center

Bucher, Katherine

1995-01-01

Examines benefits of multimedia presentation software for teachers, librarians, and elementary and secondary school students. Discusses an example of two school library media specialists working with an English class using the library's reference collection (print and CD-ROM) and HyperCard. Suggests presentation assignments for various subjects.…

Microcomputers and Workstations in Libraries: Trends and Opportunities.

ERIC Educational Resources Information Center

Welsch, Erwin K.

1990-01-01

Summarizes opinions of scholars in various disciplines on workstation history, definition, and functions. Networks and configurations for library workstations, including hardware and software recommendations, are described. The impact of workstations on the workplace resulting in task, process, and institutional transformation, is also considered.…

Exploring Planet PDA: The Librarian as Astronaut, Innovator, and Expert.

ERIC Educational Resources Information Center

Galganski, Carol; Peters, Tom; Bell, Lori

2002-01-01

Describes the integration of personal digital assistants into a medical center library's services in Illinois. Discusses training for users; hardware selection; software selection and content; technical support; the role of libraries, including the creation of policies and procedures; and future challenges. (LRW)

The Future of Library Automation in Schools.

ERIC Educational Resources Information Center

Anderson, Elaine

2000-01-01

Addresses the future of library automation programs for schools. Discusses requirements of emerging OPACs and circulation systems; the Schools Interoperability Framework (SIF), an industry initiatives to develop an open specification for ensuring that K-12 instructional and administrative software applications work together more effectively; home…

Providing Services to Virtual Patrons.

ERIC Educational Resources Information Center

Hulshof, Robert

1999-01-01

Discusses the types of services libraries need to support patrons who access the library via the Internet or e-mail. Highlights include issues in technical support; establishing policies and procedures; tools for technical support, including hardware and software; impacts of technical support on staff; and future possibilities. (LRW)

Protecting Public-Access Computers in Libraries.

ERIC Educational Resources Information Center

King, Monica

1999-01-01

Describes one public library's development of a computer-security plan, along with helpful products used. Discussion includes Internet policy, physical protection of hardware, basic protection of the operating system and software on the network, browser dilemmas and maintenance, creating clear intuitive interface, and administering fair use and…

Virtually Usable: A Test of the Information Gardens

ERIC Educational Resources Information Center

Johnson, Megan; Ochoa, Louise; Purpur, Geraldine

2007-01-01

This paper presents the results of a usability study conducted to determine the functionality of a desktop, three-dimensional virtual library designed and supported by the Appalachian State University Distance Learning Library Services team. Formative evaluations were performed with representative students utilizing Morae software. Results…

75 FR 25185 - Broadband Initiatives Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

..., excluding desktop or laptop computers, computer hardware and software (including anti-virus, anti-spyware, and other security software), audio or video equipment, computer network components... 10 desktop or laptop computers and individual workstations to be located within the rural library...

A portable structural analysis library for reaction networks.

PubMed

Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri; Medley, Kyle; Sauro, Herbert M

2018-07-01

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural). Copyright © 2018 Elsevier B.V. All rights reserved.

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Evaluation of Soft Tissue Sarcoma Tumors Electrical Conductivity Anisotropy Using Diffusion Tensor Imaging for Numerical Modeling on Electroporation.

PubMed

Ghazikhanlou-Sani, K; Firoozabadi, S M P; Agha-Ghazvini, L; Mahmoodzadeh, H

2016-06-01

There is many ways to assessing the electrical conductivity anisotropy of a tumor. Applying the values of tissue electrical conductivity anisotropy is crucial in numerical modeling of the electric and thermal field distribution in electroporation treatments. This study aims to calculate the tissues electrical conductivity anisotropy in patients with sarcoma tumors using diffusion tensor imaging technique. A total of 3 subjects were involved in this study. All of patients had clinically apparent sarcoma tumors at the extremities. The T1, T2 and DTI images were performed using a 3-Tesla multi-coil, multi-channel MRI system. The fractional anisotropy (FA) maps were performed using the FSL (FMRI software library) software regarding the DTI images. The 3D matrix of the FA maps of each area (tumor, normal soft tissue and bone/s) was reconstructed and the anisotropy matrix was calculated regarding to the FA values. The mean FA values in direction of main axis in sarcoma tumors were ranged between 0.475-0.690.  With assumption of isotropy of the electrical conductivity, the FA value of electrical conductivity at each X, Y and Z coordinate axes would be equal to 0.577. The gathered results showed that there is a mean error band of 20% in electrical conductivity, if the electrical conductivity anisotropy not concluded at the calculations. The comparison of FA values showed that there is a significant statistical difference between the mean FA value of tumor and normal soft tissues (P<0.05). DTI is a feasible technique for the assessment of electrical conductivity anisotropy of tissues.  It is crucial to quantify the electrical conductivity anisotropy data of tissues for numerical modeling of electroporation treatments.

SAM Theory Manual

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

Hu, Rui

The System Analysis Module (SAM) is an advanced and modern system analysis tool being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM development aims for advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability for reactor transient analyses. To facilitate the code development, SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SAM focuses on modeling advanced reactormore » concepts such as SFRs (sodium fast reactors), LFRs (lead-cooled fast reactors), and FHRs (fluoride-salt-cooled high temperature reactors) or MSRs (molten salt reactors). These advanced concepts are distinguished from light-water reactors in their use of single-phase, low-pressure, high-temperature, and low Prandtl number (sodium and lead) coolants. As a new code development, the initial effort has been focused on modeling and simulation capabilities of heat transfer and single-phase fluid dynamics responses in Sodium-cooled Fast Reactor (SFR) systems. The system-level simulation capabilities of fluid flow and heat transfer in general engineering systems and typical SFRs have been verified and validated. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As the code is still under ongoing development, this SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.« less

Providing Access to CD-ROM Databases in a Campus Setting. Part II: Networking CD-ROMs via a LAN.

ERIC Educational Resources Information Center

Koren, Judy

1992-01-01

The second part of a report on CD-ROM networking in libraries describes LAN (local area network) technology; networking software and towers; gateway software for connecting to campuswide networks; Macintosh LANs; and network licenses. Several product and software reviews are included, and a sidebar lists vendor addresses. (NRP)

Research flight software engineering and MUST, an integrated system of support tools

NASA Technical Reports Server (NTRS)

Straeter, T. A.; Foudriat, E. C.; Will, R. W.

1977-01-01

Consideration is given to software development to support NASA flight research. The Multipurpose User-Oriented Software Technology (MUST) program, designed to integrate digital systems into flight research, is discussed. Particular attention is given to the program's special interactive user interface, subroutine library, assemblers, compiler, automatic documentation tools, and test and simulation subsystems.

"Computers: Cure-All or Snake Oil?" Proceedings from the Spring Meeting of the Nebraska Library Association, College and University Section (Bellevue, Nebraska, April 20, 1984).

ERIC Educational Resources Information Center

Krzywkowski, Valerie I., Ed.

The 15 papers in this collection discuss various aspects of computer use in libraries and several other aspects of library service not directly related to computers. Following an introduction and a list of officers, the papers are: (1) "Criminal Justice and Related Databases" (Kate E. Adams); (2) "Software and Hard Thought:…

Using geographic information systems to identify prospective marketing areas for a special library.

PubMed

McConnaughy, Rozalynd P; Wilson, Steven P

2006-05-04

The Center for Disability Resources (CDR) Library is the largest collection of its kind in the Southeastern United States, consisting of over 5,200 books, videos/DVDs, brochures, and audiotapes covering a variety of disability-related topics, from autism to transition resources. The purpose of the library is to support the information needs of families, faculty, students, staff, and other professionals in South Carolina working with individuals with disabilities. The CDR Library is funded on a yearly basis; therefore, maintaining high usage is crucial. A variety of promotional efforts have been used to attract new patrons to the library. Anyone in South Carolina can check out materials from the library, and most of the patrons use the library remotely by requesting materials, which are then mailed to them. The goal of this project was to identify areas of low geographic usage as a means of identifying locations for future library marketing efforts. Nearly four years worth of library statistics were compiled in a spreadsheet that provided information per county on the number of checkouts, the number of renewals, and the population. Five maps were created using ArcView GIS software to create visual representations of patron checkout and renewal behavior per county. Out of the 46 counties in South Carolina, eight counties never checked out materials from the library. As expected urban areas and counties near the library's physical location have high usage totals. The visual representation of the data made identification of low usage regions easier than using a standalone database with no visual-spatial component. The low usage counties will be the focus of future Center for Disability Resources Library marketing efforts. Due to the impressive visual-spatial representations created with Geographic Information Systems, which more efficiently communicate information than stand-alone database information can, librarians may benefit from the software's use as a supplemental tool for tracking library usage and planning promotional efforts.

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

PubMed

Sand, Andreas; Kristiansen, Martin; Pedersen, Christian N S; Mailund, Thomas

2013-11-22

Hidden Markov models are widely used for genome analysis as they combine ease of modelling with efficient analysis algorithms. Calculating the likelihood of a model using the forward algorithm has worst case time complexity linear in the length of the sequence and quadratic in the number of states in the model. For genome analysis, however, the length runs to millions or billions of observations, and when maximising the likelihood hundreds of evaluations are often needed. A time efficient forward algorithm is therefore a key ingredient in an efficient hidden Markov model library. We have built a software library for efficiently computing the likelihood of a hidden Markov model. The library exploits commonly occurring substrings in the input to reuse computations in the forward algorithm. In a pre-processing step our library identifies common substrings and builds a structure over the computations in the forward algorithm which can be reused. This analysis can be saved between uses of the library and is independent of concrete hidden Markov models so one preprocessing can be used to run a number of different models.Using this library, we achieve up to 78 times shorter wall-clock time for realistic whole-genome analyses with a real and reasonably complex hidden Markov model. In one particular case the analysis was performed in less than 8 minutes compared to 9.6 hours for the previously fastest library. We have implemented the preprocessing procedure and forward algorithm as a C++ library, zipHMM, with Python bindings for use in scripts. The library is available at http://birc.au.dk/software/ziphmm/.

The JPL Library information retrieval system

NASA Technical Reports Server (NTRS)

Walsh, J.

1975-01-01

The development, capabilities, and products of the computer-based retrieval system of the Jet Propulsion Laboratory Library are described. The system handles books and documents, produces a book catalog, and provides a machine search capability. Programs and documentation are available to the public through NASA's computer software dissemination program.

Bibliographic Utilities and the Use of Microcomputers in Libraries: Current and Projected Practices.

ERIC Educational Resources Information Center

McAninch, Glen

1986-01-01

Bibliographic utilities are marketing specially designed hardware and software that permit libraries to patch together automated cataloging, acquisitions, serials control, reference, online public catalogs, circulation, interlibrary loan, and administrative functions. The increasing complexity of the technology is making it more difficult to…

Development and Evaluation of a Measure of Library Automation.

ERIC Educational Resources Information Center

Pungitore, Verna L.

1986-01-01

Construct validity and reliability estimates indicate that study designed to measure utilization of automation in public and academic libraries was successful in tentatively identifying and measuring three subdimensions of level of automation: quality of hardware, method of software development, and number of automation specialists. Questionnaire…

Public Access Workstations in the Library: New Trends.

ERIC Educational Resources Information Center

Beecher, Henry

1991-01-01

Discusses the use of microcomputer-based workstations that are provided for public access in libraries. Criteria for workstations are discussed, including standard hardware, open-design software, scalable interface, and connectivity options for networking; systems that provide full-text access are described; and the need for standards is…

Search without Boundaries Using Simple APIs

ERIC Educational Resources Information Center

Tong, Qi (Helen)

2009-01-01

The U.S. Geological Survey (USGS) Library, where the author serves as the digital services librarian, is increasingly challenged to make it easier for users to find information from many heterogeneous information sources. Information is scattered throughout different software applications (i.e., library catalog, federated search engine, link…

Ringling School of Art and Design Builds a CASTLE.

ERIC Educational Resources Information Center

Morse, Yvonne; Davis, Wendy

1984-01-01

Describes the development and installation of the Computer Automated Software for the Total Library Environment System (CASTLE), which uses a microcomputer to automate operations of small academic library in six main areas: circulation, online catalog, inventory and file maintenance, audiovisual equipment, accounting, and information and…

Imaging Technology in Libraries: Photo CD Offers New Possibilities.

ERIC Educational Resources Information Center

Beiser, Karl

1993-01-01

Describes Kodak's Photo CD technology, a format for the storage and retrieval of photographic images in electronic form. Highlights include current and future Photo CD formats; computer imaging technology; ownership issues; hardware for using Photo CD; software; library and information center applications, including image collections and…

The Quebec National Library on the Web.

ERIC Educational Resources Information Center

Kieran, Shirley; Sauve, Diane

1997-01-01

Provides an overview of the Quebec National Library (Bibliotheque Nationale du Quebec, or BNQ) Web site. Highlights include issues related to content, design, and technology; IRIS, the BNQ online public access catalog; development of the multimedia catalog; software; digitization of documents; links to bibliographic records; and future…

Going Prime Time with Live Chat Reference.

ERIC Educational Resources Information Center

Hoag, Tara J.; Cichanowicz, Edana McCaffrey

2001-01-01

Describes the development of the Suffolk Cooperative Library System's live, online chat reference service, a pilot project for public libraries in Suffolk County (New York). Topics include chat software selection; a virtual reference collection; marketing; funding; staffing; evaluation; expanded hours of service; email; and extracting data from…

Design of Inhouse Automated Library Systems.

ERIC Educational Resources Information Center

Cortez, Edwin M.

1984-01-01

Examines six steps inherent to development of in-house automated library system: (1) problem definition, (2) requirement specifications, (3) analysis of alternatives and solutions, (4, 5) design and implementation of hardware and software, and (6) evaluation. Practical method for comparing and weighting options is illustrated and explained. A…

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)

Tips for Good Electronic Presentations.

ERIC Educational Resources Information Center

Strasser, Dennis

1996-01-01

Describes library uses of presentation graphics software and offers tips for creating electronic presentations. Tips include: audience retention; visual aid options; software package options; presentation planning; presentation showing; and use of text, colors, and graphics. Sidebars note common presentation errors and popular presentation…

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries.

PubMed

Heigwer, Florian; Zhan, Tianzuo; Breinig, Marco; Winter, Jan; Brügemann, Dirk; Leible, Svenja; Boutros, Michael

2016-03-24

Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.

The Keck keyword layer

NASA Technical Reports Server (NTRS)

Conrad, A. R.; Lupton, W. F.

1992-01-01

Each Keck instrument presents a consistent software view to the user interface programmer. The view consists of a small library of functions, which are identical for all instruments, and a large set of keywords, that vary from instrument to instrument. All knowledge of the underlying task structure is hidden from the application programmer by the keyword layer. Image capture software uses the same function library to collect data for the image header. Because the image capture software and the instrument control software are built on top of the same keyword layer, a given observation can be 'replayed' by extracting keyword-value pairs from the image header and passing them back to the control system. The keyword layer features non-blocking as well as blocking I/O. A non-blocking keyword write operation (such as setting a filter position) specifies a callback to be invoked when the operation is complete. A non-blocking keyword read operation specifies a callback to be invoked whenever the keyword changes state. The keyword-callback style meshes well with the widget-callback style commonly used in X window programs. The first keyword library was built for the two Keck optical instruments. More recently, keyword libraries have been developed for the infrared instruments and for telescope control. Although the underlying mechanisms used for inter-process communication by each of these systems vary widely (Lick MUSIC, Sun RPC, and direct socket I/O, respectively), a basic user interface has been written that can be used with any of these systems. Since the keyword libraries are bound to user interface programs dynamically at run time, only a single set of user interface executables is needed. For example, the same program, 'xshow', can be used to display continuously the telescope's position, the time left in an instrument's exposure, or both values simultaneously. Less generic tools that operate on specific keywords, for example an X display that controls optical instrument exposures, have also been written using the keyword layer.

The software and algorithms for hyperspectral data processing

NASA Astrophysics Data System (ADS)

Shyrayeva, Anhelina; Martinov, Anton; Ivanov, Victor; Katkovsky, Leonid

2017-04-01

Hyperspectral remote sensing technique is widely used for collecting and processing -information about the Earth's surface objects. Hyperspectral data are combined to form a three-dimensional (x, y, λ) data cube. Department of Aerospace Research of the Institute of Applied Physical Problems of the Belarusian State University presents a general model of the software for hyperspectral image data analysis and processing. The software runs in Windows XP/7/8/8.1/10 environment on any personal computer. This complex has been has been written in C++ language using QT framework and OpenGL for graphical data visualization. The software has flexible structure that consists of a set of independent plugins. Each plugin was compiled as Qt Plugin and represents Windows Dynamic library (dll). Plugins can be categorized in terms of data reading types, data visualization (3D, 2D, 1D) and data processing The software has various in-built functions for statistical and mathematical analysis, signal processing functions like direct smoothing function for moving average, Savitzky-Golay smoothing technique, RGB correction, histogram transformation, and atmospheric correction. The software provides two author's engineering techniques for the solution of atmospheric correction problem: iteration method of refinement of spectral albedo's parameters using Libradtran and analytical least square method. The main advantages of these methods are high rate of processing (several minutes for 1 GB data) and low relative error in albedo retrieval (less than 15%). Also, the software supports work with spectral libraries, region of interest (ROI) selection, spectral analysis such as cluster-type image classification and automatic hypercube spectrum comparison by similarity criterion with similar ones from spectral libraries, and vice versa. The software deals with different kinds of spectral information in order to identify and distinguish spectrally unique materials. Also, the following advantages should be noted: fast and low memory hypercube manipulation features, user-friendly interface, modularity, and expandability.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

The challenges of archiving networked-based multimedia performances (Performance cryogenics)

NASA Astrophysics Data System (ADS)

Cohen, Elizabeth; Cooperstock, Jeremy; Kyriakakis, Chris

2002-11-01

Music archives and libraries have cultural preservation at the core of their charters. New forms of art often race ahead of the preservation infrastructure. The ability to stream multiple synchronized ultra-low latency streams of audio and video across a continent for a distributed interactive performance such as music and dance with high-definition video and multichannel audio raises a series of challenges for the architects of digital libraries and those responsible for cultural preservation. The archiving of such performances presents numerous challenges that go beyond simply recording each stream. Case studies of storage and subsequent retrieval issues for Internet2 collaborative performances are discussed. The development of shared reality and immersive environments generate issues about, What constitutes an archived performance that occurs across a network (in multiple spaces over time)? What are the families of necessary metadata to reconstruct this virtual world in another venue or era? For example, if the network exhibited changes in latency the performers most likely adapted. In a future recreation, the latency will most likely be completely different. We discuss the parameters of immersive environment acquisition and rendering, network architectures, software architecture, musical/choreographic scores, and environmental acoustics that must be considered to address this problem.

Prediction of rarefied micro-nozzle flows using the SPARTA library

NASA Astrophysics Data System (ADS)

Deschenes, Timothy R.; Grot, Jonathan

2016-11-01

The accurate numerical prediction of gas flows within micro-nozzles can help evaluate the performance and enable the design of optimal configurations for micro-propulsion systems. Viscous effects within the large boundary layers can have a strong impact on the nozzle performance. Furthermore, the variation in collision length scales from continuum to rarefied preclude the use of continuum-based computational fluid dynamics. In this paper, we describe the application of a massively parallel direct simulation Monte Carlo (DSMC) library to predict the steady-state and transient flow through a micro-nozzle. The nozzle's geometric configuration is described in a highly flexible manner to allow for the modification of the geometry in a systematic fashion. The transient simulation highlights a strong shock structure that forms within the converging portion of the nozzle when the expanded gas interacts with the nozzle walls. This structure has a strong impact on the buildup of the gas in the nozzle and affects the boundary layer thickness beyond the throat in the diverging section of the nozzle. Future work will look to examine the transient thrust and integrate this simulation capability into a web-based rarefied gas dynamics prediction software, which is currently under development.

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

von Laszewski, G.; Gawor, J.; Lane, P.

In this paper we report on the features of the Java Commodity Grid Kit (Java CoG Kit). The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus Toolkit protocols, allowing the Java CoG Kit to also communicate with the services distributed as part of the C Globus Toolkit reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well asmore » numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise and peer-to-peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus Toolkit software. In this paper we also report on the efforts to develop serverside Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Grid jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

Beam Instrument Development System

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

DOOLITTLE, LAWRENCE; HUANG, GANG; DU, QIANG

Beam Instrumentation Development System (BIDS) is a collection of common support libraries and modules developed during a series of Low-Level Radio Frequency (LLRF) control and timing/synchronization projects. BIDS includes a collection of Hardware Description Language (HDL) libraries and software libraries. The BIDS can be used for the development of any FPGA-based system, such as LLRF controllers. HDL code in this library is generic and supports common Digital Signal Processing (DSP) functions, FPGA-specific drivers (high-speed serial link wrappers, clock generation, etc.), ADC/DAC drivers, Ethernet MAC implementation, etc.

System and method for memory allocation in a multiclass memory system

DOEpatents

Loh, Gabriel; Meswani, Mitesh; Ignatowski, Michael; Nutter, Mark

2016-06-28

A system for memory allocation in a multiclass memory system includes a processor coupleable to a plurality of memories sharing a unified memory address space, and a library store to store a library of software functions. The processor identifies a type of a data structure in response to a memory allocation function call to the library for allocating memory to the data structure. Using the library, the processor allocates portions of the data structure among multiple memories of the multiclass memory system based on the type of the data structure.

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

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

Tomopy is a Python toolbox to perform x-ray data processing, image reconstruction and data exchange tasks at synchrotron facilities. The dependencies of the software are currently as follows: -Python related python standard library (http://docs.python.org/2/library/) numpy (http://www.numpy.org/) scipy (http://scipy.org/) matplotlib (http://matplotlip.org/) sphinx (http://sphinx-doc.org) pil (http://www.pythonware.com/products/pil/) pyhdf (http://pysclint.sourceforge.net/pyhdf/) h5py (http://www.h5py.org) pywt (http://www.pybytes.com/pywavelets/) file.py (https://pyspec.svn.sourceforge.net/svnroot/pyspec/trunk/pyspec/ccd/files.py) -C/C++ related: gridec (anonymous?? C-code written back in 1997 that uses standard C library) fftw (http://www.fftw.org/) tomoRecon (multi-threaded C++ verion of gridrec. Author: Mark Rivers from APS. http://cars9.uchicago.edu/software/epics/tomoRecon.html) epics (http://www.aps.anl.gov/epics/)

Particle-in-cell code library for numerical simulation of the ECR source plasma

NASA Astrophysics Data System (ADS)

Shirkov, G.; Alexandrov, V.; Preisendorf, V.; Shevtsov, V.; Filippov, A.; Komissarov, R.; Mironov, V.; Shirkova, E.; Strekalovsky, O.; Tokareva, N.; Tuzikov, A.; Vatulin, V.; Vasina, E.; Fomin, V.; Anisimov, A.; Veselov, R.; Golubev, A.; Grushin, S.; Povyshev, V.; Sadovoi, A.; Donskoi, E.; Nakagawa, T.; Yano, Y.

2003-05-01

The project ;Numerical simulation and optimization of ion accumulation and production in multicharged ion sources; is funded by the International Science and Technology Center (ISTC). A summary of recent project development and the first version of a computer code library for simulation of electron-cyclotron resonance (ECR) source plasmas based on the particle-in-cell method are presented.

Virtual Libraries: Interactive Support Software and an Application in Chaotic Models.

ERIC Educational Resources Information Center

Katsirikou, Anthi; Skiadas, Christos; Apostolou, Apostolos; Rompogiannakis, Giannis

This paper begins with a discussion of the characteristics and the singularity of chaotic systems, including dynamic systems theory, chaotic orbit, fractals, chaotic attractors, and characteristics of chaotic systems. The second section addresses the digital libraries (DL) concept and the appropriateness of chaotic models, including definition and…

Administrative Issues in Planning a Library End User Searching Program. ERIC Digest.

ERIC Educational Resources Information Center

Machovec, George S.

This digest presents a reprint of an article which examines management principles that should be considered when implementing library end user searching programs. A brief discussion of specific implementation issues includes needs assessment, hardware, software, training, budgeting, what systems to offer, publicity and marketing, policies and…

Working toward Transparency in Library Automation

ERIC Educational Resources Information Center

Breeding, Marshall

2007-01-01

In this article, the author argues the need for transparency with regard to the automation systems used in libraries. As librarians make decisions regarding automation software and services, they should have convenient access to information about the organizations it will potentially acquire technology from and about the collective experiences of…

The Librarian and the Library User: What the Future Holds.

ERIC Educational Resources Information Center

Electronic Library, 1997

1997-01-01

Discusses the role of information professionals in the future, based on a session at the Online Information 96 conference in London (England). Topics include equipment and software needs; technological advances; a trend toward distance education; how library users are adapting to change; interlibrary loans; online public access catalogs; and…

15 CFR 734.7 - Published information and software.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Ready availability at libraries open to the public or at university libraries (See supplement No. 1 to this part, Question A(6)); (3) Patents and open (published) patent applications available at any patent office; and (4) Release at an open conference, meeting, seminar, trade show, or other open gathering. (i...

15 CFR 734.7 - Published information and software.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Ready availability at libraries open to the public or at university libraries (See Supplement No. 1 to this part, Question A(6)); (3) Patents and open (published) patent applications available at any patent office; and (4) Release at an open conference, meeting, seminar, trade show, or other open gathering. (i...

Directory of Library Automation Software, Systems, and Services. 1998 Edition.

ERIC Educational Resources Information Center

Cibbarelli, Pamela R., Ed.; Cibbarelli, Shawn E., Ed.

This book includes basic information to locate and compare available options for library automation based on various criteria such as hardware requirements, operating systems, components and applications, and price, and provides the necessary contact information to allow further investigation. The major part of the directory lists 211 software…

"Library Quarterly," 1956-2004: An Exploratory Bibliometric Analysis

ERIC Educational Resources Information Center

Young, Arthur P.

2006-01-01

"Library Quarterly's" seventy-fifth anniversary invites an analysis of the journal's bibliometric dimension, including contributor attributes, various author rankings, and citation impact. Eugene Garfield's HistCite software, linked to Thomson Scientific's Web of Science, as made available by Garfield, for the period 1956-2004, was used as the…

Tracking the Integration of Library Skills in the Curriculum.

ERIC Educational Resources Information Center

Gill, Suzanne L.

2003-01-01

Describes the use of IMSeries software, a relational database capable of implementing curriculum design, in an elementary school. Topics include Big6 research skills; tracking the scope and sequence of curriculum; tying library skills to curricular disciplines; information literacy; and examples of a lesson unit and assessment strategy. (LRW)

Distance Education and Virtual Reference: Where Are We Headed?

ERIC Educational Resources Information Center

Coffman, Steve

2001-01-01

Discusses changes in distance education and considers the resulting need for new types of library services. Topics include new Web-based contact center software; how to conduct virtual reference interviews; online reference service; the role of the physical library; staffing changes; and future possibilities, including impacts on costs of library…

Making Information Available to Partially Sighted and Blind Clients.

ERIC Educational Resources Information Center

Long, C. A.

1993-01-01

Provides an empirical review of problems facing library users with visual impairments using computers, and reviews some of the technology that can help alleviate these problems. Highlights include software; GUI (Graphical User Interfaces); advising and training; library automation; and appendices that list further sources of relevant information.…

CD-ROM and Local Area Networks.

ERIC Educational Resources Information Center

Marks, Kenneth E.; And Others

1993-01-01

This special section on local area networks includes three articles: (1) a description of migration at Joyner Library, East Carolina University (North Carolina) to a new network server; (2) a discussion of factors to consider for network planning in school libraries; and (3) a directory of companies supplying cable, hardware, software, and…

Retrospective Catalog Conversion in Mid-Sized Law Libraries: Some Practical Guidelines for Automation.

ERIC Educational Resources Information Center

Riger, Robert E.

1992-01-01

Discusses retrospective catalog conversion from the viewpoint of a law firm library. Topics discussed include reasons for retrospective conversion; preplanning; suggestions for the selection of software; conducting an inventory of the collection; sources of MARC bibliographic records; setting up an online public access catalog; and marketing…

Apocalypse Soon? The Bug.

ERIC Educational Resources Information Center

Clyde, Anne

1999-01-01

Discussion of the Year 2000 (Y2K) problem, the computer-code problem that affects computer programs or computer chips, focuses on the impact on teacher-librarians. Topics include automated library systems, access to online information services, library computers and software, and other electronic equipment such as photocopiers and fax machines.…

Laser Printing for a Variety of Library Applications.

ERIC Educational Resources Information Center

Kelly, Glen J.

1988-01-01

Summarizes the current status of laser printers in terms of cost, hardware and software requirements, measurement and operational considerations, ease of use, and maintenance. The cost effectiveness of laser printing in libraries for applications such as spine labels, purchase orders, and reports, is explored. (9 notes with references) (CLB)

Assessing the Effectiveness of Online Library Instruction with Finance Students

ERIC Educational Resources Information Center

Friehs, Curt G.; Craig, Cindy L.

2008-01-01

Many academic librarians use online information literacy tutorials as an alternative or a supplement to in-class library instruction. Tutorials created with streaming media software such as Camtasia Studio have become increasingly popular. Librarians at a mid-sized Midwestern university have created several such tutorials demonstrating various…

Information Resources on Microcomputers in Libraries: Public Services. A Selected ERIC Bibliography.

ERIC Educational Resources Information Center

ERIC Clearinghouse on Information Resources, Syracuse, NY.

Twelve articles published between 1982 and 1984 and cited in "Current Index to Journals in Education" are listed in this bibliography on public service applications of microcomputers in libraries. Topics include provision of free public access to microcomputers (justification, objectives, equipment specifications, uses and software,…

Modular Filter and Source-Management Upgrade of RADAC

NASA Technical Reports Server (NTRS)

Lanzi, R. James; Smith, Donna C.

2007-01-01

In an upgrade of the Range Data Acquisition Computer (RADAC) software, a modular software object library was developed to implement required functionality for filtering of flight-vehicle-tracking data and management of tracking-data sources. (The RADAC software is used to process flight-vehicle metric data for realtime display in the Wallops Flight Facility Range Control Center and Mobile Control Center.)

An Enhanced Z39.50 Gateway to the WorldWideWeb.

ERIC Educational Resources Information Center

Cunningham, David; Sloan, Stephen

1994-01-01

Describes how a university library uses the WorldWideWeb (WWW) to enable users to access resources mounted on a local Z39.50 server and to order prints from articles stored on a CD-ROM jukebox. The software used in the construction of the system, necessary modifications to the software, and software ordering information are covered. (KRN)

Campus Energy Model for Control and Performance Validation

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

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

An Automation Survival Guide for Media Centers.

ERIC Educational Resources Information Center

Whaley, Roger E.

1989-01-01

Reviews factors that should affect the decision to automate a school media center and offers suggestions for the automation process. Topics discussed include getting the library collection ready for automation, deciding what automated functions are needed, evaluating software vendors, selecting software, and budgeting. (CLB)

Deductive Verification of Cryptographic Software

NASA Technical Reports Server (NTRS)

Almeida, Jose Barcelar; Barbosa, Manuel; Pinto, Jorge Sousa; Vieira, Barbara

2009-01-01

We report on the application of an off-the-shelf verification platform to the RC4 stream cipher cryptographic software implementation (as available in the openSSL library), and introduce a deductive verification technique based on self-composition for proving the absence of error propagation.

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Selecting Data-Base Management Software for Microcomputers in Libraries and Information Units.

ERIC Educational Resources Information Center

Pieska, K. A. O.

1986-01-01

Presents a model for the evaluation of database management systems software from the viewpoint of librarians and information specialists. The properties of data management systems, database management systems, and text retrieval systems are outlined and compared. (10 references) (CLB)

Toward a digital library strategy for a National Information Infrastructure

NASA Technical Reports Server (NTRS)

Coyne, Robert A.; Hulen, Harry

1993-01-01

Bills currently before the House and Senate would give support to the development of a National Information Infrastructure, in which digital libraries and storage systems would be an important part. A simple model is offered to show the relationship of storage systems, software, and standards to the overall information infrastructure. Some elements of a national strategy for digital libraries are proposed, based on the mission of the nonprofit National Storage System Foundation.

A verification library for multibody simulation software

NASA Technical Reports Server (NTRS)

Kim, Sung-Soo; Haug, Edward J.; Frisch, Harold P.

1989-01-01

A multibody dynamics verification library, that maintains and manages test and validation data is proposed, based on RRC Robot arm and CASE backhoe validation and a comparitive study of DADS, DISCOS, and CONTOPS that are existing public domain and commercial multibody dynamic simulation programs. Using simple representative problems, simulation results from each program are cross checked, and the validation results are presented. Functionalities of the verification library are defined, in order to automate validation procedure.

Use of OsiriX in developing a digital radiology teaching library.

PubMed

Shamshuddin, S; Matthews, H R

2014-10-01

Widespread adoption of digital imaging in clinical practice and for the image-based examinations of the Royal College of Radiologists has created a desire to provide a digital radiology teaching library in many hospital departments around the UK. This article describes our experience of using OsiriX software in developing digital radiology teaching libraries. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Integration of New Technology in Army Libraries

DTIC Science & Technology

1982-07-02

libraries in Alaska that belong to WLN. However, three of the NIorth American bibliographic utilities either are marketing minicomputer-based systems...OCLC and UT’LAS3) or a vendor will be marketing a suitable -66- modificatioxi of the software to operate on a minicomputer (WLN/BLIS). There is no...integrated and contain more II special ,features than the Claremont system which OCLC currently is marketing . -75- OCLC’s Claremont Total Library System (TLS

The Weapons Laboratory Technical Library: Automating with ’Stilas’

DTIC Science & Technology

1990-03-01

version of the system to LC in October 1988. -X- A small business specializing in library automation, SIRSI was founded in 1979 by library and...computer specialists, and has a strong reputation based upon the success of their UNIX-based Unicorn Collection Management System. SIRSI offers a complete...system based on the Unicorn and BRS/ Search systems. The contracted STILAS package includes UNISYS hardware, software written in the C language

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

The Astrophysics Source Code Library: Supporting software publication and citation

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net), established in 1999, is a free online registry for source codes used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using the unique ascl ID assigned to each code. In addition to registering codes, the ASCL can house archive files for download and assign them DOIs. The ASCL advocations for software citation on par with article citation, participates in multidiscipinary events such as Force11, OpenCon, and the annual Workshop on Sustainable Software for Science, works with journal publishers, and organizes Special Sessions and Birds of a Feather meetings at national and international conferences such as Astronomical Data Analysis Software and Systems (ADASS), European Week of Astronomy and Space Science, and AAS meetings. In this presentation, I will discuss some of the challenges of gathering credit for publishing software and ideas and efforts from other disciplines that may be useful to astronomy.

A Comparison of Science and Technology Funding for DoD’s Space and Nonspace Programs

DTIC Science & Technology

2008-01-15

Artificial intelligence for HAARP Multispectral signature libraries Environmental conditions that Ionospheric prediction HAARP Weather software for...Hardware and software for solar HAARP Electromagnetic interference for Plasma theory in the space Subproject details were not available Subproject

Software Products - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You astronomy. Available as Fortran, C, or Python source code. Current version: 3.1 Software Products by Our computer or programmable calculator. Standards Of Fundamental Astronomy (SOFA) Libraries The International

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

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

Generalized Support Software: Domain Analysis and Implementation

NASA Technical Reports Server (NTRS)

Stark, Mike; Seidewitz, Ed

1995-01-01

For the past five years, the Flight Dynamics Division (FDD) at NASA's Goddard Space Flight Center has been carrying out a detailed domain analysis effort and is now beginning to implement Generalized Support Software (GSS) based on this analysis. GSS is part of the larger Flight Dynamics Distributed System (FDDS), and is designed to run under the FDDS User Interface / Executive (UIX). The FDD is transitioning from a mainframe based environment to systems running on engineering workstations. The GSS will be a library of highly reusable components that may be configured within the standard FDDS architecture to quickly produce low-cost satellite ground support systems. The estimates for the first release is that this library will contain approximately 200,000 lines of code. The main driver for developing generalized software is development cost and schedule improvement. The goal is to ultimately have at least 80 percent of all software required for a spacecraft mission (within the domain supported by the GSS) to be configured from the generalized components.

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

acme: The Amendable Coal-Fire Modeling Exercise. A C++ Class Library for the Numerical Simulation of Coal-Fires

NASA Astrophysics Data System (ADS)

Wuttke, Manfred W.

2017-04-01

At LIAG, we use numerical models to develop and enhance understanding of coupled transport processes and to predict the dynamics of the system under consideration. Topics include geothermal heat utilization, subrosion processes, and spontaneous underground coal fires. Although the details make it inconvenient if not impossible to apply a single code implementation to all systems, their investigations go along similar paths: They all depend on the solution of coupled transport equations. We thus saw a need for a modular code system with open access for the various communities to maximize the shared synergistic effects. To this purpose we develop the oops! ( open object-oriented parallel solutions) - toolkit, a C++ class library for the numerical solution of mathematical models of coupled thermal, hydraulic and chemical processes. This is used to develop problem-specific libraries like acme( amendable coal-fire modeling exercise), a class library for the numerical simulation of coal-fires and applications like kobra (Kohlebrand, german for coal-fire), a numerical simulation code for standard coal-fire models. Basic principle of the oops!-code system is the provision of data types for the description of space and time dependent data fields, description of terms of partial differential equations (pde), their discretisation and solving methods. Coupling of different processes, described by their particular pde is modeled by an automatic timescale-ordered operator-splitting technique. acme is a derived coal-fire specific application library, depending on oops!. If specific functionalities of general interest are implemented and have been tested they will be assimilated into the main oops!-library. Interfaces to external pre- and post-processing tools are easily implemented. Thus a construction kit which can be arbitrarily amended is formed. With the kobra-application constructed with acme we study the processes and propagation of shallow coal seam fires in particular in Xinjiang, China, as well as analyze and interpret results from lab experiments.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

seismo-live: Training in Computational Seismology using Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Igel, H.; Krischer, L.; van Driel, M.; Tape, C.

2016-12-01

Practical training in computational methodologies is still underrepresented in Earth science curriculae despite the increasing use of sometimes highly sophisticated simulation technologies in research projects. At the same time well-engineered community codes make it easy to return simulation-based results yet with the danger that the inherent traps of numerical solutions are not well understood. It is our belief that training with highly simplified numerical solutions (here to the equations describing elastic wave propagation) with carefully chosen elementary ingredients of simulation technologies (e.g., finite-differencing, function interpolation, spectral derivatives, numerical integration) could substantially improve this situation. For this purpose we have initiated a community platform (www.seismo-live.org) where Python-based Jupyter notebooks can be accessed and run without and necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow combining markup language, graphics, equations with interactive, executable python codes. We demonstrate the potential with training notebooks for the finite-difference method, pseudospectral methods, finite/spectral element methods, the finite-volume and the discontinuous Galerkin method. The platform already includes general Python training, introduction to the ObsPy library for seismology as well as seismic data processing and noise analysis. Submission of Jupyter notebooks for general seismology are encouraged. The platform can be used for complementary teaching in Earth Science courses on compute-intensive research areas.

A finite-element toolbox for the stationary Gross-Pitaevskii equation with rotation

NASA Astrophysics Data System (ADS)

Vergez, Guillaume; Danaila, Ionut; Auliac, Sylvain; Hecht, Frédéric

2016-12-01

We present a new numerical system using classical finite elements with mesh adaptivity for computing stationary solutions of the Gross-Pitaevskii equation. The programs are written as a toolbox for FreeFem++ (www.freefem.org), a free finite-element software available for all existing operating systems. This offers the advantage to hide all technical issues related to the implementation of the finite element method, allowing to easily code various numerical algorithms. Two robust and optimized numerical methods were implemented to minimize the Gross-Pitaevskii energy: a steepest descent method based on Sobolev gradients and a minimization algorithm based on the state-of-the-art optimization library Ipopt. For both methods, mesh adaptivity strategies are used to reduce the computational time and increase the local spatial accuracy when vortices are present. Different run cases are made available for 2D and 3D configurations of Bose-Einstein condensates in rotation. An optional graphical user interface is also provided, allowing to easily run predefined cases or with user-defined parameter files. We also provide several post-processing tools (like the identification of quantized vortices) that could help in extracting physical features from the simulations. The toolbox is extremely versatile and can be easily adapted to deal with different physical models.

BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

PubMed Central

Vidaurre, Carmen; Sander, Tilmann H.; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. PMID:21437227

BioSig: the free and open source software library for biomedical signal processing.

PubMed

Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

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

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Guide to Library Research in Chicano Studies.

ERIC Educational Resources Information Center

Guerena, Salvador; Gonzales, Raquel Quiroz

Designed to acquaint persons conducting library research in Chicano Studies with the numerous reference materials found in the University Library at the University of California-Santa Barbara, the manual provides information on the Coleccion Tloque Nahuaque, relevant subject headings, and a useful search strategy. The Coleccion Tloque Nahuaque,…

A Literature Review of Academic Library Web Page Studies

ERIC Educational Resources Information Center

Blummer, Barbara

2007-01-01

In the early 1990s, numerous academic libraries adopted the web as a communication tool with users. The literature on academic library websites includes research on both design and navigation. Early studies typically focused on design characteristics, since websites initially merely provided information on the services and collections available in…

Using Rubrics to Assess Learning in Course-Integrated Library Instruction

ERIC Educational Resources Information Center

Gariepy, Laura W.; Stout, Jennifer A.; Hodge, Megan L.

2016-01-01

Librarians face numerous challenges when designing effective, sustainable methods for assessing student learning outcomes in one-shot, course-integrated library instruction sessions. We explore the use of rubrics to programmatically assess authentic learning exercises completed in one-shot library sessions for a large, required sophomore-level…

The Digital Marketplace and Library and Information Education in the GCC Member Nations: A Critical Review.

ERIC Educational Resources Information Center

Rehman, Sajjad ur; Al-Ansari, Husain

2003-01-01

Assessed six library and information education programs in preparing manpower for the digital environment in three countries in the Gulf Cooperation Council (GCC): Saudi Arabia, Kuwait, and Oman. Highlights include curriculum changes; student-teacher ratio; technological, physical and instructional resources; hardware; software; vendors;…

MicroUse: The Database on Microcomputer Applications in Libraries and Information Centers.

ERIC Educational Resources Information Center

Chen, Ching-chih; Wang, Xiaochu

1984-01-01

Describes MicroUse, a microcomputer-based database on microcomputer applications in libraries and information centers which was developed using relational database manager dBASE II. The description includes its system configuration, software utilized, the in-house-developed dBASE programs, multifile structure, basic functions, MicroUse records,…

Collection Analysis: Powerful Ways To Collect, Analyze, and Present Your Data.

ERIC Educational Resources Information Center

Hart, Amy

2003-01-01

Discussion of collection analysis in school libraries focuses on the kinds of data used and how to use library automation software to collect the data. Describes the use of Microsoft Excel and its chart-making capabilities to enhance the presentation of the analysis and suggests ways to use collection analysis output. (LRW)

BIBLIO: A Computer System Designed to Support the Near-Library User Model of Information Retrieval.

ERIC Educational Resources Information Center

Belew, Richard K.; Holland, Maurita Peterson

1988-01-01

Description of the development of the Information Exchange Facility, a prototype microcomputer-based personal bibliographic facility, covers software selection, user selection, overview of the system, and evaluation. The plan for an integrated system, BIBLIO, and the future role of libraries are discussed. (eight references) (MES)

Implementing LibGuides 2: An Academic Case Study

ERIC Educational Resources Information Center

Duncan, Vicky; Lucky, Shannon; McLean, Jaclyn

2015-01-01

Since 1997, the University of Saskatchewan Library has used "subject pages" to highlight key library resources. When Springshare announced it was launching LibGuides v2, a project team was assembled to transition a mixture of locally produced guides and guides created with the original LibGuides v1 software. This article synthesizes best…

VTLS Inc.: The Company, the Products, the Services, the Vision.

ERIC Educational Resources Information Center

Chachra, Vinod; And Others

1993-01-01

Describes the range of products and services offered by VTLS, a company that offers comprehensive, integrated library automation software and customer support. VTLS's growth and development in the United States and abroad is described, and nine sidebar articles detail system features and applications in public, academic, and virtual libraries. (20…

Access to Full-Text Journal Articles: Some Practical Considerations.

ERIC Educational Resources Information Center

Racine, Drew

1992-01-01

Discusses some of the issues and problems involved in using electronic full-text journals in the University of Texas at Austin libraries. Issues addressed include different standards; subjects represented and the time period covered; hardware considerations; software; printing; skills and training needed for library staff and for users; and costs.…

Library Signage: Applications for the Apple Macintosh and MacPaint.

ERIC Educational Resources Information Center

Diskin, Jill A.; FitzGerald, Patricia

1984-01-01

Describes specific applications of the Macintosh computer at Carnegie-Mellon University Libraries, where MacPaint was used as a flexible, easy to use, and powerful tool to produce informational, instructional, and promotional signage. Profiles of system hardware and software, an evaluation of the computer program MacPaint, and MacPaint signage…

The Structure of the Library Market for Scientific Journals: The Case of Chemistry.

ERIC Educational Resources Information Center

Bensman, Stephen J.

1996-01-01

An analysis of price and scientific value of chemistry journals concluded that scientific value does not play a role in the pricing of scientific journals and that consequently little relationship exists between scientific value and the prices charged libraries for journals. Describes a software package, Serials Evaluator, being developed at…

Use of Information and Communication Technology to Enhance the Information Literacy Skills of Distance Students

ERIC Educational Resources Information Center

Pastula, Matthew

2010-01-01

Information and Communication Technology (ICT) has become an integral tool in enhancing library services worldwide. This article looks at ways technology is utilized at Massey University to bridge the gap between distance students and traditional library services. There are a variety of software providers, formats and implementation practices…

Technology in the Public Library: Results from the 1992 PLDS Survey of Technology.

ERIC Educational Resources Information Center

Fidler, Linda M.; Johnson, Debra Wilcox

1994-01-01

Discusses and compares the incorporation of technology by larger public libraries in Canada and the United States. Technology mentioned includes online public access catalogs; remote and local online database searching; microcomputers and software for public use; and fax, voice mail, and Telecommunication Devices for the Deaf and Teletype writer…

The New Philanthropist: Eric Schnell--Ohio State University

ERIC Educational Resources Information Center

Library Journal, 2005

2005-01-01

As head of information technology at the Prior Health Sciences Library, Eric Schnell likes to improve products that don't fully meet his library's purposes. His first major software product, the award-winning Prospero Electronic Delivery Project, is a web-based document delivery system designed to complement Ariel[R] by converting documents to a…

An object-oriented data reduction system in Fortran

NASA Technical Reports Server (NTRS)

Bailey, J.

1992-01-01

A data reduction system for the AAO two-degree field project is being developed using an object-oriented approach. Rather than use an object-oriented language (such as C++) the system is written in Fortran and makes extensive use of existing subroutine libraries provided by the UK Starlink project. Objects are created using the extensible N-dimensional Data Format (NDF) which itself is based on the Hierarchical Data System (HDS). The software consists of a class library, with each class corresponding to a Fortran subroutine with a standard calling sequence. The methods of the classes provide operations on NDF objects at a similar level of functionality to the applications of conventional data reduction systems. However, because they are provided as callable subroutines, they can be used as building blocks for more specialist applications. The class library is not dependent on a particular software environment thought it can be used effectively in ADAM applications. It can also be used from standalone Fortran programs. It is intended to develop a graphical user interface for use with the class library to form the 2dF data reduction system.

Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

PubMed Central

Rechner, Steffen; Berger, Annabell

2016-01-01

We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

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

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

The Astrophysics Source Code Library by the numbers

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter; Berriman, G. Bruce; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Ryan, PW; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Wallin, John; Warmels, Rein

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System T-MATS

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

2018-06-01

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

The instrument control software package for the Habitable-Zone Planet Finder spectrometer

NASA Astrophysics Data System (ADS)

Bender, Chad F.; Robertson, Paul; Stefansson, Gudmundur Kari; Monson, Andrew; Anderson, Tyler; Halverson, Samuel; Hearty, Frederick; Levi, Eric; Mahadevan, Suvrath; Nelson, Matthew; Ramsey, Larry; Roy, Arpita; Schwab, Christian; Shetrone, Matthew; Terrien, Ryan

2016-08-01

We describe the Instrument Control Software (ICS) package that we have built for The Habitable-Zone Planet Finder (HPF) spectrometer. The ICS controls and monitors instrument subsystems, facilitates communication with the Hobby-Eberly Telescope facility, and provides user interfaces for observers and telescope operators. The backend is built around the asynchronous network software stack provided by the Python Twisted engine, and is linked to a suite of custom hardware communication protocols. This backend is accessed through Python-based command-line and PyQt graphical frontends. In this paper we describe several of the customized subsystem communication protocols that provide access to and help maintain the hardware systems that comprise HPF, and show how asynchronous communication benefits the numerous hardware components. We also discuss our Detector Control Subsystem, built as a set of custom Python wrappers around a C-library that provides native Linux access to the SIDECAR ASIC and Hawaii-2RG detector system used by HPF. HPF will be one of the first astronomical instruments on sky to utilize this native Linux capability through the SIDECAR Acquisition Module (SAM) electronics. The ICS we have created is very flexible, and we are adapting it for NEID, NASA's Extreme Precision Doppler Spectrometer for the WIYN telescope; we will describe this adaptation, and describe the potential for use in other astronomical instruments.

Front End Software for Online Database Searching. Part 2: The Marketplace.

ERIC Educational Resources Information Center

Levy, Louise R.; Hawkins, Donald T.

1986-01-01

This article analyzes the front end software marketplace and discusses some of the complex forces influencing it. Discussion covers intermediary market; end users (library customers, scientific and technical professionals, corporate business specialists, consumers); marketing strategies; a British front end development firm; competitive pressures;…

Interface for the documentation and compilation of a library of computer models in physiology.

PubMed Central

Summers, R. L.; Montani, J. P.

1994-01-01

A software interface for the documentation and compilation of a library of computer models in physiology was developed. The interface is an interactive program built within a word processing template in order to provide ease and flexibility of documentation. A model editor within the interface directs the model builder as to standardized requirements for incorporating models into the library and provides the user with an index to the levels of documentation. The interface and accompanying library are intended to facilitate model development, preservation and distribution and will be available for public use. PMID:7950046

AMPHION: Specification-based programming for scientific subroutine libraries

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Waldinger, Richard; Stickel, Mark

1994-01-01

AMPHION is a knowledge-based software engineering (KBSE) system that guides a user in developing a diagram representing a formal problem specification. It then automatically implements a solution to this specification as a program consisting of calls to subroutines from a library. The diagram provides an intuitive domain oriented notation for creating a specification that also facilitates reuse and modification. AMPHION'S architecture is domain independent. AMPHION is specialized to an application domain by developing a declarative domain theory. Creating a domain theory is an iterative process that currently requires the joint expertise of domain experts and experts in automated formal methods for software development.

MAVEN Data Analysis and Visualization Toolkits

NASA Astrophysics Data System (ADS)

Harter, B., Jr.; DeWolfe, A. W.; Brain, D.; Chaffin, M.

2017-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. The MAVEN Science Data Center has developed software toolkits for analyzing and visualizing the science data. Our Data Intercomparison and Visualization Development Effort (DIVIDE) toolkit is written in IDL, and utilizes the widely used "tplot" IDL libraries. Recently, we have converted DIVIDE into Python in an effort to increase the accessibility of the MAVEN data. This conversion also necessitated the development of a Python version of the tplot libraries, which we have dubbed "PyTplot". PyTplot is generalized to work with missions beyond MAVEN, and our software is available on Github.

Optimizing the Performance of Radionuclide Identification Software in the Hunt for Nuclear Security Threats

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

Fotion, Katherine A.

2016-08-18

The Radionuclide Analysis Kit (RNAK), my team’s most recent nuclide identification software, is entering the testing phase. A question arises: will removing rare nuclides from the software’s library improve its overall performance? An affirmative response indicates fundamental errors in the software’s framework, while a negative response confirms the effectiveness of the software’s key machine learning algorithms. After thorough testing, I found that the performance of RNAK cannot be improved with the library choice effect, thus verifying the effectiveness of RNAK’s algorithms—multiple linear regression, Bayesian network using the Viterbi algorithm, and branch and bound search.

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

PubMed

Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

2014-06-10

Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

The Environment for Application Software Integration and Execution (EASIE), version 1.0. Volume 2: Program integration guide

NASA Technical Reports Server (NTRS)

Jones, Kennie H.; Randall, Donald P.; Stallcup, Scott S.; Rowell, Lawrence F.

1988-01-01

The Environment for Application Software Integration and Execution, EASIE, provides a methodology and a set of software utility programs to ease the task of coordinating engineering design and analysis codes. EASIE was designed to meet the needs of conceptual design engineers that face the task of integrating many stand-alone engineering analysis programs. Using EASIE, programs are integrated through a relational data base management system. In volume 2, the use of a SYSTEM LIBRARY PROCESSOR is used to construct a DATA DICTIONARY describing all relations defined in the data base, and a TEMPLATE LIBRARY. A TEMPLATE is a description of all subsets of relations (including conditional selection criteria and sorting specifications) to be accessed as input or output for a given application. Together, these form the SYSTEM LIBRARY which is used to automatically produce the data base schema, FORTRAN subroutines to retrieve/store data from/to the data base, and instructions to a generic REVIEWER program providing review/modification of data for a given template. Automation of these functions eliminates much of the tedious, error prone work required by the usual approach to data base integration.

A web-based library consult service for evidence-based medicine: Technical development.

PubMed

Schwartz, Alan; Millam, Gregory

2006-03-16

Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement.

Planning a new library in an age of transition: the Washington University School of Medicine Library and Biomedical Communications Center.

PubMed Central

Crawford, S; Halbrook, B

1990-01-01

In an era of great technological and socioeconomic changes, the Washington University School of Medicine conceptualized and built its first Library and Biomedical Communications Center in seventy-eight years. The planning process, evolution of the electronic library, and translation of functions into operating spaces are discussed. Since 1983, when the project was approved, a whole range of information technologies and services have emerged. The authors consider the kind of library that would operate in a setting where people can do their own searches, order data and materials through an electronic network, analyze and manage information, and use software to create their own publications. Images PMID:2393757

The medical matters wiki: building a library Web site 2.0.

PubMed

Robertson, Justin; Burnham, Judy; Li, Jie; Sayed, Ellen

2008-01-01

New and innovative information technologies drive the ever-evolving library profession. From clay tablet to parchment scroll to manufactured paper to computer screen pixel, information storage, retrieval, and delivery methods continue to evolve, and each advance irrevocably affects the way libraries, and librarians, work. The Internet has forever altered information and library science, both in theory and practice, but even within this context the progression continues. Though ambiguously defined, Web 2.0 offers a new outlook and new software, presenting librarians with potentially invaluable new tools and methods. This paper discusses the creation, implementation, and maintenance of a Web 2.0 technology, the wiki, as a resource tool for an academic biomedical library.

Chapter 24: Programmatic Interfaces - IDL VOlib

NASA Astrophysics Data System (ADS)

Miller, C. J.

In this chapter, we describe a library for working with the VO using IDL (the Interactive Data Language). IDL is a software environment for data analysis, visualization, and cross-platform application development. It has wide-usage in astronomy, including NASA (e.g. http://seadas.gsfc.nasa.gov/), the Sloan Digital Sky Survey (http://www.sdss.org), and the Spitzer Infrared Spectrograph Instrument (http://ssc.spitzer.caltech.edu/archanaly/contributed/smart/). David Stern, the founder of Research Systems, Inc. (RSI), began the development of IDL while working with NASA's Mars Mariner 7 and 9 data at the Laboratory for Atmospheric and Space Physics at the University of Colorado. In 1981, IDL was rewritten in assembly language and FORTRAN for VAX/VMS. IDL's usage has expanded over the last decade into the fields of medical imaging and engineering, among many others. IDL's programming style carries over much of this FORTRAN-legacy, and has a familiar feel to many astronomers who learned their trade using FORTRAN. The spread of IDL-usage amongst astronomers can in part be attributed to the wealth of publicly astronomical libraries. The Goddard Space Flight Center (GSFC) maintains a list of astronomy-related IDL libraries, including the well known Astronomy User's Library (hereafter ASTROLIB2). We will use some of these GSFC IDL libraries. We note that while IDL is a licensed-software product, the source code of user-written procedures are typically freely available to the community. To make the most out of this section as a reader, it is important that many of the data discovery, access, and analysis protocols are understood before reading this chapter. In the next section, we provide an overview of some of the NVO terminology with which the reader should be familiar. The IDL library discussed here is specifically for use with the Virtual Observatory and is named VOlib. IDL's VOlib is available at http://nvo.noao.edu and is included with the software distrubution for this book.

STARLSE -- Starlink Extensions to the VAX Language Sensitive Editor

NASA Astrophysics Data System (ADS)

Warren-Smith, R. F.

STARLSE is a ``Starlink Sensitive'' editor based on the VAX Language Sensitive Editor (LSE). It exploits the extensibility of LSE to provide additional features which assist in the writing of portable Fortran 77 software with a standard Starlink style. STARLSE is intended mainly for use by those writing ADAM applications and subroutine libraries for distribution as part of the Starlink Software Collection, although it may also be suitable for other software projects. It is designed to integrate with the SST (Simple Software Tools) package.

Bibliographic Management Software Seminars: Funding and Implementation.

ERIC Educational Resources Information Center

Henry, Marcia

This paper contains the grant proposal and final report for a project conducted by the California State University at Northridge library to demonstrate online database searching and introduce the use of bibliographic management software to faculty and graduate students. Day-long, discipline-oriented seminars were planned to increase the…

Creating an X Window Terminal-Based Information Technology Center.

ERIC Educational Resources Information Center

Klassen, Tim W.

1997-01-01

The creation of an information technology center at the University of Oregon Science Library is described. Goals included providing access to Internet-based resources and multimedia software, platforms for running science-oriented software, and resources so students can create multimedia materials. A mixed-lab platform was created with Unix-based…

Choosing and Using Text-to-Speech Software

ERIC Educational Resources Information Center

Peters, Tom; Bell, Lori

2007-01-01

This article describes a computer-based technology for generating speech called text-to-speech (TTS). This software is ready for widespread use by libraries, other organizations, and individual users. It offers the affordable ability to turn just about any electronic text that is not image-based into an artificially spoken communication. The…

MLS data segmentation using Point Cloud Library procedures. (Polish Title: Segmentacja danych MLS z użyciem procedur Point Cloud Library)

NASA Astrophysics Data System (ADS)

Grochocka, M.

2013-12-01

Mobile laser scanning is dynamically developing measurement technology, which is becoming increasingly widespread in acquiring three-dimensional spatial information. Continuous technical progress based on the use of new tools, technology development, and thus the use of existing resources in a better way, reveals new horizons of extensive use of MLS technology. Mobile laser scanning system is usually used for mapping linear objects, and in particular the inventory of roads, railways, bridges, shorelines, shafts, tunnels, and even geometrically complex urban spaces. The measurement is done from the perspective of use of the object, however, does not interfere with the possibilities of movement and work. This paper presents the initial results of the segmentation data acquired by the MLS. The data used in this work was obtained as part of an inventory measurement infrastructure railway line. Measurement of point clouds was carried out using a profile scanners installed on the railway platform. To process the data, the tools of 'open source' Point Cloud Library was used. These tools allow to use templates of programming libraries. PCL is an open, independent project, operating on a large scale for processing 2D/3D image and point clouds. Software PCL is released under the terms of the BSD license (Berkeley Software Distribution License), which means it is a free for commercial and research use. The article presents a number of issues related to the use of this software and its capabilities. Segmentation data is based on applying the templates library pcl_ segmentation, which contains the segmentation algorithms to separate clusters. These algorithms are best suited to the processing point clouds, consisting of a number of spatially isolated regions. Template library performs the extraction of the cluster based on the fit of the model by the consensus method samples for various parametric models (planes, cylinders, spheres, lines, etc.). Most of the mathematical operation is carried out on the basis of Eigen library, a set of templates for linear algebra.

Specification of Fenix MPI Fault Tolerance library version 1.0.1

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

Gamble, Marc; Van Der Wijngaart, Rob; Teranishi, Keita

This document provides a specification of Fenix, a software library compatible with the Message Passing Interface (MPI) to support fault recovery without application shutdown. The library consists of two modules. The first, termed process recovery , restores an application to a consistent state after it has suffered a loss of one or more MPI processes (ranks). The second specifies functions the user can invoke to store application data in Fenix managed redundant storage, and to retrieve it from that storage after process recovery.

The Region 4 collaborative virtual reference project.

PubMed

Parker, Sandi K; Johnson, E Diane

2003-01-01

In May 2002, the Denison Memorial Library at the University of Colorado Health Sciences Center and the J. Otto Lottes Health Sciences Library at the University of Missouri-Columbia, with funding from the National Network of Libraries of Medicine-Midcontinental Region, embarked on a collaborative, real-time reference project using the 24/7 Reference, Inc., software package. This paper describes how the project was conceived, and includes details on the service hours, staffing, training, marketing, lessons learned, and future plans for the service.

Spending Smart: How To Budget and Finance. Making Sense of Your Budget Dollars; Success with Budget Proposals; Encumbering Grants: Managing the Money; Write a Grant? Me?; Using Microsoft[R] Excel To Plan and Budget in Your School Library; Charging Ahead; The No-Money Lottery; Coffee, Anyone?

ERIC Educational Resources Information Center

Bernstein, Allison; Baule, Steve; Farmer, Lesley S. J.; Anderson, Cyndee; Barringer, Crystal; Buchanan, Peggy; Fullner, Sheryl Kindle; Knop, Kathi; Larson, Chris

2002-01-01

Includes eight articles that address issues related to budgeting and finances in secondary school libraries. Topics include limited budgets; budget proposals; administering grants; writing grants; using Microsoft's Excel software for budgeting; using credit cards for library purchases; offering prizes for donating books; and offering coffee and…