Saturn S-2 Automatic Software System /SASS/

NASA Technical Reports Server (NTRS)

Parker, P. E.

1967-01-01

SATURN S-2 Automatic Software System /SASS/ was designed and implemented to aid SATURN S-2 program development and to increase the overall operating efficiency within the S-2 data laboratory. This program is written in FORTRAN 2 for SDS 920 computers.

Rapid Prediction of Unsteady Three-Dimensional Viscous Flows in Turbopump Geometries

NASA Technical Reports Server (NTRS)

Dorney, Daniel J.

1998-01-01

A program is underway to improve the efficiency of a three-dimensional Navier-Stokes code and generalize it for nozzle and turbopump geometries. Code modifications have included the implementation of parallel processing software, incorporation of new physical models and generalization of the multiblock capability. The final report contains details of code modifications, numerical results for several nozzle and turbopump geometries, and the implementation of the parallelization software.

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2013-01-03

staffing for the project  Implementing the necessary infrastructure ( testing, performance evaluation, needed support software, bug and issue...in the SOW The result of the planning discussions is shown in the milestone table (section 6). In addition, we selected appropriate engineering

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Near Theoretical Gigabit Link Efficiency for Distributed Data Acquisition Systems

PubMed Central

Abu-Nimeh, Faisal T.; Choong, Woon-Seng

2017-01-01

Link efficiency, data integrity, and continuity for high-throughput and real-time systems is crucial. Most of these applications require specialized hardware and operating systems as well as extensive tuning in order to achieve high efficiency. Here, we present an implementation of gigabit Ethernet data streaming which can achieve 99.26% link efficiency while maintaining no packet losses. The design and implementation are built on OpenPET, an opensource data acquisition platform for nuclear medical imaging, where (a) a crate hosting multiple OpenPET detector boards uses a User Datagram Protocol over Internet Protocol (UDP/IP) Ethernet soft-core, that is capable of understanding PAUSE frames, to stream data out to a computer workstation; (b) the receiving computer uses Netmap to allow the processing software (i.e., user space), which is written in Python, to directly receive and manage the network card’s ring buffers, bypassing the operating system kernel’s networking stack; and (c) a multi-threaded application using synchronized queues is implemented in the processing software (Python) to free up the ring buffers as quickly as possible while preserving data integrity and flow continuity. PMID:28630948

Near Theoretical Gigabit Link Efficiency for Distributed Data Acquisition Systems.

PubMed

Abu-Nimeh, Faisal T; Choong, Woon-Seng

2017-03-01

Link efficiency, data integrity, and continuity for high-throughput and real-time systems is crucial. Most of these applications require specialized hardware and operating systems as well as extensive tuning in order to achieve high efficiency. Here, we present an implementation of gigabit Ethernet data streaming which can achieve 99.26% link efficiency while maintaining no packet losses. The design and implementation are built on OpenPET, an opensource data acquisition platform for nuclear medical imaging, where (a) a crate hosting multiple OpenPET detector boards uses a User Datagram Protocol over Internet Protocol (UDP/IP) Ethernet soft-core, that is capable of understanding PAUSE frames, to stream data out to a computer workstation; (b) the receiving computer uses Netmap to allow the processing software (i.e., user space), which is written in Python, to directly receive and manage the network card's ring buffers, bypassing the operating system kernel's networking stack; and (c) a multi-threaded application using synchronized queues is implemented in the processing software (Python) to free up the ring buffers as quickly as possible while preserving data integrity and flow continuity.

Spacelab user implementation assessment study (software requirements analysis). Volume 1: Executive study

NASA Technical Reports Server (NTRS)

1976-01-01

The primary objective of this study was to develop an integrated approach for the development, implementation, and utilization of all software that is required to efficiently and cost-effectively support advanced technology laboratory flight and ground operations. It was recognized that certain aspects of the operations would be mandatory computerized services; computerization of other aspects would be optional. Thus, the analyses encompassed not only alternate computer utilization and implementations but trade studies of the programmatic effects of non-computerized versus computerized approaches to the operations. A general overview of the study is presented.

Ffuzz: Towards full system high coverage fuzz testing on binary executables.

PubMed

Zhang, Bin; Ye, Jiaxi; Bi, Xing; Feng, Chao; Tang, Chaojing

2018-01-01

Bugs and vulnerabilities in binary executables threaten cyber security. Current discovery methods, like fuzz testing, symbolic execution and manual analysis, both have advantages and disadvantages when exercising the deeper code area in binary executables to find more bugs. In this paper, we designed and implemented a hybrid automatic bug finding tool-Ffuzz-on top of fuzz testing and selective symbolic execution. It targets full system software stack testing including both the user space and kernel space. Combining these two mainstream techniques enables us to achieve higher coverage and avoid getting stuck both in fuzz testing and symbolic execution. We also proposed two key optimizations to improve the efficiency of full system testing. We evaluated the efficiency and effectiveness of our method on real-world binary software and 844 memory corruption vulnerable programs in the Juliet test suite. The results show that Ffuzz can discover software bugs in the full system software stack effectively and efficiently.

The design and implementation of a parallel unstructured Euler solver using software primitives

NASA Technical Reports Server (NTRS)

Das, R.; Mavriplis, D. J.; Saltz, J.; Gupta, S.; Ponnusamy, R.

1992-01-01

This paper is concerned with the implementation of a three-dimensional unstructured grid Euler-solver on massively parallel distributed-memory computer architectures. The goal is to minimize solution time by achieving high computational rates with a numerically efficient algorithm. An unstructured multigrid algorithm with an edge-based data structure has been adopted, and a number of optimizations have been devised and implemented in order to accelerate the parallel communication rates. The implementation is carried out by creating a set of software tools, which provide an interface between the parallelization issues and the sequential code, while providing a basis for future automatic run-time compilation support. Large practical unstructured grid problems are solved on the Intel iPSC/860 hypercube and Intel Touchstone Delta machine. The quantitative effect of the various optimizations are demonstrated, and we show that the combined effect of these optimizations leads to roughly a factor of three performance improvement. The overall solution efficiency is compared with that obtained on the CRAY-YMP vector supercomputer.

A Prolog Emulator

NASA Technical Reports Server (NTRS)

Tick, Evan

1987-01-01

This note describes an efficient software emulator for the Warren Abstract Machine (WAM) Prolog architecture. The version of the WAM implemented is called Lcode. The Lcode emulator, written in C, executes the 'naive reverse' benchmark at 3900 LIPS. The emulator is one of a set of tools used to measure the memory-referencing characteristics and performance of Prolog programs. These tools include a compiler, assembler, and memory simulators. An overview of the Lcode architecture is given here, followed by a description and listing of the emulator code implementing each Lcode instruction. This note will be of special interest to those studying the WAM and its performance characteristics. In general, this note will be of interest to those creating efficient software emulators for abstract machine architectures.

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.

PubMed

Chen, Feng; Wang, Chenghong; Dai, Wenrui; Jiang, Xiaoqian; Mohammed, Noman; Al Aziz, Md Momin; Sadat, Md Nazmus; Sahinalp, Cenk; Lauter, Kristin; Wang, Shuang

2017-07-26

Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genomic data. We present one of the first implementations of Software Guard Extension (SGX) based securely outsourced genetic testing framework, which leverages multiple cryptographic protocols and minimal perfect hash scheme to enable efficient and secure data storage and computation outsourcing. We compared the performance of the proposed PRESAGE framework with the state-of-the-art homomorphic encryption scheme, as well as the plaintext implementation. The experimental results demonstrated significant performance over the homomorphic encryption methods and a small computational overhead in comparison to plaintext implementation. The proposed PRESAGE provides an alternative solution for secure and efficient genomic data outsourcing in an untrusted cloud by using a hybrid framework that combines secure hardware and multiple crypto protocols.

Software design and implementation concepts for an interoperable medical communication framework.

PubMed

Besting, Andreas; Bürger, Sebastian; Kasparick, Martin; Strathen, Benjamin; Portheine, Frank

2018-02-23

The new IEEE 11073 service-oriented device connectivity (SDC) standard proposals for networked point-of-care and surgical devices constitutes the basis for improved interoperability due to its independence of vendors. To accelerate the distribution of the standard a reference implementation is indispensable. However, the implementation of such a framework has to overcome several non-trivial challenges. First, the high level of complexity of the underlying standard must be reflected in the software design. An efficient implementation has to consider the limited resources of the underlying hardware. Moreover, the frameworks purpose of realizing a distributed system demands a high degree of reliability of the framework itself and its internal mechanisms. Additionally, a framework must provide an easy-to-use and fail-safe application programming interface (API). In this work, we address these challenges by discussing suitable software engineering principles and practical coding guidelines. A descriptive model is developed that identifies key strategies. General feasibility is shown by outlining environments in which our implementation has been utilized.

Parallel Domain Decomposition Formulation and Software for Large-Scale Sparse Symmetrical/Unsymmetrical Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Watson, Willie R. (Technical Monitor)

2005-01-01

The overall objectives of this research work are to formulate and validate efficient parallel algorithms, and to efficiently design/implement computer software for solving large-scale acoustic problems, arised from the unified frameworks of the finite element procedures. The adopted parallel Finite Element (FE) Domain Decomposition (DD) procedures should fully take advantages of multiple processing capabilities offered by most modern high performance computing platforms for efficient parallel computation. To achieve this objective. the formulation needs to integrate efficient sparse (and dense) assembly techniques, hybrid (or mixed) direct and iterative equation solvers, proper pre-conditioned strategies, unrolling strategies, and effective processors' communicating schemes. Finally, the numerical performance of the developed parallel finite element procedures will be evaluated by solving series of structural, and acoustic (symmetrical and un-symmetrical) problems (in different computing platforms). Comparisons with existing "commercialized" and/or "public domain" software are also included, whenever possible.

Family-Based Rare Variant Association Analysis: A Fast and Efficient Method of Multivariate Phenotype Association Analysis.

PubMed

Wang, Longfei; Lee, Sungyoung; Gim, Jungsoo; Qiao, Dandi; Cho, Michael; Elston, Robert C; Silverman, Edwin K; Won, Sungho

2016-09-01

Family-based designs have been repeatedly shown to be powerful in detecting the significant rare variants associated with human diseases. Furthermore, human diseases are often defined by the outcomes of multiple phenotypes, and thus we expect multivariate family-based analyses may be very efficient in detecting associations with rare variants. However, few statistical methods implementing this strategy have been developed for family-based designs. In this report, we describe one such implementation: the multivariate family-based rare variant association tool (mFARVAT). mFARVAT is a quasi-likelihood-based score test for rare variant association analysis with multiple phenotypes, and tests both homogeneous and heterogeneous effects of each variant on multiple phenotypes. Simulation results show that the proposed method is generally robust and efficient for various disease models, and we identify some promising candidate genes associated with chronic obstructive pulmonary disease. The software of mFARVAT is freely available at http://healthstat.snu.ac.kr/software/mfarvat/, implemented in C++ and supported on Linux and MS Windows. © 2016 WILEY PERIODICALS, INC.

Advanced techniques and technology for efficient data storage, access, and transfer

NASA Technical Reports Server (NTRS)

Rice, Robert F.; Miller, Warner

1991-01-01

Advanced techniques for efficiently representing most forms of data are being implemented in practical hardware and software form through the joint efforts of three NASA centers. These techniques adapt to local statistical variations to continually provide near optimum code efficiency when representing data without error. Demonstrated in several earlier space applications, these techniques are the basis of initial NASA data compression standards specifications. Since the techniques clearly apply to most NASA science data, NASA invested in the development of both hardware and software implementations for general use. This investment includes high-speed single-chip very large scale integration (VLSI) coding and decoding modules as well as machine-transferrable software routines. The hardware chips were tested in the laboratory at data rates as high as 700 Mbits/s. A coding module's definition includes a predictive preprocessing stage and a powerful adaptive coding stage. The function of the preprocessor is to optimally process incoming data into a standard form data source that the second stage can handle.The built-in preprocessor of the VLSI coder chips is ideal for high-speed sampled data applications such as imaging and high-quality audio, but additionally, the second stage adaptive coder can be used separately with any source that can be externally preprocessed into the 'standard form'. This generic functionality assures that the applicability of these techniques and their recent high-speed implementations should be equally broad outside of NASA.

Using Deep Learning Algorithm to Enhance Image-review Software for Surveillance Cameras

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

Cui, Yonggang; Thomas, Maikael A.

We propose the development of proven deep learning algorithms to flag objects and events of interest in Next Generation Surveillance System (NGSS) surveillance to make IAEA image review more efficient. Video surveillance is one of the core monitoring technologies used by the IAEA Department of Safeguards when implementing safeguards at nuclear facilities worldwide. The current image review software GARS has limited automated functions, such as scene-change detection, black image detection and missing scene analysis, but struggles with highly cluttered backgrounds. A cutting-edge algorithm to be developed in this project will enable efficient and effective searches in images and video streamsmore » by identifying and tracking safeguards relevant objects and detect anomalies in their vicinity. In this project, we will develop the algorithm, test it with the IAEA surveillance cameras and data sets collected at simulated nuclear facilities at BNL and SNL, and implement it in a software program for potential integration into the IAEA’s IRAP (Integrated Review and Analysis Program).« less

Wireless local area network for the dental office.

PubMed

Mupparapu, Muralidhar

2004-01-01

Dental offices are no exception to the implementation of new and advanced technology, especially if it enhances productivity. In a rapidly transforming digital world, wireless technology has a special place, as it has truly "retired the wire" and contributed to the ease and efficient access to patient data and other software-based applications for diagnosis and treatment. If the office or the clinic is networked, access to patient management software, imaging software and treatment planning tools is enhanced. Access will be further enhanced and unrestricted if the entire network is wireless. As with any new, emerging technology, there will be issues that should be kept in mind before adapting to the wireless environment. Foremost is the network security involved in the installation and use of these wireless networks. This short, technical manuscript deals with standards and choices in wireless technology currently available for implementation within a dental office. The benefits of each network security protocol available to protect patient data and boost the efficiency of a modern dental office are discussed.

Experiences Supporting the Lunar Reconnaissance Orbiter Camera: the Devops Model

NASA Astrophysics Data System (ADS)

Licht, A.; Estes, N. M.; Bowman-Cisnesros, E.; Hanger, C. D.

2013-12-01

Introduction: The Lunar Reconnaissance Orbiter Camera (LROC) Science Operations Center (SOC) is responsible for instrument targeting, product processing, and archiving [1]. The LROC SOC maintains over 1,000,000 observations with over 300 TB of released data. Processing challenges compound with the acquisition of over 400 Gbits of observations daily creating the need for a robust, efficient, and reliable suite of specialized software. Development Environment: The LROC SOC's software development methodology has evolved over time. Today, the development team operates in close cooperation with the systems administration team in a model known in the IT industry as DevOps. The DevOps model enables a highly productive development environment that facilitates accomplishment of key goals within tight schedules[2]. The LROC SOC DevOps model incorporates industry best practices including prototyping, continuous integration, unit testing, code coverage analysis, version control, and utilizing existing open source software. Scientists and researchers at LROC often prototype algorithms and scripts in a high-level language such as MATLAB or IDL. After the prototype is functionally complete the solution is implemented as production ready software by the developers. Following this process ensures that all controls and requirements set by the LROC SOC DevOps team are met. The LROC SOC also strives to enhance the efficiency of the operations staff by way of weekly presentations and informal mentoring. Many small scripting tasks are assigned to the cognizant operations personnel (end users), allowing for the DevOps team to focus on more complex and mission critical tasks. In addition to leveraging open source software the LROC SOC has also contributed to the open source community by releasing Lunaserv [3]. Findings: The DevOps software model very efficiently provides smooth software releases and maintains team momentum. Scientists prototyping their work has proven to be very efficient as developers do not need to spend time iterating over small changes. Instead, these changes are realized in early prototypes and implemented before the task is seen by developers. The development practices followed by the LROC SOC DevOps team help facilitate a high level of software quality that is necessary for LROC SOC operations. Application to the Scientific Community: There is no replacement for having software developed by professional developers. While it is beneficial for scientists to write software, this activity should be seen as prototyping, which is then made production ready by professional developers. When constructed properly, even a small development team has the ability to increase the rate of software development for a research group while creating more efficient, reliable, and maintainable products. This strategy allows scientists to accomplish more, focusing on teamwork, rather than software development, which may not be their primary focus. 1. Robinson et al. (2010) Space Sci. Rev. 150, 81-124 2. DeGrandis. (2011) Cutter IT Journal. Vol 24, No. 8, 34-39 3. Estes, N.M.; Hanger, C.D.; Licht, A.A.; Bowman-Cisneros, E.; Lunaserv Web Map Service: History, Implementation Details, Development, and Uses, http://adsabs.harvard.edu/abs/2013LPICo1719.2609E.

Microcomputers: Means to Achievement. Using Information More Efficiently for Special Needs Learners.

ERIC Educational Resources Information Center

Brown, James M.

1984-01-01

Discusses database management systems for special needs student information management. Considers data access policies, implementation, software selection criteria, and special needs related uses. (SK)

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.; Olariu, Stephen

1995-01-01

The primary goal of this grant has been the design and implementation of software to be used in the conceptual design of aerospace vehicles particularly focused on the elements of geometric design, graphical user interfaces, and the interaction of the multitude of software typically used in this engineering environment. This has resulted in the development of several analysis packages and design studies. These include two major software systems currently used in the conceptual level design of aerospace vehicles. These tools are SMART, the Solid Modeling Aerospace Research Tool, and EASIE, the Environment for Software Integration and Execution. Additional software tools were designed and implemented to address the needs of the engineer working in the conceptual design environment. SMART provides conceptual designers with a rapid prototyping capability and several engineering analysis capabilities. In addition, SMART has a carefully engineered user interface that makes it easy to learn and use. Finally, a number of specialty characteristics have been built into SMART which allow it to be used efficiently as a front end geometry processor for other analysis packages. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand-alone, analysis codes. Resulting in a streamlining of the exchange of data between programs reducing errors and improving the efficiency. EASIE provides both a methodology and a collection of software tools to ease the task of coordinating engineering design and analysis codes.

Fast and Adaptive Lossless Onboard Hyperspectral Data Compression System

NASA Technical Reports Server (NTRS)

Aranki, Nazeeh I.; Keymeulen, Didier; Kimesh, Matthew A.

2012-01-01

Modern hyperspectral imaging systems are able to acquire far more data than can be downlinked from a spacecraft. Onboard data compression helps to alleviate this problem, but requires a system capable of power efficiency and high throughput. Software solutions have limited throughput performance and are power-hungry. Dedicated hardware solutions can provide both high throughput and power efficiency, while taking the load off of the main processor. Thus a hardware compression system was developed. The implementation uses a field-programmable gate array (FPGA). The implementation is based on the fast lossless (FL) compression algorithm reported in Fast Lossless Compression of Multispectral-Image Data (NPO-42517), NASA Tech Briefs, Vol. 30, No. 8 (August 2006), page 26, which achieves excellent compression performance and has low complexity. This algorithm performs predictive compression using an adaptive filtering method, and uses adaptive Golomb coding. The implementation also packetizes the coded data. The FL algorithm is well suited for implementation in hardware. In the FPGA implementation, one sample is compressed every clock cycle, which makes for a fast and practical realtime solution for space applications. Benefits of this implementation are: 1) The underlying algorithm achieves a combination of low complexity and compression effectiveness that exceeds that of techniques currently in use. 2) The algorithm requires no training data or other specific information about the nature of the spectral bands for a fixed instrument dynamic range. 3) Hardware acceleration provides a throughput improvement of 10 to 100 times vs. the software implementation. A prototype of the compressor is available in software, but it runs at a speed that does not meet spacecraft requirements. The hardware implementation targets the Xilinx Virtex IV FPGAs, and makes the use of this compressor practical for Earth satellites as well as beyond-Earth missions with hyperspectral instruments.

Ffuzz: Towards full system high coverage fuzz testing on binary executables

PubMed Central

2018-01-01

Bugs and vulnerabilities in binary executables threaten cyber security. Current discovery methods, like fuzz testing, symbolic execution and manual analysis, both have advantages and disadvantages when exercising the deeper code area in binary executables to find more bugs. In this paper, we designed and implemented a hybrid automatic bug finding tool—Ffuzz—on top of fuzz testing and selective symbolic execution. It targets full system software stack testing including both the user space and kernel space. Combining these two mainstream techniques enables us to achieve higher coverage and avoid getting stuck both in fuzz testing and symbolic execution. We also proposed two key optimizations to improve the efficiency of full system testing. We evaluated the efficiency and effectiveness of our method on real-world binary software and 844 memory corruption vulnerable programs in the Juliet test suite. The results show that Ffuzz can discover software bugs in the full system software stack effectively and efficiently. PMID:29791469

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

NASA Astrophysics Data System (ADS)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex

2018-04-01

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function g (r) of liquid Ni3Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

PubMed Central

Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

PubMed

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.

Detection And Mapping (DAM) package. Volume 4A: Software System Manual, part 1

NASA Technical Reports Server (NTRS)

Schlosser, E. H.

1980-01-01

The package is an integrated set of manual procedures, computer programs, and graphic devices designed for efficient production of precisely registered and formatted maps from digital LANDSAT multispectral scanner (MSS) data. The software can be readily implemented on any Univac 1100 series computer with standard peripheral equipment. This version of the software includes predefined spectral limits for use in classifying and mapping surface water for LANDSAT-1, LANDSAT-2, and LANDSAT-3. Tape formats supported include X, AM, and PM.

Development of a new software for analyzing 3-D fracture network

NASA Astrophysics Data System (ADS)

Um, Jeong-Gi; Noh, Young-Hwan; Choi, Yosoon

2014-05-01

A new software is presented to analyze fracture network in 3-D. Recently, we completed the software package based on information given in EGU2013. The software consists of several modules that play roles in management of borehole data, stochastic modelling of fracture network, construction of analysis domain, visualization of fracture geometry in 3-D, calculation of equivalent pipes and production of cross-section diagrams. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. A case study was performed to analyze 3-D fracture network system at the Upper Devonian Grosmont Formation in Alberta, Canada. The results have suggested that the developed software is effective in modelling and visualizing 3-D fracture network system, and can provide useful information to tackle the geomechanical problems related to strength, deformability and hydraulic behaviours of the fractured rock masses. This presentation describes the concept and details of the development and implementation of the software.

CASE tools and UML: state of the ART.

PubMed

Agarwal, S

2001-05-01

With increasing need for automated tools to assist complex systems development, software design methods are becoming popular. This article analyzes the state of art in computer-aided software engineering (CASE) tools and unified modeling language (UML), focusing on their evolution, merits, and industry usage. It identifies managerial issues for the tools' adoption and recommends an action plan to select and implement them. While CASE and UML offer inherent advantages like cheaper, shorter, and efficient development cycles, they suffer from poor user satisfaction. The critical success factors for their implementation include, among others, management and staff commitment, proper corporate infrastructure, and user training.

Testing flight software on the ground: Introducing the hardware-in-the-loop simulation method to the Alpha Magnetic Spectrometer on the International Space Station

NASA Astrophysics Data System (ADS)

Sun, Wenhao; Cai, Xudong; Meng, Qiao

2016-04-01

Complex automatic protection functions are being added to the onboard software of the Alpha Magnetic Spectrometer. A hardware-in-the-loop simulation method has been introduced to overcome the difficulties of ground testing that are brought by hardware and environmental limitations. We invented a time-saving approach by reusing the flight data as the data source of the simulation system instead of mathematical models. This is easy to implement and it works efficiently. This paper presents the system framework, implementation details and some application examples.

Team Software Development for Aerothermodynamic and Aerodynamic Analysis and Design

NASA Technical Reports Server (NTRS)

Alexandrov, N.; Atkins, H. L.; Bibb, K. L.; Biedron, R. T.; Carpenter, M. H.; Gnoffo, P. A.; Hammond, D. P.; Jones, W. T.; Kleb, W. L.; Lee-Rausch, E. M.

2003-01-01

A collaborative approach to software development is described. The approach employs the agile development techniques: project retrospectives, Scrum status meetings, and elements of Extreme Programming to efficiently develop a cohesive and extensible software suite. The software product under development is a fluid dynamics simulator for performing aerodynamic and aerothermodynamic analysis and design. The functionality of the software product is achieved both through the merging, with substantial rewrite, of separate legacy codes and the authorship of new routines. Examples of rapid implementation of new functionality demonstrate the benefits obtained with this agile software development process. The appendix contains a discussion of coding issues encountered while porting legacy Fortran 77 code to Fortran 95, software design principles, and a Fortran 95 coding standard.

Total Cost of Ownership, System Acceptance and Perceived Success of Enterprise Resource Planning Software: Simulating a Dynamic Feedback Perspective of ERP in the Higher Education Environment

ERIC Educational Resources Information Center

Fryling, Meg

2010-01-01

Enterprise Research Planning (ERP) software is advertised as the product that will "run the enterprise", improving data access and accuracy as well as enhancing business process efficiency. Unfortunately, organizations often make implementation decisions with little consideration for the maintenance phase of an ERP, resulting in significant…

Design of a fuel-efficient guidance system for a STOL aircraft

NASA Technical Reports Server (NTRS)

Mclean, J. D.; Erzberger, H.

1981-01-01

In the predictive mode, the system synthesizes a horizontal path from an initial aircraft position and heading to a desired final position and heading and then synthesizes a fuel-efficient speed-altitude profile along the path. In the track mode, the synthesized trajectory is reconstructed and tracked automatically. An analytical basis for the design of the system is presented and a description of the airborne computer implementation is given. A detailed discussion of the software, which should be helpful to those who use the actual software developed for these tests, is also provided.

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

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

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

Table-driven configuration and formatting of telemetry data in the Deep Space Network

NASA Technical Reports Server (NTRS)

Manning, Evan

1994-01-01

With a restructured software architecture for telemetry system control and data processing, the NASA/Deep Space Network (DSN) has substantially improved its ability to accommodate a wide variety of spacecraft in an era of 'better, faster, cheaper'. In the new architecture, the permanent software implements all capabilities needed by any system user, and text tables specify how these capabilities are to be used for each spacecraft. Most changes can now be made rapidly, outside of the traditional software development cycle. The system can be updated to support a new spacecraft through table changes rather than software changes, reducing the implementation, test, and delivery cycle for such a change from three months to three weeks. The mechanical separation of the text table files from the program software, with tables only loaded into memory when that mission is being supported, dramatically reduces the level of regression testing required. The format of each table is a different compromise between ease of human interpretation, efficiency of computer interpretation, and flexibility.

Solving Equations of Multibody Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Lim, Christopher

2007-01-01

Darts++ is a computer program for solving the equations of motion of a multibody system or of a multibody model of a dynamic system. It is intended especially for use in dynamical simulations performed in designing and analyzing, and developing software for the control of, complex mechanical systems. Darts++ is based on the Spatial-Operator- Algebra formulation for multibody dynamics. This software reads a description of a multibody system from a model data file, then constructs and implements an efficient algorithm that solves the dynamical equations of the system. The efficiency and, hence, the computational speed is sufficient to make Darts++ suitable for use in realtime closed-loop simulations. Darts++ features an object-oriented software architecture that enables reconfiguration of system topology at run time; in contrast, in related prior software, system topology is fixed during initialization. Darts++ provides an interface to scripting languages, including Tcl and Python, that enable the user to configure and interact with simulation objects at run time.

Radiation and scattering from printed antennas on cylindrically conformal platforms

NASA Technical Reports Server (NTRS)

Kempel, Leo C.; Volakis, John L.; Bindiganavale, Sunil

1994-01-01

The goal was to develop suitable methods and software for the analysis of antennas on cylindrical coated and uncoated platforms. Specifically, the finite element boundary integral and finite element ABC methods were employed successfully and associated software were developed for the analysis and design of wraparound and discrete cavity-backed arrays situated on cylindrical platforms. This work led to the successful implementation of analysis software for such antennas. Developments which played a role in this respect are the efficient implementation of the 3D Green's function for a metallic cylinder, the incorporation of the fast Fourier transform in computing the matrix-vector products executed in the solver of the finite element-boundary integral system, and the development of a new absorbing boundary condition for terminating the finite element mesh on cylindrical surfaces.

Modal Analysis for Grid Operation

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

MANGO software is to provide a solution for improving small signal stability of power systems through adjusting operator-controllable variables using PMU measurement. System oscillation problems are one of the major threats to the grid stability and reliability in California and the Western Interconnection. These problems result in power fluctuations, lower grid operation efficiency, and may even lead to large-scale grid breakup and outages. This MANGO software aims to solve this problem by automatically generating recommended operation procedures termed Modal Analysis for Grid Operation (MANGO) to improve damping of inter-area oscillation modes. The MANGO procedure includes three steps: recognizing small signalmore » stability problems, implementing operating point adjustment using modal sensitivity, and evaluating the effectiveness of the adjustment. The MANGO software package is designed to help implement the MANGO procedure.« less

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

PubMed

Jiang, Xiaohui; Kumar, Kamal; Hu, Xin; Wallqvist, Anders; Reifman, Jaques

2008-09-08

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability. To keep DOVIS up-to-date, we upgraded the software's docking engine to the more accurate AutoDock 4.0 code. We developed a new parallelization scheme to improve runtime efficiency and modified the AutoDock code to reduce excessive file operations during large-scale virtual screening jobs. We also implemented an algorithm to output docked ligands in an industry standard format, sd-file format, which can be easily interfaced with other modeling programs. Finally, we constructed a wrapper-script interface to enable automatic rescoring of docked ligands by arbitrarily selected third-party scoring programs. The significance of the new DOVIS 2.0 software compared with the previous version lies in its improved performance and usability. The new version makes the computation highly efficient by automating load balancing, significantly reducing excessive file operations by more than 95%, providing outputs that conform to industry standard sd-file format, and providing a general wrapper-script interface for rescoring of docked ligands. The new DOVIS 2.0 package is freely available to the public under the GNU General Public License.

Study of fault-tolerant software technology

NASA Technical Reports Server (NTRS)

Slivinski, T.; Broglio, C.; Wild, C.; Goldberg, J.; Levitt, K.; Hitt, E.; Webb, J.

1984-01-01

Presented is an overview of the current state of the art of fault-tolerant software and an analysis of quantitative techniques and models developed to assess its impact. It examines research efforts as well as experience gained from commercial application of these techniques. The paper also addresses the computer architecture and design implications on hardware, operating systems and programming languages (including Ada) of using fault-tolerant software in real-time aerospace applications. It concludes that fault-tolerant software has progressed beyond the pure research state. The paper also finds that, although not perfectly matched, newer architectural and language capabilities provide many of the notations and functions needed to effectively and efficiently implement software fault-tolerance.

Implementation methodology for interoperable personal health devices with low-voltage low-power constraints.

PubMed

Martinez-Espronceda, Miguel; Martinez, Ignacio; Serrano, Luis; Led, Santiago; Trigo, Jesús Daniel; Marzo, Asier; Escayola, Javier; Garcia, José

2011-05-01

Traditionally, e-Health solutions were located at the point of care (PoC), while the new ubiquitous user-centered paradigm draws on standard-based personal health devices (PHDs). Such devices place strict constraints on computation and battery efficiency that encouraged the International Organization for Standardization/IEEE11073 (X73) standard for medical devices to evolve from X73PoC to X73PHD. In this context, low-voltage low-power (LV-LP) technologies meet the restrictions of X73PHD-compliant devices. Since X73PHD does not approach the software architecture, the accomplishment of an efficient design falls directly on the software developer. Therefore, computational and battery performance of such LV-LP-constrained devices can even be outperformed through an efficient X73PHD implementation design. In this context, this paper proposes a new methodology to implement X73PHD into microcontroller-based platforms with LV-LP constraints. Such implementation methodology has been developed through a patterns-based approach and applied to a number of X73PHD-compliant agents (including weighing scale, blood pressure monitor, and thermometer specializations) and microprocessor architectures (8, 16, and 32 bits) as a proof of concept. As a reference, the results obtained in the weighing scale guarantee all features of X73PHD running over a microcontroller architecture based on ARM7TDMI requiring only 168 B of RAM and 2546 B of flash memory.

Many-level multilevel structural equation modeling: An efficient evaluation strategy.

PubMed

Pritikin, Joshua N; Hunter, Michael D; von Oertzen, Timo; Brick, Timothy R; Boker, Steven M

2017-01-01

Structural equation models are increasingly used for clustered or multilevel data in cases where mixed regression is too inflexible. However, when there are many levels of nesting, these models can become difficult to estimate. We introduce a novel evaluation strategy, Rampart, that applies an orthogonal rotation to the parts of a model that conform to commonly met requirements. This rotation dramatically simplifies fit evaluation in a way that becomes more potent as the size of the data set increases. We validate and evaluate the implementation using a 3-level latent regression simulation study. Then we analyze data from a state-wide child behavioral health measure administered by the Oklahoma Department of Human Services. We demonstrate the efficiency of Rampart compared to other similar software using a latent factor model with a 5-level decomposition of latent variance. Rampart is implemented in OpenMx, a free and open source software.

Binary Associative Memories as a Benchmark for Spiking Neuromorphic Hardware

PubMed Central

Stöckel, Andreas; Jenzen, Christoph; Thies, Michael; Rückert, Ulrich

2017-01-01

Large-scale neuromorphic hardware platforms, specialized computer systems for energy efficient simulation of spiking neural networks, are being developed around the world, for example as part of the European Human Brain Project (HBP). Due to conceptual differences, a universal performance analysis of these systems in terms of runtime, accuracy and energy efficiency is non-trivial, yet indispensable for further hard- and software development. In this paper we describe a scalable benchmark based on a spiking neural network implementation of the binary neural associative memory. We treat neuromorphic hardware and software simulators as black-boxes and execute exactly the same network description across all devices. Experiments on the HBP platforms under varying configurations of the associative memory show that the presented method allows to test the quality of the neuron model implementation, and to explain significant deviations from the expected reference output. PMID:28878642

Efficient QR sequential least square algorithm for high frequency GNSS precise point positioning seismic application

NASA Astrophysics Data System (ADS)

Barbu, Alina L.; Laurent-Varin, Julien; Perosanz, Felix; Mercier, Flavien; Marty, Jean-Charles

2018-01-01

The implementation into the GINS CNES geodetic software of a more efficient filter was needed to satisfy the users who wanted to compute high-rate GNSS PPP solutions. We selected the SRI approach and a QR factorization technique including an innovative algorithm which optimizes the matrix reduction step. A full description of this algorithm is given for future users. The new capacities of the software have been tested using a set of 1 Hz data from the Japanese GEONET network including the Mw 9.0 2011 Tohoku earthquake. Station coordinates solution agreed at a sub-decimeter level with previous publications as well as with solutions we computed with the National Resource Canada software. An additional benefit from the implementation of the SRI filter is the capability to estimate high-rate tropospheric parameters too. As the CPU time to estimate a 1 Hz kinematic solution from 1 h of data is now less than 1 min we could produced series of coordinates for the full 1300 stations of the Japanese network. The corresponding movie shows the impressive co-seismic deformation as well as the wave propagation along the island. The processing was straightforward using a cluster of PCs which illustrates the new potentiality of the GINS software for massive network high rate PPP processing.

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.

Practical Issues in Implementing Software Reliability Measurement

NASA Technical Reports Server (NTRS)

Nikora, Allen P.; Schneidewind, Norman F.; Everett, William W.; Munson, John C.; Vouk, Mladen A.; Musa, John D.

1999-01-01

Many ways of estimating software systems' reliability, or reliability-related quantities, have been developed over the past several years. Of particular interest are methods that can be used to estimate a software system's fault content prior to test, or to discriminate between components that are fault-prone and those that are not. The results of these methods can be used to: 1) More accurately focus scarce fault identification resources on those portions of a software system most in need of it. 2) Estimate and forecast the risk of exposure to residual faults in a software system during operation, and develop risk and safety criteria to guide the release of a software system to fielded use. 3) Estimate the efficiency of test suites in detecting residual faults. 4) Estimate the stability of the software maintenance process.

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

A real-time implementation of an advanced sensor failure detection, isolation, and accommodation algorithm

NASA Technical Reports Server (NTRS)

Delaat, J. C.; Merrill, W. C.

1983-01-01

A sensor failure detection, isolation, and accommodation algorithm was developed which incorporates analytic sensor redundancy through software. This algorithm was implemented in a high level language on a microprocessor based controls computer. Parallel processing and state-of-the-art 16-bit microprocessors are used along with efficient programming practices to achieve real-time operation.

Implementation of a departmental picture archiving and communication system: a productivity and cost analysis.

PubMed

Macyszyn, Luke; Lega, Brad; Bohman, Leif-Erik; Latefi, Ahmad; Smith, Michelle J; Malhotra, Neil R; Welch, William; Grady, Sean M

2013-09-01

Digital radiology enhances productivity and results in long-term cost savings. However, the viewing, storage, and sharing of outside imaging studies on compact discs at ambulatory offices and hospitals pose a number of unique challenges to a surgeon's efficiency and clinical workflow. To improve the efficiency and clinical workflow of an academic neurosurgical practice when evaluating patients with outside radiological studies. Open-source software and commercial hardware were used to design and implement a departmental picture archiving and communications system (PACS). The implementation of a departmental PACS system significantly improved productivity and enhanced collaboration in a variety of clinical settings. Using published data on the rate of information technology problems associated with outside studies on compact discs, this system produced a cost savings ranging from $6250 to $33600 and from $43200 to $72000 for 2 cohorts, urgent transfer and spine clinic patients, respectively, therefore justifying the costs of the system in less than a year. The implementation of a departmental PACS system using open-source software is straightforward and cost-effective and results in significant gains in surgeon productivity when evaluating patients with outside imaging studies.

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE PAGES

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; ...

2018-01-12

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

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

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Software engineering and Ada (Trademark) training: An implementation model for NASA

NASA Technical Reports Server (NTRS)

Legrand, Sue; Freedman, Glenn

1988-01-01

The choice of Ada for software engineering for projects such as the Space Station has resulted in government and industrial groups considering training programs that help workers become familiar with both a software culture and the intricacies of a new computer language. The questions of how much time it takes to learn software engineering with Ada, how much an organization should invest in such training, and how the training should be structured are considered. Software engineering is an emerging, dynamic discipline. It is defined by the author as the establishment and application of sound engineering environments, tools, methods, models, principles, and concepts combined with appropriate standards, guidelines, and practices to support computing which is correct, modifiable, reliable and safe, efficient, and understandable throughout the life cycle of the application. Neither the training programs needed, nor the content of such programs, have been well established. This study addresses the requirements for training for NASA personnel and recommends an implementation plan. A curriculum and a means of delivery are recommended. It is further suggested that a knowledgeable programmer may be able to learn Ada in 5 days, but that it takes 6 to 9 months to evolve into a software engineer who uses the language correctly and effectively. The curriculum and implementation plan can be adapted for each NASA Center according to the needs dictated by each project.

Process membership in asynchronous environments

NASA Technical Reports Server (NTRS)

Ricciardi, Aleta M.; Birman, Kenneth P.

1993-01-01

The development of reliable distributed software is simplified by the ability to assume a fail-stop failure model. The emulation of such a model in an asynchronous distributed environment is discussed. The solution proposed, called Strong-GMP, can be supported through a highly efficient protocol, and was implemented as part of a distributed systems software project at Cornell University. The precise definition of the problem, the protocol, correctness proofs, and an analysis of costs are addressed.

Parallel design patterns for a low-power, software-defined compressed video encoder

NASA Astrophysics Data System (ADS)

Bruns, Michael W.; Hunt, Martin A.; Prasad, Durga; Gunupudi, Nageswara R.; Sonachalam, Sekar

2011-06-01

Video compression algorithms such as H.264 offer much potential for parallel processing that is not always exploited by the technology of a particular implementation. Consumer mobile encoding devices often achieve real-time performance and low power consumption through parallel processing in Application Specific Integrated Circuit (ASIC) technology, but many other applications require a software-defined encoder. High quality compression features needed for some applications such as 10-bit sample depth or 4:2:2 chroma format often go beyond the capability of a typical consumer electronics device. An application may also need to efficiently combine compression with other functions such as noise reduction, image stabilization, real time clocks, GPS data, mission/ESD/user data or software-defined radio in a low power, field upgradable implementation. Low power, software-defined encoders may be implemented using a massively parallel memory-network processor array with 100 or more cores and distributed memory. The large number of processor elements allow the silicon device to operate more efficiently than conventional DSP or CPU technology. A dataflow programming methodology may be used to express all of the encoding processes including motion compensation, transform and quantization, and entropy coding. This is a declarative programming model in which the parallelism of the compression algorithm is expressed as a hierarchical graph of tasks with message communication. Data parallel and task parallel design patterns are supported without the need for explicit global synchronization control. An example is described of an H.264 encoder developed for a commercially available, massively parallel memorynetwork processor device.

Miniature EVA Software Defined Radio

NASA Technical Reports Server (NTRS)

Pozhidaev, Aleksey

2012-01-01

As NASA embarks upon developing the Next-Generation Extra Vehicular Activity (EVA) Radio for deep space exploration, the demands on EVA battery life will substantially increase. The number of modes and frequency bands required will continue to grow in order to enable efficient and complex multi-mode operations including communications, navigation, and tracking applications. Whether conducting astronaut excursions, communicating to soldiers, or first responders responding to emergency hazards, NASA has developed an innovative, affordable, miniaturized, power-efficient software defined radio that offers unprecedented power-efficient flexibility. This lightweight, programmable, S-band, multi-service, frequency- agile EVA software defined radio (SDR) supports data, telemetry, voice, and both standard and high-definition video. Features include a modular design, an easily scalable architecture, and the EVA SDR allows for both stationary and mobile battery powered handheld operations. Currently, the radio is equipped with an S-band RF section. However, its scalable architecture can accommodate multiple RF sections simultaneously to cover multiple frequency bands. The EVA SDR also supports multiple network protocols. It currently implements a Hybrid Mesh Network based on the 802.11s open standard protocol. The radio targets RF channel data rates up to 20 Mbps and can be equipped with a real-time operating system (RTOS) that can be switched off for power-aware applications. The EVA SDR's modular design permits implementation of the same hardware at all Network Nodes concept. This approach assures the portability of the same software into any radio in the system. It also brings several benefits to the entire system including reducing system maintenance, system complexity, and development cost.

Optimally analyzing and implementing of bolt fittings in steel structure based on ANSYS

NASA Astrophysics Data System (ADS)

Han, Na; Song, Shuangyang; Cui, Yan; Wu, Yongchun

2018-03-01

ANSYS simulation software for its excellent performance become outstanding one in Computer-aided Engineering (CAE) family, it is committed to the innovation of engineering simulation to help users to shorten the design process. First, a typical procedure to implement CAE was design. The framework of structural numerical analysis on ANSYS Technology was proposed. Then, A optimally analyzing and implementing of bolt fittings in beam-column join of steel structure was implemented by ANSYS, which was display the cloud chart of XY-shear stress, the cloud chart of YZ-shear stress and the cloud chart of Y component of stress. Finally, ANSYS software simulating results was compared with the measured results by the experiment. The result of ANSYS simulating and analyzing is reliable, efficient and optical. In above process, a structural performance's numerical simulating and analyzing model were explored for engineering enterprises' practice.

Simulation system architecture design for generic communications link

NASA Technical Reports Server (NTRS)

Tsang, Chit-Sang; Ratliff, Jim

1986-01-01

This paper addresses a computer simulation system architecture design for generic digital communications systems. It addresses the issues of an overall system architecture in order to achieve a user-friendly, efficient, and yet easily implementable simulation system. The system block diagram and its individual functional components are described in detail. Software implementation is discussed with the VAX/VMS operating system used as a target environment.

Microcomputer software development facilities

NASA Technical Reports Server (NTRS)

Gorman, J. S.; Mathiasen, C.

1980-01-01

A more efficient and cost effective method for developing microcomputer software is to utilize a host computer with high-speed peripheral support. Application programs such as cross assemblers, loaders, and simulators are implemented in the host computer for each of the microcomputers for which software development is a requirement. The host computer is configured to operate in a time share mode for multiusers. The remote terminals, printers, and down loading capabilities provided are based on user requirements. With this configuration a user, either local or remote, can use the host computer for microcomputer software development. Once the software is developed (through the code and modular debug stage) it can be downloaded to the development system or emulator in a test area where hardware/software integration functions can proceed. The microcomputer software program sources reside in the host computer and can be edited, assembled, loaded, and then downloaded as required until the software development project has been completed.

A LabVIEW® based generic CT scanner control software platform.

PubMed

Dierick, M; Van Loo, D; Masschaele, B; Boone, M; Van Hoorebeke, L

2010-01-01

UGCT, the Centre for X-ray tomography at Ghent University (Belgium) does research on X-ray tomography and its applications. This includes the development and construction of state-of-the-art CT scanners for scientific research. Because these scanners are built for very different purposes they differ considerably in their physical implementations. However, they all share common principle functionality. In this context a generic software platform was developed using LabVIEW® in order to provide the same interface and functionality on all scanners. This article describes the concept and features of this software, and its potential for tomography in a research setting. The core concept is to rigorously separate the abstract operation of a CT scanner from its actual physical configuration. This separation is achieved by implementing a sender-listener architecture. The advantages are that the resulting software platform is generic, scalable, highly efficient, easy to develop and to extend, and that it can be deployed on future scanners with minimal effort.

FPGA-Based Efficient Hardware/Software Co-Design for Industrial Systems with Consideration of Output Selection

NASA Astrophysics Data System (ADS)

Deliparaschos, Kyriakos M.; Michail, Konstantinos; Zolotas, Argyrios C.; Tzafestas, Spyros G.

2016-05-01

This work presents a field programmable gate array (FPGA)-based embedded software platform coupled with a software-based plant, forming a hardware-in-the-loop (HIL) that is used to validate a systematic sensor selection framework. The systematic sensor selection framework combines multi-objective optimization, linear-quadratic-Gaussian (LQG)-type control, and the nonlinear model of a maglev suspension. A robustness analysis of the closed-loop is followed (prior to implementation) supporting the appropriateness of the solution under parametric variation. The analysis also shows that quantization is robust under different controller gains. While the LQG controller is implemented on an FPGA, the physical process is realized in a high-level system modeling environment. FPGA technology enables rapid evaluation of the algorithms and test designs under realistic scenarios avoiding heavy time penalty associated with hardware description language (HDL) simulators. The HIL technique facilitates significant speed-up in the required execution time when compared to its software-based counterpart model.

Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations.

PubMed

Cario, Clinton L; Witte, John S

2018-03-15

As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments and machine learning algorithms, there is also a need for the integration of functionality across frameworks. We present orchid, a python based software package for the management, annotation and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier. Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid. Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution. JWitte@ucsf.edu. Supplementary data are available at Bioinformatics online.

Representation of Serendipitous Scientific Data

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A computer program defines and implements an innovative kind of data structure than can be used for representing information derived from serendipitous discoveries made via collection of scientific data on long exploratory spacecraft missions. Data structures capable of collecting any kind of data can easily be implemented in advance, but the task of designing a fixed and efficient data structure suitable for processing raw data into useful information and taking advantage of serendipitous scientific discovery is becoming increasingly difficult as missions go deeper into space. The present software eases the task by enabling definition of arbitrarily complex data structures that can adapt at run time as raw data are transformed into other types of information. This software runs on a variety of computers, and can be distributed in either source code or binary code form. It must be run in conjunction with any one of a number of Lisp compilers that are available commercially or as shareware. It has no specific memory requirements and depends upon the other software with which it is used. This program is implemented as a library that is called by, and becomes folded into, the other software with which it is used.

Software Quality Assurance Metrics

NASA Technical Reports Server (NTRS)

McRae, Kalindra A.

2004-01-01

Software Quality Assurance (SQA) is a planned and systematic set of activities that ensures conformance of software life cycle processes and products conform to requirements, standards and procedures. In software development, software quality means meeting requirements and a degree of excellence and refinement of a project or product. Software Quality is a set of attributes of a software product by which its quality is described and evaluated. The set of attributes includes functionality, reliability, usability, efficiency, maintainability, and portability. Software Metrics help us understand the technical process that is used to develop a product. The process is measured to improve it and the product is measured to increase quality throughout the life cycle of software. Software Metrics are measurements of the quality of software. Software is measured to indicate the quality of the product, to assess the productivity of the people who produce the product, to assess the benefits derived from new software engineering methods and tools, to form a baseline for estimation, and to help justify requests for new tools or additional training. Any part of the software development can be measured. If Software Metrics are implemented in software development, it can save time, money, and allow the organization to identify the caused of defects which have the greatest effect on software development. The summer of 2004, I worked with Cynthia Calhoun and Frank Robinson in the Software Assurance/Risk Management department. My task was to research and collect, compile, and analyze SQA Metrics that have been used in other projects that are not currently being used by the SA team and report them to the Software Assurance team to see if any metrics can be implemented in their software assurance life cycle process.

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

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

Gaenko, Alexander; Windus, Theresa L.; Sosonkina, Masha

2012-10-19

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecularmore » systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.« less

ODEion--a software module for structural identification of ordinary differential equations.

PubMed

Gennemark, Peter; Wedelin, Dag

2014-02-01

In the systems biology field, algorithms for structural identification of ordinary differential equations (ODEs) have mainly focused on fixed model spaces like S-systems and/or on methods that require sufficiently good data so that derivatives can be accurately estimated. There is therefore a lack of methods and software that can handle more general models and realistic data. We present ODEion, a software module for structural identification of ODEs. Main characteristic features of the software are: • The model space is defined by arbitrary user-defined functions that can be nonlinear in both variables and parameters, such as for example chemical rate reactions. • ODEion implements computationally efficient algorithms that have been shown to efficiently handle sparse and noisy data. It can run a range of realistic problems that previously required a supercomputer. • ODEion is easy to use and provides SBML output. We describe the mathematical problem, the ODEion system itself, and provide several examples of how the system can be used. Available at: http://www.odeidentification.org.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

The Use of Field Programmable Gate Arrays (FPGA) in Small Satellite Communication Systems

NASA Technical Reports Server (NTRS)

Varnavas, Kosta; Sims, William Herbert; Casas, Joseph

2015-01-01

This paper will describe the use of digital Field Programmable Gate Arrays (FPGA) to contribute to advancing the state-of-the-art in software defined radio (SDR) transponder design for the emerging SmallSat and CubeSat industry and to provide advances for NASA as described in the TAO5 Communication and Navigation Roadmap (Ref 4). The use of software defined radios (SDR) has been around for a long time. A typical implementation of the SDR is to use a processor and write software to implement all the functions of filtering, carrier recovery, error correction, framing etc. Even with modern high speed and low power digital signal processors, high speed memories, and efficient coding, the compute intensive nature of digital filters, error correcting and other algorithms is too much for modern processors to get efficient use of the available bandwidth to the ground. By using FPGAs, these compute intensive tasks can be done in parallel, pipelined fashion and more efficiently use every clock cycle to significantly increase throughput while maintaining low power. These methods will implement digital radios with significant data rates in the X and Ka bands. Using these state-of-the-art technologies, unprecedented uplink and downlink capabilities can be achieved in a 1/2 U sized telemetry system. Additionally, modern FPGAs have embedded processing systems, such as ARM cores, integrated inside the FPGA allowing mundane tasks such as parameter commanding to occur easily and flexibly. Potential partners include other NASA centers, industry and the DOD. These assets are associated with small satellite demonstration flights, LEO and deep space applications. MSFC currently has an SDR transponder test-bed using Hardware-in-the-Loop techniques to evaluate and improve SDR technologies.

Efficient accesses of data structures using processing near memory

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

Jayasena, Nuwan S.; Zhang, Dong Ping; Diez, Paula Aguilera

Systems, apparatuses, and methods for implementing efficient queues and other data structures. A queue may be shared among multiple processors and/or threads without using explicit software atomic instructions to coordinate access to the queue. System software may allocate an atomic queue and corresponding queue metadata in system memory and return, to the requesting thread, a handle referencing the queue metadata. Any number of threads may utilize the handle for accessing the atomic queue. The logic for ensuring the atomicity of accesses to the atomic queue may reside in a management unit in the memory controller coupled to the memory wheremore » the atomic queue is allocated.« less

A General Sparse Tensor Framework for Electronic Structure Theory

DOE PAGES

Manzer, Samuel; Epifanovsky, Evgeny; Krylov, Anna I.; ...

2017-01-24

Linear-scaling algorithms must be developed in order to extend the domain of applicability of electronic structure theory to molecules of any desired size. But, the increasing complexity of modern linear-scaling methods makes code development and maintenance a significant challenge. A major contributor to this difficulty is the lack of robust software abstractions for handling block-sparse tensor operations. We therefore report the development of a highly efficient symbolic block-sparse tensor library in order to provide access to high-level software constructs to treat such problems. Our implementation supports arbitrary multi-dimensional sparsity in all input and output tensors. We then avoid cumbersome machine-generatedmore » code by implementing all functionality as a high-level symbolic C++ language library and demonstrate that our implementation attains very high performance for linear-scaling sparse tensor contractions.« less

A Monte Carlo software for the 1-dimensional simulation of IBIC experiments

NASA Astrophysics Data System (ADS)

Forneris, J.; Jakšić, M.; Pastuović, Ž.; Vittone, E.

2014-08-01

The ion beam induced charge (IBIC) microscopy is a valuable tool for the analysis of the electronic properties of semiconductors. In this work, a recently developed Monte Carlo approach for the simulation of IBIC experiments is presented along with a self-standing software equipped with graphical user interface. The method is based on the probabilistic interpretation of the excess charge carrier continuity equations and it offers to the end-user the full control not only of the physical properties ruling the induced charge formation mechanism (i.e., mobility, lifetime, electrostatics, device's geometry), but also of the relevant experimental conditions (ionization profiles, beam dispersion, electronic noise) affecting the measurement of the IBIC pulses. Moreover, the software implements a novel model for the quantitative evaluation of the radiation damage effects on the charge collection efficiency degradation of ion-beam-irradiated devices. The reliability of the model implementation is then validated against a benchmark IBIC experiment.

openPSTD: The open source pseudospectral time-domain method for acoustic propagation

NASA Astrophysics Data System (ADS)

Hornikx, Maarten; Krijnen, Thomas; van Harten, Louis

2016-06-01

An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code.

GiNA, an efficient and high-throughput software for horticultural phenotyping

USDA-ARS?s Scientific Manuscript database

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed,...

Methodology to evaluate the performance of simulation models for alternative compiler and operating system configurations

USDA-ARS?s Scientific Manuscript database

Simulation modelers increasingly require greater flexibility for model implementation on diverse operating systems, and they demand high computational speed for efficient iterative simulations. Additionally, model users may differ in preference for proprietary versus open-source software environment...

Using Stan for Item Response Theory Models

ERIC Educational Resources Information Center

Ames, Allison J.; Au, Chi Hang

2018-01-01

Stan is a flexible probabilistic programming language providing full Bayesian inference through Hamiltonian Monte Carlo algorithms. The benefits of Hamiltonian Monte Carlo include improved efficiency and faster inference, when compared to other MCMC software implementations. Users can interface with Stan through a variety of computing…

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids by Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

SandiaMRCR

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

2012-01-05

SandiaMCR was developed to identify pure components and their concentrations from spectral data. This software efficiently implements the multivariate calibration regression alternating least squares (MCR-ALS), principal component analysis (PCA), and singular value decomposition (SVD). Version 3.37 also includes the PARAFAC-ALS Tucker-1 (for trilinear analysis) algorithms. The alternating least squares methods can be used to determine the composition without or with incomplete prior information on the constituents and their concentrations. It allows the specification of numerous preprocessing, initialization and data selection and compression options for the efficient processing of large data sets. The software includes numerous options including the definition ofmore » equality and non-negativety constraints to realistically restrict the solution set, various normalization or weighting options based on the statistics of the data, several initialization choices and data compression. The software has been designed to provide a practicing spectroscopist the tools required to routinely analysis data in a reasonable time and without requiring expert intervention.« less

JRTF: A Flexible Software Framework for Real-Time Control in Magnetic Confinement Nuclear Fusion Experiments

NASA Astrophysics Data System (ADS)

Zhang, M.; Zheng, G. Z.; Zheng, W.; Chen, Z.; Yuan, T.; Yang, C.

2016-04-01

The magnetic confinement nuclear fusion experiments require various real-time control applications like plasma control. ITER has designed the Fast Plant System Controller (FPSC) for this job. ITER provided hardware and software standards and guidelines for building a FPSC. In order to develop various real-time FPSC applications efficiently, a flexible real-time software framework called J-TEXT real-time framework (JRTF) is developed by J-TEXT tokamak team. JRTF allowed developers to implement different functions as independent and reusable modules called Application Blocks (AB). The AB developers only need to focus on implementing the control tasks or the algorithms. The timing, scheduling, data sharing and eventing are handled by the JRTF pipelines. JRTF provides great flexibility on developing ABs. Unit test against ABs can be developed easily and ABs can even be used in non-JRTF applications. JRTF also provides interfaces allowing JRTF applications to be configured and monitored at runtime. JRTF is compatible with ITER standard FPSC hardware and ITER (Control, Data Access and Communication) CODAC Core software. It can be configured and monitored using (Experimental Physics and Industrial Control System) EPICS. Moreover the JRTF can be ported to different platforms and be integrated with supervisory control software other than EPICS. The paper presents the design and implementation of JRTF as well as brief test results.

Towards a flexible middleware for context-aware pervasive and wearable systems.

PubMed

Muro, Marco; Amoretti, Michele; Zanichelli, Francesco; Conte, Gianni

2012-11-01

Ambient intelligence and wearable computing call for innovative hardware and software technologies, including a highly capable, flexible and efficient middleware, allowing for the reuse of existing pervasive applications when developing new ones. In the considered application domain, middleware should also support self-management, interoperability among different platforms, efficient communications, and context awareness. In the on-going "everything is networked" scenario scalability appears as a very important issue, for which the peer-to-peer (P2P) paradigm emerges as an appealing solution for connecting software components in an overlay network, allowing for efficient and balanced data distribution mechanisms. In this paper, we illustrate how all these concepts can be placed into a theoretical tool, called networked autonomic machine (NAM), implemented into a NAM-based middleware, and evaluated against practical problems of pervasive computing.

Research on Generating Method of Embedded Software Test Document Based on Dynamic Model

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Liu, Ying

2018-03-01

This paper provides a dynamic model-based test document generation method for embedded software that provides automatic generation of two documents: test requirements specification documentation and configuration item test documentation. This method enables dynamic test requirements to be implemented in dynamic models, enabling dynamic test demand tracking to be easily generated; able to automatically generate standardized, standardized test requirements and test documentation, improved document-related content inconsistency and lack of integrity And other issues, improve the efficiency.

A Circuit-Based Neural Network with Hybrid Learning of Backpropagation and Random Weight Change Algorithms

PubMed Central

Yang, Changju; Kim, Hyongsuk; Adhikari, Shyam Prasad; Chua, Leon O.

2016-01-01

A hybrid learning method of a software-based backpropagation learning and a hardware-based RWC learning is proposed for the development of circuit-based neural networks. The backpropagation is known as one of the most efficient learning algorithms. A weak point is that its hardware implementation is extremely difficult. The RWC algorithm, which is very easy to implement with respect to its hardware circuits, takes too many iterations for learning. The proposed learning algorithm is a hybrid one of these two. The main learning is performed with a software version of the BP algorithm, firstly, and then, learned weights are transplanted on a hardware version of a neural circuit. At the time of the weight transplantation, a significant amount of output error would occur due to the characteristic difference between the software and the hardware. In the proposed method, such error is reduced via a complementary learning of the RWC algorithm, which is implemented in a simple hardware. The usefulness of the proposed hybrid learning system is verified via simulations upon several classical learning problems. PMID:28025566

A Capital Assets Preservation Program.

ERIC Educational Resources Information Center

Heiman, Ralph

1989-01-01

New York State officials have created an efficient capital planning system that is a prescribed set of procedures and actions within a program planning manual and two software modules. The program is a series of logical steps that school districts must take to successfully implement their preservation plans. (MLF)

An Application Development Platform for Neuromorphic Computing

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

Dean, Mark; Chan, Jason; Daffron, Christopher

2016-01-01

Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic computing systems developed as a hardware based approach to the implementation of neural networks. They feature highly adaptive and programmable structural elements, which model arti cial neural networks with spiking behavior. We design them to solve problems using evolutionary optimization. In this paper, we highlight the current hardware and software implementations of DANNA, including their features, functionalities and performance. We then describe the development of an Application Development Platform (ADP) to support efficient application implementation and testing of DANNA based solutions. We conclude with future directions.

Metadata-driven Delphi rating on the Internet.

PubMed

Deshpande, Aniruddha M; Shiffman, Richard N; Nadkarni, Prakash M

2005-01-01

Paper-based data collection and analysis for consensus development is inefficient and error-prone. Computerized techniques that could improve efficiency, however, have been criticized as costly, inconvenient and difficult to use. We designed and implemented a metadata-driven Web-based Delphi rating and analysis tool, employing the flexible entity-attribute-value schema to create generic, reusable software. The software can be applied to various domains by altering the metadata; the programming code remains intact. This approach greatly reduces the marginal cost of re-using the software. We implemented our software to prepare for the Conference on Guidelines Standardization. Twenty-three invited experts completed the first round of the Delphi rating on the Web. For each participant, the software generated individualized reports that described the median rating and the disagreement index (calculated from the Interpercentile Range Adjusted for Symmetry) as defined by the RAND/UCLA Appropriateness Method. We evaluated the software with a satisfaction survey using a five-level Likert scale. The panelists felt that Web data entry was convenient (median 4, interquartile range [IQR] 4.0-5.0), acceptable (median 4.5, IQR 4.0-5.0) and easily accessible (median 5, IQR 4.0-5.0). We conclude that Web-based Delphi rating for consensus development is a convenient and acceptable alternative to the traditional paper-based method.

Implementation of Systematic Review Tools in IRIS | Science ...

EPA Pesticide Factsheets

Currently, the number of chemicals present in the environment exceeds the ability of public health scientists to efficiently screen the available data in order to produce well-informed human health risk assessments in a timely manner. For this reason, the US EPA’s Integrated Risk Information System (IRIS) program has started implementing new software tools into the hazard characterization workflow. These automated tools aid in multiple phases of the systematic review process including scoping and problem formulation, literature search, and identification and screening of available published studies. The increased availability of these tools lays the foundation for automating or semi-automating multiple phases of the systematic review process. Some of these software tools include modules to facilitate a structured approach to study quality evaluation of human and animal data, although approaches are generally lacking for assessing complex mechanistic information, in particular “omics”-based evidence tools are starting to become available to evaluate these types of studies. We will highlight how new software programs, online tools, and approaches for assessing study quality can be better integrated to allow for a more efficient and transparent workflow of the risk assessment process as well as identify tool gaps that would benefit future risk assessments. Disclaimer: The views expressed here are those of the authors and do not necessarily represent the view

Application of industry-standard guidelines for the validation of avionics software

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.; Shagnea, Anita M.

1990-01-01

The application of industry standards to the development of avionics software is discussed, focusing on verification and validation activities. It is pointed out that the procedures that guide the avionics software development and testing process are under increased scrutiny. The DO-178A guidelines, Software Considerations in Airborne Systems and Equipment Certification, are used by the FAA for certifying avionics software. To investigate the effectiveness of the DO-178A guidelines for improving the quality of avionics software, guidance and control software (GCS) is being developed according to the DO-178A development method. It is noted that, due to the extent of the data collection and configuration management procedures, any phase in the life cycle of a GCS implementation can be reconstructed. Hence, a fundamental development and testing platform has been established that is suitable for investigating the adequacy of various software development processes. In particular, the overall effectiveness and efficiency of the development method recommended by the DO-178A guidelines are being closely examined.

Study of a unified hardware and software fault-tolerant architecture

NASA Technical Reports Server (NTRS)

Lala, Jaynarayan; Alger, Linda; Friend, Steven; Greeley, Gregory; Sacco, Stephen; Adams, Stuart

1989-01-01

A unified architectural concept, called the Fault Tolerant Processor Attached Processor (FTP-AP), that can tolerate hardware as well as software faults is proposed for applications requiring ultrareliable computation capability. An emulation of the FTP-AP architecture, consisting of a breadboard Motorola 68010-based quadruply redundant Fault Tolerant Processor, four VAX 750s as attached processors, and four versions of a transport aircraft yaw damper control law, is used as a testbed in the AIRLAB to examine a number of critical issues. Solutions of several basic problems associated with N-Version software are proposed and implemented on the testbed. This includes a confidence voter to resolve coincident errors in N-Version software. A reliability model of N-Version software that is based upon the recent understanding of software failure mechanisms is also developed. The basic FTP-AP architectural concept appears suitable for hosting N-Version application software while at the same time tolerating hardware failures. Architectural enhancements for greater efficiency, software reliability modeling, and N-Version issues that merit further research are identified.

IMPLEMENTATION OF A CAPE-OPEN COMPLIANT PROCESS SIMULATOR USING MICROSOFT'S VISUAL STUDIO.NET AND THE .NET FRAMEWORK

EPA Science Inventory

The United States Environmental Protection Agency is developing a Computer
Aided Process Engineering (CAPE) software tool for the metal finishing
industry that helps users design efficient metal finishing processes that
are less polluting to the environment. Metal finish...

Modeling survival of juvenile salmon during downriver migration in the Columbia River on a microcomputer

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

Peloquin, R.A.; McKenzie, D.H.

1994-10-01

A compartmental model has been implemented on a microcomputer as an aid in the analysis of alternative solutions to a problem. The model, entitled Smolt Survival Simulator, simulates the survival of juvenile salmon during their downstream migration and passage of hydroelectric dams in the Columbia River. The model is designed to function in a workshop environment where resource managers and fisheries biologists can study alternative measures that may potentially increase juvenile anadromous fish survival during downriver migration. The potential application of the model has placed several requirements on the implementing software. It must be available for use in workshop settings.more » The software must be easily to use with minimal computer knowledge. Scenarios must be created and executed quickly and efficiently. Results must be immediately available. Software design emphasis vas placed on the user interface because of these requirements. The discussion focuses on methods used in the development of the SSS software user interface. These methods should reduce user stress and alloy thorough and easy parameter modification.« less

Near-Infrared Neuroimaging with NinPy

PubMed Central

Strangman, Gary E.; Zhang, Quan; Zeffiro, Thomas

2009-01-01

There has been substantial recent growth in the use of non-invasive optical brain imaging in studies of human brain function in health and disease. Near-infrared neuroimaging (NIN) is one of the most promising of these techniques and, although NIN hardware continues to evolve at a rapid pace, software tools supporting optical data acquisition, image processing, statistical modeling, and visualization remain less refined. Python, a modular and computationally efficient development language, can support functional neuroimaging studies of diverse design and implementation. In particular, Python's easily readable syntax and modular architecture allow swift prototyping followed by efficient transition to stable production systems. As an introduction to our ongoing efforts to develop Python software tools for structural and functional neuroimaging, we discuss: (i) the role of non-invasive diffuse optical imaging in measuring brain function, (ii) the key computational requirements to support NIN experiments, (iii) our collection of software tools to support NIN, called NinPy, and (iv) future extensions of these tools that will allow integration of optical with other structural and functional neuroimaging data sources. Source code for the software discussed here will be made available at www.nmr.mgh.harvard.edu/Neural_SystemsGroup/software.html. PMID:19543449

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Current And Future Directions Of Lens Design Software

NASA Astrophysics Data System (ADS)

Gustafson, Darryl E.

1983-10-01

The most effective environment for doing lens design continues to evolve as new computer hardware and software tools become available. Important recent hardware developments include: Low-cost but powerful interactive multi-user 32 bit computers with virtual memory that are totally software-compatible with prior larger and more expensive members of the family. A rapidly growing variety of graphics devices for both hard-copy and screen graphics, including many with color capability. In addition, with optical design software readily accessible in many forms, optical design has become a part-time activity for a large number of engineers instead of being restricted to a small number of full-time specialists. A designer interface that is friendly for the part-time user while remaining efficient for the full-time designer is thus becoming more important as well as more practical. Along with these developments, software tools in other scientific and engineering disciplines are proliferating. Thus, the optical designer is less and less unique in his use of computer-aided techniques and faces the challenge and opportunity of efficiently communicating his designs to other computer-aided-design (CAD), computer-aided-manufacturing (CAM), structural, thermal, and mechanical software tools. This paper will address the impact of these developments on the current and future directions of the CODE VTM optical design software package, its implementation, and the resulting lens design environment.

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines.

PubMed

Wojdyla, Justyna Aleksandra; Kaminski, Jakub W; Panepucci, Ezequiel; Ebner, Simon; Wang, Xiaoqiang; Gabadinho, Jose; Wang, Meitian

2018-01-01

Data acquisition software is an essential component of modern macromolecular crystallography (MX) beamlines, enabling efficient use of beam time at synchrotron facilities. Developed at the Paul Scherrer Institute, the DA+ data acquisition software is implemented at all three Swiss Light Source (SLS) MX beamlines. DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. The major components of DA+ are the user interface, acquisition engine, online processing and database. Immediate data quality feedback is achieved with distributed automatic data analysis routines. The software architecture enables exploration of the full potential of the latest instrumentation at the SLS MX beamlines, such as the SmarGon goniometer and the EIGER X 16M detector, and development of new data collection methods.

APRON: A Cellular Processor Array Simulation and Hardware Design Tool

NASA Astrophysics Data System (ADS)

Barr, David R. W.; Dudek, Piotr

2009-12-01

We present a software environment for the efficient simulation of cellular processor arrays (CPAs). This software (APRON) is used to explore algorithms that are designed for massively parallel fine-grained processor arrays, topographic multilayer neural networks, vision chips with SIMD processor arrays, and related architectures. The software uses a highly optimised core combined with a flexible compiler to provide the user with tools for the design of new processor array hardware architectures and the emulation of existing devices. We present performance benchmarks for the software processor array implemented on standard commodity microprocessors. APRON can be configured to use additional processing hardware if necessary and can be used as a complete graphical user interface and development environment for new or existing CPA systems, allowing more users to develop algorithms for CPA systems.

Geometric modeling for computer aided design

NASA Technical Reports Server (NTRS)

Schwing, James L.

1992-01-01

The goal was the design and implementation of software to be used in the conceptual design of aerospace vehicles. Several packages and design studies were completed, including two software tools currently used in the conceptual level design of aerospace vehicles. These tools are the Solid Modeling Aerospace Research Tool (SMART) and the Environment for Software Integration and Execution (EASIE). SMART provides conceptual designers with a rapid prototyping capability and additionally provides initial mass property analysis. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand alone analysis codes that result in the streamlining of the exchange of data between programs, reducing errors and improving efficiency.

Efficient FIR Filter Implementations for Multichannel BCIs Using Xilinx System Generator.

PubMed

Ghani, Usman; Wasim, Muhammad; Khan, Umar Shahbaz; Mubasher Saleem, Muhammad; Hassan, Ali; Rashid, Nasir; Islam Tiwana, Mohsin; Hamza, Amir; Kashif, Amir

2018-01-01

Background . Brain computer interface (BCI) is a combination of software and hardware communication protocols that allow brain to control external devices. Main purpose of BCI controlled external devices is to provide communication medium for disabled persons. Now these devices are considered as a new way to rehabilitate patients with impunities. There are certain potentials present in electroencephalogram (EEG) that correspond to specific event. Main issue is to detect such event related potentials online in such a low signal to noise ratio (SNR). In this paper we propose a method that will facilitate the concept of online processing by providing an efficient filtering implementation in a hardware friendly environment by switching to finite impulse response (FIR). Main focus of this research is to minimize latency and computational delay of preprocessing related to any BCI application. Four different finite impulse response (FIR) implementations along with large Laplacian filter are implemented in Xilinx System Generator. Efficiency of 25% is achieved in terms of reduced number of coefficients and multiplications which in turn reduce computational delays accordingly.

Interfacing An Intelligent Decision-Maker To A Real-Time Control System

NASA Astrophysics Data System (ADS)

Evers, D. C.; Smith, D. M.; Staros, C. J.

1984-06-01

This paper discusses some of the practical aspects of implementing expert systems in a real-time environment. There is a conflict between the needs of a process control system and the computational load imposed by intelligent decision-making software. The computation required to manage a real-time control problem is primarily concerned with routine calculations which must be executed in real time. On most current hardware, non-trivial AI software should not be forced to operate under real-time constraints. In order for the system to work efficiently, the two processes must be separated by a well-defined interface. Although the precise nature of the task separation will vary with the application, the definition of the interface will need to follow certain fundamental principles in order to provide functional separation. This interface was successfully implemented in the expert scheduling software currently running the automated chemical processing facility at Lockheed-Georgia. Potential applications of this concept in the areas of airborne avionics and robotics will be discussed.

Pattern classification by memristive crossbar circuits using ex situ and in situ training.

PubMed

Alibart, Fabien; Zamanidoost, Elham; Strukov, Dmitri B

2013-01-01

Memristors are memory resistors that promise the efficient implementation of synaptic weights in artificial neural networks. Whereas demonstrations of the synaptic operation of memristors already exist, the implementation of even simple networks is more challenging and has yet to be reported. Here we demonstrate pattern classification using a single-layer perceptron network implemented with a memrisitive crossbar circuit and trained using the perceptron learning rule by ex situ and in situ methods. In the first case, synaptic weights, which are realized as conductances of titanium dioxide memristors, are calculated on a precursor software-based network and then imported sequentially into the crossbar circuit. In the second case, training is implemented in situ, so the weights are adjusted in parallel. Both methods work satisfactorily despite significant variations in the switching behaviour of the memristors. These results give hope for the anticipated efficient implementation of artificial neuromorphic networks and pave the way for dense, high-performance information processing systems.

Pattern classification by memristive crossbar circuits using ex situ and in situ training

NASA Astrophysics Data System (ADS)

Alibart, Fabien; Zamanidoost, Elham; Strukov, Dmitri B.

2013-06-01

Memristors are memory resistors that promise the efficient implementation of synaptic weights in artificial neural networks. Whereas demonstrations of the synaptic operation of memristors already exist, the implementation of even simple networks is more challenging and has yet to be reported. Here we demonstrate pattern classification using a single-layer perceptron network implemented with a memrisitive crossbar circuit and trained using the perceptron learning rule by ex situ and in situ methods. In the first case, synaptic weights, which are realized as conductances of titanium dioxide memristors, are calculated on a precursor software-based network and then imported sequentially into the crossbar circuit. In the second case, training is implemented in situ, so the weights are adjusted in parallel. Both methods work satisfactorily despite significant variations in the switching behaviour of the memristors. These results give hope for the anticipated efficient implementation of artificial neuromorphic networks and pave the way for dense, high-performance information processing systems.

Study of Huizhou architecture component point cloud in surface reconstruction

NASA Astrophysics Data System (ADS)

Zhang, Runmei; Wang, Guangyin; Ma, Jixiang; Wu, Yulu; Zhang, Guangbin

2017-06-01

Surface reconfiguration softwares have many problems such as complicated operation on point cloud data, too many interaction definitions, and too stringent requirements for inputing data. Thus, it has not been widely popularized so far. This paper selects the unique Huizhou Architecture chuandou wooden beam framework as the research object, and presents a complete set of implementation in data acquisition from point, point cloud preprocessing and finally implemented surface reconstruction. Firstly, preprocessing the acquired point cloud data, including segmentation and filtering. Secondly, the surface’s normals are deduced directly from the point cloud dataset. Finally, the surface reconstruction is studied by using Greedy Projection Triangulation Algorithm. Comparing the reconstructed model with the three-dimensional surface reconstruction softwares, the results show that the proposed scheme is more smooth, time efficient and portable.

Developing Interactive Educational Engineering Software for the World Wide Web with Java.

ERIC Educational Resources Information Center

Reed, John A.; Afjeh, Abdollah A.

1998-01-01

Illustrates the design and implementation of a Java applet for use in educational propulsion engineering curricula. The Java Gas Turbine Simulator applet provides an interactive graphical environment which allows the rapid, efficient construction and analysis of arbitrary gas turbine systems. The simulator can be easily accessed from the World…

Computer-intensive simulation of solid-state NMR experiments using SIMPSON.

PubMed

Tošner, Zdeněk; Andersen, Rasmus; Stevensson, Baltzar; Edén, Mattias; Nielsen, Niels Chr; Vosegaard, Thomas

2014-09-01

Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden-Fletcher-Goldfarb-Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations. Copyright © 2014 Elsevier Inc. All rights reserved.

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

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.

An Implicit Algorithm for the Numerical Simulation of Shape-Memory Alloys

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

Becker, R; Stolken, J; Jannetti, C

Shape-memory alloys (SMA) have the potential to be used in a variety of interesting applications due to their unique properties of pseudoelasticity and the shape-memory effect. However, in order to design SMA devices efficiently, a physics-based constitutive model is required to accurately simulate the behavior of shape-memory alloys. The scope of this work is to extend the numerical capabilities of the SMA constitutive model developed by Jannetti et. al. (2003), to handle large-scale polycrystalline simulations. The constitutive model is implemented within the finite-element software ABAQUS/Standard using a user defined material subroutine, or UMAT. To improve the efficiency of the numericalmore » simulations, so that polycrystalline specimens of shape-memory alloys can be modeled, a fully implicit algorithm has been implemented to integrate the constitutive equations. Using an implicit integration scheme increases the efficiency of the UMAT over the previously implemented explicit integration method by a factor of more than 100 for single crystal simulations.« less

Applying the metro map to software development management

NASA Astrophysics Data System (ADS)

Aguirregoitia, Amaia; Dolado, J. Javier; Presedo, Concepción

2010-01-01

This paper presents MetroMap, a new graphical representation model for controlling and managing the software development process. Metromap uses metaphors and visual representation techniques to explore several key indicators in order to support problem detection and resolution. The resulting visualization addresses diverse management tasks, such as tracking of deviations from the plan, analysis of patterns of failure detection and correction, overall assessment of change management policies, and estimation of product quality. The proposed visualization uses a metaphor with a metro map along with various interactive techniques to represent information concerning the software development process and to deal efficiently with multivariate visual queries. Finally, the paper shows the implementation of the tool in JavaFX with data of a real project and the results of testing the tool with the aforementioned data and users attempting several information retrieval tasks. The conclusion shows the results of analyzing user response time and efficiency using the MetroMap visualization system. The utility of the tool was positively evaluated.

Finite-difference method Stokes solver (FDMSS) for 3D pore geometries: Software development, validation and case studies

NASA Astrophysics Data System (ADS)

Gerke, Kirill M.; Vasilyev, Roman V.; Khirevich, Siarhei; Collins, Daniel; Karsanina, Marina V.; Sizonenko, Timofey O.; Korost, Dmitry V.; Lamontagne, Sébastien; Mallants, Dirk

2018-05-01

Permeability is one of the fundamental properties of porous media and is required for large-scale Darcian fluid flow and mass transport models. Whilst permeability can be measured directly at a range of scales, there are increasing opportunities to evaluate permeability from pore-scale fluid flow simulations. We introduce the free software Finite-Difference Method Stokes Solver (FDMSS) that solves Stokes equation using a finite-difference method (FDM) directly on voxelized 3D pore geometries (i.e. without meshing). Based on explicit convergence studies, validation on sphere packings with analytically known permeabilities, and comparison against lattice-Boltzmann and other published FDM studies, we conclude that FDMSS provides a computationally efficient and accurate basis for single-phase pore-scale flow simulations. By implementing an efficient parallelization and code optimization scheme, permeability inferences can now be made from 3D images of up to 109 voxels using modern desktop computers. Case studies demonstrate the broad applicability of the FDMSS software for both natural and artificial porous media.

Ramses-GPU: Second order MUSCL-Handcock finite volume fluid solver

NASA Astrophysics Data System (ADS)

Kestener, Pierre

2017-10-01

RamsesGPU is a reimplementation of RAMSES (ascl:1011.007) which drops the adaptive mesh refinement (AMR) features to optimize 3D uniform grid algorithms for modern graphics processor units (GPU) to provide an efficient software package for astrophysics applications that do not need AMR features but do require a very large number of integration time steps. RamsesGPU provides an very efficient C++/CUDA/MPI software implementation of a second order MUSCL-Handcock finite volume fluid solver for compressible hydrodynamics as a magnetohydrodynamics solver based on the constraint transport technique. Other useful modules includes static gravity, dissipative terms (viscosity, resistivity), and forcing source term for turbulence studies, and special care was taken to enhance parallel input/output performance by using state-of-the-art libraries such as HDF5 and parallel-netcdf.

PREMIX: PRivacy-preserving EstiMation of Individual admiXture.

PubMed

Chen, Feng; Dow, Michelle; Ding, Sijie; Lu, Yao; Jiang, Xiaoqian; Tang, Hua; Wang, Shuang

2016-01-01

In this paper we proposed a framework: PRivacy-preserving EstiMation of Individual admiXture (PREMIX) using Intel software guard extensions (SGX). SGX is a suite of software and hardware architectures to enable efficient and secure computation over confidential data. PREMIX enables multiple sites to securely collaborate on estimating individual admixture within a secure enclave inside Intel SGX. We implemented a feature selection module to identify most discriminative Single Nucleotide Polymorphism (SNP) based on informativeness and an Expectation Maximization (EM)-based Maximum Likelihood estimator to identify the individual admixture. Experimental results based on both simulation and 1000 genome data demonstrated the efficiency and accuracy of the proposed framework. PREMIX ensures a high level of security as all operations on sensitive genomic data are conducted within a secure enclave using SGX.

Enhanced autocompensating quantum cryptography system.

PubMed

Bethune, Donald S; Navarro, Martha; Risk, William P

2002-03-20

We have improved the hardware and software of our autocompensating system for quantum key distribution by replacing bulk optical components at the end stations with fiber-optic equivalents and implementing software that synchronizes end-station activities, communicates basis choices, corrects errors, and performs privacy amplification over a local area network. The all-fiber-optic arrangement provides stable, efficient, and high-contrast routing of the photons. The low-bit error rate leads to high error-correction efficiency and minimizes data sacrifice during privacy amplification. Characterization measurements made on a number of commercial avalanche photodiodes are presented that highlight the need for improved devices tailored specifically for quantum information applications. A scheme for frequency shifting the photons returning from Alice's station to allow them to be distinguished from backscattered noise photons is also described.

Implementation of an object oriented track reconstruction model into multiple LHC experiments*

NASA Astrophysics Data System (ADS)

Gaines, Irwin; Gonzalez, Saul; Qian, Sijin

2001-10-01

An Object Oriented (OO) model (Gaines et al., 1996; 1997; Gaines and Qian, 1998; 1999) for track reconstruction by the Kalman filtering method has been designed for high energy physics experiments at high luminosity hadron colliders. The model has been coded in the C++ programming language and has been successfully implemented into the OO computing environments of both the CMS (1994) and ATLAS (1994) experiments at the future Large Hadron Collider (LHC) at CERN. We shall report: how the OO model was adapted, with largely the same code, to different scenarios and serves the different reconstruction aims in different experiments (i.e. the level-2 trigger software for ATLAS and the offline software for CMS); how the OO model has been incorporated into different OO environments with a similar integration structure (demonstrating the ease of re-use of OO program); what are the OO model's performance, including execution time, memory usage, track finding efficiency and ghost rate, etc.; and additional physics performance based on use of the OO tracking model. We shall also mention the experience and lessons learned from the implementation of the OO model into the general OO software framework of the experiments. In summary, our practice shows that the OO technology really makes the software development and the integration issues straightforward and convenient; this may be particularly beneficial for the general non-computer-professional physicists.

Mercury⊕: An evidential reasoning image classifier

NASA Astrophysics Data System (ADS)

Peddle, Derek R.

1995-12-01

MERCURY⊕ is a multisource evidential reasoning classification software system based on the Dempster-Shafer theory of evidence. The design and implementation of this software package is described for improving the classification and analysis of multisource digital image data necessary for addressing advanced environmental and geoscience applications. In the remote-sensing context, the approach provides a more appropriate framework for classifying modern, multisource, and ancillary data sets which may contain a large number of disparate variables with different statistical properties, scales of measurement, and levels of error which cannot be handled using conventional Bayesian approaches. The software uses a nonparametric, supervised approach to classification, and provides a more objective and flexible interface to the evidential reasoning framework using a frequency-based method for computing support values from training data. The MERCURY⊕ software package has been implemented efficiently in the C programming language, with extensive use made of dynamic memory allocation procedures and compound linked list and hash-table data structures to optimize the storage and retrieval of evidence in a Knowledge Look-up Table. The software is complete with a full user interface and runs under Unix, Ultrix, VAX/VMS, MS-DOS, and Apple Macintosh operating system. An example of classifying alpine land cover and permafrost active layer depth in northern Canada is presented to illustrate the use and application of these ideas.

International Conference on Stiff Computation Held at Park City, Utah on April 12, 13 and 14, 1982.

DTIC Science & Technology

1983-05-31

algorithm should be designed which can analyse a system description and find out for the user ~to which class of problems his system belongs... Dove...processors designed to implement aspecific solution process. yrne: IEE floating point chip design " used by INE and others is an example (Xahan)...the...hardware speciaList has designed his computer such that the paraL#L features can be addressed convenientLy and !! ’) efficientLy, and 4;) the software

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

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

Jiang, S; Dolly, S; Cai, B

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deepmore » modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.« less

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.

PubMed

Modolo, Laurent; Lerat, Emmanuelle

2015-04-29

Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various quality statistics. Moreover, current quality control procedures that provide a "good quality" data set, are not optimal and discard many informative nucleotides. To address these drawbacks, we present a new quality control method, implemented in UrQt software, for Unsupervised Quality trimming of Next Generation Sequencing reads. Our trimming procedure relies on a well-defined probabilistic framework to detect the best segmentation between two segments of unreliable nucleotides, framing a segment of informative nucleotides. Our software only requires one user-friendly parameter to define the minimal quality threshold (phred score) to consider a nucleotide to be informative, which is independent of both the experiment and the quality of the data. This procedure is implemented in C++ in an efficient and parallelized software with a low memory footprint. We tested the performances of UrQt compared to the best-known trimming programs, on seven RNA and DNA sequencing experiments and demonstrated its optimality in the resulting tradeoff between the number of trimmed nucleotides and the quality objective. By finding the best segmentation to delimit a segment of good quality nucleotides, UrQt greatly increases the number of reads and of nucleotides that can be retained for a given quality objective. UrQt source files, binary executables for different operating systems and documentation are freely available (under the GPLv3) at the following address: https://lbbe.univ-lyon1.fr/-UrQt-.html .

A Simplified Mesh Deformation Method Using Commercial Structural Analysis Software

NASA Technical Reports Server (NTRS)

Hsu, Su-Yuen; Chang, Chau-Lyan; Samareh, Jamshid

2004-01-01

Mesh deformation in response to redefined or moving aerodynamic surface geometries is a frequently encountered task in many applications. Most existing methods are either mathematically too complex or computationally too expensive for usage in practical design and optimization. We propose a simplified mesh deformation method based on linear elastic finite element analyses that can be easily implemented by using commercially available structural analysis software. Using a prescribed displacement at the mesh boundaries, a simple structural analysis is constructed based on a spatially varying Young s modulus to move the entire mesh in accordance with the surface geometry redefinitions. A variety of surface movements, such as translation, rotation, or incremental surface reshaping that often takes place in an optimization procedure, may be handled by the present method. We describe the numerical formulation and implementation using the NASTRAN software in this paper. The use of commercial software bypasses tedious reimplementation and takes advantage of the computational efficiency offered by the vendor. A two-dimensional airfoil mesh and a three-dimensional aircraft mesh were used as test cases to demonstrate the effectiveness of the proposed method. Euler and Navier-Stokes calculations were performed for the deformed two-dimensional meshes.

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines

PubMed Central

Wojdyla, Justyna Aleksandra; Kaminski, Jakub W.; Ebner, Simon; Wang, Xiaoqiang; Gabadinho, Jose; Wang, Meitian

2018-01-01

Data acquisition software is an essential component of modern macromolecular crystallography (MX) beamlines, enabling efficient use of beam time at synchrotron facilities. Developed at the Paul Scherrer Institute, the DA+ data acquisition software is implemented at all three Swiss Light Source (SLS) MX beamlines. DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. The major components of DA+ are the user interface, acquisition engine, online processing and database. Immediate data quality feedback is achieved with distributed automatic data analysis routines. The software architecture enables exploration of the full potential of the latest instrumentation at the SLS MX beamlines, such as the SmarGon goniometer and the EIGER X 16M detector, and development of new data collection methods. PMID:29271779

Implementation of a parallel unstructured Euler solver on shared and distributed memory architectures

NASA Technical Reports Server (NTRS)

Mavriplis, D. J.; Das, Raja; Saltz, Joel; Vermeland, R. E.

1992-01-01

An efficient three dimensional unstructured Euler solver is parallelized on a Cray Y-MP C90 shared memory computer and on an Intel Touchstone Delta distributed memory computer. This paper relates the experiences gained and describes the software tools and hardware used in this study. Performance comparisons between two differing architectures are made.

Automatic finite element generators

NASA Technical Reports Server (NTRS)

Wang, P. S.

1984-01-01

The design and implementation of a software system for generating finite elements and related computations are described. Exact symbolic computational techniques are employed to derive strain-displacement matrices and element stiffness matrices. Methods for dealing with the excessive growth of symbolic expressions are discussed. Automatic FORTRAN code generation is described with emphasis on improving the efficiency of the resultant code.

Advantages of Brahms for Specifying and Implementing a Multiagent Human-Robotic Exploration System

NASA Technical Reports Server (NTRS)

Clancey, William J.; Sierhuis, Maarten; Kaskiris, Charis; vanHoof, Ron

2003-01-01

We have developed a model-based, distributed architecture that integrates diverse components in a system designed for lunar and planetary surface operations: an astronaut's space suit, cameras, all-terrain vehicles, robotic assistant, crew in a local habitat, and mission support team. Software processes ('agents') implemented in the Brahms language, run on multiple, mobile platforms. These mobile agents interpret and transform available data to help people and robotic systems coordinate their actions to make operations more safe and efficient. The Brahms-based mobile agent architecture (MAA) uses a novel combination of agent types so the software agents may understand and facilitate communications between people and between system components. A state-of-the-art spoken dialogue interface is integrated with Brahms models, supporting a speech-driven field observation record and rover command system. An important aspect of the methodology involves first simulating the entire system in Brahms, then configuring the agents into a runtime system Thus, Brahms provides a language, engine, and system builder's toolkit for specifying and implementing multiagent systems.

Design Approach and Implementation of Application Specific Instruction Set Processor for SHA-3 BLAKE Algorithm

NASA Astrophysics Data System (ADS)

Zhang, Yuli; Han, Jun; Weng, Xinqian; He, Zhongzhu; Zeng, Xiaoyang

This paper presents an Application Specific Instruction-set Processor (ASIP) for the SHA-3 BLAKE algorithm family by instruction set extensions (ISE) from an RISC (reduced instruction set computer) processor. With a design space exploration for this ASIP to increase the performance and reduce the area cost, we accomplish an efficient hardware and software implementation of BLAKE algorithm. The special instructions and their well-matched hardware function unit improve the calculation of the key section of the algorithm, namely G-functions. Also, relaxing the time constraint of the special function unit can decrease its hardware cost, while keeping the high data throughput of the processor. Evaluation results reveal the ASIP achieves 335Mbps and 176Mbps for BLAKE-256 and BLAKE-512. The extra area cost is only 8.06k equivalent gates. The proposed ASIP outperforms several software approaches on various platforms in cycle per byte. In fact, both high throughput and low hardware cost achieved by this programmable processor are comparable to that of ASIC implementations.

Numerical implementation of the S-matrix algorithm for modeling of relief diffraction gratings

NASA Astrophysics Data System (ADS)

Yaremchuk, Iryna; Tamulevičius, Tomas; Fitio, Volodymyr; Gražulevičiūte, Ieva; Bobitski, Yaroslav; Tamulevičius, Sigitas

2013-11-01

A new numerical implementation is developed to calculate the diffraction efficiency of relief diffraction gratings. In the new formulation, vectors containing the expansion coefficients of electric and magnetic fields on boundaries of the grating layer are expressed by additional constants. An S-matrix algorithm has been systematically described in detail and adapted to a simple matrix form. This implementation is suitable for the study of optical characteristics of periodic structures by using modern object-oriented programming languages and different standard mathematical software. The modeling program has been developed on the basis of this numerical implementation and tested by comparison with other commercially available programs and experimental data. Numerical examples are given to show the usefulness of the new implementation.

[Implementation of a new electronic patient record in surgery].

PubMed

Eggli, S; Holm, J

2001-12-01

The increasing amount of clinical data, intensified interest of patients in medical information, medical quality management and the recent cost explosion in health care systems have forced medical institutions to improve their strategy in handling medical data. In the orthopedic department (3,600 surgeries, 75 beds, 14,000 consultations) software application for comprehensive patient data management has been developed. When implementing the electronic patient history following criteria were evaluated: 1. software evaluation, 2. implementation, 3. work flow, 4. data security/system stability. In the first phase the functional character was defined. Implementation required 3 months after parametrization. The expense amounted to 130,000 DM (30 clients). The training requirements were one afternoon for the secretaries and a 2-h session for the residents. The access speed on medically relevant data averaged under 3 s. The average saving in working hours was approximately 5 h/week for the secretaries and 4 h/week for the residents. The saving in paper amounted to 36,000 sheets/year. In 3 operational years there were 3 server breakdowns. Evaluation of the saving on working hours showed that such a system can amortize within a year. The latest improvements in hardware and software technology made the electronic medical record with integrated quality-control practicable without massive expenditure. The system supplies an extensive platform of information for patient treatment and an instrument to evaluate the efficiency of therapy strategies independent of the clinical field.

Parallel processing architecture for H.264 deblocking filter on multi-core platforms

NASA Astrophysics Data System (ADS)

Prasad, Durga P.; Sonachalam, Sekar; Kunchamwar, Mangesh K.; Gunupudi, Nageswara Rao

2012-03-01

Massively parallel computing (multi-core) chips offer outstanding new solutions that satisfy the increasing demand for high resolution and high quality video compression technologies such as H.264. Such solutions not only provide exceptional quality but also efficiency, low power, and low latency, previously unattainable in software based designs. While custom hardware and Application Specific Integrated Circuit (ASIC) technologies may achieve lowlatency, low power, and real-time performance in some consumer devices, many applications require a flexible and scalable software-defined solution. The deblocking filter in H.264 encoder/decoder poses difficult implementation challenges because of heavy data dependencies and the conditional nature of the computations. Deblocking filter implementations tend to be fixed and difficult to reconfigure for different needs. The ability to scale up for higher quality requirements such as 10-bit pixel depth or a 4:2:2 chroma format often reduces the throughput of a parallel architecture designed for lower feature set. A scalable architecture for deblocking filtering, created with a massively parallel processor based solution, means that the same encoder or decoder will be deployed in a variety of applications, at different video resolutions, for different power requirements, and at higher bit-depths and better color sub sampling patterns like YUV, 4:2:2, or 4:4:4 formats. Low power, software-defined encoders/decoders may be implemented using a massively parallel processor array, like that found in HyperX technology, with 100 or more cores and distributed memory. The large number of processor elements allows the silicon device to operate more efficiently than conventional DSP or CPU technology. This software programing model for massively parallel processors offers a flexible implementation and a power efficiency close to that of ASIC solutions. This work describes a scalable parallel architecture for an H.264 compliant deblocking filter for multi core platforms such as HyperX technology. Parallel techniques such as parallel processing of independent macroblocks, sub blocks, and pixel row level are examined in this work. The deblocking architecture consists of a basic cell called deblocking filter unit (DFU) and dependent data buffer manager (DFM). The DFU can be used in several instances, catering to different performance needs the DFM serves the data required for the different number of DFUs, and also manages all the neighboring data required for future data processing of DFUs. This approach achieves the scalability, flexibility, and performance excellence required in deblocking filters.

Quantum machine learning.

PubMed

Biamonte, Jacob; Wittek, Peter; Pancotti, Nicola; Rebentrost, Patrick; Wiebe, Nathan; Lloyd, Seth

2017-09-13

Fuelled by increasing computer power and algorithmic advances, machine learning techniques have become powerful tools for finding patterns in data. Quantum systems produce atypical patterns that classical systems are thought not to produce efficiently, so it is reasonable to postulate that quantum computers may outperform classical computers on machine learning tasks. The field of quantum machine learning explores how to devise and implement quantum software that could enable machine learning that is faster than that of classical computers. Recent work has produced quantum algorithms that could act as the building blocks of machine learning programs, but the hardware and software challenges are still considerable.

Quantum machine learning

NASA Astrophysics Data System (ADS)

Biamonte, Jacob; Wittek, Peter; Pancotti, Nicola; Rebentrost, Patrick; Wiebe, Nathan; Lloyd, Seth

2017-09-01

Fuelled by increasing computer power and algorithmic advances, machine learning techniques have become powerful tools for finding patterns in data. Quantum systems produce atypical patterns that classical systems are thought not to produce efficiently, so it is reasonable to postulate that quantum computers may outperform classical computers on machine learning tasks. The field of quantum machine learning explores how to devise and implement quantum software that could enable machine learning that is faster than that of classical computers. Recent work has produced quantum algorithms that could act as the building blocks of machine learning programs, but the hardware and software challenges are still considerable.

A time-efficient algorithm for implementing the Catmull-Clark subdivision method

NASA Astrophysics Data System (ADS)

Ioannou, G.; Savva, A.; Stylianou, V.

2015-10-01

Splines are the most popular methods in Figure Modeling and CAGD (Computer Aided Geometric Design) in generating smooth surfaces from a number of control points. The control points define the shape of a figure and splines calculate the required number of points which when displayed on a computer screen the result is a smooth surface. However, spline methods are based on a rectangular topological structure of points, i.e., a two-dimensional table of vertices, and thus cannot generate complex figures, such as the human and animal bodies that their complex structure does not allow them to be defined by a regular rectangular grid. On the other hand surface subdivision methods, which are derived by splines, generate surfaces which are defined by an arbitrary topology of control points. This is the reason that during the last fifteen years subdivision methods have taken the lead over regular spline methods in all areas of modeling in both industry and research. The cost of executing computer software developed to read control points and calculate the surface is run-time, due to the fact that the surface-structure required for handling arbitrary topological grids is very complicate. There are many software programs that have been developed related to the implementation of subdivision surfaces however, not many algorithms are documented in the literature, to support developers for writing efficient code. This paper aims to assist programmers by presenting a time-efficient algorithm for implementing subdivision splines. The Catmull-Clark which is the most popular of the subdivision methods has been employed to illustrate the algorithm.

Spitzer observatory operations: increasing efficiency in mission operations

NASA Astrophysics Data System (ADS)

Scott, Charles P.; Kahr, Bolinda E.; Sarrel, Marc A.

2006-06-01

This paper explores the how's and why's of the Spitzer Mission Operations System's (MOS) success, efficiency, and affordability in comparison to other observatory-class missions. MOS exploits today's flight, ground, and operations capabilities, embraces automation, and balances both risk and cost. With operational efficiency as the primary goal, MOS maintains a strong control process by translating lessons learned into efficiency improvements, thereby enabling the MOS processes, teams, and procedures to rapidly evolve from concept (through thorough validation) into in-flight implementation. Operational teaming, planning, and execution are designed to enable re-use. Mission changes, unforeseen events, and continuous improvement have often times forced us to learn to fly anew. Collaborative spacecraft operations and remote science and instrument teams have become well integrated, and worked together to improve and optimize each human, machine, and software-system element. Adaptation to tighter spacecraft margins has facilitated continuous operational improvements via automated and autonomous software coupled with improved human analysis. Based upon what we now know and what we need to improve, adapt, or fix, the projected mission lifetime continues to grow - as does the opportunity for numerous scientific discoveries.

SVM classifier on chip for melanoma detection.

PubMed

Afifi, Shereen; GholamHosseini, Hamid; Sinha, Roopak

2017-07-01

Support Vector Machine (SVM) is a common classifier used for efficient classification with high accuracy. SVM shows high accuracy for classifying melanoma (skin cancer) clinical images within computer-aided diagnosis systems used by skin cancer specialists to detect melanoma early and save lives. We aim to develop a medical low-cost handheld device that runs a real-time embedded SVM-based diagnosis system for use in primary care for early detection of melanoma. In this paper, an optimized SVM classifier is implemented onto a recent FPGA platform using the latest design methodology to be embedded into the proposed device for realizing online efficient melanoma detection on a single system on chip/device. The hardware implementation results demonstrate a high classification accuracy of 97.9% and a significant acceleration factor of 26 from equivalent software implementation on an embedded processor, with 34% of resources utilization and 2 watts for power consumption. Consequently, the implemented system meets crucial embedded systems constraints of high performance and low cost, resources utilization and power consumption, while achieving high classification accuracy.

Building Diagnostic Market Deployment - Final Report

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

Katipamula, S.; Gayeski, N.

2012-04-30

Operational faults are pervasive across the commercial buildings sector, wasting energy and increasing energy costs by up to about 30% (Mills 2009, Liu et al. 2003, Claridge et al. 2000, Katipamula and Brambley 2008, and Brambley and Katipamula 2009). Automated fault detection and diagnostic (AFDD) tools provide capabilities essential for detecting and correcting these problems and eliminating the associated energy waste and costs. The U.S. Department of Energy's (DOE) Building Technology Program (BTP) has previously invested in developing and testing of such diagnostic tools for whole-building (and major system) energy use, air handlers, chillers, cooling towers, chilled-water distribution systems, andmore » boilers. These diagnostic processes can be used to make the commercial buildings more energy efficient. The work described in this report was done as part of a Cooperative Research and Development Agreement (CRADA) between the U.S. Department of Energy's Pacific Northwest National Laboratory (PNNL) and KGS Building LLC (KGS). PNNL and KGS both believe that the widespread adoption of AFDD tools will result in significant reduction to energy and peak energy consumption. The report provides an introduction and summary of the various tasks performed under the CRADA. The CRADA project had three major focus areas: (1) Technical Assistance for Whole Building Energy Diagnostician (WBE) Commercialization, (2) Market Transfer of the Outdoor Air/Economizer Diagnostician (OAE), and (3) Development and Deployment of Automated Diagnostics to Improve Large Commercial Building Operations. PNNL has previously developed two diagnostic tools: (1) whole building energy (WBE) diagnostician and (2) outdoor air/economizer (OAE) diagnostician. WBE diagnostician is currently licensed non-exclusively to one company. As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite, Clockworks. PNNL also provided validation data sets and the WBE software tool to validate the KGS implementation. OAE diagnostician automatically detects and diagnoses problems with outdoor air ventilation and economizer operation for air handling units (AHUs) in commercial buildings using data available from building automation systems (BASs). As part of this CRADA, PNNL developed implementation documentation and provided technical support to KGS to implement the tool into their software suite. PNNL also provided validation data sets and the OAE software tool to validate the KGS implementation. Finally, as part of this CRADA project, PNNL developed new processes to automate parts of the re-tuning process and transfer those process to KGS for integration into their software product. The transfer of DOE-funded technologies will transform the commercial buildings sector by making buildings more energy efficient and also reducing the carbon footprint from the buildings. As part of the CRADA with PNNL, KGS implemented the whole building energy diagnostician, a portion of outdoor air economizer diagnostician and a number of measures that automate the identification of re-tuning measures.« less

RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.

PubMed

Na, Dokyun; Lee, Doheon

2010-10-15

RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol., 4, 71). The program additionally incorporates the effect on translation efficiency of the spacer length between a Shine-Dalgarno (SD) sequence and an AUG codon, which is crucial for the incorporation of fMet-tRNA into the ribosome. RBSDesigner provides a graphical user interface (GUI) for the convenient design of synthetic RBSs. RBSDesigner is written in Python and Microsoft Visual Basic 6.0 and is publicly available as precompiled stand-alone software on the web (http://rbs.kaist.ac.kr). dhlee@kaist.ac.kr

Sybil--efficient constraint-based modelling in R.

PubMed

Gelius-Dietrich, Gabriel; Desouki, Abdelmoneim Amer; Fritzemeier, Claus Jonathan; Lercher, Martin J

2013-11-13

Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users. Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model. Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Fault-tolerant software - Experiment with the sift operating system. [Software Implemented Fault Tolerance computer

NASA Technical Reports Server (NTRS)

Brunelle, J. E.; Eckhardt, D. E., Jr.

1985-01-01

Results are presented of an experiment conducted in the NASA Avionics Integrated Research Laboratory (AIRLAB) to investigate the implementation of fault-tolerant software techniques on fault-tolerant computer architectures, in particular the Software Implemented Fault Tolerance (SIFT) computer. The N-version programming and recovery block techniques were implemented on a portion of the SIFT operating system. The results indicate that, to effectively implement fault-tolerant software design techniques, system requirements will be impacted and suggest that retrofitting fault-tolerant software on existing designs will be inefficient and may require system modification.

UK Health and Social Care Case Studies: Iterative Technology Development.

PubMed

Blanchard, Adie; Gilbert, Laura; Dawson, Tom

2017-01-01

As a result of increasing demand in the face of reducing resources, technology has been implemented in many social and health care services to improve service efficiency. This paper outlines the experiences of deploying a 'Software as a Service' application in the UK social and health care sectors. The case studies demonstrate that every implementation is different, and unique to each organisation. Technology design and integration can be facilitated by ongoing engagement and collaboration with all stakeholders, flexible design, and attention to interoperability to suit services and their workflows.

The Particle Physics Data Grid. Final Report

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

Livny, Miron

2002-08-16

The main objective of the Particle Physics Data Grid (PPDG) project has been to implement and evaluate distributed (Grid-enabled) data access and management technology for current and future particle and nuclear physics experiments. The specific goals of PPDG have been to design, implement, and deploy a Grid-based software infrastructure capable of supporting the data generation, processing and analysis needs common to the physics experiments represented by the participants, and to adapt experiment-specific software to operate in the Grid environment and to exploit this infrastructure. To accomplish these goals, the PPDG focused on the implementation and deployment of several critical services:more » reliable and efficient file replication service, high-speed data transfer services, multisite file caching and staging service, and reliable and recoverable job management services. The focus of the activity was the job management services and the interplay between these services and distributed data access in a Grid environment. Software was developed to study the interaction between HENP applications and distributed data storage fabric. One key conclusion was the need for a reliable and recoverable tool for managing large collections of interdependent jobs. An attached document provides an overview of the current status of the Directed Acyclic Graph Manager (DAGMan) with its main features and capabilities.« less

Data Standards for Flow Cytometry

PubMed Central

SPIDLEN, JOSEF; GENTLEMAN, ROBERT C.; HAALAND, PERRY D.; LANGILLE, MORGAN; MEUR, NOLWENN LE; OCHS, MICHAEL F.; SCHMITT, CHARLES; SMITH, CLAYTON A.; TREISTER, ADAM S.; BRINKMAN, RYAN R.

2009-01-01

Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of large FCM datasets. We are implementing a standardized approach to capturing, analyzing, and disseminating FCM data that will facilitate both more complex analyses and analysis of datasets that could not previously be efficiently studied. Initial work has focused on developing a community-based guideline for recording and reporting the details of FCM experiments. Open source software tools that implement this standard are being created, with an emphasis on facilitating reproducible and extensible data analyses. As well, tools for electronic collaboration will assist the integrated access and comprehension of experiments to empower users to collaborate on FCM analyses. This coordinated, joint development of bioinformatics standards and software tools for FCM data analysis has the potential to greatly facilitate both basic and clinical research—impacting a notably diverse range of medical and environmental research areas. PMID:16901228

Infrared small target detection technology based on OpenCV

NASA Astrophysics Data System (ADS)

Liu, Lei; Huang, Zhijian

2013-05-01

Accurate and fast detection of infrared (IR) dim target has very important meaning for infrared precise guidance, early warning, video surveillance, etc. In this paper, some basic principles and the implementing flow charts of a series of algorithms for target detection are described. These algorithms are traditional two-frame difference method, improved three-frame difference method, background estimate and frame difference fusion method, and building background with neighborhood mean method. On the foundation of above works, an infrared target detection software platform which is developed by OpenCV and MFC is introduced. Three kinds of tracking algorithms are integrated in this software. In order to explain the software clearly, the framework and the function are described in this paper. At last, the experiments are performed for some real-life IR images. The whole algorithm implementing processes and results are analyzed, and those algorithms for detection targets are evaluated from the two aspects of subjective and objective. The results prove that the proposed method has satisfying detection effectiveness and robustness. Meanwhile, it has high detection efficiency and can be used for real-time detection.

Infrared small target detection technology based on OpenCV

NASA Astrophysics Data System (ADS)

Liu, Lei; Huang, Zhijian

2013-09-01

Accurate and fast detection of infrared (IR) dim target has very important meaning for infrared precise guidance, early warning, video surveillance, etc. In this paper, some basic principles and the implementing flow charts of a series of algorithms for target detection are described. These algorithms are traditional two-frame difference method, improved three-frame difference method, background estimate and frame difference fusion method, and building background with neighborhood mean method. On the foundation of above works, an infrared target detection software platform which is developed by OpenCV and MFC is introduced. Three kinds of tracking algorithms are integrated in this software. In order to explain the software clearly, the framework and the function are described in this paper. At last, the experiments are performed for some real-life IR images. The whole algorithm implementing processes and results are analyzed, and those algorithms for detection targets are evaluated from the two aspects of subjective and objective. The results prove that the proposed method has satisfying detection effectiveness and robustness. Meanwhile, it has high detection efficiency and can be used for real-time detection.

Software control and system configuration management - A process that works

NASA Technical Reports Server (NTRS)

Petersen, K. L.; Flores, C., Jr.

1983-01-01

A comprehensive software control and system configuration management process for flight-crucial digital control systems of advanced aircraft has been developed and refined to insure efficient flight system development and safe flight operations. Because of the highly complex interactions among the hardware, software, and system elements of state-of-the-art digital flight control system designs, a systems-wide approach to configuration control and management has been used. Specific procedures are implemented to govern discrepancy reporting and reconciliation, software and hardware change control, systems verification and validation testing, and formal documentation requirements. An active and knowledgeable configuration control board reviews and approves all flight system configuration modifications and revalidation tests. This flexible process has proved effective during the development and flight testing of several research aircraft and remotely piloted research vehicles with digital flight control systems that ranged from relatively simple to highly complex, integrated mechanizations.

Software control and system configuration management: A systems-wide approach

NASA Technical Reports Server (NTRS)

Petersen, K. L.; Flores, C., Jr.

1984-01-01

A comprehensive software control and system configuration management process for flight-crucial digital control systems of advanced aircraft has been developed and refined to insure efficient flight system development and safe flight operations. Because of the highly complex interactions among the hardware, software, and system elements of state-of-the-art digital flight control system designs, a systems-wide approach to configuration control and management has been used. Specific procedures are implemented to govern discrepancy reporting and reconciliation, software and hardware change control, systems verification and validation testing, and formal documentation requirements. An active and knowledgeable configuration control board reviews and approves all flight system configuration modifications and revalidation tests. This flexible process has proved effective during the development and flight testing of several research aircraft and remotely piloted research vehicles with digital flight control systems that ranged from relatively simple to highly complex, integrated mechanizations.

Uncertainty quantification in Rothermel's Model using an efficient sampling method

Treesearch

Edwin Jimenez; M. Yousuff Hussaini; Scott L. Goodrick

2007-01-01

The purpose of the present work is to quantify parametric uncertainty in Rothermel’s wildland fire spread model (implemented in software such as BehavePlus3 and FARSITE), which is undoubtedly among the most widely used fire spread models in the United States. This model consists of a nonlinear system of equations that relates environmental variables (input parameter...

Diffusion pseudotime robustly reconstructs lineage branching.

PubMed

Haghverdi, Laleh; Büttner, Maren; Wolf, F Alexander; Buettner, Florian; Theis, Fabian J

2016-10-01

The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.

SYN-OP-SYS™: A Computerized Management Information System for Quality Assurance and Risk Management

PubMed Central

Thomas, David J.; Weiner, Jayne; Lippincott, Ronald C.

1985-01-01

SYN·OP·SYS™ is a computerized management information system for quality assurance and risk management. Computer software for the efficient collection and analysis of “occurrences” and the clinical data associated with these kinds of patient events is described. The system is evaluated according to certain computer design criteria, and the system's implementation is assessed.

System Testing of Ground Cooling System Components

NASA Technical Reports Server (NTRS)

Ensey, Tyler Steven

2014-01-01

This internship focused primarily upon software unit testing of Ground Cooling System (GCS) components, one of the three types of tests (unit, integrated, and COTS/regression) utilized in software verification. Unit tests are used to test the software of necessary components before it is implemented into the hardware. A unit test determines that the control data, usage procedures, and operating procedures of a particular component are tested to determine if the program is fit for use. Three different files are used to make and complete an efficient unit test. These files include the following: Model Test file (.mdl), Simulink SystemTest (.test), and autotest (.m). The Model Test file includes the component that is being tested with the appropriate Discrete Physical Interface (DPI) for testing. The Simulink SystemTest is a program used to test all of the requirements of the component. The autotest tests that the component passes Model Advisor and System Testing, and puts the results into proper files. Once unit testing is completed on the GCS components they can then be implemented into the GCS Schematic and the software of the GCS model as a whole can be tested using integrated testing. Unit testing is a critical part of software verification; it allows for the testing of more basic components before a model of higher fidelity is tested, making the process of testing flow in an orderly manner.

Integrating personalized medical test contents with XML and XSL-FO.

PubMed

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents. Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents. The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion. The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

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.

Stencil computations for PDE-based applications with examples from DUNE and hypre

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

Engwer, C.; Falgout, R. D.; Yang, U. M.

Here, stencils are commonly used to implement efficient on–the–fly computations of linear operators arising from partial differential equations. At the same time the term “stencil” is not fully defined and can be interpreted differently depending on the application domain and the background of the software developers. Common features in stencil codes are the preservation of the structure given by the discretization of the partial differential equation and the benefit of minimal data storage. We discuss stencil concepts of different complexity, show how they are used in modern software packages like hypre and DUNE, and discuss recent efforts to extend themore » software to enable stencil computations of more complex problems and methods such as inf–sup–stable Stokes discretizations and mixed finite element discretizations.« less

IBM system/360 assembly language interval arithmetic software

NASA Technical Reports Server (NTRS)

Phillips, E. J.

1972-01-01

Computer software designed to perform interval arithmetic is described. An interval is defined as the set of all real numbers between two given numbers including or excluding one or both endpoints. Interval arithmetic consists of the various elementary arithmetic operations defined on the set of all intervals, such as interval addition, subtraction, union, etc. One of the main applications of interval arithmetic is in the area of error analysis of computer calculations. For example, it has been used sucessfully to compute bounds on sounding errors in the solution of linear algebraic systems, error bounds in numerical solutions of ordinary differential equations, as well as integral equations and boundary value problems. The described software enables users to implement algorithms of the type described in references efficiently on the IBM 360 system.

Stencil computations for PDE-based applications with examples from DUNE and hypre

DOE PAGES

Engwer, C.; Falgout, R. D.; Yang, U. M.

2017-02-24

Here, stencils are commonly used to implement efficient on–the–fly computations of linear operators arising from partial differential equations. At the same time the term “stencil” is not fully defined and can be interpreted differently depending on the application domain and the background of the software developers. Common features in stencil codes are the preservation of the structure given by the discretization of the partial differential equation and the benefit of minimal data storage. We discuss stencil concepts of different complexity, show how they are used in modern software packages like hypre and DUNE, and discuss recent efforts to extend themore » software to enable stencil computations of more complex problems and methods such as inf–sup–stable Stokes discretizations and mixed finite element discretizations.« less

Flight dynamics software in a distributed network environment

NASA Technical Reports Server (NTRS)

Jeletic, J.; Weidow, D.; Boland, D.

1995-01-01

As with all NASA facilities, the announcement of reduced budgets, reduced staffing, and the desire to implement smaller/quicker/cheaper missions has required the Agency's organizations to become more efficient in what they do. To accomplish these objectives, the FDD has initiated the development of the Flight Dynamics Distributed System (FDDS). The underlying philosophy of FDDS is to build an integrated system that breaks down the traditional barriers of attitude, mission planning, and navigation support software to provide a uniform approach to flight dynamics applications. Through the application of open systems concepts and state-of-the-art technologies, including object-oriented specification concepts, object-oriented software, and common user interface, communications, data management, and executive services, the FDD will reengineer most of its six million lines of code.

A complexity-scalable software-based MPEG-2 video encoder.

PubMed

Chen, Guo-bin; Lu, Xin-ning; Wang, Xing-guo; Liu, Ji-lin

2004-05-01

With the development of general-purpose processors (GPP) and video signal processing algorithms, it is possible to implement a software-based real-time video encoder on GPP, and its low cost and easy upgrade attract developers' interests to transfer video encoding from specialized hardware to more flexible software. In this paper, the encoding structure is set up first to support complexity scalability; then a lot of high performance algorithms are used on the key time-consuming modules in coding process; finally, at programming level, processor characteristics are considered to improve data access efficiency and processing parallelism. Other programming methods such as lookup table are adopted to reduce the computational complexity. Simulation results showed that these ideas could not only improve the global performance of video coding, but also provide great flexibility in complexity regulation.

Digital Library Storage using iRODS Data Grids

NASA Astrophysics Data System (ADS)

Hedges, Mark; Blanke, Tobias; Hasan, Adil

Digital repository software provides a powerful and flexible infrastructure for managing and delivering complex digital resources and metadata. However, issues can arise in managing the very large, distributed data files that may constitute these resources. This paper describes an implementation approach that combines the Fedora digital repository software with a storage layer implemented as a data grid, using the iRODS middleware developed by DICE (Data Intensive Cyber Environments) as the successor to SRB. This approach allows us to use Fedoras flexible architecture to manage the structure of resources and to provide application- layer services to users. The grid-based storage layer provides efficient support for managing and processing the underlying distributed data objects, which may be very large (e.g. audio-visual material). The Rule Engine built into iRODS is used to integrate complex workflows at the data level that need not be visible to users, e.g. digital preservation functionality.

Modular and configurable optimal sequence alignment software: Cola.

PubMed

Zamani, Neda; Sundström, Görel; Höppner, Marc P; Grabherr, Manfred G

2014-01-01

The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignment does not always reflect the patterns by which nucleotides mutate. Efficiently implemented algorithms that can be parameterised to accommodate more complex non-linear scoring schemes are thus desirable. We present Cola, alignment software that implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved motifs, and less on the surrounding nucleotides, which can be more diverged. To illustrate the differences, we report results from aligning 14,100 sequences from 3' untranslated regions of human genes to 25 of their mammalian counterparts, where we found that a nonlinear scoring scheme is more consistent than a linear scheme in detecting short, conserved motifs. Cola is freely available under LPGL from https://github.com/nedaz/cola.

BEST Winery Guidebook: Benchmarking and Energy and Water SavingsTool for the Wine Industry

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

Galitsky, Christina; Worrell, Ernst; Radspieler, Anthony

2005-10-15

Not all industrial facilities have the staff or the opportunity to perform a detailed audit of their operations. The lack of knowledge of energy efficiency opportunities provides an important barrier to improving efficiency. Benchmarking has demonstrated to help energy users understand energy use and the potential for energy efficiency improvement, reducing the information barrier. In California, the wine making industry is not only one of the economic pillars of the economy; it is also a large energy consumer, with a considerable potential for energy-efficiency improvement. Lawrence Berkeley National Laboratory and Fetzer Vineyards developed an integrated benchmarking and self-assessment tool formore » the California wine industry called ''BEST''(Benchmarking and Energy and water Savings Tool) Winery. BEST Winery enables a winery to compare its energy efficiency to a best practice winery, accounting for differences in product mix and other characteristics of the winery. The tool enables the user to evaluate the impact of implementing energy and water efficiency measures. The tool facilitates strategic planning of efficiency measures, based on the estimated impact of the measures, their costs and savings. BEST Winery is available as a software tool in an Excel environment. This report serves as background material, documenting assumptions and information on the included energy and water efficiency measures. It also serves as a user guide for the software package.« less

75 FR 27341 - Increasing Market and Planning Efficiency Through Improved Software; Notice of Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-14

... Market and Planning Efficiency Through Improved Software; Notice of Technical Conference To Discuss Increasing Market and Planning Efficiency Through Improved Software May 7, 2010. Take notice that Commission... planning efficiency through improved software. [[Page 27342

Fault Management Architectures and the Challenges of Providing Software Assurance

NASA Technical Reports Server (NTRS)

Savarino, Shirley; Fitz, Rhonda; Fesq, Lorraine; Whitman, Gerek

2015-01-01

Fault Management (FM) is focused on safety, the preservation of assets, and maintaining the desired functionality of the system. How FM is implemented varies among missions. Common to most missions is system complexity due to a need to establish a multi-dimensional structure across hardware, software and spacecraft operations. FM is necessary to identify and respond to system faults, mitigate technical risks and ensure operational continuity. Generally, FM architecture, implementation, and software assurance efforts increase with mission complexity. Because FM is a systems engineering discipline with a distributed implementation, providing efficient and effective verification and validation (V&V) is challenging. A breakout session at the 2012 NASA Independent Verification & Validation (IV&V) Annual Workshop titled "V&V of Fault Management: Challenges and Successes" exposed this issue in terms of V&V for a representative set of architectures. NASA's Software Assurance Research Program (SARP) has provided funds to NASA IV&V to extend the work performed at the Workshop session in partnership with NASA's Jet Propulsion Laboratory (JPL). NASA IV&V will extract FM architectures across the IV&V portfolio and evaluate the data set, assess visibility for validation and test, and define software assurance methods that could be applied to the various architectures and designs. This SARP initiative focuses efforts on FM architectures from critical and complex projects within NASA. The identification of particular FM architectures and associated V&V/IV&V techniques provides a data set that can enable improved assurance that a system will adequately detect and respond to adverse conditions. Ultimately, results from this activity will be incorporated into the NASA Fault Management Handbook providing dissemination across NASA, other agencies and the space community. This paper discusses the approach taken to perform the evaluations and preliminary findings from the research.

Fault Management Architectures and the Challenges of Providing Software Assurance

NASA Technical Reports Server (NTRS)

Savarino, Shirley; Fitz, Rhonda; Fesq, Lorraine; Whitman, Gerek

2015-01-01

The satellite systems Fault Management (FM) is focused on safety, the preservation of assets, and maintaining the desired functionality of the system. How FM is implemented varies among missions. Common to most is system complexity due to a need to establish a multi-dimensional structure across hardware, software and operations. This structure is necessary to identify and respond to system faults, mitigate technical risks and ensure operational continuity. These architecture, implementation and software assurance efforts increase with mission complexity. Because FM is a systems engineering discipline with a distributed implementation, providing efficient and effective verification and validation (VV) is challenging. A breakout session at the 2012 NASA Independent Verification Validation (IVV) Annual Workshop titled VV of Fault Management: Challenges and Successes exposed these issues in terms of VV for a representative set of architectures. NASA's IVV is funded by NASA's Software Assurance Research Program (SARP) in partnership with NASA's Jet Propulsion Laboratory (JPL) to extend the work performed at the Workshop session. NASA IVV will extract FM architectures across the IVV portfolio and evaluate the data set for robustness, assess visibility for validation and test, and define software assurance methods that could be applied to the various architectures and designs. This work focuses efforts on FM architectures from critical and complex projects within NASA. The identification of particular FM architectures, visibility, and associated VVIVV techniques provides a data set that can enable higher assurance that a satellite system will adequately detect and respond to adverse conditions. Ultimately, results from this activity will be incorporated into the NASA Fault Management Handbook providing dissemination across NASA, other agencies and the satellite community. This paper discusses the approach taken to perform the evaluations and preliminary findings from the research including identification of FM architectures, visibility observations, and methods utilized for VVIVV.

A Comparison of Four Software Programs for Implementing Decision Analytic Cost-Effectiveness Models.

PubMed

Hollman, Chase; Paulden, Mike; Pechlivanoglou, Petros; McCabe, Christopher

2017-08-01

The volume and technical complexity of both academic and commercial research using decision analytic modelling has increased rapidly over the last two decades. The range of software programs used for their implementation has also increased, but it remains true that a small number of programs account for the vast majority of cost-effectiveness modelling work. We report a comparison of four software programs: TreeAge Pro, Microsoft Excel, R and MATLAB. Our focus is on software commonly used for building Markov models and decision trees to conduct cohort simulations, given their predominance in the published literature around cost-effectiveness modelling. Our comparison uses three qualitative criteria as proposed by Eddy et al.: "transparency and validation", "learning curve" and "capability". In addition, we introduce the quantitative criterion of processing speed. We also consider the cost of each program to academic users and commercial users. We rank the programs based on each of these criteria. We find that, whilst Microsoft Excel and TreeAge Pro are good programs for educational purposes and for producing the types of analyses typically required by health technology assessment agencies, the efficiency and transparency advantages of programming languages such as MATLAB and R become increasingly valuable when more complex analyses are required.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Software engineering the mixed model for genome-wide association studies on large samples.

PubMed

Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

2009-11-01

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

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

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Software defined photon counting system for time resolved x-ray experiments.

PubMed

Acremann, Y; Chembrolu, V; Strachan, J P; Tyliszczak, T; Stöhr, J

2007-01-01

The time structure of synchrotron radiation allows time resolved experiments with sub-100 ps temporal resolution using a pump-probe approach. However, the relaxation time of the samples may require a lower repetition rate of the pump pulse compared to the full repetition rate of the x-ray pulses from the synchrotron. The use of only the x-ray pulse immediately following the pump pulse is not efficient and often requires special operation modes where only a few buckets of the storage ring are filled. We designed a novel software defined photon counting system that allows to implement a variety of pump-probe schemes at the full repetition rate. The high number of photon counters allows to detect the response of the sample at multiple time delays simultaneously, thus improving the efficiency of the experiment. The system has been successfully applied to time resolved scanning transmission x-ray microscopy. However, this technique is applicable more generally.

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data

PubMed Central

2013-01-01

Background RNA-Seq technology has been used widely in transcriptome study, and one of the most important applications is to estimate the expression level of genes and their alternative splicing isoforms. There have been several algorithms published to estimate the expression based on different models. Recently Wu et al. published a method that can accurately estimate isoform level expression by considering position-related sequencing biases using nonparametric models. The method has advantages in handling different read distributions, but there hasn’t been an efficient program to implement this algorithm. Results We developed an efficient implementation of the algorithm in the program NURD. It uses a binary interval search algorithm. The program can correct both the global tendency of sequencing bias in the data and local sequencing bias specific to each gene. The correction makes the isoform expression estimation more reliable under various read distributions. And the implementation is computationally efficient in both the memory cost and running time and can be readily scaled up for huge datasets. Conclusion NURD is an efficient and reliable tool for estimating the isoform expression level. Given the reads mapping result and gene annotation file, NURD will output the expression estimation result. The package is freely available for academic use at http://bioinfo.au.tsinghua.edu.cn/software/NURD/. PMID:23837734

Specialized Computer Systems for Environment Visualization

NASA Astrophysics Data System (ADS)

Al-Oraiqat, Anas M.; Bashkov, Evgeniy A.; Zori, Sergii A.

2018-06-01

The need for real time image generation of landscapes arises in various fields as part of tasks solved by virtual and augmented reality systems, as well as geographic information systems. Such systems provide opportunities for collecting, storing, analyzing and graphically visualizing geographic data. Algorithmic and hardware software tools for increasing the realism and efficiency of the environment visualization in 3D visualization systems are proposed. This paper discusses a modified path tracing algorithm with a two-level hierarchy of bounding volumes and finding intersections with Axis-Aligned Bounding Box. The proposed algorithm eliminates the branching and hence makes the algorithm more suitable to be implemented on the multi-threaded CPU and GPU. A modified ROAM algorithm is used to solve the qualitative visualization of reliefs' problems and landscapes. The algorithm is implemented on parallel systems—cluster and Compute Unified Device Architecture-networks. Results show that the implementation on MPI clusters is more efficient than Graphics Processing Unit/Graphics Processing Clusters and allows real-time synthesis. The organization and algorithms of the parallel GPU system for the 3D pseudo stereo image/video synthesis are proposed. With realizing possibility analysis on a parallel GPU-architecture of each stage, 3D pseudo stereo synthesis is performed. An experimental prototype of a specialized hardware-software system 3D pseudo stereo imaging and video was developed on the CPU/GPU. The experimental results show that the proposed adaptation of 3D pseudo stereo imaging to the architecture of GPU-systems is efficient. Also it accelerates the computational procedures of 3D pseudo-stereo synthesis for the anaglyph and anamorphic formats of the 3D stereo frame without performing optimization procedures. The acceleration is on average 11 and 54 times for test GPUs.

Software-implemented fault insertion: An FTMP example

NASA Technical Reports Server (NTRS)

Czeck, Edward W.; Siewiorek, Daniel P.; Segall, Zary Z.

1987-01-01

This report presents a model for fault insertion through software; describes its implementation on a fault-tolerant computer, FTMP; presents a summary of fault detection, identification, and reconfiguration data collected with software-implemented fault insertion; and compares the results to hardware fault insertion data. Experimental results show detection time to be a function of time of insertion and system workload. For the fault detection time, there is no correlation between software-inserted faults and hardware-inserted faults; this is because hardware-inserted faults must manifest as errors before detection, whereas software-inserted faults immediately exercise the error detection mechanisms. In summary, the software-implemented fault insertion is able to be used as an evaluation technique for the fault-handling capabilities of a system in fault detection, identification and recovery. Although the software-inserted faults do not map directly to hardware-inserted faults, experiments show software-implemented fault insertion is capable of emulating hardware fault insertion, with greater ease and automation.

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

Seaworthy Quantum Key Distribution Design and Validation (SEAKEY)

DTIC Science & Technology

2014-10-30

to single photon detection, at comparable detection efficiencies. On the other hand, error-correction codes are better developed for small-alphabet...protocol is several orders of magnitude better than the Shapiro protocol, which needs entangled states. The bits/mode performance achieved by our...putting together a software tool implemented in MATLAB , which talks to the MODTRAN database via an intermediate numerical dump of transmission data

Energy Assessment Helps Kaiser Aluminum Save Energy and Improve Productivity; DOE Software Adopted as Standard for Analyzing Plant Process Heating Systems Company-Wide

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

Not Available

2008-07-01

This case study describes how the Kaiser Aluminum plant in Sherman, Texas, achieved annual savings of $360,000 and 45,000 MMBtu, and improved furnace energy intensity by 11.1% after receiving a DOE Save Energy Now energy assessment and implementing recommendations to improve the efficiency of its process heating system.

nmsBuilder: Freeware to create subject-specific musculoskeletal models for OpenSim.

PubMed

Valente, Giordano; Crimi, Gianluigi; Vanella, Nicola; Schileo, Enrico; Taddei, Fulvia

2017-12-01

Musculoskeletal modeling and simulations of movement have been increasingly used in orthopedic and neurological scenarios, with increased attention to subject-specific applications. In general, musculoskeletal modeling applications have been facilitated by the development of dedicated software tools; however, subject-specific studies have been limited also by time-consuming modeling workflows and high skilled expertise required. In addition, no reference tools exist to standardize the process of musculoskeletal model creation and make it more efficient. Here we present a freely available software application, nmsBuilder 2.0, to create musculoskeletal models in the file format of OpenSim, a widely-used open-source platform for musculoskeletal modeling and simulation. nmsBuilder 2.0 is the result of a major refactoring of a previous implementation that moved a first step toward an efficient workflow for subject-specific model creation. nmsBuilder includes a graphical user interface that provides access to all functionalities, based on a framework for computer-aided medicine written in C++. The operations implemented can be used in a workflow to create OpenSim musculoskeletal models from 3D surfaces. A first step includes data processing to create supporting objects necessary to create models, e.g. surfaces, anatomical landmarks, reference systems; and a second step includes the creation of OpenSim objects, e.g. bodies, joints, muscles, and the corresponding model. We present a case study using nmsBuilder 2.0: the creation of an MRI-based musculoskeletal model of the lower limb. The model included four rigid bodies, five degrees of freedom and 43 musculotendon actuators, and was created from 3D surfaces of the segmented images of a healthy subject through the modeling workflow implemented in the software application. We have presented nmsBuilder 2.0 for the creation of musculoskeletal OpenSim models from image-based data, and made it freely available via nmsbuilder.org. This application provides an efficient workflow for model creation and helps standardize the process. We hope this would help promote personalized applications in musculoskeletal biomechanics, including larger sample size studies, and might also represent a basis for future developments for specific applications. Copyright © 2017 Elsevier B.V. All rights reserved.

SPP: A data base processor data communications protocol

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1983-01-01

The design and implementation of a data communications protocol for the Intel Data Base Processor (DBP) is defined. The protocol is termed SPP (Service Port Protocol) since it enables data transfer between the host computer and the DBP service port. The protocol implementation is extensible in that it is explicitly layered and the protocol functionality is hierarchically organized. Extensive trace and performance capabilities have been supplied with the protocol software to permit optional efficient monitoring of the data transfer between the host and the Intel data base processor. Machine independence was considered to be an important attribute during the design and implementation of SPP. The protocol source is fully commented and is included in Appendix A of this report.

Environmental concept for engineering software on MIMD computers

NASA Technical Reports Server (NTRS)

Lopez, L. A.; Valimohamed, K.

1989-01-01

The issues related to developing an environment in which engineering systems can be implemented on MIMD machines are discussed. The problem is presented in terms of implementing the finite element method under such an environment. However, neither the concepts nor the prototype implementation environment are limited to this application. The topics discussed include: the ability to schedule and synchronize tasks efficiently; granularity of tasks; load balancing; and the use of a high level language to specify parallel constructs, manage data, and achieve portability. The objective of developing a virtual machine concept which incorporates solutions to the above issues leads to a design that can be mapped onto loosely coupled, tightly coupled, and hybrid systems.

77 FR 19280 - Increasing Market and Planning Efficiency Through Improved Software; Notice of Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-30

... Market and Planning Efficiency Through Improved Software; Notice of Technical Conference: Increasing Real-Time and Day- Ahead Market Efficiency Through Improved Software Take notice that Commission staff will...-time and day-ahead market efficiency through improved software. A detailed agenda with the list of and...

76 FR 28022 - Increasing Market and Planning Efficiency Through Improved Software; Notice of Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-13

... Market and Planning Efficiency Through Improved Software; Notice of Technical Conference: Increasing Real-Time and Day- Ahead Market Efficiency Through Improved Software Take notice that Commission staff will... for increasing real-time and day-ahead market efficiency through improved software. This conference...

Cost-Sensitive Radial Basis Function Neural Network Classifier for Software Defect Prediction

PubMed Central

Venkatesan, R.

2016-01-01

Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers. This testing phase should be carefully operated in an effective manner to release a defect-free (bug-free) software product to the customers. In order to improve the software testing process, fault prediction methods identify the software parts that are more noted to be defect-prone. This paper proposes a prediction approach based on conventional radial basis function neural network (RBFNN) and the novel adaptive dimensional biogeography based optimization (ADBBO) model. The developed ADBBO based RBFNN model is tested with five publicly available datasets from the NASA data program repository. The computed results prove the effectiveness of the proposed ADBBO-RBFNN classifier approach with respect to the considered metrics in comparison with that of the early predictors available in the literature for the same datasets. PMID:27738649

Cost-Sensitive Radial Basis Function Neural Network Classifier for Software Defect Prediction.

PubMed

Kumudha, P; Venkatesan, R

Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers. This testing phase should be carefully operated in an effective manner to release a defect-free (bug-free) software product to the customers. In order to improve the software testing process, fault prediction methods identify the software parts that are more noted to be defect-prone. This paper proposes a prediction approach based on conventional radial basis function neural network (RBFNN) and the novel adaptive dimensional biogeography based optimization (ADBBO) model. The developed ADBBO based RBFNN model is tested with five publicly available datasets from the NASA data program repository. The computed results prove the effectiveness of the proposed ADBBO-RBFNN classifier approach with respect to the considered metrics in comparison with that of the early predictors available in the literature for the same datasets.

SPICODYN: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings.

PubMed

Pastore, Vito Paolo; Godjoski, Aleksandar; Martinoia, Sergio; Massobrio, Paolo

2018-01-01

We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis. In particular, for inferring network connectivity, a new implementation of the transfer entropy method is presented dealing with multiple time delays (temporal extension) and with multiple binary patterns (high order extension). SPICODYN is specifically tailored to process data coming from different Multi-Electrode Arrays setups, guarantying, in those specific cases, automated processing. The optimized implementation of the Delayed Transfer Entropy and the High-Order Transfer Entropy algorithms, allows performing accurate and rapid analysis on multiple spike trains from thousands of electrodes.

Software Coherence in Multiprocessor Memory Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Bolosky, William Joseph

1993-01-01

Processors are becoming faster and multiprocessor memory interconnection systems are not keeping up. Therefore, it is necessary to have threads and the memory they access as near one another as possible. Typically, this involves putting memory or caches with the processors, which gives rise to the problem of coherence: if one processor writes an address, any other processor reading that address must see the new value. This coherence can be maintained by the hardware or with software intervention. Systems of both types have been built in the past; the hardware-based systems tended to outperform the software ones. However, the ratio of processor to interconnect speed is now so high that the extra overhead of the software systems may no longer be significant. This issue is explored both by implementing a software maintained system and by introducing and using the technique of offline optimal analysis of memory reference traces. It finds that in properly built systems, software maintained coherence can perform comparably to or even better than hardware maintained coherence. The architectural features necessary for efficient software coherence to be profitable include a small page size, a fast trap mechanism, and the ability to execute instructions while remote memory references are outstanding.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Daily Planet Redesign: eZ Publish Web Content Management Implementation

NASA Technical Reports Server (NTRS)

Dutra, Jayne E.

2006-01-01

This viewgraph presentation reviews the process of the redesign of the Daily . Planet news letter as a content management implementation project. This is a site that is an internal news site that acts as a communication vehicle for a large volume of content. The Objectives for the site redesign was: (1) Clean visual design, (2) Facilitation of publication processes, (3) More efficient maintenance mode, (4) Automated publishing to internal portal, (5) Better navigation through improved site IA, (6) Archiving and retrieval functionality, (7) Back to basics on fundamental business goals. The CM is a process not a software package

Challenges at Petascale for Pseudo-Spectral Methods on Spheres (A Last Hurrah?)

NASA Technical Reports Server (NTRS)

Clune, Thomas

2011-01-01

Conclusions: a) Proper software abstractions should enable rapid-exploration of platform-specific optimizations/ tradeoffs. b) Pseudo-spectra! methods are marginally viable for at least some classes of petascaie problems. i.e., GPU based machine with good bisection would be best. c) Scalability at exascale is possible, but the necessary resolution will make algorithm prohibitively expensive. Efficient implementations of realistic global transposes are mtricate and tedious in MPI. PS at petascaie requires exploration of a variety of strategies for spreading local and remote communic3tions. PGAS allows far simpler implementation and thus rapid exploration of variants.

The Ames Virtual Environment Workstation: Implementation issues and requirements

NASA Technical Reports Server (NTRS)

Fisher, Scott S.; Jacoby, R.; Bryson, S.; Stone, P.; Mcdowall, I.; Bolas, M.; Dasaro, D.; Wenzel, Elizabeth M.; Coler, C.; Kerr, D.

1991-01-01

This presentation describes recent developments in the implementation of a virtual environment workstation in the Aerospace Human Factors Research Division of NASA's Ames Research Center. Introductory discussions are presented on the primary research objectives and applications of the system and on the system's current hardware and software configuration. Principle attention is then focused on unique issues and problems encountered in the workstation's development with emphasis on its ability to meet original design specifications for computational graphics performance and for associated human factors requirements necessary to provide compelling sense of presence and efficient interaction in the virtual environment.

Evolution of International Space Station Program Safety Review Processes and Tools

NASA Technical Reports Server (NTRS)

Ratterman, Christian D.; Green, Collin; Guibert, Matt R.; McCracken, Kristle I.; Sang, Anthony C.; Sharpe, Matthew D.; Tollinger, Irene V.

2013-01-01

The International Space Station Program at NASA is constantly seeking to improve the processes and systems that support safe space operations. To that end, the ISS Program decided to upgrade their Safety and Hazard data systems with 3 goals: make safety and hazard data more accessible; better support the interconnection of different types of safety data; and increase the efficiency (and compliance) of safety-related processes. These goals are accomplished by moving data into a web-based structured data system that includes strong process support and supports integration with other information systems. Along with the data systems, ISS is evolving its submission requirements and safety process requirements to support the improved model. In contrast to existing operations (where paper processes and electronic file repositories are used for safety data management) the web-based solution provides the program with dramatically faster access to records, the ability to search for and reference specific data within records, reduced workload for hazard updates and approval, and process support including digital signatures and controlled record workflow. In addition, integration with other key data systems provides assistance with assessments of flight readiness, more efficient review and approval of operational controls and better tracking of international safety certifications. This approach will also provide new opportunities to streamline the sharing of data with ISS international partners while maintaining compliance with applicable laws and respecting restrictions on proprietary data. One goal of this paper is to outline the approach taken by the ISS Progrm to determine requirements for the new system and to devise a practical and efficient implementation strategy. From conception through implementation, ISS and NASA partners utilized a user-centered software development approach focused on user research and iterative design methods. The user-centered approach used on the new ISS hazard system utilized focused user research and iterative design methods employed by the Human Computer Interaction Group at NASA Ames Research Center. Particularly, the approach emphasized the reduction of workload associated with document and data management activities so more resources can be allocated to the operational use of data in problem solving, safety analysis, and recurrence control. The methods and techniques used to understand existing processes and systems, to recognize opportunities for improvement, and to design and review improvements are described with the intent that similar techniques can be employed elsewhere in safety operations. A second goal of this paper is to provide and overview of the web-based data system implemented by ISS. The software selected for the ISS hazard systemMission Assurance System (MAS)is a NASA-customized vairant of the open source software project Bugzilla. The origin and history of MAS as a NASA software project and the rationale for (and advantages of) using open-source software are documented elsewhere (Green, et al., 2009).

76 FR 41790 - Increasing Market and Planning Efficiency Through Improved Software; Notice Establishing Date for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

... Market and Planning Efficiency Through Improved Software; Notice Establishing Date for Comments From June... real-time and day- ahead market efficiency through improved software.\\1\\ \\1\\ Notice of technical conference: increasing real-time and day-ahead market efficiency through improved software, 76 Fed. Reg. 28...

An Efficient Scheme for Updating Sparse Cholesky Factors

NASA Technical Reports Server (NTRS)

Raghavan, Padma

2002-01-01

Raghavan had earlier developed the software package DCSPACK which can be used for solving sparse linear systems where the coefficient matrix is symmetric and positive definite (this project was not funded by NASA but by agencies such as NSF). DSCPACK-S is the serial code and DSCPACK-P is a parallel implementation suitable for multiprocessors or networks-of-workstations with message passing using MCI. The main algorithm used is the Cholesky factorization of a sparse symmetric positive positive definite matrix A = LL(T). The code can also compute the factorization A = LDL(T). The complexity of the software arises from several factors relating to the sparsity of the matrix A. A sparse N x N matrix A has typically less that cN nonzeroes where c is a small constant. If the matrix were dense, it would have O(N2) nonzeroes. The most complicated part of such sparse Cholesky factorization relates to fill-in, i.e., zeroes in the original matrix that become nonzeroes in the factor L. An efficient implementation depends to a large extent on complex data structures and on techniques from graph theory to reduce, identify, and manage fill. DSCPACK is based on an efficient multifrontal implementation with fill-managing algorithms and implementation arising from earlier research by Raghavan and others. Sparse Cholesky factorization is typically a four step process: (1) ordering to compute a fill-reducing numbering, (2) symbolic factorization to determine the nonzero structure of L, (3) numeric factorization to compute L, and, (4) triangular solution to solve L(T)x = y and Ly = b. The first two steps are symbolic and are performed using the graph of the matrix. The numeric factorization step is of dominant cost and there are several schemes for improving performance by exploiting the nested and dense structure of groups of columns in the factor. The latter are aimed at better utilization of the cache-memory hierarchy on modem processors to prevent cache-misses and provide execution rates (operations/second) that are close to the peak rates for dense matrix computations. Currently, EPISCOPACY is being used in an application at NASA directed by J. Newman and M. James. We propose the implementation of efficient schemes for updating the LL(T) or LDL(T) factors computed in DSCPACK-S to meet the computational requirements of their project. A brief description is provided in the next section.

Spacelab user implementation assessment study. (Software requirements analysis). Volume 2: Technical report

NASA Technical Reports Server (NTRS)

1976-01-01

The engineering analyses and evaluation studies conducted for the Software Requirements Analysis are discussed. Included are the development of the study data base, synthesis of implementation approaches for software required by both mandatory onboard computer services and command/control functions, and identification and implementation of software for ground processing activities.

Touchscreen questionnaire patient data collection in rheumatology practice: development of a highly successful system using process redesign.

PubMed

Newman, Eric D; Lerch, Virginia; Jones, J B; Stewart, Walter

2012-04-01

While questionnaires have been developed to capture patient-reported outcomes (PROs) in rheumatology practice, these instruments are not widely used. We developed a touchscreen interface designed to provide reliable and efficient data collection. Using the touchscreen to obtain PROs, we compared 2 different workflow models implemented separately in 2 rheumatology clinics. The Plan-Do-Study-Act methodology was used in 2 cycles of workflow redesign. Cycle 1 relied on off-the-shelf questionnaire builder software, and cycle 2 relied on a custom programmed software solution. During cycle 1, clinic 1 (private practice model, resource replete, simple flow) demonstrated a high completion rate at the start, averaging between 74% and 92% for the first 12 weeks. Clinic 2 (academic model, resource deficient, complex flow) did not achieve a consistent completion rate above 60%. The revised cycle 2 implementation protocol incorporated a 15-minute "nurse visit," an instant messaging system, and a streamlined authentication process, all of which contributed to substantial improvement in touchscreen questionnaire completion rates of ∼80% that were sustained without the need for any additional clinic staff support. Process redesign techniques and touchscreen technology were used to develop a highly successful, efficient, and effective process for the routine collection of PROs in a busy, complex, and resource-depleted academic practice and in typical private practice. The successful implementation required both a touchscreen questionnaire, human behavioral redesign, and other technical solutions. Copyright © 2012 by the American College of Rheumatology.

Analyzing gene perturbation screens with nested effects models in R and bioconductor.

PubMed

Fröhlich, Holger; Beissbarth, Tim; Tresch, Achim; Kostka, Dennis; Jacob, Juby; Spang, Rainer; Markowetz, F

2008-11-01

Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or cell morphology. NEMs reverse engineer upstream/downstream relations of cellular signaling cascades. NEMs take as input a set of candidate pathway genes and phenotypic profiles of perturbing these genes. NEMs return a pathway structure explaining the observed perturbation effects. Here, we describe the package nem, an open-source software to efficiently infer NEMs from data. Our software implements several search algorithms for model fitting and is applicable to a wide range of different data types and representations. The methods we present summarize the current state-of-the-art in NEMs. Our software is written in the R language and freely avail-able via the Bioconductor project at http://www.bioconductor.org.

Software Infrastructure for Computer-aided Drug Discovery and Development, a Practical Example with Guidelines.

PubMed

Moretti, Loris; Sartori, Luca

2016-09-01

In the field of Computer-Aided Drug Discovery and Development (CADDD) the proper software infrastructure is essential for everyday investigations. The creation of such an environment should be carefully planned and implemented with certain features in order to be productive and efficient. Here we describe a solution to integrate standard computational services into a functional unit that empowers modelling applications for drug discovery. This system allows users with various level of expertise to run in silico experiments automatically and without the burden of file formatting for different software, managing the actual computation, keeping track of the activities and graphical rendering of the structural outcomes. To showcase the potential of this approach, performances of five different docking programs on an Hiv-1 protease test set are presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tools for Implementing Science Practice in a Large Introductory Class

NASA Astrophysics Data System (ADS)

Prothero, W. A.

2008-12-01

Scientists must have in-depth background knowledge of their subject area and know where current knowledge can be advanced. They perform experiments that gather data to test new or existing theories, present their findings at meetings, publish their results, critically review the results of others, and respond to the reviews of their own work. In the context of a course, these activities correspond to learning the background material by listening to lectures or reading a text, formulating a problem, exploring data using student friendly data access and plotting software, giving brief talks to classmates in a small class or lab setting, writing a science paper or lab report, reviewing the writing of their peers, and receiving feedback (and grades) from their instructors and/or peers. These activities can be supported using course management software and online resources. The "LearningWithData" software system allows solid Earth (focused on plate tectonics) data exploration and plotting. Ocean data access, display, and plotting are also supported. Background material is delivered using animations and slide show type displays. Students are accountable for their learning through included homework assignments. Lab and small group activities provide support for data exploration and interpretation. Writing is most efficiently implemented using the "Calibrated Peer Review" method. This methodology is available at http://cpr.molsci.ucla.edu/. These methods have been successfully implemented in a large oceanography class at UCSB.

A Low-Cost and Energy-Efficient Multiprocessor System-on-Chip for UWB MAC Layer

NASA Astrophysics Data System (ADS)

Xiao, Hao; Isshiki, Tsuyoshi; Khan, Arif Ullah; Li, Dongju; Kunieda, Hiroaki; Nakase, Yuko; Kimura, Sadahiro

Ultra-wideband (UWB) technology has attracted much attention recently due to its high data rate and low emission power. Its media access control (MAC) protocol, WiMedia MAC, promises a lot of facilities for high-speed and high-quality wireless communication. However, these benefits in turn involve a large amount of computational load, which challenges the traditional uniprocessor architecture based implementation method to provide the required performance. However, the constrained cost and power budget, on the other hand, makes using commercial multiprocessor solutions unrealistic. In this paper, a low-cost and energy-efficient multiprocessor system-on-chip (MPSoC), which tackles at once the aspects of system design, software migration and hardware architecture, is presented for the implementation of UWB MAC layer. Experimental results show that the proposed MPSoC, based on four simple RISC processors and shared-memory infrastructure, achieves up to 45% performance improvement and 65% power saving, but takes 15% less area than the uniprocessor implementation.

Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

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

Aktulga, Hasan Metin; Coffman, Paul; Shan, Tzu-Ray

2015-12-01

Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups inmore » the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.« less

Abstracted Workow Framework with a Structure from Motion Application

NASA Astrophysics Data System (ADS)

Rossi, Adam J.

In scientific and engineering disciplines, from academia to industry, there is an increasing need for the development of custom software to perform experiments, construct systems, and develop products. The natural mindset initially is to shortcut and bypass all overhead and process rigor in order to obtain an immediate result for the problem at hand, with the misconception that the software will simply be thrown away at the end. In a majority of the cases, it turns out the software persists for many years, and likely ends up in production systems for which it was not initially intended. In the current study, a framework that can be used in both industry and academic applications mitigates underlying problems associated with developing scientific and engineering software. This results in software that is much more maintainable, documented, and usable by others, specifically allowing new users to extend capabilities of components already implemented in the framework. There is a multi-disciplinary need in the fields of imaging science, computer science, and software engineering for a unified implementation model, which motivates the development of an abstracted software framework. Structure from motion (SfM) has been identified as one use case where the abstracted workflow framework can improve research efficiencies and eliminate implementation redundancies in scientific fields. The SfM process begins by obtaining 2D images of a scene from different perspectives. Features from the images are extracted and correspondences are established. This provides a sufficient amount of information to initialize the problem for fully automated processing. Transformations are established between views, and 3D points are established via triangulation algorithms. The parameters for the camera models for all views / images are solved through bundle adjustment, establishing a highly consistent point cloud. The initial sparse point cloud and camera matrices are used to generate a dense point cloud through patch based techniques or densification algorithms such as Semi-Global Matching (SGM). The point cloud can be visualized or exploited by both humans and automated techniques. In some cases the point cloud is "draped" with original imagery in order to enhance the 3D model for a human viewer. The SfM workflow can be implemented in the abstracted framework, making it easily leverageable and extensible by multiple users. Like many processes in scientific and engineering domains, the workflow described for SfM is complex and requires many disparate components to form a functional system, often utilizing algorithms implemented by many users in different languages / environments and without knowledge of how the component fits into the larger system. In practice, this generally leads to issues interfacing the components, building the software for desired platforms, understanding its concept of operations, and how it can be manipulated in order to fit the desired function for a particular application. In addition, other scientists and engineers instinctively wish to analyze the performance of the system, establish new algorithms, optimize existing processes, and establish new functionality based on current research. This requires a framework whereby new components can be easily plugged in without affecting the current implemented functionality. The need for a universal programming environment establishes the motivation for the development of the abstracted workflow framework. This software implementation, named Catena, provides base classes from which new components must derive in order to operate within the framework. The derivation mandates requirements be satisfied in order to provide a complete implementation. Additionally, the developer must provide documentation of the component in terms of its overall function and inputs. The interface input and output values corresponding to the component must be defined in terms of their respective data types, and the implementation uses mechanisms within the framework to retrieve and send the values. This process requires the developer to componentize their algorithm rather than implement it monolithically. Although the requirements of the developer are slightly greater, the benefits realized from using Catena far outweigh the overhead, and results in extensible software. This thesis provides a basis for the abstracted workflow framework concept and the Catena software implementation. The benefits are also illustrated using a detailed examination of the SfM process as an example application.

Software-Defined Architectures for Spectrally Efficient Cognitive Networking in Extreme Environments

NASA Astrophysics Data System (ADS)

Sklivanitis, Georgios

The objective of this dissertation is the design, development, and experimental evaluation of novel algorithms and reconfigurable radio architectures for spectrally efficient cognitive networking in terrestrial, airborne, and underwater environments. Next-generation wireless communication architectures and networking protocols that maximize spectrum utilization efficiency in congested/contested or low-spectral availability (extreme) communication environments can enable a rich body of applications with unprecedented societal impact. In recent years, underwater wireless networks have attracted significant attention for military and commercial applications including oceanographic data collection, disaster prevention, tactical surveillance, offshore exploration, and pollution monitoring. Unmanned aerial systems that are autonomously networked and fully mobile can assist humans in extreme or difficult-to-reach environments and provide cost-effective wireless connectivity for devices without infrastructure coverage. Cognitive radio (CR) has emerged as a promising technology to maximize spectral efficiency in dynamically changing communication environments by adaptively reconfiguring radio communication parameters. At the same time, the fast developing technology of software-defined radio (SDR) platforms has enabled hardware realization of cognitive radio algorithms for opportunistic spectrum access. However, existing algorithmic designs and protocols for shared spectrum access do not effectively capture the interdependencies between radio parameters at the physical (PHY), medium-access control (MAC), and network (NET) layers of the network protocol stack. In addition, existing off-the-shelf radio platforms and SDR programmable architectures are far from fulfilling runtime adaptation and reconfiguration across PHY, MAC, and NET layers. Spectrum allocation in cognitive networks with multi-hop communication requirements depends on the location, network traffic load, and interference profile at each network node. As a result, the development and implementation of algorithms and cross-layer reconfigurable radio platforms that can jointly treat space, time, and frequency as a unified resource to be dynamically optimized according to inter- and intra-network interference constraints is of fundamental importance. In the next chapters, we present novel algorithmic and software/hardware implementation developments toward the deployment of spectrally efficient terrestrial, airborne, and underwater wireless networks. In Chapter 1 we review the state-of-art in commercially available SDR platforms, describe their software and hardware capabilities, and classify them based on their ability to enable rapid prototyping and advance experimental research in wireless networks. Chapter 2 discusses system design and implementation details toward real-time evaluation of a software-radio platform for all-spectrum cognitive channelization in the presence of narrowband or wideband primary stations. All-spectrum channelization is achieved by designing maximum signal-to-interference-plus-noise ratio (SINR) waveforms that span the whole continuum of the device-accessible spectrum, while satisfying peak power and interference temperature (IT) constraints for the secondary and primary users, respectively. In Chapter 3, we introduce the concept of all-spectrum channelization based on max-SINR optimized sparse-binary waveforms, we propose optimal and suboptimal waveform design algorithms, and evaluate their SINR and bit-error-rate (BER) performance in an SDR testbed. Chapter 4 considers the problem of channel estimation with minimal pilot signaling in multi-cell multi-user multi-input multi-output (MIMO) systems with very large antenna arrays at the base station, and proposes a least-squares (LS)-type algorithm that iteratively extracts channel and data estimates from a short record of data measurements. Our algorithmic developments toward spectrally-efficient cognitive networking through joint optimization of channel access code-waveforms and routes in a multi-hop network are described in Chapter 5. Algorithmic designs are software optimized on heterogeneous multi-core general-purpose processor (GPP)-based SDR architectures by leveraging a novel software-radio framework that offers self-optimization and real-time adaptation capabilities at the PHY, MAC, and NET layers of the network protocol stack. Our system design approach is experimentally validated under realistic conditions in a large-scale hybrid ground-air testbed deployment. Chapter 6 reviews the state-of-art in software and hardware platforms for underwater wireless networking and proposes a software-defined acoustic modem prototype that enables (i) cognitive reconfiguration of PHY/MAC parameters, and (ii) cross-technology communication adaptation. The proposed modem design is evaluated in terms of effective communication data rate in both water tank and lake testbed setups. In Chapter 7, we present a novel receiver configuration for code-waveform-based multiple-access underwater communications. The proposed receiver is fully reconfigurable and executes (i) all-spectrum cognitive channelization, and (ii) combined synchronization, channel estimation, and demodulation. Experimental evaluation in terms of SINR and BER show that all-spectrum channelization is a powerful proposition for underwater communications. At the same time, the proposed receiver design can significantly enhance bandwidth utilization. Finally, in Chapter 8, we focus on challenging practical issues that arise in underwater acoustic sensor network setups where co-located multi-antenna sensor deployment is not feasible due to power, computation, and hardware limitations, and design, implement, and evaluate an underwater receiver structure that accounts for multiple carrier frequency and timing offsets in virtual (distributed) MIMO underwater systems.

Efficient Scalable Median Filtering Using Histogram-Based Operations.

PubMed

Green, Oded

2018-05-01

Median filtering is a smoothing technique for noise removal in images. While there are various implementations of median filtering for a single-core CPU, there are few implementations for accelerators and multi-core systems. Many parallel implementations of median filtering use a sorting algorithm for rearranging the values within a filtering window and taking the median of the sorted value. While using sorting algorithms allows for simple parallel implementations, the cost of the sorting becomes prohibitive as the filtering windows grow. This makes such algorithms, sequential and parallel alike, inefficient. In this work, we introduce the first software parallel median filtering that is non-sorting-based. The new algorithm uses efficient histogram-based operations. These reduce the computational requirements of the new algorithm while also accessing the image fewer times. We show an implementation of our algorithm for both the CPU and NVIDIA's CUDA supported graphics processing unit (GPU). The new algorithm is compared with several other leading CPU and GPU implementations. The CPU implementation has near perfect linear scaling with a speedup on a quad-core system. The GPU implementation is several orders of magnitude faster than the other GPU implementations for mid-size median filters. For small kernels, and , comparison-based approaches are preferable as fewer operations are required. Lastly, the new algorithm is open-source and can be found in the OpenCV library.

PopED lite: An optimal design software for preclinical pharmacokinetic and pharmacodynamic studies.

PubMed

Aoki, Yasunori; Sundqvist, Monika; Hooker, Andrew C; Gennemark, Peter

2016-04-01

Optimal experimental design approaches are seldom used in preclinical drug discovery. The objective is to develop an optimal design software tool specifically designed for preclinical applications in order to increase the efficiency of drug discovery in vivo studies. Several realistic experimental design case studies were collected and many preclinical experimental teams were consulted to determine the design goal of the software tool. The tool obtains an optimized experimental design by solving a constrained optimization problem, where each experimental design is evaluated using some function of the Fisher Information Matrix. The software was implemented in C++ using the Qt framework to assure a responsive user-software interaction through a rich graphical user interface, and at the same time, achieving the desired computational speed. In addition, a discrete global optimization algorithm was developed and implemented. The software design goals were simplicity, speed and intuition. Based on these design goals, we have developed the publicly available software PopED lite (http://www.bluetree.me/PopED_lite). Optimization computation was on average, over 14 test problems, 30 times faster in PopED lite compared to an already existing optimal design software tool. PopED lite is now used in real drug discovery projects and a few of these case studies are presented in this paper. PopED lite is designed to be simple, fast and intuitive. Simple, to give many users access to basic optimal design calculations. Fast, to fit a short design-execution cycle and allow interactive experimental design (test one design, discuss proposed design, test another design, etc). Intuitive, so that the input to and output from the software tool can easily be understood by users without knowledge of the theory of optimal design. In this way, PopED lite is highly useful in practice and complements existing tools. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Implementation of customized health information technology in diabetes self management programs.

PubMed

Alexander, Susan; Frith, Karen H; O'Keefe, Louise; Hennigan, Michael A

2011-01-01

The project was a nurse-led implementation of a software application, designed to combine clinical and demographic records for a diabetes education program, which would result in secure, long-term record storage. Clinical information systems may be prohibitively expensive for small practices and require extensive training for implementation. A review of the literature suggests that the use of simple, practice-based registries offer an economical method of monitoring the outcomes of diabetic patients. The database was designed using a common software application, Microsoft Access. The theory used to guide implementation and staff training was Rogers' Diffusion of Innovations theory (1995). Outcomes after a 3-month period included incorporation of 100% of new clinical and demographic patient records into the database and positive changes in staff attitudes regarding software applications used in diabetes self-management training. These objectives were met while keeping project costs under budgeted amounts. As a function of the clinical nurse specialist (CNS) researcher role, there is a need for CNSs to identify innovative and economical methods of data collection. The success of this nurse-led project reinforces suggestions in the literature for less costly methods of data maintenance in small practice settings. Ongoing utilization and enhancement have resulted in the creation of a robust database that could aid in the research of multiple clinical issues. Clinical nurse specialists can use existing evidence to guide and improve both their own practice and outcomes for patients and organizations. Further research regarding specific factors that predict efficient transition of informatics applications, how these factors vary according to practice settings, and the role of the CNS in implementation of such applications is needed.

Fault tolerant software modules for SIFT

NASA Technical Reports Server (NTRS)

Hecht, M.; Hecht, H.

1982-01-01

The implementation of software fault tolerance is investigated for critical modules of the Software Implemented Fault Tolerance (SIFT) operating system to support the computational and reliability requirements of advanced fly by wire transport aircraft. Fault tolerant designs generated for the error reported and global executive are examined. A description of the alternate routines, implementation requirements, and software validation are included.

Software system for data management and distributed processing of multichannel biomedical signals.

PubMed

Franaszczuk, P J; Jouny, C C

2004-01-01

The presented software is designed for efficient utilization of cluster of PC computers for signal analysis of multichannel physiological data. The system consists of three main components: 1) a library of input and output procedures, 2) a database storing additional information about location in a storage system, 3) a user interface for selecting data for analysis, choosing programs for analysis, and distributing computing and output data on cluster nodes. The system allows for processing multichannel time series data in multiple binary formats. The description of data format, channels and time of recording are included in separate text files. Definition and selection of multiple channel montages is possible. Epochs for analysis can be selected both manually and automatically. Implementation of a new signal processing procedures is possible with a minimal programming overhead for the input/output processing and user interface. The number of nodes in cluster used for computations and amount of storage can be changed with no major modification to software. Current implementations include the time-frequency analysis of multiday, multichannel recordings of intracranial EEG of epileptic patients as well as evoked response analyses of repeated cognitive tasks.

TGeoCad: an Interface between ROOT and CAD Systems

NASA Astrophysics Data System (ADS)

Luzzi, C.; Carminati, F.

2014-06-01

In the simulation of High Energy Physics experiment a very high precision in the description of the detector geometry is essential to achieve the required performances. The physicists in charge of Monte Carlo Simulation of the detector need to collaborate efficiently with the engineers working at the mechanical design of the detector. Often, this collaboration is made hard by the usage of different and incompatible software. ROOT is an object-oriented C++ framework used by physicists for storing, analyzing and simulating data produced by the high-energy physics experiments while CAD (Computer-Aided Design) software is used for mechanical design in the engineering field. The necessity to improve the level of communication between physicists and engineers led to the implementation of an interface between the ROOT geometrical modeler used by the virtual Monte Carlo simulation software and the CAD systems. In this paper we describe the design and implementation of the TGeoCad Interface that has been developed to enable the use of ROOT geometrical models in several CAD systems. To achieve this goal, the ROOT geometry description is converted into STEP file format (ISO 10303), which can be imported and used by many CAD systems.

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.

A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging.

PubMed

Gallio, Elena; Rampado, Osvaldo; Gianaria, Elena; Bianchi, Silvio Diego; Ropolo, Roberto

2015-01-01

Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies.

Successful Municipal Separate Storm Sewer System Programs Implemented in the Navy - NESDI #494

DTIC Science & Technology

2014-06-01

account. Lastly, upon speaking with numerous stormwater personnel who use a spreadsheet software for data tracking, they recommended that staying well...existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding...an organized manner. In the long-term, a comprehensive electronic methodology is recommended to keep data organized, be more efficient and to keep

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

PubMed

Bradley, Anthony R; Rose, Alexander S; Pavelka, Antonín; Valasatava, Yana; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

2017-06-01

Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

PubMed Central

Pavelka, Antonín; Valasatava, Yana; Prlić, Andreas

2017-01-01

Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis. PMID:28574982

A Model Independent S/W Framework for Search-Based Software Testing

PubMed Central

Baik, Jongmoon

2014-01-01

In Model-Based Testing (MBT) area, Search-Based Software Testing (SBST) has been employed to generate test cases from the model of a system under test. However, many types of models have been used in MBT. If the type of a model has changed from one to another, all functions of a search technique must be reimplemented because the types of models are different even if the same search technique has been applied. It requires too much time and effort to implement the same algorithm over and over again. We propose a model-independent software framework for SBST, which can reduce redundant works. The framework provides a reusable common software platform to reduce time and effort. The software framework not only presents design patterns to find test cases for a target model but also reduces development time by using common functions provided in the framework. We show the effectiveness and efficiency of the proposed framework with two case studies. The framework improves the productivity by about 50% when changing the type of a model. PMID:25302314

General guidelines for biomedical software development

PubMed Central

Silva, Luis Bastiao; Jimenez, Rafael C.; Blomberg, Niklas; Luis Oliveira, José

2017-01-01

Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic. PMID:28443186

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Software Framework for Advanced Power Plant Simulations

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

John Widmann; Sorin Munteanu; Aseem Jain

2010-08-01

This report summarizes the work accomplished during the Phase II development effort of the Advanced Process Engineering Co-Simulator (APECS). The objective of the project is to develop the tools to efficiently combine high-fidelity computational fluid dynamics (CFD) models with process modeling software. During the course of the project, a robust integration controller was developed that can be used in any CAPE-OPEN compliant process modeling environment. The controller mediates the exchange of information between the process modeling software and the CFD software. Several approaches to reducing the time disparity between CFD simulations and process modeling have been investigated and implemented. Thesemore » include enabling the CFD models to be run on a remote cluster and enabling multiple CFD models to be run simultaneously. Furthermore, computationally fast reduced-order models (ROMs) have been developed that can be 'trained' using the results from CFD simulations and then used directly within flowsheets. Unit operation models (both CFD and ROMs) can be uploaded to a model database and shared between multiple users.« less

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.

Parallel Fortran-MPI software for numerical inversion of the Laplace transform and its application to oscillatory water levels in groundwater environments

USGS Publications Warehouse

Zhan, X.

2005-01-01

A parallel Fortran-MPI (Message Passing Interface) software for numerical inversion of the Laplace transform based on a Fourier series method is developed to meet the need of solving intensive computational problems involving oscillatory water level's response to hydraulic tests in a groundwater environment. The software is a parallel version of ACM (The Association for Computing Machinery) Transactions on Mathematical Software (TOMS) Algorithm 796. Running 38 test examples indicated that implementation of MPI techniques with distributed memory architecture speedups the processing and improves the efficiency. Applications to oscillatory water levels in a well during aquifer tests are presented to illustrate how this package can be applied to solve complicated environmental problems involved in differential and integral equations. The package is free and is easy to use for people with little or no previous experience in using MPI but who wish to get off to a quick start in parallel computing. ?? 2004 Elsevier Ltd. All rights reserved.

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

Ramos, Marcel; Schiffer, Lucas; Re, Angela; Azhar, Rimsha; Basunia, Azfar; Rodriguez, Carmen; Chan, Tiffany; Chapman, Phil; Davis, Sean R; Gomez-Cabrero, David; Culhane, Aedin C; Haibe-Kains, Benjamin; Hansen, Kasper D; Kodali, Hanish; Louis, Marie S; Mer, Arvind S; Riester, Markus; Morgan, Martin; Carey, Vince; Waldron, Levi

2017-11-01

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR . ©2017 American Association for Cancer Research.

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.

Web Implementation of Quality Assurance (QA) for X-ray Units in Balkanic Medical Institutions.

PubMed

Urošević, Vlade; Ristić, Olga; Milošević, Danijela; Košutić, Duško

2015-08-01

Diagnostic radiology is the major contributor to the total dose of the population from all artificial sources. In order to reduce radiation exposure and optimize diagnostic x-ray image quality, it is necessary to increase the quality and efficiency of quality assurance (QA) and audit programs. This work presents a web application providing completely new QA solutions for x-ray modalities and facilities. The software gives complete online information (using European standards) with which the corresponding institutions and individuals can evaluate and control a facility's Radiation Safety and QA program. The software enables storage of all data in one place and sharing the same information (data), regardless of whether the measured data is used by an individual user or by an authorized institution. The software overcomes the distance and time separation of institutions and individuals who take part in QA. Upgrading the software will enable assessment of the medical exposure level to ionizing radiation.

45 CFR 153.350 - Risk adjustment data validation standards.

Code of Federal Regulations, 2012 CFR

2012-10-01

... implementation of any risk adjustment software and ensure proper validation of a statistically valid sample of... respect to implementation of risk adjustment software or as a result of data validation conducted pursuant... implementation of risk adjustment software or data validation. ...

Open source cardiology electronic health record development for DIGICARDIAC implementation

NASA Astrophysics Data System (ADS)

Dugarte, Nelson; Medina, Rubén.; Huiracocha, Lourdes; Rojas, Rubén.

2015-12-01

This article presents the development of a Cardiology Electronic Health Record (CEHR) system. Software consists of a structured algorithm designed under Health Level-7 (HL7) international standards. Novelty of the system is the integration of high resolution ECG (HRECG) signal acquisition and processing tools, patient information management tools and telecardiology tools. Acquisition tools are for management and control of the DIGICARDIAC electrocardiograph functions. Processing tools allow management of HRECG signal analysis searching for indicative patterns of cardiovascular pathologies. Telecardiology tools incorporation allows system communication with other health care centers decreasing access time to the patient information. CEHR system was completely developed using open source software. Preliminary results of process validation showed the system efficiency.

MIDAS: Software for the detection and analysis of lunar impact flashes

NASA Astrophysics Data System (ADS)

Madiedo, José M.; Ortiz, José L.; Morales, Nicolás; Cabrera-Caño, Jesús

2015-06-01

Since 2009 we are running a project to identify flashes produced by the impact of meteoroids on the surface of the Moon. For this purpose we are employing small telescopes and high-sensitivity CCD video cameras. To automatically identify these events a software package called MIDAS was developed and tested. This package can also perform the photometric analysis of these flashes and estimate the value of the luminous efficiency. Besides, we have implemented in MIDAS a new method to establish which is the likely source of the meteoroids (known meteoroid stream or sporadic background). The main features of this computer program are analyzed here, and some examples of lunar impact events are presented.

Real-time computing platform for spiking neurons (RT-spike).

PubMed

Ros, Eduardo; Ortigosa, Eva M; Agís, Rodrigo; Carrillo, Richard; Arnold, Michael

2006-07-01

A computing platform is described for simulating arbitrary networks of spiking neurons in real time. A hybrid computing scheme is adopted that uses both software and hardware components to manage the tradeoff between flexibility and computational power; the neuron model is implemented in hardware and the network model and the learning are implemented in software. The incremental transition of the software components into hardware is supported. We focus on a spike response model (SRM) for a neuron where the synapses are modeled as input-driven conductances. The temporal dynamics of the synaptic integration process are modeled with a synaptic time constant that results in a gradual injection of charge. This type of model is computationally expensive and is not easily amenable to existing software-based event-driven approaches. As an alternative we have designed an efficient time-based computing architecture in hardware, where the different stages of the neuron model are processed in parallel. Further improvements occur by computing multiple neurons in parallel using multiple processing units. This design is tested using reconfigurable hardware and its scalability and performance evaluated. Our overall goal is to investigate biologically realistic models for the real-time control of robots operating within closed action-perception loops, and so we evaluate the performance of the system on simulating a model of the cerebellum where the emulation of the temporal dynamics of the synaptic integration process is important.

Implementation of Chaotic Gaussian Particle Swarm Optimization for Optimize Learning-to-Rank Software Defect Prediction Model Construction

NASA Astrophysics Data System (ADS)

Buchari, M. A.; Mardiyanto, S.; Hendradjaya, B.

2018-03-01

Finding the existence of software defect as early as possible is the purpose of research about software defect prediction. Software defect prediction activity is required to not only state the existence of defects, but also to be able to give a list of priorities which modules require a more intensive test. Therefore, the allocation of test resources can be managed efficiently. Learning to rank is one of the approach that can provide defect module ranking data for the purposes of software testing. In this study, we propose a meta-heuristic chaotic Gaussian particle swarm optimization to improve the accuracy of learning to rank software defect prediction approach. We have used 11 public benchmark data sets as experimental data. Our overall results has demonstrated that the prediction models construct using Chaotic Gaussian Particle Swarm Optimization gets better accuracy on 5 data sets, ties in 5 data sets and gets worse in 1 data sets. Thus, we conclude that the application of Chaotic Gaussian Particle Swarm Optimization in Learning-to-Rank approach can improve the accuracy of the defect module ranking in data sets that have high-dimensional features.

The Elements of an Effective Software Development Plan - Software Development Process Guidebook

DTIC Science & Technology

2011-11-11

standards and practices required for all XMPL software development. This SDP implements the <corporate> Standard Software Process (SSP). as tailored...Developing and integrating reusable software products • Approach to managing COTS/Reuse software implementation • COTS/Reuse software selection...final selection and submit to change board for approval MAINTENANCE Monitor current products for obsolescence or end of support Track new

Industrial energy systems and assessment opportunities

NASA Astrophysics Data System (ADS)

Barringer, Frank Leonard, III

Industrial energy assessments are performed primarily to increase energy system efficiency and reduce energy costs in industrial facilities. The most common energy systems are lighting, compressed air, steam, process heating, HVAC, pumping, and fan systems, and these systems are described in this document. ASME has produced energy assessment standards for four energy systems, and these systems include compressed air, steam, process heating, and pumping systems. ASHRAE has produced an energy assessment standard for HVAC systems. Software tools for energy systems were developed for the DOE, and there are software tools for almost all of the most common energy systems. The software tools are AIRMaster+ and LogTool for compressed air systems, SSAT and 3E Plus for steam systems, PHAST and 3E Plus for process heating systems, eQUEST for HVAC systems, PSAT for pumping systems, and FSAT for fan systems. The recommended assessment procedures described in this thesis are used to set up an energy assessment for an industrial facility, collect energy system data, and analyze the energy system data. The assessment recommendations (ARs) are opportunities to increase efficiency and reduce energy consumption for energy systems. A set of recommended assessment procedures and recommended assessment opportunities are presented for each of the most common energy systems. There are many assessment opportunities for industrial facilities, and this thesis describes forty-three ARs for the seven different energy systems. There are seven ARs for lighting systems, ten ARs for compressed air systems, eight ARs for boiler and steam systems, four ARs for process heating systems, six ARs for HVAC systems, and four ARs for both pumping and fan systems. Based on a history of past assessments, average potential energy savings and typical implementation costs are shared in this thesis for most ARs. Implementing these ARs will increase efficiency and reduce energy consumption for energy systems in industrial facilities. This thesis does not explain all energy saving ARs that are available, but does describe the most common ARs.

78 FR 31916 - Increasing Market and Planning Efficiency Through Improved Software; Supplemental Agenda Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-28

... Market and Planning Efficiency Through Improved Software; Supplemental Agenda Notice Take notice that... for increasing real-time and day-ahead market efficiency through improved software. A detailed agenda..., the software industry, government, research centers and academia and is intended to build on the...

Theoretical and experimental fundamentals of designing promising technological equipment to improve efficiency and environmental safety of highly viscous oil recovery from deep oil reservoirs

NASA Astrophysics Data System (ADS)

Moiseyev, V. A.; Nazarov, V. P.; Zhuravlev, V. Y.; Zhuykov, D. A.; Kubrikov, M. V.; Klokotov, Y. N.

2016-12-01

The development of new technological equipment for the implementation of highly effective methods of recovering highly viscous oil from deep reservoirs is an important scientific and technical challenge. Thermal recovery methods are promising approaches to solving the problem. It is necessary to carry out theoretical and experimental research aimed at developing oil-well tubing (OWT) with composite heatinsulating coatings on the basis of basalt and glass fibers. We used the method of finite element analysis in Nastran software, which implements complex scientific and engineering calculations, including the calculation of the stress-strain state of mechanical systems, the solution of problems of heat transfer, the study of nonlinear static, the dynamic transient analysis of frequency characteristics, etc. As a result, we obtained a mathematical model of thermal conductivity which describes the steady-state temperature and changes in the fibrous highly porous material with the heat loss by Stefan-Boltzmann's radiation. It has been performed for the first time using the method of computer modeling in Nastran software environments. The results give grounds for further implementation of the real design of the OWT when implementing thermal methods for increasing the rates of oil production and mitigating environmental impacts.

Managing the Implementation of Mission Operations Automation

NASA Technical Reports Server (NTRS)

Sodano, R.; Crouse, P.; Odendahl, S.; Fatig, M.; McMahon, K.; Lakin, J.

2006-01-01

Reducing the cost of mission operations has necessitated a high level of automation both on spacecraft and ground systems. While automation on spacecraft is implemented during the design phase, ground system automation tends to be implemented during the prime mission operations phase. Experience has shown that this tendency for late automation development can be hindered by several factors: additional hardware and software resources may need to be procured; software must be developed and tested on a non-interference basis with primary operations with limited manpower; and established procedures may not be suited for automation requiring substantial rework. In this paper we will review the experience of successfully automating mission operations for seven on-orbit missions: the Compton Gamma Ray Observatory (CGRO), the Rossi X-Ray Timing Explorer (RXTE), the Advanced Composition Explorer (ACE), the Far Ultraviolet Spectroscopic Explorer (FUSE), Interplanetary Physics Laboratory (WIND), Polar Plasma Laboratory (POLAR), and the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE). We will provide lessons learned in areas such as: spacecraft recorder management, procedure development, lights out commanding from the ground system vs. stored command loads, spacecraft contingency response time, and ground station interfaces. Implementing automation strategies during the mission concept and spacecraft integration and test phase as the most efficient method will be discussed.

Software organization for a prolog-based prototyping system for machine vision

NASA Astrophysics Data System (ADS)

Jones, Andrew C.; Hack, Ralf; Batchelor, Bruce G.

1996-11-01

We describe PIP (prolog image processing)--a prototype system for interactive image processing using Prolog, implemented on an Apple Macintosh computer. PIP is the latest in a series of products that the third author has been involved in the implementation of, under the collective title Prolog+. PIP differs from our previous systems in two particularly important respects. The first is that whereas we previously required dedicated image processing hardware, the present system implements image processing routines using software. The second difference is that our present system is hierarchical in structure, where the top level of the hierarchy emulates Prolog+, but there is a flexible infrastructure which supports more sophisticated image manipulation which we will be able to exploit in due course . We discuss the impact of the Apple Macintosh operating system upon the implementation of the image processing functions, and the interface between these functions and the Prolog system. We also explain how the existing set of Prolog+ commands has been implemented. PIP is now nearing maturity, and we will make a version of it generally available in the near future. However, although the represent version of PIP constitutes a complete image processing tool, there are a number of ways in which we are intending to enhance future versions, with a view to added flexibility and efficiency: we discuss these ideas briefly near the end of the present paper.

C to VHDL compiler

NASA Astrophysics Data System (ADS)

Berdychowski, Piotr P.; Zabolotny, Wojciech M.

2010-09-01

The main goal of C to VHDL compiler project is to make FPGA platform more accessible for scientists and software developers. FPGA platform offers unique ability to configure the hardware to implement virtually any dedicated architecture, and modern devices provide sufficient number of hardware resources to implement parallel execution platforms with complex processing units. All this makes the FPGA platform very attractive for those looking for efficient heterogeneous, computing environment. Current industry standard in development of digital systems on FPGA platform is based on HDLs. Although very effective and expressive in hands of hardware development specialists, these languages require specific knowledge and experience, unreachable for most scientists and software programmers. C to VHDL compiler project attempts to remedy that by creating an application, that derives initial VHDL description of a digital system (for further compilation and synthesis), from purely algorithmic description in C programming language. This idea itself is not new, and the C to VHDL compiler combines the best approaches from existing solutions developed over many previous years, with the introduction of some new unique improvements.

Efficient Process Migration for Parallel Processing on Non-Dedicated Networks of Workstations

NASA Technical Reports Server (NTRS)

Chanchio, Kasidit; Sun, Xian-He

1996-01-01

This paper presents the design and preliminary implementation of MpPVM, a software system that supports process migration for PVM application programs in a non-dedicated heterogeneous computing environment. New concepts of migration point as well as migration point analysis and necessary data analysis are introduced. In MpPVM, process migrations occur only at previously inserted migration points. Migration point analysis determines appropriate locations to insert migration points; whereas, necessary data analysis provides a minimum set of variables to be transferred at each migration pint. A new methodology to perform reliable point-to-point data communications in a migration environment is also discussed. Finally, a preliminary implementation of MpPVM and its experimental results are presented, showing the correctness and promising performance of our process migration mechanism in a scalable non-dedicated heterogeneous computing environment. While MpPVM is developed on top of PVM, the process migration methodology introduced in this study is general and can be applied to any distributed software environment.

Software Defined Networking challenges and future direction: A case study of implementing SDN features on OpenStack private cloud

NASA Astrophysics Data System (ADS)

Shamugam, Veeramani; Murray, I.; Leong, J. A.; Sidhu, Amandeep S.

2016-03-01

Cloud computing provides services on demand instantly, such as access to network infrastructure consisting of computing hardware, operating systems, network storage, database and applications. Network usage and demands are growing at a very fast rate and to meet the current requirements, there is a need for automatic infrastructure scaling. Traditional networks are difficult to automate because of the distributed nature of their decision making process for switching or routing which are collocated on the same device. Managing complex environments using traditional networks is time-consuming and expensive, especially in the case of generating virtual machines, migration and network configuration. To mitigate the challenges, network operations require efficient, flexible, agile and scalable software defined networks (SDN). This paper discuss various issues in SDN and suggests how to mitigate the network management related issues. A private cloud prototype test bed was setup to implement the SDN on the OpenStack platform to test and evaluate the various network performances provided by the various configurations.

Extreme Ultraviolet Imaging Telescope (EIT)

NASA Technical Reports Server (NTRS)

Lemen, J. R.; Freeland, S. L.

1997-01-01

Efforts concentrated on development and implementation of the SolarSoft (SSW) data analysis system. From an EIT analysis perspective, this system was designed to facilitate efficient reuse and conversion of software developed for Yohkoh/SXT and to take advantage of a large existing body of software developed by the SDAC, Yohkoh, and SOHO instrument teams. Another strong motivation for this system was to provide an EIT analysis environment which permits coordinated analysis of EIT data in conjunction with data from important supporting instruments, including Yohkoh/SXT and the other SOHO coronal instruments; CDS, SUMER, and LASCO. In addition, the SSW system will support coordinated EIT/TRACE analysis (by design) when TRACE data is available; TRACE launch is currently planned for March 1998. Working with Jeff Newmark, the Chianti software package (K.P. Dere et al) and UV /EUV data base was fully integrated into the SSW system to facilitate EIT temperature and emission analysis.

BIM cost analysis of transport infrastructure projects

NASA Astrophysics Data System (ADS)

Volkov, Andrey; Chelyshkov, Pavel; Grossman, Y.; Khromenkova, A.

2017-10-01

The article describes the method of analysis of the energy costs of transport infrastructure objects using BIM software. The paper consideres several options of orientation of a building using SketchUp and IES VE software programs. These options allow to choose the best direction of the building facades. Particular attention is given to a distribution of a temperature field in a cross-section of the wall according to the calculation made in the ELCUT software. The issues related to calculation of solar radiation penetration into a building and selection of translucent structures are considered in the paper. The article presents data on building codes relating to the transport sector, on the basis of which the calculations were made. The author emphasizes that BIM-programs should be implemented and used in order to optimize a thermal behavior of a building and increase its energy efficiency using climatic data.

Ndarts

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2011-01-01

Ndarts software provides algorithms for computing quantities associated with the dynamics of articulated, rigid-link, multibody systems. It is designed as a general-purpose dynamics library that can be used for the modeling of robotic platforms, space vehicles, molecular dynamics, and other such applications. The architecture and algorithms in Ndarts are based on the Spatial Operator Algebra (SOA) theory for computational multibody and robot dynamics developed at JPL. It uses minimal, internal coordinate models. The algorithms are low-order, recursive scatter/ gather algorithms. In comparison with the earlier Darts++ software, this version has a more general and cleaner design needed to support a larger class of computational dynamics needs. It includes a frames infrastructure, allows algorithms to operate on subgraphs of the system, and implements lazy and deferred computation for better efficiency. Dynamics modeling modules such as Ndarts are core building blocks of control and simulation software for space, robotic, mechanism, bio-molecular, and material systems modeling.

A Business Analytics Software Tool for Monitoring and Predicting Radiology Throughput Performance.

PubMed

Jones, Stephen; Cournane, Seán; Sheehy, Niall; Hederman, Lucy

2016-12-01

Business analytics (BA) is increasingly being utilised by radiology departments to analyse and present data. It encompasses statistical analysis, forecasting and predictive modelling and is used as an umbrella term for decision support and business intelligence systems. The primary aim of this study was to determine whether utilising BA technologies could contribute towards improved decision support and resource management within radiology departments. A set of information technology requirements were identified with key stakeholders, and a prototype BA software tool was designed, developed and implemented. A qualitative evaluation of the tool was carried out through a series of semi-structured interviews with key stakeholders. Feedback was collated, and emergent themes were identified. The results indicated that BA software applications can provide visibility of radiology performance data across all time horizons. The study demonstrated that the tool could potentially assist with improving operational efficiencies and management of radiology resources.

Design study of Software-Implemented Fault-Tolerance (SIFT) computer

NASA Technical Reports Server (NTRS)

Wensley, J. H.; Goldberg, J.; Green, M. W.; Kutz, W. H.; Levitt, K. N.; Mills, M. E.; Shostak, R. E.; Whiting-Okeefe, P. M.; Zeidler, H. M.

1982-01-01

Software-implemented fault tolerant (SIFT) computer design for commercial aviation is reported. A SIFT design concept is addressed. Alternate strategies for physical implementation are considered. Hardware and software design correctness is addressed. System modeling and effectiveness evaluation are considered from a fault-tolerant point of view.

Improving glycemic control with the adjunct use of a data management software program.

PubMed

Reed, Charles C; Richa, Jacqueline M; Berndt, Andrea E; Beadle, Randy D; Gerhardt, Susan D; Stewart, Ronald; Corneille, Michael

2012-01-01

Published studies have supported the implementation of tight glucose control (TGC) programs to improve patient outcomes and reduce mortality rates. However, measuring a program's efficiency is challenging, because of a lack of systems that capture data, allow access to data, and support analysis and interpretation in a near prospective time frame. We hypothesized that providing clinicians access to real-time blood glucose (BG) results reports could improve the efficacy of our TGC program. We performed a retrospective review of BG data during a 12-month period in a surgical trauma intensive care unit at a level I trauma center. A unit-specific insulin algorithm was used throughout the study. We compared BG values before and after the implementation of a data management software program that allowed clinicians access to real-time BG results reports. Reports were run daily and weekly to monitor the unit's TGC program. A total of 70 616 BG values from 1044 patients were analyzed. An overall decrease was observed in the BG level mean, from 121 mg/dL to 112 mg/dL (P < .001), as well as a decrease in the aggregated mean across patients, from 132 mg/dL to 119 mg/dL (P < .001), after implementation of the software. The percentage of values within the target range of 80 to 110 mg/dL increased from 38.9% to 50.4% (P < .001). The percentage of BG values less than 70 increased from 2.7% to 3.4% (P < .001). However, the percentage of severe hypoglyce-mic episodes (≤ 40 mg/dL) remained unchanged. Access to real-time aggregated BG data reports through the use of a data management software program improved the efficacy of our TGC program.

Finite element method for calculating spectral and optical characteristics of axially symmetric quantum dots

NASA Astrophysics Data System (ADS)

Gusev, A. A.; Chuluunbaatar, O.; Vinitsky, S. I.; Derbov, V. L.; Hai, L. L.; Kazaryan, E. M.; Sarkisyan, H. A.

2018-04-01

We present new calculation schemes using high-order finite element method implemented on unstructured grids with triangle elements for solving boundary-value problems that describe axially symmetric quantum dots. The efficiency of the algorithms and software is demonstrated by benchmark calculations of the energy spectrum, the envelope eigenfunctions of electron, hole and exciton states, and the direct interband light absorption in conical and spheroidal impenetrable quantum dots.

Development of a Dynamic Time Sharing Scheduled Environment Final Report CRADA No. TC-824-94E

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

Jette, M.; Caliga, D.

Massively parallel computers, such as the Cray T3D, have historically supported resource sharing solely with space sharing. In that method, multiple problems are solved by executing them on distinct processors. This project developed a dynamic time- and space-sharing scheduler to achieve greater interactivity and throughput than could be achieved with space-sharing alone. CRI and LLNL worked together on the design, testing, and review aspects of this project. There were separate software deliverables. CFU implemented a general purpose scheduling system as per the design specifications. LLNL ported the local gang scheduler software to the LLNL Cray T3D. In this approach, processorsmore » are allocated simultaneously to aU components of a parallel program (in a “gang”). Program execution is preempted as needed to provide for interactivity. Programs are also reIocated to different processors as needed to efficiently pack the computer’s torus of processors. In phase one, CRI developed an interface specification after discussions with LLNL for systemlevel software supporting a time- and space-sharing environment on the LLNL T3D. The two parties also discussed interface specifications for external control tools (such as scheduling policy tools, system administration tools) and applications programs. CRI assumed responsibility for the writing and implementation of all the necessary system software in this phase. In phase two, CRI implemented job-rolling on the Cray T3D, a mechanism for preempting a program, saving its state to disk, and later restoring its state to memory for continued execution. LLNL ported its gang scheduler to the LLNL T3D utilizing the CRI interface implemented in phases one and two. During phase three, the functionality and effectiveness of the LLNL gang scheduler was assessed to provide input to CRI time- and space-sharing, efforts. CRI will utilize this information in the development of general schedulers suitable for other sites and future architectures.« less

75 FR 45623 - Increasing Market and Planning Efficiency Through Improved Software; Notice Establishing Date for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-03

... Market and Planning Efficiency Through Improved Software; Notice Establishing Date for Comments July 27... software related to wholesale electricity markets and planning: \\1\\ \\1\\ Notice of Technical Conference to Discuss Increasing Market and Planning Efficiency Through Improved Software, 75 FR 27,341 (2010). June 2-3...

Design of a Knowledge Driven HIS

PubMed Central

Pryor, T. Allan; Clayton, Paul D.; Haug, Peter J.; Wigertz, Ove

1987-01-01

Design of the software architecture for a knowledge driven HIS is presented. In our design the frame has been used as the basic unit of knowledge representation. The structure of the frame is being designed to be sufficiently universal to contain knowledge required to implement not only expert systems, but almost all traditional HIS functions including ADT, order entry and results review. The design incorporates a two level format for the knowledge. The first level as ASCII records is used to maintain the knowledge base while the second level converted by special knowledge compilers to standard computer languages is used for efficient implementation of the knowledge applications.

Robot welding process control

NASA Technical Reports Server (NTRS)

Romine, Peter L.

1991-01-01

This final report documents the development and installation of software and hardware for Robotic Welding Process Control. Primary emphasis is on serial communications between the CYRO 750 robotic welder, Heurikon minicomputer running Hunter & Ready VRTX, and an IBM PC/AT, for offline programming and control and closed-loop welding control. The requirements for completion of the implementation of the Rocketdyne weld tracking control are discussed. The procedure for downloading programs from the Intergraph, over the network, is discussed. Conclusions are made on the results of this task, and recommendations are made for efficient implementation of communications, weld process control development, and advanced process control procedures using the Heurikon.

Traditional versus rule-based programming techniques: Application to the control of optional flight information

NASA Technical Reports Server (NTRS)

Ricks, Wendell R.; Abbott, Kathy H.

1987-01-01

To the software design community, the concern over the costs associated with a program's execution time and implementation is great. It is always desirable, and sometimes imperative, that the proper programming technique is chosen which minimizes all costs for a given application or type of application. A study is described that compared cost-related factors associated with traditional programming techniques to rule-based programming techniques for a specific application. The results of this study favored the traditional approach regarding execution efficiency, but favored the rule-based approach regarding programmer productivity (implementation ease). Although this study examined a specific application, the results should be widely applicable.

Fast and Adaptive Lossless On-Board Hyperspectral Data Compression System for Space Applications

NASA Technical Reports Server (NTRS)

Aranki, Nazeeh; Bakhshi, Alireza; Keymeulen, Didier; Klimesh, Matthew

2009-01-01

Efficient on-board lossless hyperspectral data compression reduces the data volume necessary to meet NASA and DoD limited downlink capabilities. The techniques also improves signature extraction, object recognition and feature classification capabilities by providing exact reconstructed data on constrained downlink resources. At JPL a novel, adaptive and predictive technique for lossless compression of hyperspectral data was recently developed. This technique uses an adaptive filtering method and achieves a combination of low complexity and compression effectiveness that far exceeds state-of-the-art techniques currently in use. The JPL-developed 'Fast Lossless' algorithm requires no training data or other specific information about the nature of the spectral bands for a fixed instrument dynamic range. It is of low computational complexity and thus well-suited for implementation in hardware, which makes it practical for flight implementations of pushbroom instruments. A prototype of the compressor (and decompressor) of the algorithm is available in software, but this implementation may not meet speed and real-time requirements of some space applications. Hardware acceleration provides performance improvements of 10x-100x vs. the software implementation (about 1M samples/sec on a Pentium IV machine). This paper describes a hardware implementation of the JPL-developed 'Fast Lossless' compression algorithm on a Field Programmable Gate Array (FPGA). The FPGA implementation targets the current state of the art FPGAs (Xilinx Virtex IV and V families) and compresses one sample every clock cycle to provide a fast and practical real-time solution for Space applications.

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

PubMed Central

Kumar, Rajendra; Sobhy, Haitham

2017-01-01

Abstract Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community. PMID:28973466

The MR-Base platform supports systematic causal inference across the human phenome

PubMed Central

Wade, Kaitlin H; Haberland, Valeriia; Baird, Denis; Laurin, Charles; Burgess, Stephen; Bowden, Jack; Langdon, Ryan; Tan, Vanessa Y; Yarmolinsky, James; Shihab, Hashem A; Timpson, Nicholas J; Evans, David M; Relton, Caroline; Martin, Richard M; Davey Smith, George

2018-01-01

Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base (http://www.mrbase.org): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies. PMID:29846171

Arra: Tas::89 0227::Tas Recovery Act 100g Ftp: An Ultra-High Speed Data Transfer Service Over Next Generation 100 Gigabit Per Second Network

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

YU, DANTONG; Jin, Shudong

2014-03-01

Data-intensive applications, including high energy and nuclear physics, astrophysics, climate modeling, nano-scale materials science, genomics, and financing, are expected to generate exabytes of data over the coming years, which must be transferred, visualized, and analyzed by geographically distributed teams of users. High-performance network capabilities must be available to these users at the application level in a transparent, virtualized manner. Moreover, the application users must have the capability to move large datasets from local and remote locations across network environments to their home institutions. To solve these challenges, the main goal of our project is to design and evaluate high-performance datamore » transfer software to support various data-intensive applications. First, we have designed a middleware software that provides access to Remote Direct Memory Access (RDMA) functionalities. This middleware integrates network access, memory management and multitasking in its core design. We address a number of issues related to its efficient implementation, for instance, explicit buffer management and memory registration, and parallelization of RDMA operations, which are vital to delivering the benefit of RDMA to the applications. Built on top of this middleware, an implementation and experimental evaluation of the RDMA-based FTP software, RFTP, is described and evaluated. This application has been implemented by our team to exploit the full capabilities of advanced RDMA mechanisms for ultra-high speed bulk data transfer applications on Energy Sciences Network (ESnet). Second, we designed our data transfer software to optimize TCP/IP based data transfer performance such that RFTP can be fully compatible with today’s Internet. Our kernel optimization techniques with Linux system calls sendfile and splice, can reduce data copy cost. In this report, we summarize the technical challenges of our project, the primary software design methods, the major project milestones achieved, as well as the testbed evaluation work and demonstrations during our project life time.« less

Modeling Complex Workflow in Molecular Diagnostics

PubMed Central

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert

PubMed Central

2015-01-01

We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data. Specifically, a new wavelet-based peak-picker (CantWaiT) and a precursor charge determination algorithm (Turbocharger) have been implemented. These additions into ProteoWizard provide universal tools that are independent of vendor platform for tandem mass spectrometry analyses and have particular utility for intralaboratory studies requiring the advantages of different platforms convergent on a particular workflow or for interlaboratory investigations spanning multiple platforms. We compared results from these tools to those obtained using vendor and commercial software, finding that in all cases our algorithms resulted in a comparable number of identified peptides for simple and complex samples measured on Waters, Agilent, and AB SCIEX quadrupole time-of-flight and Thermo Q-Exactive mass spectrometers. The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools. Additionally, typical analysis runtimes (∼1–100 ms per MS/MS spectrum) were short enough to enable the practical use of these high-quality signal processing tools for large clinical and research data sets. PMID:25411686

INDDGO: Integrated Network Decomposition & Dynamic programming for Graph Optimization

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

Groer, Christopher S; Sullivan, Blair D; Weerapurage, Dinesh P

2012-10-01

It is well-known that dynamic programming algorithms can utilize tree decompositions to provide a way to solve some \\emph{NP}-hard problems on graphs where the complexity is polynomial in the number of nodes and edges in the graph, but exponential in the width of the underlying tree decomposition. However, there has been relatively little computational work done to determine the practical utility of such dynamic programming algorithms. We have developed software to construct tree decompositions using various heuristics and have created a fast, memory-efficient dynamic programming implementation for solving maximum weighted independent set. We describe our software and the algorithms wemore » have implemented, focusing on memory saving techniques for the dynamic programming. We compare the running time and memory usage of our implementation with other techniques for solving maximum weighted independent set, including a commercial integer programming solver and a semi-definite programming solver. Our results indicate that it is possible to solve some instances where the underlying decomposition has width much larger than suggested by the literature. For certain types of problems, our dynamic programming code runs several times faster than these other methods.« less

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.

PubMed

French, William R; Zimmerman, Lisa J; Schilling, Birgit; Gibson, Bradford W; Miller, Christine A; Townsend, R Reid; Sherrod, Stacy D; Goodwin, Cody R; McLean, John A; Tabb, David L

2015-02-06

We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data. Specifically, a new wavelet-based peak-picker (CantWaiT) and a precursor charge determination algorithm (Turbocharger) have been implemented. These additions into ProteoWizard provide universal tools that are independent of vendor platform for tandem mass spectrometry analyses and have particular utility for intralaboratory studies requiring the advantages of different platforms convergent on a particular workflow or for interlaboratory investigations spanning multiple platforms. We compared results from these tools to those obtained using vendor and commercial software, finding that in all cases our algorithms resulted in a comparable number of identified peptides for simple and complex samples measured on Waters, Agilent, and AB SCIEX quadrupole time-of-flight and Thermo Q-Exactive mass spectrometers. The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools. Additionally, typical analysis runtimes (∼1-100 ms per MS/MS spectrum) were short enough to enable the practical use of these high-quality signal processing tools for large clinical and research data sets.

A Specification for a Godunov-type Eulerian 2-D Hydrocode, Revision 0

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

Nystrom, William D; Robey, Jonathan M

2012-05-01

The purpose of this code specification is to describe an algorithm for solving the Euler equations of hydrodynamics in a 2D rectangular region in sufficient detail to allow a software developer to produce an implementation on their target platform using their programming language of choice without requiring detailed knowledge and experience in the field of computational fluid dynamics. It should be possible for a software developer who is proficient in the programming language of choice and is knowledgable of the target hardware to produce an efficient implementation of this specification if they also possess a thorough working knowledge of parallelmore » programming and have some experience in scientific programming using fields and meshes. On modern architectures, it will be important to focus on issues related to the exploitation of the fine grain parallelism and data locality present in this algorithm. This specification aims to make that task easier by presenting the essential details of the algorithm in a systematic and language neutral manner while also avoiding the inclusion of implementation details that would likely be specific to a particular type of programming paradigm or platform architecture.« less

Machine learning on-a-chip: a high-performance low-power reusable neuron architecture for artificial neural networks in ECG classifications.

PubMed

Sun, Yuwen; Cheng, Allen C

2012-07-01

Artificial neural networks (ANNs) are a promising machine learning technique in classifying non-linear electrocardiogram (ECG) signals and recognizing abnormal patterns suggesting risks of cardiovascular diseases (CVDs). In this paper, we propose a new reusable neuron architecture (RNA) enabling a performance-efficient and cost-effective silicon implementation for ANN. The RNA architecture consists of a single layer of physical RNA neurons, each of which is designed to use minimal hardware resource (e.g., a single 2-input multiplier-accumulator is used to compute the dot product of two vectors). By carefully applying the principal of time sharing, RNA can multiplexs this single layer of physical neurons to efficiently execute both feed-forward and back-propagation computations of an ANN while conserving the area and reducing the power dissipation of the silicon. A three-layer 51-30-12 ANN is implemented in RNA to perform the ECG classification for CVD detection. This RNA hardware also allows on-chip automatic training update. A quantitative design space exploration in area, power dissipation, and execution speed between RNA and three other implementations representative of different reusable hardware strategies is presented and discussed. Compared with an equivalent software implementation in C executed on an embedded microprocessor, the RNA ASIC achieves three orders of magnitude improvements in both the execution speed and the energy efficiency. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2016-03-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2016 Elsevier Inc. All rights reserved.

Connectivity-enhanced route selection and adaptive control for the Chevrolet Volt

DOE PAGES

Gonder, Jeffrey; Wood, Eric; Rajagopalan, Sai

2016-01-01

The National Renewable Energy Laboratory and General Motors evaluated connectivity-enabled efficiency enhancements for the Chevrolet Volt. A high-level model was developed to predict vehicle fuel and electricity consumption based on driving characteristics and vehicle state inputs. These techniques were leveraged to optimize energy efficiency via green routing and intelligent control mode scheduling, which were evaluated using prospective driving routes between tens of thousands of real-world origin/destination pairs. The overall energy savings potential of green routing and intelligent mode scheduling was estimated at 5% and 3%, respectively. Furthermore, these represent substantial opportunities considering that they only require software adjustments to implement.

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2015-06-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2015 Elsevier Inc. All rights reserved.

Maintaining Quality and Confidence in Open-Source, Evolving Software: Lessons Learned with PFLOTRAN

NASA Astrophysics Data System (ADS)

Frederick, J. M.; Hammond, G. E.

2017-12-01

Software evolution in an open-source framework poses a major challenge to a geoscientific simulator, but when properly managed, the pay-off can be enormous for both the developers and the community at large. Developers must juggle implementing new scientific process models, adopting increasingly efficient numerical methods and programming paradigms, changing funding sources (or total lack of funding), while also ensuring that legacy code remains functional and reported bugs are fixed in a timely manner. With robust software engineering and a plan for long-term maintenance, a simulator can evolve over time incorporating and leveraging many advances in the computational and domain sciences. In this positive light, what practices in software engineering and code maintenance can be employed within open-source development to maximize the positive aspects of software evolution and community contributions while minimizing its negative side effects? This presentation will discusses steps taken in the development of PFLOTRAN (www.pflotran.org), an open source, massively parallel subsurface simulator for multiphase, multicomponent, and multiscale reactive flow and transport processes in porous media. As PFLOTRAN's user base and development team continues to grow, it has become increasingly important to implement strategies which ensure sustainable software development while maintaining software quality and community confidence. In this presentation, we will share our experiences and "lessons learned" within the context of our open-source development framework and community engagement efforts. Topics discussed will include how we've leveraged both standard software engineering principles, such as coding standards, version control, and automated testing, as well unique advantages of object-oriented design in process model coupling, to ensure software quality and confidence. We will also be prepared to discuss the major challenges faced by most open-source software teams, such as on-boarding new developers or one-time contributions, dealing with competitors or lookie-loos, and other downsides of complete transparency, as well as our approach to community engagement, including a user group email list, hosting short courses and workshops for new users, and maintaining a website. SAND2017-8174A

Analysis of key technologies for virtual instruments metrology

NASA Astrophysics Data System (ADS)

Liu, Guixiong; Xu, Qingui; Gao, Furong; Guan, Qiuju; Fang, Qiang

2008-12-01

Virtual instruments (VIs) require metrological verification when applied as measuring instruments. Owing to the software-centered architecture, metrological evaluation of VIs includes two aspects: measurement functions and software characteristics. Complexity of software imposes difficulties on metrological testing of VIs. Key approaches and technologies for metrology evaluation of virtual instruments are investigated and analyzed in this paper. The principal issue is evaluation of measurement uncertainty. The nature and regularity of measurement uncertainty caused by software and algorithms can be evaluated by modeling, simulation, analysis, testing and statistics with support of powerful computing capability of PC. Another concern is evaluation of software features like correctness, reliability, stability, security and real-time of VIs. Technologies from software engineering, software testing and computer security domain can be used for these purposes. For example, a variety of black-box testing, white-box testing and modeling approaches can be used to evaluate the reliability of modules, components, applications and the whole VI software. The security of a VI can be assessed by methods like vulnerability scanning and penetration analysis. In order to facilitate metrology institutions to perform metrological verification of VIs efficiently, an automatic metrological tool for the above validation is essential. Based on technologies of numerical simulation, software testing and system benchmarking, a framework for the automatic tool is proposed in this paper. Investigation on implementation of existing automatic tools that perform calculation of measurement uncertainty, software testing and security assessment demonstrates the feasibility of the automatic framework advanced.

Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access.

PubMed

Chacón, Alejandro; Marco-Sola, Santiago; Espinosa, Antonio; Ribeca, Paolo; Moure, Juan Carlos

2015-01-01

The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8 × faster than a comparable multi-core CPU version, and about 3 × to 5 × faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.

A comparative study of the A* heuristic search algorithm used to solve efficiently a puzzle game

NASA Astrophysics Data System (ADS)

Iordan, A. E.

2018-01-01

The puzzle game presented in this paper consists in polyhedra (prisms, pyramids or pyramidal frustums) which can be moved using the free available spaces. The problem requires to be found the minimum number of movements in order the game reaches to a goal configuration starting from an initial configuration. Because the problem is enough complex, the principal difficulty in solving it is given by dimension of search space, that leads to necessity of a heuristic search. The improving of the search method consists into determination of a strong estimation by the heuristic function which will guide the search process to the most promising side of the search tree. The comparative study is realized among Manhattan heuristic and the Hamming heuristic using A* search algorithm implemented in Java. This paper also presents the necessary stages in object oriented development of a software used to solve efficiently this puzzle game. The modelling of the software is achieved through specific UML diagrams representing the phases of analysis, design and implementation, the system thus being described in a clear and practical manner. With the purpose to confirm the theoretical results which demonstrates that Manhattan heuristic is more efficient was used space complexity criterion. The space complexity was measured by the number of generated nodes from the search tree, by the number of the expanded nodes and by the effective branching factor. From the experimental results obtained by using the Manhattan heuristic, improvements were observed regarding space complexity of A* algorithm versus Hamming heuristic.

UTM TCL2 Software Requirements

NASA Technical Reports Server (NTRS)

Smith, Irene S.; Rios, Joseph L.; McGuirk, Patrick O.; Mulfinger, Daniel G.; Venkatesan, Priya; Smith, David R.; Baskaran, Vijayakumar; Wang, Leo

2017-01-01

The Unmanned Aircraft Systems (UAS) Traffic Management (UTM) Technical Capability Level (TCL) 2 software implements the UTM TCL 2 software requirements described herein. These software requirements are linked to the higher level UTM TCL 2 System Requirements. Each successive TCL implements additional UTM functionality, enabling additional use cases. TCL 2 demonstrated how to enable expanded multiple operations by implementing automation for beyond visual line-of-sight, tracking operations, and operations flying over sparsely populated areas.

FUEL-FLEXIBLE GASIFICATION-COMBUSTION TECHNOLOGY FOR PRODUCTION OF H2 AND SEQUESTRATION-READY CO2

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

George Rizeq; Janice West; Arnaldo Frydman

Further development of a combustion Large Eddy Simulation (LES) code for the design of advanced gaseous combustion systems is described in this sixth quarterly report. CFD Research Corporation (CFDRC) is developing the LES module within the parallel, unstructured solver included in the commercial CFD-ACE+ software. In this quarter, in-situ adaptive tabulation (ISAT) for efficient chemical rate storage and retrieval was implemented and tested within the Linear Eddy Model (LEM). ISAT type 3 is being tested so that extrapolation can be performed and further improve the retrieval rate. Further testing of the LEM for subgrid chemistry was performed for parallel applicationsmore » and for multi-step chemistry. Validation of the software on backstep and bluff-body reacting cases were performed. Initial calculations of the SimVal experiment at Georgia Tech using their LES code were performed. Georgia Tech continues the effort to parameterize the LEM over composition space so that a neural net can be used efficiently in the combustion LES code. A new and improved Artificial Neural Network (ANN), with log-transformed output, for the 1-step chemistry was implemented in CFDRC's LES code and gave reasonable results. This quarter, the 2nd consortium meeting was held at CFDRC. Next quarter, LES software development and testing will continue. Alpha testing of the code will continue to be performed on cases of interest to the industrial consortium. Optimization of subgrid models will be pursued, particularly with the ISAT approach. Also next quarter, the demonstration of the neural net approach, for multi-step chemical kinetics speed-up in CFD-ACE+, will be accomplished.« less

Mapping of H.264 decoding on a multiprocessor architecture

NASA Astrophysics Data System (ADS)

van der Tol, Erik B.; Jaspers, Egbert G.; Gelderblom, Rob H.

2003-05-01

Due to the increasing significance of development costs in the competitive domain of high-volume consumer electronics, generic solutions are required to enable reuse of the design effort and to increase the potential market volume. As a result from this, Systems-on-Chip (SoCs) contain a growing amount of fully programmable media processing devices as opposed to application-specific systems, which offered the most attractive solutions due to a high performance density. The following motivates this trend. First, SoCs are increasingly dominated by their communication infrastructure and embedded memory, thereby making the cost of the functional units less significant. Moreover, the continuously growing design costs require generic solutions that can be applied over a broad product range. Hence, powerful programmable SoCs are becoming increasingly attractive. However, to enable power-efficient designs, that are also scalable over the advancing VLSI technology, parallelism should be fully exploited. Both task-level and instruction-level parallelism can be provided by means of e.g. a VLIW multiprocessor architecture. To provide the above-mentioned scalability, we propose to partition the data over the processors, instead of traditional functional partitioning. An advantage of this approach is the inherent locality of data, which is extremely important for communication-efficient software implementations. Consequently, a software implementation is discussed, enabling e.g. SD resolution H.264 decoding with a two-processor architecture, whereas High-Definition (HD) decoding can be achieved with an eight-processor system, executing the same software. Experimental results show that the data communication considerably reduces up to 65% directly improving the overall performance. Apart from considerable improvement in memory bandwidth, this novel concept of partitioning offers a natural approach for optimally balancing the load of all processors, thereby further improving the overall speedup.

Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh

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

Brown, W Michael; Kohlmeyer, Axel; Plimpton, Steven J

The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. In this paper, we present a continuation of previous work implementing algorithms for using accelerators into the LAMMPS molecular dynamics software for distributed memory parallel hybrid machines. In our previous work, we focused on acceleration for short-range models with anmore » approach intended to harness the processing power of both the accelerator and (multi-core) CPUs. To augment the existing implementations, we present an efficient implementation of long-range electrostatic force calculation for molecular dynamics. Specifically, we present an implementation of the particle-particle particle-mesh method based on the work by Harvey and De Fabritiis. We present benchmark results on the Keeneland InfiniBand GPU cluster. We provide a performance comparison of the same kernels compiled with both CUDA and OpenCL. We discuss limitations to parallel efficiency and future directions for improving performance on hybrid or heterogeneous computers.« less

The Use of Smartphones in Norwegian Social Care Services.

PubMed

Hansen, Linda Iren Mihaila; Fruhling, Ann; Fossum, Mariann

2016-01-01

This study aims to understand how smartphone technology was perceived by social workers responsible for piloting social services software and the experiences of involving end-users as co-developers. The pilot resulted in an improved match between the smartphone software and workflow as well as mutual learning experiences among the social workers, clients, and the vendor. The pilot study revealed several graphical user interface (GUI) and functionality challenges. Implementing an ICT social service smartphone application may further improve efficiencies for social workers serving citizens, however; this study validates the importance to study end-users' experiences with communication and the real-time use of the system in order reap the anticipated benefits of ICT capabilities for smart phone social service applications.

Comparison of matrix method and ray tracing in the study of complex optical systems

NASA Astrophysics Data System (ADS)

Anterrieu, Eric; Perez, Jose-Philippe

2000-06-01

In the context of the classical study of optical systems within the geometrical Gauss approximation, the cardinal elements are efficiently obtained with the aid of the transfer matrix between the input and output planes of the system. In order to take into account the geometrical aberrations, a ray tracing approach, using the Snell- Descartes laws, has been implemented in an interactive software. Both methods are applied for measuring the correction to be done to a human eye suffering from ametropia. This software may be used by optometrists and ophthalmologists for solving the problems encountered when considering this pathology. The ray tracing approach gives a significant improvement and could be very helpful for a better understanding of an eventual surgical act.

System for Better Spacing of Airplanes En Route

NASA Technical Reports Server (NTRS)

Green, Steven; Erzberger, Heinz

2004-01-01

An improved method of computing the spacing of airplanes en route, and software to implement the method, have been invented. The purpose of the invention is to help air-traffic controllers minimize those deviations of the airplanes from the trajectories preferred by their pilots that are needed to make the airplanes comply with miles-in-trail spacing requirements. The software is meant to be a modular component of the Center TRACON Automation System (CTAS) (TRACON signifies "terminal radar approach control"). The invention reduces controllers workloads and reduces fuel consumption by reducing the number of corrective clearances needed to achieve conformance with specified flow rates, without causing conflicts, while providing for more efficient distribution of spacing workload upstream and across air-traffic-control sectors.

StochKit2: software for discrete stochastic simulation of biochemical systems with events.

PubMed

Sanft, Kevin R; Wu, Sheng; Roh, Min; Fu, Jin; Lim, Rone Kwei; Petzold, Linda R

2011-09-01

StochKit2 is the first major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a flexible framework for extending its functionality. StochKit2 runs on Linux/Unix, Mac OS X and Windows. It is freely available under GPL version 3 and can be downloaded from http://sourceforge.net/projects/stochkit/. petzold@engineering.ucsb.edu.

Improving Cognitive Abilities and e-Inclusion in Children with Cerebral Palsy

NASA Astrophysics Data System (ADS)

Martinengo, Chiara; Curatelli, Francesco

Besides overcoming the motor barriers for accessing to computers and Internet, ICT tools can provide a very useful, and often necessary, support for the cognitive development of motor-impaired children with cerebral palsy. In fact, software tools for computation and communication allow teachers to put into effect, in a more complete and efficient way, the learning methods and the educational plans studied for the child. In the present article, after a brief analysis of the general objectives to be pursued for favouring the learning for children with cerebral palsy, we take account of some specific difficulties in the logical-linguistic and logical-mathematical fields, and we show how they can be overcome using general ICT tools and specifically implemented software programs.

mz5: space- and time-efficient storage of mass spectrometry data sets.

PubMed

Wilhelm, Mathias; Kirchner, Marc; Steen, Judith A J; Steen, Hanno

2012-01-01

Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to ∼54% and increases linear read and write speeds ∼3-4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5.

High-Density Liquid-State Machine Circuitry for Time-Series Forecasting.

PubMed

Rosselló, Josep L; Alomar, Miquel L; Morro, Antoni; Oliver, Antoni; Canals, Vincent

2016-08-01

Spiking neural networks (SNN) are the last neural network generation that try to mimic the real behavior of biological neurons. Although most research in this area is done through software applications, it is in hardware implementations in which the intrinsic parallelism of these computing systems are more efficiently exploited. Liquid state machines (LSM) have arisen as a strategic technique to implement recurrent designs of SNN with a simple learning methodology. In this work, we show a new low-cost methodology to implement high-density LSM by using Boolean gates. The proposed method is based on the use of probabilistic computing concepts to reduce hardware requirements, thus considerably increasing the neuron count per chip. The result is a highly functional system that is applied to high-speed time series forecasting.

Algorithms for optimized maximum entropy and diagnostic tools for analytic continuation.

PubMed

Bergeron, Dominic; Tremblay, A-M S

2016-08-01

Analytic continuation of numerical data obtained in imaginary time or frequency has become an essential part of many branches of quantum computational physics. It is, however, an ill-conditioned procedure and thus a hard numerical problem. The maximum-entropy approach, based on Bayesian inference, is the most widely used method to tackle that problem. Although the approach is well established and among the most reliable and efficient ones, useful developments of the method and of its implementation are still possible. In addition, while a few free software implementations are available, a well-documented, optimized, general purpose, and user-friendly software dedicated to that specific task is still lacking. Here we analyze all aspects of the implementation that are critical for accuracy and speed and present a highly optimized approach to maximum entropy. Original algorithmic and conceptual contributions include (1) numerical approximations that yield a computational complexity that is almost independent of temperature and spectrum shape (including sharp Drude peaks in broad background, for example) while ensuring quantitative accuracy of the result whenever precision of the data is sufficient, (2) a robust method of choosing the entropy weight α that follows from a simple consistency condition of the approach and the observation that information- and noise-fitting regimes can be identified clearly from the behavior of χ^{2} with respect to α, and (3) several diagnostics to assess the reliability of the result. Benchmarks with test spectral functions of different complexity and an example with an actual physical simulation are presented. Our implementation, which covers most typical cases for fermions, bosons, and response functions, is available as an open source, user-friendly software.

Algorithms for optimized maximum entropy and diagnostic tools for analytic continuation

NASA Astrophysics Data System (ADS)

Bergeron, Dominic; Tremblay, A.-M. S.

2016-08-01

Analytic continuation of numerical data obtained in imaginary time or frequency has become an essential part of many branches of quantum computational physics. It is, however, an ill-conditioned procedure and thus a hard numerical problem. The maximum-entropy approach, based on Bayesian inference, is the most widely used method to tackle that problem. Although the approach is well established and among the most reliable and efficient ones, useful developments of the method and of its implementation are still possible. In addition, while a few free software implementations are available, a well-documented, optimized, general purpose, and user-friendly software dedicated to that specific task is still lacking. Here we analyze all aspects of the implementation that are critical for accuracy and speed and present a highly optimized approach to maximum entropy. Original algorithmic and conceptual contributions include (1) numerical approximations that yield a computational complexity that is almost independent of temperature and spectrum shape (including sharp Drude peaks in broad background, for example) while ensuring quantitative accuracy of the result whenever precision of the data is sufficient, (2) a robust method of choosing the entropy weight α that follows from a simple consistency condition of the approach and the observation that information- and noise-fitting regimes can be identified clearly from the behavior of χ2 with respect to α , and (3) several diagnostics to assess the reliability of the result. Benchmarks with test spectral functions of different complexity and an example with an actual physical simulation are presented. Our implementation, which covers most typical cases for fermions, bosons, and response functions, is available as an open source, user-friendly software.

An FPGA-Based People Detection System

NASA Astrophysics Data System (ADS)

Nair, Vinod; Laprise, Pierre-Olivier; Clark, James J.

2005-12-01

This paper presents an FPGA-based system for detecting people from video. The system is designed to use JPEG-compressed frames from a network camera. Unlike previous approaches that use techniques such as background subtraction and motion detection, we use a machine-learning-based approach to train an accurate detector. We address the hardware design challenges involved in implementing such a detector, along with JPEG decompression, on an FPGA. We also present an algorithm that efficiently combines JPEG decompression with the detection process. This algorithm carries out the inverse DCT step of JPEG decompression only partially. Therefore, it is computationally more efficient and simpler to implement, and it takes up less space on the chip than the full inverse DCT algorithm. The system is demonstrated on an automated video surveillance application and the performance of both hardware and software implementations is analyzed. The results show that the system can detect people accurately at a rate of about[InlineEquation not available: see fulltext.] frames per second on a Virtex-II 2V1000 using a MicroBlaze processor running at[InlineEquation not available: see fulltext.], communicating with dedicated hardware over FSL links.

Internet Usage In The Fresh Produce Supply Chainin China

NASA Astrophysics Data System (ADS)

Xu, Xiaoxiao; Duan, Yanqing; Fu, Zetian; Liu, Xue

Although effective implementation of the Internet technologies has a great potential for improving efficiency and reducing wastage within the fresh produce supply chain. the situation of the Internet usage by SMEs (small and medium sized enterprises) in the fresh produce supply chain is still unclear in China. As the main players, SMEs haven't been given enough attention from both academics and governments. Therefore, this research attempts to address this issue by, first, investigating the current usage of the Internet and related software by Chinese SMEs in the fresh produce supply chain, and then, by identifying enablers and barriers faced by SMEs to call government's attention. As a part of an EU-Asia IT&C funded project, a survey was carried out with SMEs in this industry from five major cities in China. The results reveal that in the relatively developed areas of China, SMEs in the fresh produce supply chain are rapidly adopting the Internet and software packages, but the level of adoption varies greatly and there is a significant lack of integration among the supply chain partners. Chinese SMEs are keen to embrace emerging technologies and have acted to adopt new software and tools. Given that cost of implementation is not a barrier, their concern over legal protection and online security must be addressed for further development.

AIRNOISE: A Tool for Preliminary Noise-Abatement Terminal Approach Route Design

NASA Technical Reports Server (NTRS)

Li, Jinhua; Sridhar, Banavar; Xue, Min; Ng, Hok

2016-01-01

Noise from aircraft in the airport vicinity is one of the leading aviation-induced environmental issues. The FAA developed the Integrated Noise Model (INM) and its replacement Aviation Environmental Design Tool (AEDT) software to assess noise impact resulting from all aviation activities. However, a software tool is needed that is simple to use for terminal route modification, quick and reasonably accurate for preliminary noise impact evaluation and flexible to be used for iterative design of optimal noise-abatement terminal routes. In this paper, we extend our previous work on developing a noise-abatement terminal approach route design tool, named AIRNOISE, to satisfy this criterion. First, software efficiency has been significantly increased by over tenfold using the C programming language instead of MATLAB. Moreover, a state-of-the-art high performance GPU-accelerated computing module is implemented that was tested to be hundreds time faster than the C implementation. Secondly, a Graphical User Interface (GUI) was developed allowing users to import current terminal approach routes and modify the routes interactively to design new terminal approach routes. The corresponding noise impacts are then calculated and displayed in the GUI in seconds. Finally, AIRNOISE was applied to Baltimore-Washington International Airport terminal approach route to demonstrate its usage.

An adaptive software defined radio design based on a standard space telecommunication radio system API

NASA Astrophysics Data System (ADS)

Xiong, Wenhao; Tian, Xin; Chen, Genshe; Pham, Khanh; Blasch, Erik

2017-05-01

Software defined radio (SDR) has become a popular tool for the implementation and testing for communications performance. The advantage of the SDR approach includes: a re-configurable design, adaptive response to changing conditions, efficient development, and highly versatile implementation. In order to understand the benefits of SDR, the space telecommunication radio system (STRS) was proposed by NASA Glenn research center (GRC) along with the standard application program interface (API) structure. Each component of the system uses a well-defined API to communicate with other components. The benefit of standard API is to relax the platform limitation of each component for addition options. For example, the waveform generating process can support a field programmable gate array (FPGA), personal computer (PC), or an embedded system. As long as the API defines the requirements, the generated waveform selection will work with the complete system. In this paper, we demonstrate the design and development of adaptive SDR following the STRS and standard API protocol. We introduce step by step the SDR testbed system including the controlling graphic user interface (GUI), database, GNU radio hardware control, and universal software radio peripheral (USRP) tranceiving front end. In addition, a performance evaluation in shown on the effectiveness of the SDR approach for space telecommunication.

A web-based library consult service for evidence-based medicine: Technical development

PubMed Central

Schwartz, Alan; Millam, Gregory

2006-01-01

Background 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. Results 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. Conclusion A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement. PMID:16542453

Design and Implementation of Integrated Software Research and Community Service at State Polytechnic of Manado

NASA Astrophysics Data System (ADS)

Saroinsong, T.; A. S Kondoj, M.; Kandiyoh, G.; Pontoh, G.

2018-01-01

The State Polytechnic of Manado (Polimdo) is one of the reliable institutions in North Sulawesi that first implemented ISO 9001. But the accreditation of the institution has not been satisfactory, it means there is still much to be prepared to achieve the expected target. One of the criteria of assessment of institutional accreditation is related to research activities and social work in accordance with the standard seven. Data documentation systems related to research activities and social work are not well integrated and well documented in all existing work units. This causes the process of gathering information related to the activities and the results of research and social work in order to support the accreditation activities of the institution is still not efficient. This study aims to build an integrated software in all work units in Polimdo to obtain documentation and data synchronization in support of activities or reporting of documents accreditation institution in accordance with standard seven specifically in terms of submission of research proposal and dedication. The software will be developed using RUP method with analysis using data flow diagram and ERM so that the result of this research is documentation and synchronization of data and information of research activity and community service which can be used in preparing documents report for accreditation institution.

Hydrological Monitoring System Design and Implementation Based on IOT

NASA Astrophysics Data System (ADS)

Han, Kun; Zhang, Dacheng; Bo, Jingyi; Zhang, Zhiguang

In this article, an embedded system development platform based on GSM communication is proposed. Through its application in hydrology monitoring management, the author makes discussion about communication reliability and lightning protection, suggests detail solutions, and also analyzes design and realization of upper computer software. Finally, communication program is given. Hydrology monitoring system from wireless communication network is a typical practical application of embedded system, which has realized intelligence, modernization, high-efficiency and networking of hydrology monitoring management.

Efficient XML Interchange (EXI) Compression and Performance Benefits: Development, Implementation and Evaluation

DTIC Science & Technology

2010-03-01

to a graphics card , and not the redesign of XML. The justification is that if XML is going to be prevalent, special optimized hardware is...the answer, similar to the specialized functions of a video card .  Given the Moore’s law that processing power doubles every few years, let the...and numerous multimedia players such as iTunes from Apple. These applications are free to use, but the source is restricted by software licenses

A Multiscale Software Tool for Field/Circuit Co-Simulation

DTIC Science & Technology

2011-12-15

technology fields: Number of graduating undergraduates who achieved a 3.5 GPA to 4.0 (4.0 max scale): Number of graduating undergraduates funded by a...times more efficient than FDTD for such a problem in 3D . The techniques in class (c) above include the discontinuous Galerkin method and multidomain...implements a finite-differential-time-domain method on single field propagation in a 3D space. We consider a cavity model which includes two electric

Rapid Prediction of Unsteady Three-Dimensional Viscous Flows in Turbopump Geometries

NASA Technical Reports Server (NTRS)

Dorney, Daniel J.

1998-01-01

A program is underway to improve the efficiency of a three-dimensional Navier-Stokes code and generalize it for nozzle and turbopump geometries. Code modifications will include the implementation of parallel processing software, incorporating new physical models and generalizing the multi-block capability to allow the simultaneous simulation of nozzle and turbopump configurations. The current report contains details of code modifications, numerical results of several flow simulations and the status of the parallelization effort.

Arithmetic functions in torus and tree networks

DOEpatents

Bhanot, Gyan; Blumrich, Matthias A.; Chen, Dong; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Steinmacher-Burow, Burkhard D.; Vranas, Pavlos M.

2007-12-25

Methods and systems for performing arithmetic functions. In accordance with a first aspect of the invention, methods and apparatus are provided, working in conjunction of software algorithms and hardware implementation of class network routing, to achieve a very significant reduction in the time required for global arithmetic operation on the torus. Therefore, it leads to greater scalability of applications running on large parallel machines. The invention involves three steps in improving the efficiency and accuracy of global operations: (1) Ensuring, when necessary, that all the nodes do the global operation on the data in the same order and so obtain a unique answer, independent of roundoff error; (2) Using the topology of the torus to minimize the number of hops and the bidirectional capabilities of the network to reduce the number of time steps in the data transfer operation to an absolute minimum; and (3) Using class function routing to reduce latency in the data transfer. With the method of this invention, every single element is injected into the network only once and it will be stored and forwarded without any further software overhead. In accordance with a second aspect of the invention, methods and systems are provided to efficiently implement global arithmetic operations on a network that supports the global combining operations. The latency of doing such global operations are greatly reduced by using these methods.

IMPROVING TACONITE PROCESSING PLANT EFFICIENCY BY COMPUTER SIMULATION, Final Report

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

William M. Bond; Salih Ersayin

2007-03-30

This project involved industrial scale testing of a mineral processing simulator to improve the efficiency of a taconite processing plant, namely the Minorca mine. The Concentrator Modeling Center at the Coleraine Minerals Research Laboratory, University of Minnesota Duluth, enhanced the capabilities of available software, Usim Pac, by developing mathematical models needed for accurate simulation of taconite plants. This project provided funding for this technology to prove itself in the industrial environment. As the first step, data representing existing plant conditions were collected by sampling and sample analysis. Data were then balanced and provided a basis for assessing the efficiency ofmore » individual devices and the plant, and also for performing simulations aimed at improving plant efficiency. Performance evaluation served as a guide in developing alternative process strategies for more efficient production. A large number of computer simulations were then performed to quantify the benefits and effects of implementing these alternative schemes. Modification of makeup ball size was selected as the most feasible option for the target performance improvement. This was combined with replacement of existing hydrocyclones with more efficient ones. After plant implementation of these modifications, plant sampling surveys were carried out to validate findings of the simulation-based study. Plant data showed very good agreement with the simulated data, confirming results of simulation. After the implementation of modifications in the plant, several upstream bottlenecks became visible. Despite these bottlenecks limiting full capacity, concentrator energy improvement of 7% was obtained. Further improvements in energy efficiency are expected in the near future. The success of this project demonstrated the feasibility of a simulation-based approach. Currently, the Center provides simulation-based service to all the iron ore mining companies operating in northern Minnesota, and future proposals are pending with non-taconite mineral processing applications.« less

A model of cloud application assignments in software-defined storages

NASA Astrophysics Data System (ADS)

Bolodurina, Irina P.; Parfenov, Denis I.; Polezhaev, Petr N.; E Shukhman, Alexander

2017-01-01

The aim of this study is to analyze the structure and mechanisms of interaction of typical cloud applications and to suggest the approaches to optimize their placement in storage systems. In this paper, we describe a generalized model of cloud applications including the three basic layers: a model of application, a model of service, and a model of resource. The distinctive feature of the model suggested implies analyzing cloud resources from the user point of view and from the point of view of a software-defined infrastructure of the virtual data center (DC). The innovation character of this model is in describing at the same time the application data placements, as well as the state of the virtual environment, taking into account the network topology. The model of software-defined storage has been developed as a submodel within the resource model. This model allows implementing the algorithm for control of cloud application assignments in software-defined storages. Experimental researches returned this algorithm decreases in cloud application response time and performance growth in user request processes. The use of software-defined data storages allows the decrease in the number of physical store devices, which demonstrates the efficiency of our algorithm.

Fast software-based volume rendering using multimedia instructions on PC platforms and its application to virtual endoscopy

NASA Astrophysics Data System (ADS)

Mori, Kensaku; Suenaga, Yasuhito; Toriwaki, Jun-ichiro

2003-05-01

This paper describes a software-based fast volume rendering (VolR) method on a PC platform by using multimedia instructions, such as SIMD instructions, which are currently available in PCs' CPUs. This method achieves fast rendering speed through highly optimizing software rather than an improved rendering algorithm. In volume rendering using a ray casting method, the system requires fast execution of the following processes: (a) interpolation of voxel or color values at sample points, (b) computation of normal vectors (gray-level gradient vectors), (c) calculation of shaded values obtained by dot-products of normal vectors and light source direction vectors, (d) memory access to a huge area, and (e) efficient ray skipping at translucent regions. The proposed software implements these fundamental processes in volume rending by using special instruction sets for multimedia processing. The proposed software can generate virtual endoscopic images of a 3-D volume of 512x512x489 voxel size by volume rendering with perspective projection, specular reflection, and on-the-fly normal vector computation on a conventional PC without any special hardware at thirteen frames per second. Semi-translucent display is also possible.

A Unified Algebraic and Logic-Based Framework Towards Safe Routing Implementations

DTIC Science & Technology

2015-08-13

Software - defined Networks ( SDN ). We developed a declarative platform for implementing SDN protocols using declarative...and debugging several SDN applications. Example-based SDN synthesis. Recent emergence of software - defined networks offers an opportunity to design...domain of Software - defined Networks ( SDN ). We developed a declarative platform for implementing SDN protocols using declarative networking

Modification of infant hypothyroidism and phenylketonuria screening program using electronic tools.

PubMed

Taheri, Behjat; Haddadpoor, Asefeh; Mirkhalafzadeh, Mahmood; Mazroei, Fariba; Aghdak, Pezhman; Nasri, Mehran; Bahrami, Gholamreza

2017-01-01

Congenital hypothyroidism and phenylketonuria (PKU) are the most common cause for preventable mental retardation in infants worldwide. Timely diagnosis and treatment of these disorders can have lasting effects on the mental development of newborns. However, there are several problems at different stages of screening programs that along with imposing heavy costs can reduce the precision of the screening, increasing the chance of undiagnosed cases which in turn can have damaging consequences for the society. Therefore, given these problems and the importance of information systems in facilitating the management and improving the quality of health care the aim of this study was to improve the screening process of hypothyroidism and PKU in infants with the help of electronic resources. The current study is a qualitative, action research designed to improve the quality of screening, services, performance, implementation effectiveness, and management of hypothyroidism and PKU screening program in Isfahan province. To this end, web-based software was designed. Programming was carried out using Delphi.net software and used SQL Server 2008 for database management. Given the weaknesses, problems, and limitations of hypothyroidism and PKU screening program, and the importance of these diseases in a national scale, this study resulted in design of hypothyroidism and PKU screening software for infants in Isfahan province. The inputs and outputs of the software were designed in three levels including Health Care Centers in charge of the screening program, provincial reference lab, and health and treatment network of Isfahan province. Immediate registration of sample data at the time and location of sampling, providing the provincial reference Laboratory and Health Centers of different eparchies with the ability to instantly observe, monitor, and follow-up on the samples at any moment, online verification of samples by reference lab, creating a daily schedule for reference lab, and receiving of the results from analysis equipment; and entering the results into the database without the need for user input are among the features of this software. The implementation of hypothyroidism screening software led to an increase in the quality and efficiency of the screening program; minimized the risk of human error in the process and solved many of the previous limitations of the screening program which were the main goals for implementation of this software. The implementation of this software also resulted in improvement in precision and quality of services provided for these two diseases and better accuracy and precision for data inputs by providing the possibility of entering the sample data at the place and time of sampling which then resulted in the possibility of management based on precise data and also helped develop a comprehensive database and improved the satisfaction of service recipients.

An NAFP Project: Use of Object Oriented Methodologies and Design Patterns to Refactor Software Design

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali; Baggs, Rhoda

2007-01-01

In the early problem-solution era of software programming, functional decompositions were mainly used to design and implement software solutions. In functional decompositions, functions and data are introduced as two separate entities during the design phase, and are followed as such in the implementation phase. Functional decompositions make use of refactoring through optimizing the algorithms, grouping similar functionalities into common reusable functions, and using abstract representations of data where possible; all these are done during the implementation phase. This paper advocates the usage of object-oriented methodologies and design patterns as the centerpieces of refactoring software solutions. Refactoring software is a method of changing software design while explicitly preserving its external functionalities. The combined usage of object-oriented methodologies and design patterns to refactor should also benefit the overall software life cycle cost with improved software.

Methods and implementation of a central biosample and data management in a three-centre clinical study.

PubMed

Angelow, Aniela; Schmidt, Matthias; Weitmann, Kerstin; Schwedler, Susanne; Vogt, Hannes; Havemann, Christoph; Hoffmann, Wolfgang

2008-07-01

In our report we describe concept, strategies and implementation of a central biosample and data management (CSDM) system in the three-centre clinical study of the Transregional Collaborative Research Centre "Inflammatory Cardiomyopathy - Molecular Pathogenesis and Therapy" SFB/TR 19, Germany. Following the requirements of high system resource availability, data security, privacy protection and quality assurance, a web-based CSDM was developed based on Java 2 Enterprise Edition using an Oracle database. An efficient and reliable sample documentation system using bar code labelling, a partitioning storage algorithm and an online documentation software was implemented. An online electronic case report form is used to acquire patient-related data. Strict rules for access to the online applications and secure connections are used to account for privacy protection and data security. Challenges for the implementation of the CSDM resided at project, technical and organisational level as well as at staff level.

Quadratic Blind Linear Unmixing: A Graphical User Interface for Tissue Characterization

PubMed Central

Gutierrez-Navarro, O.; Campos-Delgado, D.U.; Arce-Santana, E. R.; Jo, Javier A.

2016-01-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. PMID:26589467

Quadratic blind linear unmixing: A graphical user interface for tissue characterization.

PubMed

Gutierrez-Navarro, O; Campos-Delgado, D U; Arce-Santana, E R; Jo, Javier A

2016-02-01

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

SIM_EXPLORE: Software for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

Burl, Michael; Wang, Esther; Enke, Brian; Merline, William J.

2013-01-01

Physics-based numerical simulation codes are widely used in science and engineering to model complex systems that would be infeasible to study otherwise. While such codes may provide the highest- fidelity representation of system behavior, they are often so slow to run that insight into the system is limited. Trying to understand the effects of inputs on outputs by conducting an exhaustive grid-based sweep over the input parameter space is simply too time-consuming. An alternative approach called "directed exploration" has been developed to harvest information from numerical simulators more efficiently. The basic idea is to employ active learning and supervised machine learning to choose cleverly at each step which simulation trials to run next based on the results of previous trials. SIM_EXPLORE is a new computer program that uses directed exploration to explore efficiently complex systems represented by numerical simulations. The software sequentially identifies and runs simulation trials that it believes will be most informative given the results of previous trials. The results of new trials are incorporated into the software's model of the system behavior. The updated model is then used to pick the next round of new trials. This process, implemented as a closed-loop system wrapped around existing simulation code, provides a means to improve the speed and efficiency with which a set of simulations can yield scientifically useful results. The software focuses on the case in which the feedback from the simulation trials is binary-valued, i.e., the learner is only informed of the success or failure of the simulation trial to produce a desired output. The software offers a number of choices for the supervised learning algorithm (the method used to model the system behavior given the results so far) and a number of choices for the active learning strategy (the method used to choose which new simulation trials to run given the current behavior model). The software also makes use of the LEGION distributed computing framework to leverage the power of a set of compute nodes. The approach has been demonstrated on a planetary science application in which numerical simulations are used to study the formation of asteroid families.

QUEST/Ada (Query Utility Environment for Software Testing of Ada): The development of a prgram analysis environment for Ada, task 1, phase 2

NASA Technical Reports Server (NTRS)

Brown, David B.

1990-01-01

The results of research and development efforts are described for Task one, Phase two of a general project entitled The Development of a Program Analysis Environment for Ada. The scope of this task includes the design and development of a prototype system for testing Ada software modules at the unit level. The system is called Query Utility Environment for Software Testing of Ada (QUEST/Ada). The prototype for condition coverage provides a platform that implements expert system interaction with program testing. The expert system can modify data in the instrument source code in order to achieve coverage goals. Given this initial prototype, it is possible to evaluate the rule base in order to develop improved rules for test case generation. The goals of Phase two are the following: (1) to continue to develop and improve the current user interface to support the other goals of this research effort (i.e., those related to improved testing efficiency and increased code reliable); (2) to develop and empirically evaluate a succession of alternative rule bases for the test case generator such that the expert system achieves coverage in a more efficient manner; and (3) to extend the concepts of the current test environment to address the issues of Ada concurrency.

Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

PubMed Central

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

2013-01-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803

Space station advanced automation

NASA Technical Reports Server (NTRS)

Woods, Donald

1990-01-01

In the development of a safe, productive and maintainable space station, Automation and Robotics (A and R) has been identified as an enabling technology which will allow efficient operation at a reasonable cost. The Space Station Freedom's (SSF) systems are very complex, and interdependent. The usage of Advanced Automation (AA) will help restructure, and integrate system status so that station and ground personnel can operate more efficiently. To use AA technology for the augmentation of system management functions requires a development model which consists of well defined phases of: evaluation, development, integration, and maintenance. The evaluation phase will consider system management functions against traditional solutions, implementation techniques and requirements; the end result of this phase should be a well developed concept along with a feasibility analysis. In the development phase the AA system will be developed in accordance with a traditional Life Cycle Model (LCM) modified for Knowledge Based System (KBS) applications. A way by which both knowledge bases and reasoning techniques can be reused to control costs is explained. During the integration phase the KBS software must be integrated with conventional software, and verified and validated. The Verification and Validation (V and V) techniques applicable to these KBS are based on the ideas of consistency, minimal competency, and graph theory. The maintenance phase will be aided by having well designed and documented KBS software.

Structuring software anthropometric variables on CD Rom as a facilitator of the process of design of work situations.

PubMed

Zanuncio, Sharinna Venturim; Mafra, Simone Caldas Tavares; Antônio, Carlos Emílio Barbosa; Lisboa Filho, Jugurta; Guimarães, Elza Maria Vidigal; da Silva, Vania Eugênia; de Souza, Amaury Paulo; Minette, Luciano José

2012-01-01

The environment where everyday activities are developed, these should be appropriate and the individual who will execute them, for greater efficiency of their work and even if you feel safe, comfortable and satisfied when interacting with that space, expending less energy to this interaction. Given this context, this study aims to structure a software with the results obtained in the field, from anthropometric measure to subsidize the furniture industry in manufacturing of furniture, definition work situations, considering the different anthropometric measurements made between 2001 and 2010, using data from this sample of adults aged 18 to 65 years old and children between 6 and 11 years old. It was convenient to make the software with a site, only instead of staying on the Web has been recorded on CD Rom. Tests with the prototype allow navigation through the structure of the software. The data needed to implement the remaining modules were also raised. Issues related to system layout and usability of the interface also were not considered, because it is an initial prototype.

G-Guidance Interface Design for Small Body Mission Simulation

NASA Technical Reports Server (NTRS)

Acikmese, Behcet; Carson, John; Phan, Linh

2008-01-01

The G-Guidance software implements a guidance and control (G and C) algorithm for small-body, autonomous proximity operations, developed under the Small Body GN and C task at JPL. The software is written in Matlab and interfaces with G-OPT, a JPL-developed optimization package written in C that provides G-Guidance with guaranteed convergence to a solution in a finite computation time with a prescribed accuracy. The resulting program is computationally efficient and is a prototype of an onboard, real-time algorithm for autonomous guidance and control. Two thruster firing schemes are available in G-Guidance, allowing tailoring of the software for specific mission maneuvers. For example, descent, landing, or rendezvous benefit from a thruster firing at the maneuver termination to mitigate velocity errors. Conversely, ascent or separation maneuvers benefit from an immediate firing to avoid potential drift toward a second body. The guidance portion of this software explicitly enforces user-defined control constraints and thruster silence times while minimizing total fuel usage. This program is currently specialized to small-body proximity operations, but the underlying method can be generalized to other applications.

Using virtual reality for science mission planning: A Mars Pathfinder case

NASA Technical Reports Server (NTRS)

Kim, Jacqueline H.; Weidner, Richard J.; Sacks, Allan L.

1994-01-01

NASA's Mars Pathfinder Project requires a Ground Data System (GDS) that supports both engineering and scientific payloads with reduced mission operations staffing, and short planning schedules. Also, successful surface operation of the lander camera requires efficient mission planning and accurate pointing of the camera. To meet these challenges, a new software strategy that integrates virtual reality technology with existing navigational ancillary information and image processing capabilities. The result is an interactive workstation based applications software that provides a high resolution, 3-dimensial, stereo display of Mars as if it were viewed through the lander camera. The design, implementation strategy and parametric specification phases for the development of this software were completed, and the prototype tested. When completed, the software will allow scientists and mission planners to access simulated and actual scenes of Mars' surface. The perspective from the lander camera will enable scientists to plan activities more accurately and completely. The application will also support the sequence and command generation process and will allow testing and verification of camera pointing commands via simulation.

Development of preoperative planning software for transforaminal endoscopic surgery and the guidance for clinical applications.

PubMed

Chen, Xiaojun; Cheng, Jun; Gu, Xin; Sun, Yi; Politis, Constantinus

2016-04-01

Preoperative planning is of great importance for transforaminal endoscopic techniques applied in percutaneous endoscopic lumbar discectomy. In this study, a modular preoperative planning software for transforaminal endoscopic surgery was developed and demonstrated. The path searching method is based on collision detection, and the oriented bounding box was constructed for the anatomical models. Then, image reformatting algorithms were developed for multiplanar reconstruction which provides detailed anatomical information surrounding the virtual planned path. Finally, multithread technique was implemented to realize the steady-state condition of the software. A preoperative planning software for transforaminal endoscopic surgery (TE-Guider) was developed; seven cases of patients with symptomatic lumbar disc herniations were planned preoperatively using TE-Guider. The distances to the midlines and the direction of the optimal paths were exported, and each result was in line with the empirical value. TE-Guider provides an efficient and cost-effective way to search the ideal path and entry point for the puncture. However, more clinical cases will be conducted to demonstrate its feasibility and reliability.

Design and implementation of H.264 based embedded video coding technology

NASA Astrophysics Data System (ADS)

Mao, Jian; Liu, Jinming; Zhang, Jiemin

2016-03-01

In this paper, an embedded system for remote online video monitoring was designed and developed to capture and record the real-time circumstances in elevator. For the purpose of improving the efficiency of video acquisition and processing, the system selected Samsung S5PV210 chip as the core processor which Integrated graphics processing unit. And the video was encoded with H.264 format for storage and transmission efficiently. Based on S5PV210 chip, the hardware video coding technology was researched, which was more efficient than software coding. After running test, it had been proved that the hardware video coding technology could obviously reduce the cost of system and obtain the more smooth video display. It can be widely applied for the security supervision [1].

Experimental research control software system

NASA Astrophysics Data System (ADS)

Cohn, I. A.; Kovalenko, A. G.; Vystavkin, A. N.

2014-05-01

A software system, intended for automation of a small scale research, has been developed. The software allows one to control equipment, acquire and process data by means of simple scripts. The main purpose of that development is to increase experiment automation easiness, thus significantly reducing experimental setup automation efforts. In particular, minimal programming skills are required and supervisors have no reviewing troubles. Interactions between scripts and equipment are managed automatically, thus allowing to run multiple scripts simultaneously. Unlike well-known data acquisition commercial software systems, the control is performed by an imperative scripting language. This approach eases complex control and data acquisition algorithms implementation. A modular interface library performs interaction with external interfaces. While most widely used interfaces are already implemented, a simple framework is developed for fast implementations of new software and hardware interfaces. While the software is in continuous development with new features being implemented, it is already used in our laboratory for automation of a helium-3 cryostat control and data acquisition. The software is open source and distributed under Gnu Public License.

Implementing Educational Software and Evaluating Its Academic Effectiveness: Part I.

ERIC Educational Resources Information Center

Jolicoeur, Karen; Berger, Dale E.

1988-01-01

This basic plan for implementing educational software in the classroom incorporates a research design for evaluating its effectiveness. A study of fifth grade classrooms using game and tutorial software for spelling and fractions is used as an example. Topics discussed include software selection, selecting groups of comparable ability, and use of…

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Large-scale virtual screening on public cloud resources with Apache Spark.

PubMed

Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin; Spjuth, Ola

2017-01-01

Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against [Formula: see text]2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries. Our implementation is named Spark-VS and it is freely available as open source from GitHub (https://github.com/mcapuccini/spark-vs).Graphical abstract.

Enterprise resource planning (ERP) implementation using the value engineering methodology and Six Sigma tools

NASA Astrophysics Data System (ADS)

Leu, Jun-Der; Lee, Larry Jung-Hsing

2017-09-01

Enterprise resource planning (ERP) is a software solution that integrates the operational processes of the business functions of an enterprise. However, implementing ERP systems is a complex process. In addition to the technical issues, companies must address problems associated with business process re-engineering, time and budget control, and organisational change. Numerous industrial studies have shown that the failure rate of ERP implementation is high, even for well-designed systems. Thus, ERP projects typically require a clear methodology to support the project execution and effectiveness. In this study, we propose a theoretical model for ERP implementation. The value engineering (VE) method forms the basis of the proposed framework, which integrates Six Sigma tools. The proposed framework encompasses five phases: knowledge generation, analysis, creation, development and execution. In the VE method, potential ERP problems related to software, hardware, consultation and organisation are analysed in a group-decision manner and in relation to value, and Six Sigma tools are applied to avoid any project defects. We validate the feasibility of the proposed model by applying it to an international manufacturing enterprise in Taiwan. The results show improvements in customer response time and operational efficiency in terms of work-in-process and turnover of materials. Based on the evidence from the case study, the theoretical framework is discussed together with the study's limitations and suggestions for future research.

Transient loads analysis for space flight applications

NASA Technical Reports Server (NTRS)

Thampi, S. K.; Vidyasagar, N. S.; Ganesan, N.

1992-01-01

A significant part of the flight readiness verification process involves transient analysis of the coupled Shuttle-payload system to determine the low frequency transient loads. This paper describes a methodology for transient loads analysis and its implementation for the Spacelab Life Sciences Mission. The analysis is carried out using two major software tools - NASTRAN and an external FORTRAN code called EZTRAN. This approach is adopted to overcome some of the limitations of NASTRAN's standard transient analysis capabilities. The method uses Data Recovery Matrices (DRM) to improve computational efficiency. The mode acceleration method is fully implemented in the DRM formulation to recover accurate displacements, stresses, and forces. The advantages of the method are demonstrated through a numerical example.

On Designing Lightweight Threads for Substrate Software

NASA Technical Reports Server (NTRS)

Haines, Matthew

1997-01-01

Existing user-level thread packages employ a 'black box' design approach, where the implementation of the threads is hidden from the user. While this approach is often sufficient for application-level programmers, it hides critical design decisions that system-level programmers must be able to change in order to provide efficient service for high-level systems. By applying the principles of Open Implementation Analysis and Design, we construct a new user-level threads package that supports common thread abstractions and a well-defined meta-interface for altering the behavior of these abstractions. As a result, system-level programmers will have the advantages of using high-level thread abstractions without having to sacrifice performance, flexibility or portability.

Benchmarking of Computational Models for NDE and SHM of Composites

NASA Technical Reports Server (NTRS)

Wheeler, Kevin; Leckey, Cara; Hafiychuk, Vasyl; Juarez, Peter; Timucin, Dogan; Schuet, Stefan; Hafiychuk, Halyna

2016-01-01

Ultrasonic wave phenomena constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials such as carbon-fiber-reinforced polymer (CFRP) laminates. Computational models of ultrasonic guided-wave excitation, propagation, scattering, and detection in quasi-isotropic laminates can be extremely valuable in designing practically realizable NDE and SHM hardware and software with desired accuracy, reliability, efficiency, and coverage. This paper presents comparisons of guided-wave simulations for CFRP composites implemented using three different simulation codes: two commercial finite-element analysis packages, COMSOL and ABAQUS, and a custom code implementing the Elastodynamic Finite Integration Technique (EFIT). Comparisons are also made to experimental laser Doppler vibrometry data and theoretical dispersion curves.

Study on light weight design of truss structures of spacecrafts

NASA Astrophysics Data System (ADS)

Zeng, Fuming; Yang, Jianzhong; Wang, Jian

2015-08-01

Truss structure is usually adopted as the main structure form for spacecrafts due to its high efficiency in supporting concentrated loads. Light-weight design is now becoming the primary concern during conceptual design of spacecrafts. Implementation of light-weight design on truss structure always goes through three processes: topology optimization, size optimization and composites optimization. During each optimization process, appropriate algorithm such as the traditional optimality criterion method, mathematical programming method and the intelligent algorithms which simulate the growth and evolution processes in nature will be selected. According to the practical processes and algorithms, combined with engineering practice and commercial software, summary is made for the implementation of light-weight design on truss structure for spacecrafts.

Photonic reservoir computing: a new approach to optical information processing

NASA Astrophysics Data System (ADS)

Vandoorne, Kristof; Fiers, Martin; Verstraeten, David; Schrauwen, Benjamin; Dambre, Joni; Bienstman, Peter

2010-06-01

Despite ever increasing computational power, recognition and classification problems remain challenging to solve. Recently, advances have been made by the introduction of the new concept of reservoir computing. This is a methodology coming from the field of machine learning and neural networks that has been successfully used in several pattern classification problems, like speech and image recognition. Thus far, most implementations have been in software, limiting their speed and power efficiency. Photonics could be an excellent platform for a hardware implementation of this concept because of its inherent parallelism and unique nonlinear behaviour. Moreover, a photonic implementation offers the promise of massively parallel information processing with low power and high speed. We propose using a network of coupled Semiconductor Optical Amplifiers (SOA) and show in simulation that it could be used as a reservoir by comparing it to conventional software implementations using a benchmark speech recognition task. In spite of the differences with classical reservoir models, the performance of our photonic reservoir is comparable to that of conventional implementations and sometimes slightly better. As our implementation uses coherent light for information processing, we find that phase tuning is crucial to obtain high performance. In parallel we investigate the use of a network of photonic crystal cavities. The coupled mode theory (CMT) is used to investigate these resonators. A new framework is designed to model networks of resonators and SOAs. The same network topologies are used, but feedback is added to control the internal dynamics of the system. By adjusting the readout weights of the network in a controlled manner, we can generate arbitrary periodic patterns.

Improving urban district heating systems and assessing the efficiency of the energy usage therein

NASA Astrophysics Data System (ADS)

Orlov, M. E.; Sharapov, V. I.

2017-11-01

The report describes issues in connection with improving urban district heating systems from combined heat power plants (CHPs), to propose the ways for improving the reliability and the efficiency of the energy usage (often referred to as “energy efficiency”) in such systems. The main direction of such urban district heating systems improvement suggests transition to combined heating systems that include structural elements of both centralized and decentralized systems. Such systems provide the basic part of thermal power via highly efficient methods for extracting thermal power plants turbines steam, while peak loads are covered by decentralized peak thermal power sources to be mounted at consumers’ locations, with the peak sources being also reserve thermal power sources. The methodology was developed for assessing energy efficiency of the combined district heating systems, implemented as a computer software product capable of comparatively calculating saving on reference fuel for the system.

Eigenvalue routines in NASTRAN: A comparison with the Block Lanczos method

NASA Technical Reports Server (NTRS)

Tischler, V. A.; Venkayya, Vipperla B.

1993-01-01

The NASA STRuctural ANalysis (NASTRAN) program is one of the most extensively used engineering applications software in the world. It contains a wealth of matrix operations and numerical solution techniques, and they were used to construct efficient eigenvalue routines. The purpose of this paper is to examine the current eigenvalue routines in NASTRAN and to make efficiency comparisons with a more recent implementation of the Block Lanczos algorithm by Boeing Computer Services (BCS). This eigenvalue routine is now available in the BCS mathematics library as well as in several commercial versions of NASTRAN. In addition, CRAY maintains a modified version of this routine on their network. Several example problems, with a varying number of degrees of freedom, were selected primarily for efficiency bench-marking. Accuracy is not an issue, because they all gave comparable results. The Block Lanczos algorithm was found to be extremely efficient, in particular, for very large size problems.

Design and Multicentric Implementation of a Generic Software Architecture for Patient Recruitment Systems Re-Using Existing HIS Tools and Routine Patient Data

PubMed Central

Trinczek, B.; Köpcke, F.; Leusch, T.; Majeed, R.W.; Schreiweis, B.; Wenk, J.; Bergh, B.; Ohmann, C.; Röhrig, R.; Prokosch, H.U.; Dugas, M.

2014-01-01

Summary Objective (1) To define features and data items of a Patient Recruitment System (PRS); (2) to design a generic software architecture of such a system covering the requirements; (3) to identify implementation options available within different Hospital Information System (HIS) environments; (4) to implement five PRS following the architecture and utilizing the implementation options as proof of concept. Methods Existing PRS were reviewed and interviews with users and developers conducted. All reported PRS features were collected and prioritized according to their published success and user’s request. Common feature sets were combined into software modules of a generic software architecture. Data items to process and transfer were identified for each of the modules. Each site collected implementation options available within their respective HIS environment for each module, provided a prototypical implementation based on available implementation possibilities and supported the patient recruitment of a clinical trial as a proof of concept. Results 24 commonly reported and requested features of a PRS were identified, 13 of them prioritized as being mandatory. A UML version 2 based software architecture containing 5 software modules covering these features was developed. 13 data item groups processed by the modules, thus required to be available electronically, have been identified. Several implementation options could be identified for each module, most of them being available at multiple sites. Utilizing available tools, a PRS could be implemented in each of the five participating German university hospitals. Conclusion A set of required features and data items of a PRS has been described for the first time. The software architecture covers all features in a clear, well-defined way. The variety of implementation options and the prototypes show that it is possible to implement the given architecture in different HIS environments, thus enabling more sites to successfully support patient recruitment in clinical trials. PMID:24734138

Design and multicentric implementation of a generic software architecture for patient recruitment systems re-using existing HIS tools and routine patient data.

PubMed

Trinczek, B; Köpcke, F; Leusch, T; Majeed, R W; Schreiweis, B; Wenk, J; Bergh, B; Ohmann, C; Röhrig, R; Prokosch, H U; Dugas, M

2014-01-01

(1) To define features and data items of a Patient Recruitment System (PRS); (2) to design a generic software architecture of such a system covering the requirements; (3) to identify implementation options available within different Hospital Information System (HIS) environments; (4) to implement five PRS following the architecture and utilizing the implementation options as proof of concept. Existing PRS were reviewed and interviews with users and developers conducted. All reported PRS features were collected and prioritized according to their published success and user's request. Common feature sets were combined into software modules of a generic software architecture. Data items to process and transfer were identified for each of the modules. Each site collected implementation options available within their respective HIS environment for each module, provided a prototypical implementation based on available implementation possibilities and supported the patient recruitment of a clinical trial as a proof of concept. 24 commonly reported and requested features of a PRS were identified, 13 of them prioritized as being mandatory. A UML version 2 based software architecture containing 5 software modules covering these features was developed. 13 data item groups processed by the modules, thus required to be available electronically, have been identified. Several implementation options could be identified for each module, most of them being available at multiple sites. Utilizing available tools, a PRS could be implemented in each of the five participating German university hospitals. A set of required features and data items of a PRS has been described for the first time. The software architecture covers all features in a clear, well-defined way. The variety of implementation options and the prototypes show that it is possible to implement the given architecture in different HIS environments, thus enabling more sites to successfully support patient recruitment in clinical trials.

Efficient Translation of LTL Formulae into Buchi Automata

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Lerda, Flavio

2001-01-01

Model checking is a fully automated technique for checking that a system satisfies a set of required properties. With explicit-state model checkers, properties are typically defined in linear-time temporal logic (LTL), and are translated into B chi automata in order to be checked. This report presents how we have combined and improved existing techniques to obtain an efficient LTL to B chi automata translator. In particular, we optimize the core of existing tableau-based approaches to generate significantly smaller automata. Our approach has been implemented and is being released as part of the Java PathFinder software (JPF), an explicit state model checker under development at the NASA Ames Research Center.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

LightForce Photon-Pressure Collision Avoidance: Updated Efficiency Analysis Utilizing a Highly Parallel Simulation Approach

DTIC Science & Technology

2014-09-01

simulation time frame from 30 days to one year. This was enabled by porting the simulation to the Pleiades supercomputer at NASA Ames Research Center, a...including the motivation for changes to our past approach. We then present the software implementation (3) on the NASA Ames Pleiades supercomputer...significantly updated since last year’s paper [25]. The main incentive for that was the shift to a highly parallel approach in order to utilize the Pleiades

Efficient abstract data type components for distributed and parallel systems

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

Bastani, F.; Hilal, W.; Iyengar, S.S.

1987-10-01

One way of improving software system's comprehensibility and maintainability is to decompose it into several components, each of which encapsulates some information concerning the system. These components can be classified into four categories, namely, abstract data type, functional, interface, and control components. Such a classfication underscores the need for different specification, implementation, and performance-improvement methods for different types of components. This article focuses on the development of high-performance abstract data type components for distributed and parallel environments.

Grand challenges in mass storage: A system integrator's perspective

NASA Technical Reports Server (NTRS)

Mintz, Dan; Lee, Richard

1993-01-01

The grand challenges are the following: to develop more innovation in approach; to expand the I/O barrier; to achieve increased volumetric efficiency and incremental cost improvements; to reinforce the 'weakest link' software; to implement improved architectures; and to minimize the impact of self-destructing technologies. Mass storage is defined as any type of storage system exceeding 100 GBytes in total size, under the control of a centralized file management scheme. The topics covered are presented in viewgraph form.

IGDS/TRAP Interface Program (ITIP). Software Design Document

NASA Technical Reports Server (NTRS)

Jefferys, Steve; Johnson, Wendell

1981-01-01

The preliminary design of the IGDS/TRAP Interface Program (ITIP) is described. The ITIP is implemented on the PDP 11/70 and interfaces directly with the Interactive Graphics Design System and the Data Management and Retrieval System. The program provides an efficient method for developing a network flow diagram. Performance requirements, operational rquirements, and design requirements are discussed along with sources and types of input and destination and types of output. Information processing functions and data base requirements are also covered.

ASDC Advances in the Utilization of Microservices and Hybrid Cloud Environments

NASA Astrophysics Data System (ADS)

Baskin, W. E.; Herbert, A.; Mazaika, A.; Walter, J.

2017-12-01

The Atmospheric Science Data Center (ASDC) is transitioning many of its software tools and applications to standalone microservices deployable in a hybrid cloud, offering benefits such as scalability and efficient environment management. This presentation features several projects the ASDC staff have implemented leveraging the OpenShift Container Application Platform and OpenStack Hybrid Cloud Environment focusing on key tools and techniques applied to: Earth Science data processing Spatial-Temporal metadata generation, validation, repair, and curation Archived Data discovery, visualization, and access

Design of a Novel Electro-hydraulic Drive Downhole Tractor

NASA Astrophysics Data System (ADS)

Fang, Delei; Shang, Jianzhong; Yang, Junhong; Wang, Zhuo; Wu, Wei

2018-02-01

In order to improve the traction ability and the work efficiency of downhole tractor in oil field, a novel electro-hydraulic drive downhole tractor was designed. The tractor’s supporting mechanism and moving mechanism were analyzed based on the tractor mechanical structure. Through the introduction of hydraulic system, the hydraulic drive mechanism and the implementation process were researched. Based on software, analysis of tractor hydraulic drive characteristic and movement performance were simulated, which provide theoretical basis for the development of tractor prototype.

Development of a demand assignment/TDMA system for international business satellite communications

NASA Astrophysics Data System (ADS)

Nohara, Mitsuo; Takeuchi, Yoshio; Takahata, Fumio; Hirata, Yasuo; Yamazaki, Yoshiharu

An experimental IBS (international business satellite) communications system based on a demand assignment and TDMA (time-division multiple-access) operation has been developed. The system utilizes a limited satellite resource efficiently and provides various kinds of ISDN services totally. A discussion is presented of the IBS network configurations suitable to international communications and describes the developed communications system from the viewpoint of the hardware and software implementation. The performance in terms of the transmission quality and call processing is also demonstrated.

Space Station: NASA's software development approach increases safety and cost risks. Report to the Chairman, Committee on Science, Space, and Technology, House of Representatives

NASA Astrophysics Data System (ADS)

1992-06-01

The House Committee on Science, Space, and Technology asked NASA to study software development issues for the space station. How well NASA has implemented key software engineering practices for the station was asked. Specifically, the objectives were to determine: (1) if independent verification and validation techniques are being used to ensure that critical software meets specified requirements and functions; (2) if NASA has incorporated software risk management techniques into program; (3) whether standards are in place that will prescribe a disciplined, uniform approach to software development; and (4) if software support tools will help, as intended, to maximize efficiency in developing and maintaining the software. To meet the objectives, NASA proceeded: (1) reviewing and analyzing software development objectives and strategies contained in NASA conference publications; (2) reviewing and analyzing NASA, other government, and industry guidelines for establishing good software development practices; (3) reviewing and analyzing technical proposals and contracts; (4) reviewing and analyzing software management plans, risk management plans, and program requirements; (4) reviewing and analyzing reports prepared by NASA and contractor officials that identified key issues and challenges facing the program; (5) obtaining expert opinions on what constitutes appropriate independent V-and-V and software risk management activities; (6) interviewing program officials at NASA headquarters in Washington, DC; at the Space Station Program Office in Reston, Virginia; and at the three work package centers; Johnson in Houston, Texas; Marshall in Huntsville, Alabama; and Lewis in Cleveland, Ohio; and (7) interviewing contractor officials doing work for NASA at Johnson and Marshall. The audit work was performed in accordance with generally accepted government auditing standards, between April 1991 and May 1992.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

PubMed

Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

2011-01-01

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

Advanced engineering software for in-space assembly and manned planetary spacecraft

NASA Technical Reports Server (NTRS)

Delaquil, Donald; Mah, Robert

1990-01-01

Meeting the objectives of the Lunar/Mars initiative to establish safe and cost-effective extraterrestrial bases requires an integrated software/hardware approach to operational definitions and systems implementation. This paper begins this process by taking a 'software-first' approach to systems design, for implementing specific mission scenarios in the domains of in-space assembly and operations of the manned Mars spacecraft. The technological barriers facing implementation of robust operational systems within these two domains are discussed, and preliminary software requirements and architectures that resolve these barriers are provided.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

Enhanced method of fast re-routing with load balancing in software-defined networks

NASA Astrophysics Data System (ADS)

Lemeshko, Oleksandr; Yeremenko, Oleksandra

2017-11-01

A two-level method of fast re-routing with load balancing in a software-defined network (SDN) is proposed. The novelty of the method consists, firstly, in the introduction of a two-level hierarchy of calculating the routing variables responsible for the formation of the primary and backup paths, and secondly, in ensuring a balanced load of the communication links of the network, which meets the requirements of the traffic engineering concept. The method provides implementation of link, node, path, and bandwidth protection schemes for fast re-routing in SDN. The separation in accordance with the interaction prediction principle along two hierarchical levels of the calculation functions of the primary (lower level) and backup (upper level) routes allowed to abandon the initial sufficiently large and nonlinear optimization problem by transiting to the iterative solution of linear optimization problems of half the dimension. The analysis of the proposed method confirmed its efficiency and effectiveness in terms of obtaining optimal solutions for ensuring balanced load of communication links and implementing the required network element protection schemes for fast re-routing in SDN.

Simplified Novel Application (SNApp) framework: a guide to developing and implementing second-generation mobile applications for behavioral health research.

PubMed

Fillo, Jennifer; Staplefoote-Boynton, B Lynette; Martinez, Angel; Sontag-Padilla, Lisa; Shadel, William G; Martino, Steven C; Setodji, Claude M; Meeker, Daniella; Scharf, Deborah

2016-12-01

Advances in mobile technology and mobile applications (apps) have opened up an exciting new frontier for behavioral health researchers, with a "second generation" of apps allowing for the simultaneous collection of multiple streams of data in real time. With this comes a host of technical decisions and ethical considerations unique to this evolving approach to research. Drawing on our experience developing a second-generation app for the simultaneous collection of text message, voice, and self-report data, we provide a framework for researchers interested in developing and using second-generation mobile apps to study health behaviors. Our Simplified Novel Application (SNApp) framework breaks the app development process into four phases: (1) information and resource gathering, (2) software and hardware decisions, (3) software development and testing, and (4) study start-up and implementation. At each phase, we address common challenges and ethical issues and make suggestions for effective and efficient app development. Our goal is to help researchers effectively balance priorities related to the function of the app with the realities of app development, human subjects issues, and project resource constraints.

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

NASA Astrophysics Data System (ADS)

Lippert, Ross A.; Predescu, Cristian; Ierardi, Douglas J.; Mackenzie, Kenneth M.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2013-10-01

In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the additional variables along with the particle positions and momenta at each time step. We present a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostat and barostat updates to be applied infrequently. Such infrequent updates provide a particularly substantial performance advantage for simulations parallelized across many computer processors, because thermostat and barostat updates typically require communication among all processors. Infrequent updates can also improve accuracy by alleviating certain sources of error associated with limited-precision arithmetic. In addition, separating the barostat, thermostat, and particle motion update steps reduces certain truncation errors, bringing the time-average pressure closer to its target value. Finally, this framework, which we have implemented on both general-purpose and special-purpose hardware, reduces software complexity and improves software modularity.

Using Compilers to Enhance Cryptographic Product Development

NASA Astrophysics Data System (ADS)

Bangerter, E.; Barbosa, M.; Bernstein, D.; Damgård, I.; Page, D.; Pagter, J. I.; Sadeghi, A.-R.; Sovio, S.

Developing high-quality software is hard in the general case, and it is significantly more challenging in the case of cryptographic software. A high degree of new skill and understanding must be learnt and applied without error to avoid vulnerability and inefficiency. This is often beyond the financial, manpower or intellectual resources avail-able. In this paper we present the motivation for the European funded CACE (Computer Aided Cryptography Engineering) project The main objective of CACE is to provide engineers (with limited or no expertise in cryptography) with a toolbox that allows them to generate robust and efficient implementations of cryptographic primitives. We also present some preliminary results already obtained in the early stages of this project, and discuss the relevance of the project as perceived by stakeholders in the mobile device arena.

Use of application containers and workflows for genomic data analysis.

PubMed

Schulz, Wade L; Durant, Thomas J S; Siddon, Alexa J; Torres, Richard

2016-01-01

The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

Description of the U.S. Geological Survey Geo Data Portal data integration framework

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Lucido, Jessica M.

2012-01-01

The U.S. Geological Survey has developed an open-standard data integration framework for working efficiently and effectively with large collections of climate and other geoscience data. A web interface accesses catalog datasets to find data services. Data resources can then be rendered for mapping and dataset metadata are derived directly from these web services. Algorithm configuration and information needed to retrieve data for processing are passed to a server where all large-volume data access and manipulation takes place. The data integration strategy described here was implemented by leveraging existing free and open source software. Details of the software used are omitted; rather, emphasis is placed on how open-standard web services and data encodings can be used in an architecture that integrates common geographic and atmospheric data.

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

Hammitzsch, Martin; Fritzsch, Bernadette; Reusser, Dominik; Brembs, Björn; Deinzer, Gernot; Loewe, Peter; Fenner, Martin; van Edig, Xenia; Bertelmann, Roland; Pampel, Heinz; Klump, Jens; Wächter, Joachim

2015-04-01

Scientific software has become an indispensable commodity for the production, processing and analysis of empirical data but also for modelling and simulation of complex processes. Software has a significant influence on the quality of research results. For strengthening the recognition of the academic performance of scientific software development, for increasing its visibility and for promoting the reproducibility of research results, concepts for the publication of scientific software have to be developed, tested, evaluated, and then transferred into operations. For this, the publication and citability of scientific software have to fulfil scientific criteria by means of defined processes and the use of persistent identifiers, similar to data publications. The SciForge project is addressing these challenges. Based on interviews a blueprint for a scientific software publishing platform and a systematic implementation plan has been designed. In addition, the potential of journals, software repositories and persistent identifiers have been evaluated to improve the publication and dissemination of reusable software solutions. It is important that procedures for publishing software as well as methods and tools for software engineering are reflected in the architecture of the platform, in order to improve the quality of the software and the results of research. In addition, it is necessary to work continuously on improving specific conditions that promote the adoption and sustainable utilization of scientific software publications. Among others, this would include policies for the development and publication of scientific software in the institutions but also policies for establishing the necessary competencies and skills of scientists and IT personnel. To implement the concepts developed in SciForge a combined bottom-up / top-down approach is considered that will be implemented in parallel in different scientific domains, e.g. in earth sciences, climate research and the life sciences. Based on the developed blueprints a scientific software publishing platform will be iteratively implemented, tested, and evaluated. Thus the platform should be developed continuously on the basis of gained experiences and results. The platform services will be extended one by one corresponding to the requirements of the communities. Thus the implemented platform for the publication of scientific software can be improved and stabilized incrementally as a tool with software, science, publishing, and user oriented features.

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.

Tough2{_}MP: A parallel version of TOUGH2

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

Zhang, Keni; Wu, Yu-Shu; Ding, Chris

2003-04-09

TOUGH2{_}MP is a massively parallel version of TOUGH2. It was developed for running on distributed-memory parallel computers to simulate large simulation problems that may not be solved by the standard, single-CPU TOUGH2 code. The new code implements an efficient massively parallel scheme, while preserving the full capacity and flexibility of the original TOUGH2 code. The new software uses the METIS software package for grid partitioning and AZTEC software package for linear-equation solving. The standard message-passing interface is adopted for communication among processors. Numerical performance of the current version code has been tested on CRAY-T3E and IBM RS/6000 SP platforms. Inmore » addition, the parallel code has been successfully applied to real field problems of multi-million-cell simulations for three-dimensional multiphase and multicomponent fluid and heat flow, as well as solute transport. In this paper, we will review the development of the TOUGH2{_}MP, and discuss the basic features, modules, and their applications.« less

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

LSDCat: Detection and cataloguing of emission-line sources in integral-field spectroscopy datacubes

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Wisotzki, Lutz

2017-06-01

We present a robust, efficient, and user-friendly algorithm for detecting faint emission-line sources in large integral-field spectroscopic datacubes together with the public release of the software package Line Source Detection and Cataloguing (LSDCat). LSDCat uses a three-dimensional matched filter approach, combined with thresholding in signal-to-noise, to build a catalogue of individual line detections. In a second pass, the detected lines are grouped into distinct objects, and positions, spatial extents, and fluxes of the detected lines are determined. LSDCat requires only a small number of input parameters, and we provide guidelines for choosing appropriate values. The software is coded in Python and capable of processing very large datacubes in a short time. We verify the implementation with a source insertion and recovery experiment utilising a real datacube taken with the MUSE instrument at the ESO Very Large Telescope. The LSDCat software is available for download at http://muse-vlt.eu/science/tools and via the Astrophysics Source Code Library at http://ascl.net/1612.002

Evaluating a digital ship design tool prototype: Designers' perceptions of novel ergonomics software.

PubMed

Mallam, Steven C; Lundh, Monica; MacKinnon, Scott N

2017-03-01

Computer-aided solutions are essential for naval architects to manage and optimize technical complexities when developing a ship's design. Although there are an array of software solutions aimed to optimize the human element in design, practical ergonomics methodologies and technological solutions have struggled to gain widespread application in ship design processes. This paper explores how a new ergonomics technology is perceived by naval architecture students using a mixed-methods framework. Thirteen Naval Architecture and Ocean Engineering Masters students participated in the study. Overall, results found participants perceived the software and its embedded ergonomics tools to benefit their design work, increasing their empathy and ability to understand the work environment and work demands end-users face. However, participant's questioned if ergonomics could be practically and efficiently implemented under real-world project constraints. This revealed underlying social biases and a fundamental lack of understanding in engineering postgraduate students regarding applied ergonomics in naval architecture. Copyright © 2016 Elsevier Ltd. All rights reserved.

RCTS: A flexible environment for sensor integration and control of robot systems; the distributed processing approach

NASA Technical Reports Server (NTRS)

Allard, R.; Mack, B.; Bayoumi, M. M.

1989-01-01

Most robot systems lack a suitable hardware and software environment for the efficient research of new control and sensing schemes. Typically, engineers and researchers need to be experts in control, sensing, programming, communication and robotics in order to implement, integrate and test new ideas in a robot system. In order to reduce this time, the Robot Controller Test Station (RCTS) has been developed. It uses a modular hardware and software architecture allowing easy physical and functional reconfiguration of a robot. This is accomplished by emphasizing four major design goals: flexibility, portability, ease of use, and ease of modification. An enhanced distributed processing version of RCTS is described. It features an expanded and more flexible communication system design. Distributed processing results in the availability of more local computing power and retains the low cost of microprocessors. A large number of possible communication, control and sensing schemes can therefore be easily introduced and tested, using the same basic software structure.

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NASA Technical Reports Server (NTRS)

Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

2006-01-01

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies.

PubMed

Pedretti, Alessandro; Mazzolari, Angelica; Vistoli, Giulio

2018-05-21

The manuscript describes WarpEngine, a novel platform implemented within the VEGA ZZ suite of software for performing distributed simulations both in local and wide area networks. Despite being tailored for structure-based virtual screening campaigns, WarpEngine possesses the required flexibility to carry out distributed calculations utilizing various pieces of software, which can be easily encapsulated within this platform without changing their source codes. WarpEngine takes advantages of all cheminformatics features implemented in the VEGA ZZ program as well as of its largely customizable scripting architecture thus allowing an efficient distribution of various time-demanding simulations. To offer an example of the WarpEngine potentials, the manuscript includes a set of virtual screening campaigns based on the ACE data set of the DUD-E collections using PLANTS as the docking application. Benchmarking analyses revealed a satisfactory linearity of the WarpEngine performances, the speed-up values being roughly equal to the number of utilized cores. Again, the computed scalability values emphasized that a vast majority (i.e., >90%) of the performed simulations benefit from the distributed platform presented here. WarpEngine can be freely downloaded along with the VEGA ZZ program at www.vegazz.net .

Multivariate and repeated measures (MRM): A new toolbox for dependent and multimodal group-level neuroimaging data

PubMed Central

McFarquhar, Martyn; McKie, Shane; Emsley, Richard; Suckling, John; Elliott, Rebecca; Williams, Stephen

2016-01-01

Repeated measurements and multimodal data are common in neuroimaging research. Despite this, conventional approaches to group level analysis ignore these repeated measurements in favour of multiple between-subject models using contrasts of interest. This approach has a number of drawbacks as certain designs and comparisons of interest are either not possible or complex to implement. Unfortunately, even when attempting to analyse group level data within a repeated-measures framework, the methods implemented in popular software packages make potentially unrealistic assumptions about the covariance structure across the brain. In this paper, we describe how this issue can be addressed in a simple and efficient manner using the multivariate form of the familiar general linear model (GLM), as implemented in a new MATLAB toolbox. This multivariate framework is discussed, paying particular attention to methods of inference by permutation. Comparisons with existing approaches and software packages for dependent group-level neuroimaging data are made. We also demonstrate how this method is easily adapted for dependency at the group level when multiple modalities of imaging are collected from the same individuals. Follow-up of these multimodal models using linear discriminant functions (LDA) is also discussed, with applications to future studies wishing to integrate multiple scanning techniques into investigating populations of interest. PMID:26921716

Implementation of a flexible and scalable particle-in-cell method for massively parallel computations in the mantle convection code ASPECT

NASA Astrophysics Data System (ADS)

Gassmöller, Rene; Bangerth, Wolfgang

2016-04-01

Particle-in-cell methods have a long history and many applications in geodynamic modelling of mantle convection, lithospheric deformation and crustal dynamics. They are primarily used to track material information, the strain a material has undergone, the pressure-temperature history a certain material region has experienced, or the amount of volatiles or partial melt present in a region. However, their efficient parallel implementation - in particular combined with adaptive finite-element meshes - is complicated due to the complex communication patterns and frequent reassignment of particles to cells. Consequently, many current scientific software packages accomplish this efficient implementation by specifically designing particle methods for a single purpose, like the advection of scalar material properties that do not evolve over time (e.g., for chemical heterogeneities). Design choices for particle integration, data storage, and parallel communication are then optimized for this single purpose, making the code relatively rigid to changing requirements. Here, we present the implementation of a flexible, scalable and efficient particle-in-cell method for massively parallel finite-element codes with adaptively changing meshes. Using a modular plugin structure, we allow maximum flexibility of the generation of particles, the carried tracer properties, the advection and output algorithms, and the projection of properties to the finite-element mesh. We present scaling tests ranging up to tens of thousands of cores and tens of billions of particles. Additionally, we discuss efficient load-balancing strategies for particles in adaptive meshes with their strengths and weaknesses, local particle-transfer between parallel subdomains utilizing existing communication patterns from the finite element mesh, and the use of established parallel output algorithms like the HDF5 library. Finally, we show some relevant particle application cases, compare our implementation to a modern advection-field approach, and demonstrate under which conditions which method is more efficient. We implemented the presented methods in ASPECT (aspect.dealii.org), a freely available open-source community code for geodynamic simulations. The structure of the particle code is highly modular, and segregated from the PDE solver, and can thus be easily transferred to other programs, or adapted for various application cases.

Capability Maturity Model (CMM) for Software Process Improvements

NASA Technical Reports Server (NTRS)

Ling, Robert Y.

2000-01-01

This slide presentation reviews the Avionic Systems Division's implementation of the Capability Maturity Model (CMM) for improvements in the software development process. The presentation reviews the process involved in implementing the model and the benefits of using CMM to improve the software development process.

Flight software requirements and design support system

NASA Technical Reports Server (NTRS)

Riddle, W. E.; Edwards, B.

1980-01-01

The desirability and feasibility of computer-augmented support for the pre-implementation activities occurring during the development of flight control software was investigated. The specific topics to be investigated were the capabilities to be included in a pre-implementation support system for flight control software system development, and the specification of a preliminary design for such a system. Further, the pre-implementation support system was to be characterized and specified under the constraints that it: (1) support both description and assessment of flight control software requirements definitions and design specification; (2) account for known software description and assessment techniques; (3) be compatible with existing and planned NASA flight control software development support system; and (4) does not impose, but may encourage, specific development technologies. An overview of the results is given.

Software Defined Radio with Parallelized Software Architecture

NASA Technical Reports Server (NTRS)

Heckler, Greg

2013-01-01

This software implements software-defined radio procession over multicore, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to approx.50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.

Software Defined Radio with Parallelized Software Architecture

NASA Technical Reports Server (NTRS)

Heckler, Greg

2013-01-01

This software implements software-defined radio procession over multi-core, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to .50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.

ELIPS: Toward a Sensor Fusion Processor on a Chip

NASA Technical Reports Server (NTRS)

Daud, Taher; Stoica, Adrian; Tyson, Thomas; Li, Wei-te; Fabunmi, James

1998-01-01

The paper presents the concept and initial tests from the hardware implementation of a low-power, high-speed reconfigurable sensor fusion processor. The Extended Logic Intelligent Processing System (ELIPS) processor is developed to seamlessly combine rule-based systems, fuzzy logic, and neural networks to achieve parallel fusion of sensor in compact low power VLSI. The first demonstration of the ELIPS concept targets interceptor functionality; other applications, mainly in robotics and autonomous systems are considered for the future. The main assumption behind ELIPS is that fuzzy, rule-based and neural forms of computation can serve as the main primitives of an "intelligent" processor. Thus, in the same way classic processors are designed to optimize the hardware implementation of a set of fundamental operations, ELIPS is developed as an efficient implementation of computational intelligence primitives, and relies on a set of fuzzy set, fuzzy inference and neural modules, built in programmable analog hardware. The hardware programmability allows the processor to reconfigure into different machines, taking the most efficient hardware implementation during each phase of information processing. Following software demonstrations on several interceptor data, three important ELIPS building blocks (a fuzzy set preprocessor, a rule-based fuzzy system and a neural network) have been fabricated in analog VLSI hardware and demonstrated microsecond-processing times.

High assurance SPIRAL

NASA Astrophysics Data System (ADS)

Franchetti, Franz; Sandryhaila, Aliaksei; Johnson, Jeremy R.

2014-06-01

In this paper we introduce High Assurance SPIRAL to solve the last mile problem for the synthesis of high assurance implementations of controllers for vehicular systems that are executed in today's and future embedded and high performance embedded system processors. High Assurance SPIRAL is a scalable methodology to translate a high level specification of a high assurance controller into a highly resource-efficient, platform-adapted, verified control software implementation for a given platform in a language like C or C++. High Assurance SPIRAL proves that the implementation is equivalent to the specification written in the control engineer's domain language. Our approach scales to problems involving floating-point calculations and provides highly optimized synthesized code. It is possible to estimate the available headroom to enable assurance/performance trade-offs under real-time constraints, and enables the synthesis of multiple implementation variants to make attacks harder. At the core of High Assurance SPIRAL is the Hybrid Control Operator Language (HCOL) that leverages advanced mathematical constructs expressing the controller specification to provide high quality translation capabilities. Combined with a verified/certified compiler, High Assurance SPIRAL provides a comprehensive complete solution to the efficient synthesis of verifiable high assurance controllers. We demonstrate High Assurance SPIRALs capability by co-synthesizing proofs and implementations for attack detection and sensor spoofing algorithms and deploy the code as ROS nodes on the Landshark unmanned ground vehicle and on a Synthetic Car in a real-time simulator.

A Custom Robotic System for Inspecting HEPA Filters in the Payload Changeout Room at the NASA Kennedy Space Center

NASA Technical Reports Server (NTRS)

Spencer, James E., Jr.; Looney, Joe

1994-01-01

In this paper, the prime objective is to describe a custom 4-dof (degree-of-freedom) robotic arm capable of autonomously or telerobotically performing systematic HEPA filter inspection and certification in the Shuttle Launch Pad Payload Changeout Rooms (PCR's) on pads A and B at the Kennedy Space Center, Florida. This HEPA filter inspection robot (HFIR) has been designed to be easily deployable and is equipped with the necessary sensory devices, control hardware, software and man-machine interfaces needed to implement HEPA filter inspection reliably and efficiently without damaging the filters or colliding with existing PCR structures or filters. The main purpose of the HFIR is to implement an automated positioning system to move special inspection sensors in pre-defined or manual patterns for the purpose of verifying filter integrity and efficiency. This will ultimately relieve NASA Payload Operations from significant problems associated with time, cost and personnel safety, impacts realized during non-automated PCR HFIR filter certification.

Usability evaluation of user interface of thesis title review system

NASA Astrophysics Data System (ADS)

Tri, Y.; Erna, A.; Gellysa, U.

2018-03-01

Presentation of programs with user interface that can be accessed online through the website of course greatly provide user benefits. User can easily access the program they need. There are usability values that serve as a benchmark for the success of a user accessible program, ie efficiency, effectiveness, and convenience. These usability values also determine the development of the program for the better use. Therefore, on the review title thesis program that will be implemented in STT Dumai was measured usability evaluation. It aims to see which sides are not yet perfect and need to be improved to improve the performance and utilization of the program. Usability evaluation was measured by using smartPLS software. Database used was the result of respondent questionnaires that include questions about the experience when they used program. The result of a review of thesis title program implemented in STT Dumai has an efficiency value of 22.615, the effectiveness of 20.612, and satisfaction of 33.177.

The U.S./IAEA Workshop on Software Sustainability for Safeguards Instrumentation: Report to the NNSA DOE Office of International Nuclear Safeguards (NA-241)

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

Pepper, Susan E.; Pickett, Chris A.; Queirolo, Al

The U.S Department of Energy (DOE) National Nuclear Security Administration (NNSA) Next Generation Safeguards Initiative (NGSI) and the International Atomic Energy Agency (IAEA) convened a workshop on Software Sustainability for Safeguards Instrumentation in Vienna, Austria, May 6-8, 2014. Safeguards instrumentation software must be sustained in a changing environment to ensure existing instruments can continue to perform as designed, with improved security. The approaches to the development and maintenance of instrument software used in the past may not be the best model for the future and, therefore, the organizers’ goal was to investigate these past approaches and to determine an optimalmore » path forward. The purpose of this report is to provide input for the DOE NNSA Office of International Nuclear Safeguards (NA-241) and other stakeholders that can be utilized when making decisions related to the development and maintenance of software used in the implementation of international nuclear safeguards. For example, this guidance can be used when determining whether to fund the development, upgrade, or replacement of a particular software product. The report identifies the challenges related to sustaining software, and makes recommendations for addressing these challenges, supported by summaries and detailed notes from the workshop discussions. In addition the authors provide a set of recommendations for institutionalizing software sustainability practices in the safeguards community. The term “software sustainability” was defined for this workshop as ensuring that safeguards instrument software and algorithm functionality can be maintained efficiently throughout the instrument lifecycle, without interruption and providing the ability to continue to improve that software as needs arise.« less

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

PubMed

Abella, Jayvee R; Cheng, Sara Y; Wang, Qiantao; Yang, Wei; Ren, Pengyu

2014-07-08

The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.

Impedance matching wireless power transmission system for biomedical devices.

PubMed

Lum, Kin Yun; Lindén, Maria; Tan, Tian Swee

2015-01-01

For medical application, the efficiency and transmission distance of the wireless power transfer (WPT) are always the main concern. Research has been showing that the impedance matching is one of the critical factors for dealing with the problem. However, there is not much work performed taking both the source and load sides into consideration. Both sides matching is crucial in achieving an optimum overall performance, and the present work proposes a circuit model analysis for design and implementation. The proposed technique was validated against experiment and software simulation. Result was showing an improvement in transmission distance up to 6 times, and efficiency at this transmission distance had been improved up to 7 times as compared to the impedance mismatch system. The system had demonstrated a near-constant transfer efficiency for an operating range of 2cm-12cm.

Intelligent Software Agents: Sensor Integration and Response

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

Kulesz, James J; Lee, Ronald W

2013-01-01

Abstract In a post Macondo world the buzzwords are Integrity Management and Incident Response Management. The twin processes are not new but the opportunity to link the two is novel. Intelligent software agents can be used with sensor networks in distributed and centralized computing systems to enhance real-time monitoring of system integrity as well as manage the follow-on incident response to changing, and potentially hazardous, environmental conditions. The software components are embedded at the sensor network nodes in surveillance systems used for monitoring unusual events. When an event occurs, the software agents establish a new concept of operation at themore » sensing node, post the event status to a blackboard for software agents at other nodes to see , and then react quickly and efficiently to monitor the scale of the event. The technology addresses a current challenge in sensor networks that prevents a rapid and efficient response when a sensor measurement indicates that an event has occurred. By using intelligent software agents - which can be stationary or mobile, interact socially, and adapt to changing situations - the technology offers features that are particularly important when systems need to adapt to active circumstances. For example, when a release is detected, the local software agent collaborates with other agents at the node to exercise the appropriate operation, such as: targeted detection, increased detection frequency, decreased detection frequency for other non-alarming sensors, and determination of environmental conditions so that adjacent nodes can be informed that an event is occurring and when it will arrive. The software agents at the nodes can also post the data in a targeted manner, so that agents at other nodes and the command center can exercise appropriate operations to recalibrate the overall sensor network and associated intelligence systems. The paper describes the concepts and provides examples of real-world implementations including the Threat Detection and Analysis System (TDAS) at the International Port of Memphis and the Biological Warning and Incident Characterization System (BWIC) Environmental Monitoring (EM) Component. Technologies developed for these 24/7 operational systems have applications for improved real-time system integrity awareness as well as provide incident response (as needed) for production and field applications.« less

Exploring Cognition Using Software Defined Radios for NASA Missions

NASA Technical Reports Server (NTRS)

Mortensen, Dale J.; Reinhart, Richard C.

2016-01-01

NASA missions typically operate using a communication infrastructure that requires significant schedule planning with limited flexibility when the needs of the mission change. Parameters such as modulation, coding scheme, frequency, and data rate are fixed for the life of the mission. This is due to antiquated hardware and software for both the space and ground assets and a very complex set of mission profiles. Automated techniques in place by commercial telecommunication companies are being explored by NASA to determine their usability by NASA to reduce cost and increase science return. Adding cognition the ability to learn from past decisions and adjust behavior is also being investigated. Software Defined Radios are an ideal way to implement cognitive concepts. Cognition can be considered in many different aspects of the communication system. Radio functions, such as frequency, modulation, data rate, coding and filters can be adjusted based on measurements of signal degradation. Data delivery mechanisms and route changes based on past successes and failures can be made to more efficiently deliver the data to the end user. Automated antenna pointing can be added to improve gain, coverage, or adjust the target. Scheduling improvements and automation to reduce the dependence on humans provide more flexible capabilities. The Cognitive Communications project, funded by the Space Communication and Navigation Program, is exploring these concepts and using the SCaN Testbed on board the International Space Station to implement them as they evolve. The SCaN Testbed contains three Software Defined Radios and a flight computer. These four computing platforms, along with a tracking antenna system and the supporting ground infrastructure, will be used to implement various concepts in a system similar to those used by missions. Multiple universities and SBIR companies are supporting this investigation. This paper will describe the cognitive system ideas under consideration and the plan for implementing them on platforms, including the SCaN Testbed. Discussions in the paper will include how these concepts might be used to reduce cost and improve the science return for NASA missions.

The MeqTrees software system and its use for third-generation calibration of radio interferometers

NASA Astrophysics Data System (ADS)

Noordam, J. E.; Smirnov, O. M.

2010-12-01

Context. The formulation of the radio interferometer measurement equation (RIME) for a generic radio telescope by Hamaker et al. has provided us with an elegant mathematical apparatus for better understanding, simulation and calibration of existing and future instruments. The calibration of the new radio telescopes (LOFAR, SKA) would be unthinkable without the RIME formalism, and new software to exploit it. Aims: The MeqTrees software system is designed to implement numerical models, and to solve for arbitrary subsets of their parameters. It may be applied to many problems, but was originally geared towards implementing Measurement Equations in radio astronomy for the purposes of simulation and calibration. The technical goal of MeqTrees is to provide a tool for rapid implementation of such models, while offering performance comparable to hand-written code. We are also pursuing the wider goal of increasing the rate of evolution of radio astronomical software, by offering a tool that facilitates rapid experimentation, and exchange of ideas (and scripts). Methods: MeqTrees is implemented as a Python-based front-end called the meqbrowser, and an efficient (C++-based) computational back-end called the meqserver. Numerical models are defined on the front-end via a Python-based Tree Definition Language (TDL), then rapidly executed on the back-end. The use of TDL facilitates an extremely short turn-around time (hours rather than weeks or months) for experimentation with new ideas. This is also helped by unprecedented visualization capabilities for all final and intermediate results. A flexible data model and a number of important optimizations in the back-end ensures that the numerical performance is comparable to that of hand-written code. Results: MeqTrees is already widely used as the simulation tool for new instruments (LOFAR, SKA) and technologies (focal plane arrays). It has demonstrated that it can achieve a noise-limited dynamic range in excess of a million, on WSRT data. It is the only package that is specifically designed to handle what we propose to call third-generation calibration (3GC), which is needed for the new generation of giant radio telescopes, but can also improve the calibration of existing instruments.

mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets*

PubMed Central

Wilhelm, Mathias; Kirchner, Marc; Steen, Judith A. J.; Steen, Hanno

2012-01-01

Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to ∼54% and increases linear read and write speeds ∼3–4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5. PMID:21960719

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.

PubMed

Rosenberg, David M; Horn, Charles C

2016-08-01

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus-a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software-an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research. Copyright © 2016 the American Physiological Society.

A Methodology and Implementation for Annotating Digital Images for Context-appropriate Use in an Academic Health Care Environment

PubMed Central

Goede, Patricia A.; Lauman, Jason R.; Cochella, Christopher; Katzman, Gregory L.; Morton, David A.; Albertine, Kurt H.

2004-01-01

Use of digital medical images has become common over the last several years, coincident with the release of inexpensive, mega-pixel quality digital cameras and the transition to digital radiology operation by hospitals. One problem that clinicians, medical educators, and basic scientists encounter when handling images is the difficulty of using business and graphic arts commercial-off-the-shelf (COTS) software in multicontext authoring and interactive teaching environments. The authors investigated and developed software-supported methodologies to help clinicians, medical educators, and basic scientists become more efficient and effective in their digital imaging environments. The software that the authors developed provides the ability to annotate images based on a multispecialty methodology for annotation and visual knowledge representation. This annotation methodology is designed by consensus, with contributions from the authors and physicians, medical educators, and basic scientists in the Departments of Radiology, Neurobiology and Anatomy, Dermatology, and Ophthalmology at the University of Utah. The annotation methodology functions as a foundation for creating, using, reusing, and extending dynamic annotations in a context-appropriate, interactive digital environment. The annotation methodology supports the authoring process as well as output and presentation mechanisms. The annotation methodology is the foundation for a Windows implementation that allows annotated elements to be represented as structured eXtensible Markup Language and stored separate from the image(s). PMID:14527971

Selected Systems Engineering Process Deficiencies and Their Consequences

NASA Technical Reports Server (NTRS)

Thomas, Lawrence Dale

2006-01-01

The systems engineering process is well established and well understood. While this statement could be argued in the light of the many systems engineering guidelines and that have been developed, comparative review of these respective descriptions reveal that they differ primarily in the number of discrete steps or other nuances, and are at their core essentially common. Likewise, the systems engineering textbooks differ primarily in the context for application of systems engineering or in the utilization of evolved tools and techniques, not in the basic method. Thus, failures in systems engineering cannot credibly be attributed to implementation of the wrong systems engineering process among alternatives. However, numerous systems failures can be attributed to deficient implementation of the systems engineering process. What may clearly be perceived as a system engineering deficiency in retrospect can appear to be a well considered system engineering efficiency in real time - an efficiency taken to reduce cost or meet a schedule, or more often both. Typically these efficiencies are grounded on apparently solid rationale, such as reuse of heritage hardware or software. Over time, unintended consequences of a systems engineering process deficiency may begin to be realized, and unfortunately often the consequence is system failure. This paper describes several actual cases of system failures that resulted from deficiencies in their systems engineering process implementation, including the Ariane 5 and the Hubble Space Telescope.

Selected systems engineering process deficiencies and their consequences

NASA Astrophysics Data System (ADS)

Thomas, L. Dale

2007-06-01

The systems engineering process is well established and well understood. While this statement could be argued in the light of the many systems engineering guidelines and that have been developed, comparative review of these respective descriptions reveal that they differ primarily in the number of discrete steps or other nuances, and are at their core essentially common. Likewise, the systems engineering textbooks differ primarily in the context for application of systems engineering or in the utilization of evolved tools and techniques, not in the basic method. Thus, failures in systems engineering cannot credibly be attributed to implementation of the wrong systems engineering process among alternatives. However, numerous system failures can be attributed to deficient implementation of the systems engineering process. What may clearly be perceived as a systems engineering deficiency in retrospect can appear to be a well considered system engineering efficiency in real time—an efficiency taken to reduce cost or meet a schedule, or more often both. Typically these efficiencies are grounded on apparently solid rationale, such as reuse of heritage hardware or software. Over time, unintended consequences of a systems engineering process deficiency may begin to be realized, and unfortunately often the consequence is systems failure. This paper describes several actual cases of system failures that resulted from deficiencies in their systems engineering process implementation, including the Ariane 5 and the Hubble Space Telescope.

Simulink/PARS Integration Support

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

Vacaliuc, B.; Nakhaee, N.

2013-12-18

The state of the art for signal processor hardware has far out-paced the development tools for placing applications on that hardware. In addition, signal processors are available in a variety of architectures, each uniquely capable of handling specific types of signal processing efficiently. With these processors becoming smaller and demanding less power, it has become possible to group multiple processors, a heterogeneous set of processors, into single systems. Different portions of the desired problem set can be assigned to different processor types as appropriate. As software development tools do not keep pace with these processors, especially when multiple processors ofmore » different types are used, a method is needed to enable software code portability among multiple processors and multiple types of processors along with their respective software environments. Sundance DSP, Inc. has developed a software toolkit called “PARS”, whose objective is to provide a framework that uses suites of tools provided by different vendors, along with modeling tools and a real time operating system, to build an application that spans different processor types. The software language used to express the behavior of the system is a very high level modeling language, “Simulink”, a MathWorks product. ORNL has used this toolkit to effectively implement several deliverables. This CRADA describes this collaboration between ORNL and Sundance DSP, Inc.« less

The GenABEL Project for statistical genomics.

PubMed

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

Project SYNERGY: Software Support for Underprepared Students. Software Implementation Report.

ERIC Educational Resources Information Center

Anandam, Kamala; And Others

Miami-Dade Community College's (MDCC's) implementation and assessment of computer software as a part of Project SYNERGY, a multi-institutional project funded by the International Business Machines (IBM) Corporation designed to seek technological solutions for helping students underprepared in reading, writing and mathematics, is described in this…

Genome-wide regression and prediction with the BGLR statistical package.

PubMed

Pérez, Paulino; de los Campos, Gustavo

2014-10-01

Many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). Implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using Bayesian methods. This approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. The BGLR R-package implements a large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (Bayesian reproducing kernel Hilbert spaces regressions, RKHS). The software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. The response can be continuous (censored or not) or categorical (either binary or ordinal). The algorithm is based on a Gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled C and Fortran routines. In this article we describe the methods implemented in BGLR, present examples of the use of the package, and discuss practical issues emerging in real-data analysis. Copyright © 2014 by the Genetics Society of America.

Efficient Open Source Lidar for Desktop Users

NASA Astrophysics Data System (ADS)

Flanagan, Jacob P.

Lidar --- Light Detection and Ranging --- is a remote sensing technology that utilizes a device similar to a rangefinder to determine a distance to a target. A laser pulse is shot at an object and the time it takes for the pulse to return in measured. The distance to the object is easily calculated using the speed property of light. For lidar, this laser is moved (primarily in a rotational movement usually accompanied by a translational movement) and records the distances to objects several thousands of times per second. From this, a 3 dimensional structure can be procured in the form of a point cloud. A point cloud is a collection of 3 dimensional points with at least an x, a y and a z attribute. These 3 attributes represent the position of a single point in 3 dimensional space. Other attributes can be associated with the points that include properties such as the intensity of the return pulse, the color of the target or even the time the point was recorded. Another very useful, post processed attribute is point classification where a point is associated with the type of object the point represents (i.e. ground.). Lidar has gained popularity and advancements in the technology has made its collection easier and cheaper creating larger and denser datasets. The need to handle this data in a more efficiently manner has become a necessity; The processing, visualizing or even simply loading lidar can be computationally intensive due to its very large size. Standard remote sensing and geographical information systems (GIS) software (ENVI, ArcGIS, etc.) was not originally built for optimized point cloud processing and its implementation is an afterthought and therefore inefficient. Newer, more optimized software for point cloud processing (QTModeler, TopoDOT, etc.) usually lack more advanced processing tools, requires higher end computers and are very costly. Existing open source lidar approaches the loading and processing of lidar in an iterative fashion that requires implementing batch coding and processing time that could take months for a standard lidar dataset. This project attempts to build a software with the best approach for creating, importing and exporting, manipulating and processing lidar, especially in the environmental field. Development of this software is described in 3 sections - (1) explanation of the search methods for efficiently extracting the "area of interest" (AOI) data from disk (file space), (2) using file space (for storage), budgeting memory space (for efficient processing) and moving between the two, and (3) method development for creating lidar products (usually raster based) used in environmental modeling and analysis (i.e.: hydrology feature extraction, geomorphological studies, ecology modeling, etc.).

A Prototype for the Support of Integrated Software Process Development and Improvement

NASA Astrophysics Data System (ADS)

Porrawatpreyakorn, Nalinpat; Quirchmayr, Gerald; Chutimaskul, Wichian

An efficient software development process is one of key success factors for quality software. Not only can the appropriate establishment but also the continuous improvement of integrated project management and of the software development process result in efficiency. This paper hence proposes a software process maintenance framework which consists of two core components: an integrated PMBOK-Scrum model describing how to establish a comprehensive set of project management and software engineering processes and a software development maturity model advocating software process improvement. Besides, a prototype tool to support the framework is introduced.

Improved treatment of exact exchange in Quantum ESPRESSO

DOE PAGES

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre; ...

2017-01-18

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

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

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace.

PubMed

Biczok, R; Bozsoky, P; Eisenmann, P; Ernst, J; Ribizel, T; Scholz, F; Trefzer, A; Weber, F; Hamann, M; Stamatakis, A

2018-05-08

The presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace. In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous 3rd party python implementation. The source codes are available under GNU GPL at https://github.com/terraphast. Alexandros.Stamatakis@h-its.org. Supplementary data are available at Bioinformatics online.

Scalable Implementation of Finite Elements by NASA _ Implicit (ScIFEi)

NASA Technical Reports Server (NTRS)

Warner, James E.; Bomarito, Geoffrey F.; Heber, Gerd; Hochhalter, Jacob D.

2016-01-01

Scalable Implementation of Finite Elements by NASA (ScIFEN) is a parallel finite element analysis code written in C++. ScIFEN is designed to provide scalable solutions to computational mechanics problems. It supports a variety of finite element types, nonlinear material models, and boundary conditions. This report provides an overview of ScIFEi (\\Sci-Fi"), the implicit solid mechanics driver within ScIFEN. A description of ScIFEi's capabilities is provided, including an overview of the tools and features that accompany the software as well as a description of the input and output le formats. Results from several problems are included, demonstrating the efficiency and scalability of ScIFEi by comparing to finite element analysis using a commercial code.

FAILSAFE Health Management for Embedded Systems

NASA Technical Reports Server (NTRS)

Horvath, Gregory A.; Wagner, David A.; Wen, Hui Ying; Barry, Matthew

2010-01-01

The FAILSAFE project is developing concepts and prototype implementations for software health management in mission- critical, real-time embedded systems. The project unites features of the industry-standard ARINC 653 Avionics Application Software Standard Interface and JPL s Mission Data System (MDS) technology (see figure). The ARINC 653 standard establishes requirements for the services provided by partitioned, real-time operating systems. The MDS technology provides a state analysis method, canonical architecture, and software framework that facilitates the design and implementation of software-intensive complex systems. The MDS technology has been used to provide the health management function for an ARINC 653 application implementation. In particular, the focus is on showing how this combination enables reasoning about, and recovering from, application software problems.

Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data.

PubMed

Schäfer, Christian; Schmidt, Alexander H; Sauter, Jürgen

2017-05-30

Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records. To meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data. Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.

A New Method for Control of the Efficiency of Gear Reducers

NASA Astrophysics Data System (ADS)

E Kozlov, K.; Egorov, A. V.; Belogusev, V. N.

2017-04-01

This article proposes a new method to control the energy efficiency of gear reducers. The method allows evaluating the friction losses in a drive motor, drive motor bearing assemblies, and toothing both at the stage of control of the finished product and in the course of its operation, maintenance, and repair. The proposed method, unlike currently used methods for control of the efficiency of gear reducers, allows determining the friction losses without the use of strain measurement, which requires calibration of tensometric sensors and expensive equipment. The method is based on the idea of invariability of mechanical characteristics of the induction motor at constant voltage, resistance of windings, and mains frequency, regardless of the driven inertia mass. This paper presents experimental results which verify the theoretical predictions. The proposed method can be implemented in the procedure of acceptance test at the companies that manufacture gear reducers, thereby assess their effectiveness and the level of degradation processes that significantly affect the service life of the research object. The method can be implemented both with universal and with specialized hardware and software complexes. At that, both an increment of the inertia moment and acceleration time of a gear reducer may serve as a performance criterion.

75 FR 30010 - Improving Market and Planning Efficiency Through Improved Software; Notice of Agenda and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-28

... Market and Planning Efficiency Through Improved Software; Notice of Agenda and Procedures for Staff... conference to be held on June 2, 2010 and June 3, 2010, to discuss issues related to unit commitment software... Unit Commitment Software Federal Energy Regulatory Commission June 2, 2010 8 a.m Richard O'Neill, FERC...

75 FR 30387 - Improving Market and Planning Efficiency Through Improved Software; Notice of Agenda and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-01

... Market and Planning Efficiency Through Improved Software; Notice of Agenda and Procedures for Staff... planning models and software. The technical conference will be held from 8 a.m. to 5:30 p.m. (EDT) on June.... Agenda for AD10-12 Staff Technical Conference on Planning Models and Software Federal Energy Regulatory...

Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites.

PubMed

Dickerson, Jane A; Schmeling, Michael; Hoofnagle, Andrew N; Hoffman, Noah G

2013-01-16

Mass spectrometry provides a powerful platform for performing quantitative, multiplexed assays in the clinical laboratory, but at the cost of increased complexity of analysis and quality assurance calculations compared to other methodologies. Here we describe the design and implementation of a software application that performs quality control calculations for a complex, multiplexed, mass spectrometric analysis of opioids and opioid metabolites. The development and implementation of this application improved our data analysis and quality assurance processes in several ways. First, use of the software significantly improved the procedural consistency for performing quality control calculations. Second, it reduced the amount of time technologists spent preparing and reviewing the data, saving on average over four hours per run, and in some cases improving turnaround time by a day. Third, it provides a mechanism for coupling procedural and software changes with the results of each analysis. We describe several key details of the implementation including the use of version control software and automated unit tests. These generally useful software engineering principles should be considered for any software development project in the clinical lab. Copyright © 2012 Elsevier B.V. All rights reserved.

Permanent magnet synchronous motor servo system control based on μC/OS

NASA Astrophysics Data System (ADS)

Shi, Chongyang; Chen, Kele; Chen, Xinglong

2015-10-01

When Opto-Electronic Tracking system operates in complex environments, every subsystem must operate efficiently and stably. As a important part of Opto-Electronic Tracking system, the performance of PMSM(Permanent Magnet Synchronous Motor) servo system affects the Opto-Electronic Tracking system's accuracy and speed greatly[1][2]. This paper applied embedded real-time operating system μC/OS to the control of PMSM servo system, implemented SVPWM(Space Vector Pulse Width Modulation) algorithm in PMSM servo system, optimized the stability of PMSM servo system. Pointing on the characteristics of the Opto-Electronic Tracking system, this paper expanded μC/OS with software redundancy processes, remote debugging and upgrading. As a result, the Opto- Electronic Tracking system performs efficiently and stably.

DEVELOPMENTS IN GRworkbench

NASA Astrophysics Data System (ADS)

Moylan, Andrew; Scott, Susan M.; Searle, Anthony C.

2006-02-01

The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, GRworkbench has been significantly extended to facilitate numerical experimentation in analytically-defined space-times. The numerical differential geometric engine has been rewritten using functional programming techniques, enabling objects which are normally defined as functions in the formalism of differential geometry and General Relativity to be directly represented as function variables in the C++ code of GRworkbench. The new functional differential geometric engine allows for more accurate and efficient visualisation of objects in space-times and makes new, efficient computational techniques available. Motivated by the desire to investigate a recent scientific claim using GRworkbench, new tools for numerical experimentation have been implemented, allowing for the simulation of complex physical situations.

Using Decision Procedures to Build Domain-Specific Deductive Synthesis Systems

NASA Technical Reports Server (NTRS)

VanBaalen, Jeffrey; Roach, Steven; Lau, Sonie (Technical Monitor)

1998-01-01

This paper describes a class of decision procedures that we have found useful for efficient, domain-specific deductive synthesis. These procedures are called closure-based ground literal satisfiability procedures. We argue that this is a large and interesting class of procedures and show how to interface these procedures to a theorem prover for efficient deductive synthesis. Finally, we describe some results we have observed from our implementation. Amphion/NAIF is a domain-specific, high-assurance software synthesis system. It takes an abstract specification of a problem in solar system mechanics, such as 'when will a signal sent from the Cassini spacecraft to Earth be blocked by the planet Saturn?', and automatically synthesizes a FORTRAN program to solve it.

Neural network-based retrieval from software reuse repositories

NASA Technical Reports Server (NTRS)

Eichmann, David A.; Srinivas, Kankanahalli

1992-01-01

A significant hurdle confronts the software reuser attempting to select candidate components from a software repository - discriminating between those components without resorting to inspection of the implementation(s). We outline an approach to this problem based upon neural networks which avoids requiring the repository administrators to define a conceptual closeness graph for the classification vocabulary.

Enhancing Architecture-Implementation Conformance with Change Management and Support for Behavioral Mapping

ERIC Educational Resources Information Center

Zheng, Yongjie

2012-01-01

Software architecture plays an increasingly important role in complex software development. Its further application, however, is challenged by the fact that software architecture, over time, is often found not conformant to its implementation. This is usually caused by frequent development changes made to both artifacts. Against this background,…

Extensive Evaluation of Using a Game Project in a Software Architecture Course

ERIC Educational Resources Information Center

Wang, Alf Inge

2011-01-01

This article describes an extensive evaluation of introducing a game project to a software architecture course. In this project, university students have to construct and design a type of software architecture, evaluate the architecture, implement an application based on the architecture, and test this implementation. In previous years, the domain…

Mitigating Motion Base Safety Issues: The NASA LaRC CMF Implementation

NASA Technical Reports Server (NTRS)

Bryant, Richard B., Jr.; Grupton, Lawrence E.; Martinez, Debbie; Carrelli, David J.

2005-01-01

The NASA Langley Research Center (LaRC), Cockpit Motion Facility (CMF) motion base design has taken advantage of inherent hydraulic characteristics to implement safety features using hardware solutions only. Motion system safety has always been a concern and its implementation is addressed differently by each organization. Some approaches rely heavily on software safety features. Software which performs safety functions is subject to more scrutiny making its approval, modification, and development time consuming and expensive. The NASA LaRC's CMF motion system is used for research and, as such, requires that the software be updated or modified frequently. The CMF's customers need the ability to update the simulation software frequently without the associated cost incurred with safety critical software. This paper describes the CMF engineering team's approach to achieving motion base safety by designing and implementing all safety features in hardware, resulting in applications software (including motion cueing and actuator dynamic control) being completely independent of the safety devices. This allows the CMF safety systems to remain intact and unaffected by frequent research system modifications.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

PubMed

Chen, Haochuan; Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

2018-06-18

Extended adaptive biasing force (eABF), a collective variable (CV)-based importance-sampling algorithm, has proven to be very robust and efficient compared with the original ABF algorithm. Its implementation in Colvars, a software addition to molecular dynamics (MD) engines, is, however, currently limited to NAMD and LAMMPS. To broaden the scope of eABF and its variants, like its generalized form (egABF), and make them available to other MD engines, e.g., GROMACS, AMBER, CP2K, and openMM, we present a PLUMED-based implementation, called extended-Lagrangian free energy calculation (ELF). This implementation can be used as a stand-alone gradient estimator for other CV-based sampling algorithms, such as temperature-accelerated MD (TAMD) and extended-Lagrangian metadynamics (MtD). ELF provides the end user with a convenient framework to help select the best-suited importance-sampling algorithm for a given application without any commitment to a particular MD engine.

Test Methods for Robot Agility in Manufacturing.

PubMed

Downs, Anthony; Harrison, William; Schlenoff, Craig

2016-01-01

The paper aims to define and describe test methods and metrics to assess industrial robot system agility in both simulation and in reality. The paper describes test methods and associated quantitative and qualitative metrics for assessing robot system efficiency and effectiveness which can then be used for the assessment of system agility. The paper describes how the test methods were implemented in a simulation environment and real world environment. It also shows how the metrics are measured and assessed as they would be in a future competition. The test methods described in this paper will push forward the state of the art in software agility for manufacturing robots, allowing small and medium manufacturers to better utilize robotic systems. The paper fulfills the identified need for standard test methods to measure and allow for improvement in software agility for manufacturing robots.

Use of application containers and workflows for genomic data analysis

PubMed Central

Schulz, Wade L.; Durant, Thomas J. S.; Siddon, Alexa J.; Torres, Richard

2016-01-01

Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia. PMID:28163975

ANNIE - INTERACTIVE PROCESSING OF DATA BASES FOR HYDROLOGIC MODELS.

USGS Publications Warehouse

Lumb, Alan M.; Kittle, John L.

1985-01-01

ANNIE is a data storage and retrieval system that was developed to reduce the time and effort required to calibrate, verify, and apply watershed models that continuously simulate water quantity and quality. Watershed models have three categories of input: parameters to describe segments of a drainage area, linkage of the segments, and time-series data. Additional goals for ANNIE include the development of software that is easily implemented on minicomputers and some microcomputers and software that has no special requirements for interactive display terminals. Another goal is for the user interaction to be based on the experience of the user so that ANNIE is helpful to the inexperienced user and yet efficient and brief for the experienced user. Finally, the code should be designed so that additional hydrologic models can easily be added to ANNIE.

[Investigation on Mobile Phone Based Thermal Imaging System and Its Preliminary Application].

PubMed

Li, Fufeng; Chen, Feng; Liu, Jing

2015-03-01

The technical structure of a low-cost thermal imaging system (TIM) lunched on a mobile phone was investigated, which consists of a thermal infrared module and mobile phone and application software. The designing strategies and technical factors toward realizing various TIM array performances are interpreted, including sensor cost and Noise Equivalent Temperature Difference (NETD). In the software algorithm, a mechanism for scene-change detection was implemented to optimize the efficiency of non-uniformity correction (NUC). The performance experiments and analysis indicate that the NETD of the system can be smaller than 150 mK when the integration time is larger than 16 frames. Furthermore, a practical application for human temperature monitoring during physical exercise is proposed and interpreted. The measurement results support the feasibility and facility of the system in the medical application.

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Center for Efficient Exascale Discretizations Software Suite

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

Kolev, Tzanio; Dobrev, Veselin; Tomov, Vladimir

The CEED Software suite is a collection of generally applicable software tools focusing on the following computational motives: PDE discretizations on unstructured meshes, high-order finite element and spectral element methods and unstructured adaptive mesh refinement. All of this software is being developed as part of CEED, a co-design Center for Efficient Exascale Discretizations, within DOE's Exascale Computing Project (ECP) program.

Object oriented development of engineering software using CLIPS

NASA Technical Reports Server (NTRS)

Yoon, C. John

1991-01-01

Engineering applications involve numeric complexity and manipulations of a large amount of data. Traditionally, numeric computation has been the concern in developing an engineering software. As engineering application software became larger and more complex, management of resources such as data, rather than the numeric complexity, has become the major software design problem. Object oriented design and implementation methodologies can improve the reliability, flexibility, and maintainability of the resulting software; however, some tasks are better solved with the traditional procedural paradigm. The C Language Integrated Production System (CLIPS), with deffunction and defgeneric constructs, supports the procedural paradigm. The natural blending of object oriented and procedural paradigms has been cited as the reason for the popularity of the C++ language. The CLIPS Object Oriented Language's (COOL) object oriented features are more versatile than C++'s. A software design methodology based on object oriented and procedural approaches appropriate for engineering software, and to be implemented in CLIPS was outlined. A method for sensor placement for Space Station Freedom is being implemented in COOL as a sample problem.

Design and implementation of handheld and desktop software for the structured reporting of hepatic masses using the LI-RADS schema.

PubMed

Clark, Toshimasa J; McNeeley, Michael F; Maki, Jeffrey H

2014-04-01

The Liver Imaging Reporting and Data System (LI-RADS) can enhance communication between radiologists and clinicians if applied consistently. We identified an institutional need to improve liver imaging report standardization and developed handheld and desktop software to serve this purpose. We developed two complementary applications that implement the LI-RADS schema. A mobile application for iOS devices written in the Objective-C language allows for rapid characterization of hepatic observations under a variety of circumstances. A desktop application written in the Java language allows for comprehensive observation characterization and standardized report text generation. We chose the applications' languages and feature sets based on the computing resources of target platforms, anticipated usage scenarios, and ease of application installation, deployment, and updating. Our primary results are the publication of the core source code implementing the LI-RADS algorithm and the availability of the applications for use worldwide via our website, http://www.liradsapp.com/. The Java application is free open-source software that can be integrated into nearly any vendor's reporting system. The iOS application is distributed through Apple's iTunes App Store. Observation categorizations of both programs have been manually validated to be correct. The iOS application has been used to characterize liver tumors during multidisciplinary conferences of our institution, and several faculty members, fellows, and residents have adopted the generated text of Java application into their diagnostic reports. Although these two applications were developed for the specific reporting requirements of our liver tumor service, we intend to apply this development model to other diseases as well. Through semiautomated structured report generation and observation characterization, we aim to improve patient care while increasing radiologist efficiency. Published by Elsevier Inc.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

Considerations for Software Defined Networking (SDN): Approaches and use cases

NASA Astrophysics Data System (ADS)

Bakshi, K.

Software Defined Networking (SDN) is an evolutionary approach to network design and functionality based on the ability to programmatically modify the behavior of network devices. SDN uses user-customizable and configurable software that's independent of hardware to enable networked systems to expand data flow control. SDN is in large part about understanding and managing a network as a unified abstraction. It will make networks more flexible, dynamic, and cost-efficient, while greatly simplifying operational complexity. And this advanced solution provides several benefits including network and service customizability, configurability, improved operations, and increased performance. There are several approaches to SDN and its practical implementation. Among them, two have risen to prominence with differences in pedigree and implementation. This paper's main focus will be to define, review, and evaluate salient approaches and use cases of the OpenFlow and Virtual Network Overlay approaches to SDN. OpenFlow is a communication protocol that gives access to the forwarding plane of a network's switches and routers. The Virtual Network Overlay relies on a completely virtualized network infrastructure and services to abstract the underlying physical network, which allows the overlay to be mobile to other physical networks. This is an important requirement for cloud computing, where applications and associated network services are migrated to cloud service providers and remote data centers on the fly as resource demands dictate. The paper will discuss how and where SDN can be applied and implemented, including research and academia, virtual multitenant data center, and cloud computing applications. Specific attention will be given to the cloud computing use case, where automated provisioning and programmable overlay for scalable multi-tenancy is leveraged via the SDN approach.

The effect of nursing participation in the design of a critical care information system: a case study in a Chinese hospital.

PubMed

Qin, Yanhong; Zhou, Ranyun; Wu, Qiong; Huang, Xiaodi; Chen, Xinli; Wang, Weiwei; Wang, Xun; Xu, Hua; Zheng, Jing; Qian, Siyu; Bai, Changqing; Yu, Ping

2017-12-06

Intensive care information systems (ICIS) are continuously evolving to meet the ever changing information needs of intensive care units (ICUs), providing the backbone for a safe, intelligent and efficient patient care environment. Although beneficial for the international advancement in building smart environments to transform ICU services, knowledge about the contemporary development of ICIS worldwide, their usage and impacts is limited. This study aimed to fill this knowledge gap by researching the development and implementation of an ICIS in a Chinese hospital, nurses' use of the system, and the impact of system use on critical care nursing processes and outcomes. This descriptive case study was conducted in a 14-bed Respiratory ICU in a tertiary hospital in Beijing. Participative design was the method used for ICU nurses, hospital IT department and a software company to collaboratively research and develop the ICIS. Focus group discussions were conducted to understand the subjective perceptions of the nurses toward the ICIS. Nursing documentation time and quality were compared before and after system implementation. ICU nursing performance was extracted from the annual nursing performance data collected by the hospital. A participative design process was followed by the nurses in the ICU, the hospital IT staff and the software engineers in the company to develop and implement a highly useful ICIS. Nursing documentation was fully digitized and was significantly improved in quality and efficiency. The wrong data, missing data items and calculation errors were significantly reduced. Nurses spent more time on direct patient care after the introduction of the ICIS. The accuracy and efficiency of medication administration was also improved. The outcome was improvement in ward nursing performance as measured by ward management, routine nursing practices, disinfection and isolation, infection rate and mortality rate. Nurses in this ICU unit in China actively participated in the ICIS development and fully used the system to document care. Introduction of the ICIS led to significant improvement in quality and efficiency in nursing documentation, medication order transcription and administration. It allowed nurses to spend more time with patients to improve quality of care. These led to improvement in overall nursing performance. Further study should investigate how the ICIS system contributes to the improvement in decision making of ICU nurses and intensivists.

Software Development Life Cycle Security Issues

NASA Astrophysics Data System (ADS)

Kaur, Daljit; Kaur, Parminder

2011-12-01

Security is now-a-days one of the major problems because of many reasons. Security is now-a-days one of the major problems because of many reasons. The main cause is that software can't withstand security attacks because of vulnerabilities in it which are caused by defective specifications design and implementation. We have conducted a survey asking software developers, project managers and other people in software development about their security awareness and implementation in Software Development Life Cycle (SDLC). The survey was open to participation for three weeks and this paper explains the survey results.

Reference software implementation for GIFTS ground data processing

NASA Astrophysics Data System (ADS)

Garcia, R. K.; Howell, H. B.; Knuteson, R. O.; Martin, G. D.; Olson, E. R.; Smuga-Otto, M. J.

2006-08-01

Future satellite weather instruments such as high spectral resolution imaging interferometers pose a challenge to the atmospheric science and software development communities due to the immense data volumes they will generate. An open-source, scalable reference software implementation demonstrating the calibration of radiance products from an imaging interferometer, the Geosynchronous Imaging Fourier Transform Spectrometer1 (GIFTS), is presented. This paper covers essential design principles laid out in summary system diagrams, lessons learned during implementation and preliminary test results from the GIFTS Information Processing System (GIPS) prototype.

Recipe for Success: Digital Viewables

NASA Technical Reports Server (NTRS)

LaPha, Steven; Gaydos, Frank

2014-01-01

The Engineering Services Contract (ESC) and Information Management Communication Support contract (IMCS) at Kennedy Space Center (KSC) provide services to NASA in respect to flight and ground systems design and development. These groups provides the necessary tools, aid, and best practice methodologies required for efficient, optimized design and process development. The team is responsible for configuring and implementing systems, software, along with training, documentation, and administering standards. The team supports over 200 engineers and design specialists with the use of Windchill, Creo Parametric, NX, AutoCAD, and a variety of other design and analysis tools.

Software For Fault-Tree Diagnosis Of A System

NASA Technical Reports Server (NTRS)

Iverson, Dave; Patterson-Hine, Ann; Liao, Jack

1993-01-01

Fault Tree Diagnosis System (FTDS) computer program is automated-diagnostic-system program identifying likely causes of specified failure on basis of information represented in system-reliability mathematical models known as fault trees. Is modified implementation of failure-cause-identification phase of Narayanan's and Viswanadham's methodology for acquisition of knowledge and reasoning in analyzing failures of systems. Knowledge base of if/then rules replaced with object-oriented fault-tree representation. Enhancement yields more-efficient identification of causes of failures and enables dynamic updating of knowledge base. Written in C language, C++, and Common LISP.

Study on generation and sharing of on-demand global seamless data—Taking MODIS NDVI as an example

NASA Astrophysics Data System (ADS)

Shen, Dayong; Deng, Meixia; Di, Liping; Han, Weiguo; Peng, Chunming; Yagci, Ali Levent; Yu, Genong; Chen, Zeqiang

2013-04-01

By applying advanced Geospatial Data Abstraction Library (GDAL) and BigTIFF technology in a Geographical Information System (GIS) with Service Oriented Architecture (SOA), this study has derived global datasets using tile-based input data and implemented Virtual Web Map Service (VWMS) and Virtual Web Coverage Service (VWCS) to provide software tools for visualization and acquisition of global data. Taking MODIS Normalized Difference Vegetation Index (NDVI) as an example, this study proves the feasibility, efficiency and features of the proposed approach.

Designing a low cost bedside workstation for intensive care units.

PubMed Central

Michel, A.; Zörb, L.; Dudeck, J.

1996-01-01

The paper describes the design and implementation of a software architecture for a low cost bedside workstation for intensive care units. The development is fully integrated into the information infrastructure of the existing hospital information system (HIS) at the University Hospital of Giessen. It provides cost efficient and reliable access for data entry and review from the HIS database from within patient rooms, even in very space limited environments. The architecture further supports automatical data input from medical devices. First results from three different intensive care units are reported. PMID:8947771

Development of a space-systems network testbed

NASA Technical Reports Server (NTRS)

Lala, Jaynarayan; Alger, Linda; Adams, Stuart; Burkhardt, Laura; Nagle, Gail; Murray, Nicholas

1988-01-01

This paper describes a communications network testbed which has been designed to allow the development of architectures and algorithms that meet the functional requirements of future NASA communication systems. The central hardware components of the Network Testbed are programmable circuit switching communication nodes which can be adapted by software or firmware changes to customize the testbed to particular architectures and algorithms. Fault detection, isolation, and reconfiguration has been implemented in the Network with a hybrid approach which utilizes features of both centralized and distributed techniques to provide efficient handling of faults within the Network.

Industrial Technology Modernization Program. Project 80. Increase Efficiency of Card Test/Device Test Areas by the Usage of Improved Material Handling Systems. Revision 1. Phase 2

DTIC Science & Technology

1988-03-01

INDUSTRY ANALYSIS/FINDINGS 132 12 EQUIPMENT/MACHINERY ALTERNATIVES 134 13 MIS REQUIREMENTS/IMPROVEMENTS 135 14 COST BENEFIT ANALYSIS AND PROCEDURE 137 15...SOFTWARE DIAGRAM 14.0-1 COST BENEFIT ANALYSIS METHODOLOGY 138 14.3-1 PROJECT 80 EXPENDITURE SCHEDULE 141 14.4-1 PROJECT 80 CASH FLOWS 142 15.1-1 PROJECT 80...testing, streamlining work flow, and installation of ergonomically designed work cell/work centers. The benefits associated with the implementation of ITM

Redesigning a risk-management process for tracking injuries.

PubMed

Wenzel, G R

1998-01-01

The changing responsibilities of registered nurses are challenging even the most dedicated professionals. To survive within her newly-defined roles, one nurse used a total quality improvement model to understand, analyze, and improve a medical center's system for tracking inpatient injuries. This process led to the drafting of an original software design that implemented a nursing informatics tracking system. It has resulted in significant savings of time and money and has far surpassed the accuracy, efficiency, and scope of the previous method. This article presents an overview of the design process.

The control system of the 12-m medium-size telescope prototype: a test-ground for the CTA array control

NASA Astrophysics Data System (ADS)

Oya, I.; Anguner, E. A.; Behera, B.; Birsin, E.; Fuessling, M.; Lindemann, R.; Melkumyan, D.; Schlenstedt, S.; Schmidt, T.; Schwanke, U.; Sternberger, R.; Wegner, P.; Wiesand, S.

2014-07-01

The Cherenkov Telescope Array (CTA) will be the next generation ground-based very-high energy -ray observatory. CTA will consist of two arrays: one in the Northern hemisphere composed of about 20 telescopes, and the other one in the Southern hemisphere composed of about 100 telescopes, both arrays containing telescopes of different sizes and types and in addition numerous auxiliary devices. In order to provide a test-ground for the CTA array control, the steering software of the 12-m medium size telescope (MST) prototype deployed in Berlin has been implemented using the tools and design concepts under consideration to be used for the control of the CTA array. The prototype control system is implemented based on the Atacama Large Millimeter/submillimeter Array (ALMA) Common Software (ACS) control middleware, with components implemented in Java, C++ and Python. The interfacing to the hardware is standardized via the Object Linking and Embedding for Process Control Unified Architecture (OPC UA). In order to access the OPC UA servers from the ACS framework in a common way, a library has been developed that allows to tie the OPC UA server nodes, methods and events to the equivalents in ACS components. The front-end of the archive system is able to identify the deployed components and to perform the sampling of the monitoring points of each component following time and value change triggers according to the selected configurations. The back-end of the archive system of the prototype is composed by two different databases: MySQL and MongoDB. MySQL has been selected as storage of the system configurations, while MongoDB is used to have an efficient storage of device monitoring data, CCD images, logging and alarm information. In this contribution, the details and conclusions on the implementation of the control software of the MST prototype are presented.

Modelling and Implementation of Catalogue Cards Using FreeMarker

ERIC Educational Resources Information Center

Radjenovic, Jelen; Milosavljevic, Branko; Surla, Dusan

2009-01-01

Purpose: The purpose of this paper is to report on a study involving the specification (using Unified Modelling Language (UML) 2.0) of information requirements and implementation of the software components for generating catalogue cards. The implementation in a Java environment is developed using the FreeMarker software.…

78 FR 79564 - Discontinuance of Annual Financial Assessments-Delay in Implementation

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-30

... that due to delays in modifying computer software, VA is postponing implementation of this change. FOR... computer matching of income reported to the Internal Revenue Service (IRS) and Social Security... implemented by December 31, 2013. Due to delays in revising and updating supporting computer software, VA is...

Hierarchical MFMO Circuit Modules for an Energy-Efficient SDR DBF

NASA Astrophysics Data System (ADS)

Mar, Jeich; Kuo, Chi-Cheng; Wu, Shin-Ru; Lin, You-Rong

The hierarchical multi-function matrix operation (MFMO) circuit modules are designed using coordinate rotations digital computer (CORDIC) algorithm for realizing the intensive computation of matrix operations. The paper emphasizes that the designed hierarchical MFMO circuit modules can be used to develop a power-efficient software-defined radio (SDR) digital beamformer (DBF). The formulas of the processing time for the scalable MFMO circuit modules implemented in field programmable gate array (FPGA) are derived to allocate the proper logic resources for the hardware reconfiguration. The hierarchical MFMO circuit modules are scalable to the changing number of array branches employed for the SDR DBF to achieve the purpose of power saving. The efficient reuse of the common MFMO circuit modules in the SDR DBF can also lead to energy reduction. Finally, the power dissipation and reconfiguration function in the different modes of the SDR DBF are observed from the experiment results.

Common Misconceptions About Service-Oriented Architecture

DTIC Science & Technology

2007-11-01

addition, the architect(s) must make decisions on how services are implemented. Service implementations may involve developing new software , wrapping a...legacy software system, incor- porating services provided by third par- ties, or a combination of these options. Information about the quality attrib...temperature. However, there 28 CROSSTALK The Journal of Defense Software Engineering November 2007 Common Misconceptions About Service -Oriented

The Holistic Targeting (HOT) Methodology as the Means to Improve Information Operations (IO) Target Development and Prioritization

DTIC Science & Technology

2008-09-01

software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi-automated means to...the use of compendium software facilitate targeting problem understanding and the network analysis tool, Palantir , as an efficient and tailored semi...OBJECTIVES USING COMPENDIUM SOFTWARE .....63 E. HOT TARGET PRIORITIZATION AND DEVELOPMENT USING PALANTIR SOFTWARE .................................69 1

Multivariate and repeated measures (MRM): A new toolbox for dependent and multimodal group-level neuroimaging data.

PubMed

McFarquhar, Martyn; McKie, Shane; Emsley, Richard; Suckling, John; Elliott, Rebecca; Williams, Stephen

2016-05-15

Repeated measurements and multimodal data are common in neuroimaging research. Despite this, conventional approaches to group level analysis ignore these repeated measurements in favour of multiple between-subject models using contrasts of interest. This approach has a number of drawbacks as certain designs and comparisons of interest are either not possible or complex to implement. Unfortunately, even when attempting to analyse group level data within a repeated-measures framework, the methods implemented in popular software packages make potentially unrealistic assumptions about the covariance structure across the brain. In this paper, we describe how this issue can be addressed in a simple and efficient manner using the multivariate form of the familiar general linear model (GLM), as implemented in a new MATLAB toolbox. This multivariate framework is discussed, paying particular attention to methods of inference by permutation. Comparisons with existing approaches and software packages for dependent group-level neuroimaging data are made. We also demonstrate how this method is easily adapted for dependency at the group level when multiple modalities of imaging are collected from the same individuals. Follow-up of these multimodal models using linear discriminant functions (LDA) is also discussed, with applications to future studies wishing to integrate multiple scanning techniques into investigating populations of interest. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Experimental model of a wind energy conversion system

NASA Astrophysics Data System (ADS)

Vasar, C.; Rat, C. L.; Prostean, O.

2018-01-01

The renewable energy domain represents an important issue for the sustainable development of the mankind in the actual context of increasing demand for energy along with the increasing pollution that affect the environment. A significant quota of the clean energy is represented by the wind energy. As a consequence, the developing of wind energy conversion systems (WECS) in order to achieve high energetic performances (efficiency, stability, availability, competitive cost etc) represents a topic of permanent actuality. Testing and developing of an optimized control strategy for a WECS direct implemented on a real energetic site is quite difficult and not cost efficient. Thus a more convenient solution consists in a flexible laboratory setup which requires an experimental model of a WECS. Such approach would allow the simulation of various real conditions very similar with existing energetic sites. This paper presents a grid-connected wind turbine emulator. The wind turbine is implemented through a real-time Hardware-in-the-Loop (HIL) emulator, which will be analyzed extensively in the paper. The HIL system uses software implemented in the LabVIEW programming environment to control an ABB ACS800 electric drive. ACS800 has the task of driving an induction machine coupled to a permanent magnet synchronous generator. The power obtained from the synchronous generator is rectified, filtered and sent to the main grid through a controlled inverter. The control strategy is implemented on a NI CompactRIO (cRIO) platform.

An efficient and general approach for implementing thermodynamic phase equilibria information in geophysical and geodynamic studies

NASA Astrophysics Data System (ADS)

Afonso, Juan Carlos; Zlotnik, Sergio; Díez, Pedro

2015-10-01

We present a flexible, general, and efficient approach for implementing thermodynamic phase equilibria information (in the form of sets of physical parameters) into geophysical and geodynamic studies. The approach is based on Tensor Rank Decomposition methods, which transform the original multidimensional discrete information into a separated representation that contains significantly fewer terms, thus drastically reducing the amount of information to be stored in memory during a numerical simulation or geophysical inversion. Accordingly, the amount and resolution of the thermodynamic information that can be used in a simulation or inversion increases substantially. In addition, the method is independent of the actual software used to obtain the primary thermodynamic information, and therefore, it can be used in conjunction with any thermodynamic modeling program and/or database. Also, the errors associated with the decomposition procedure are readily controlled by the user, depending on her/his actual needs (e.g., preliminary runs versus full resolution runs). We illustrate the benefits, generality, and applicability of our approach with several examples of practical interest for both geodynamic modeling and geophysical inversion/modeling. Our results demonstrate that the proposed method is a competitive and attractive candidate for implementing thermodynamic constraints into a broad range of geophysical and geodynamic studies. MATLAB implementations of the method and examples are provided as supporting information and can be downloaded from the journal's website.

Nektar++: An open-source spectral/ hp element framework

NASA Astrophysics Data System (ADS)

Cantwell, C. D.; Moxey, D.; Comerford, A.; Bolis, A.; Rocco, G.; Mengaldo, G.; De Grazia, D.; Yakovlev, S.; Lombard, J.-E.; Ekelschot, D.; Jordi, B.; Xu, H.; Mohamied, Y.; Eskilsson, C.; Nelson, B.; Vos, P.; Biotto, C.; Kirby, R. M.; Sherwin, S. J.

2015-07-01

Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/ hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/ hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.

Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data

PubMed Central

Combrisson, Etienne; Vallat, Raphael; Eichenlaub, Jean-Baptiste; O'Reilly, Christian; Lajnef, Tarek; Guillot, Aymeric; Ruby, Perrine M.; Jerbi, Karim

2017-01-01

We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module. PMID:28983246

Parameter optimization for the visco-hyperelastic constitutive model of tendon using FEM.

PubMed

Tang, C Y; Ng, G Y F; Wang, Z W; Tsui, C P; Zhang, G

2011-01-01

Numerous constitutive models describing the mechanical properties of tendons have been proposed during the past few decades. However, few were widely used owing to the lack of implementation in the general finite element (FE) software, and very few systematic studies have been done on selecting the most appropriate parameters for these constitutive laws. In this work, the visco-hyperelastic constitutive model of the tendon implemented through the use of three-parameter Mooney-Rivlin form and sixty-four-parameter Prony series were firstly analyzed using ANSYS FE software. Afterwards, an integrated optimization scheme was developed by coupling two optimization toolboxes (OPTs) of ANSYS and MATLAB for estimating these unknown constitutive parameters of the tendon. Finally, a group of Sprague-Dawley rat tendons was used to execute experimental and numerical simulation investigation. The simulated results showed good agreement with the experimental data. An important finding revealed that too many Maxwell elements was not necessary for assuring accuracy of the model, which is often neglected in most open literatures. Thus, all these proved that the constitutive parameter optimization scheme was reliable and highly efficient. Furthermore, the approach can be extended to study other tendons or ligaments, as well as any visco-hyperelastic solid materials.

A Comparative Study on Java Technologies for Focus and Cursor Handling in Accessible Dynamic Interactions.

PubMed

Jitngernmadan, Prajaks; Miesenberger, Klaus

2015-01-01

For an interactive application, supporting and guiding the user in fulfilling tasks is most important. The behavior of the application that will guide users through the procedures until they finish the task has to be designed intuitively and well guiding, especially if the users has only restricted or no access to the visual and spatial arrangement on the screen. Therefore, the focus/cursor management plays an important role for orientation and navigating through the interaction. In the frame of ongoing research on a software tool supporting blind people in more efficiently doing mathematical calculations, we researched how Java technologies support implementing an accessible Graphical User Interface (GUI) with an additional focus on usable accessibility in terms of guiding blind users through the process of solving mathematical calculations. We used Java Swing [1] and Eclipse SWT [2] APIs for creating a series of prototypes. We tested a) accessibility and usability of the prototypes for blind people when using screen reader software and refreshable Braille display and b) the implementation support to developers provided by both technologies. It turned out that Eclipse SWT API delivered best results under Windows operating system.

Sleep: An Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data.

PubMed

Combrisson, Etienne; Vallat, Raphael; Eichenlaub, Jean-Baptiste; O'Reilly, Christian; Lajnef, Tarek; Guillot, Aymeric; Ruby, Perrine M; Jerbi, Karim

2017-01-01

We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.

Augmenting SCA project management and automation framework

NASA Astrophysics Data System (ADS)

Iyapparaja, M.; Sharma, Bhanupriya

2017-11-01

In our daily life we need to keep the records of the things in order to manage it in more efficient and proper way. Our Company manufactures semiconductor chips and sale it to the buyer. Sometimes it manufactures the entire product and sometimes partially and sometimes it sales the intermediary product obtained during manufacturing, so for the better management of the entire process there is a need to keep the track record of all the entity involved in it. Materials and Methods: Therefore to overcome with the problem the need raised to develop the framework for the maintenance of the project and for the automation testing. Project management framework provides an architecture which supports in managing the project by marinating the records of entire requirements, the test cases that were created for testing each unit of the software, defect raised from the past years. So through this the quality of the project can be maintained. Results: Automation framework provides the architecture which supports the development and implementation of the automation test script for the software testing process. Conclusion: For implementing project management framework the product of HP that is Application Lifecycle management is used which provides central repository to maintain the project.

ZOOM Lite: next-generation sequencing data mapping and visualization software

PubMed Central

Zhang, Zefeng; Lin, Hao; Ma, Bin

2010-01-01

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/. PMID:20530531

Transform-Based Channel-Data Compression to Improve the Performance of a Real-Time GPU-Based Software Beamformer.

PubMed

Lok, U-Wai; Li, Pai-Chi

2016-03-01

Graphics processing unit (GPU)-based software beamforming has advantages over hardware-based beamforming of easier programmability and a faster design cycle, since complicated imaging algorithms can be efficiently programmed and modified. However, the need for a high data rate when transferring ultrasound radio-frequency (RF) data from the hardware front end to the software back end limits the real-time performance. Data compression methods can be applied to the hardware front end to mitigate the data transfer issue. Nevertheless, most decompression processes cannot be performed efficiently on a GPU, thus becoming another bottleneck of the real-time imaging. Moreover, lossless (or nearly lossless) compression is desirable to avoid image quality degradation. In a previous study, we proposed a real-time lossless compression-decompression algorithm and demonstrated that it can reduce the overall processing time because the reduction in data transfer time is greater than the computation time required for compression/decompression. This paper analyzes the lossless compression method in order to understand the factors limiting the compression efficiency. Based on the analytical results, a nearly lossless compression is proposed to further enhance the compression efficiency. The proposed method comprises a transformation coding method involving modified lossless compression that aims at suppressing amplitude data. The simulation results indicate that the compression ratio (CR) of the proposed approach can be enhanced from nearly 1.8 to 2.5, thus allowing a higher data acquisition rate at the front end. The spatial and contrast resolutions with and without compression were almost identical, and the process of decompressing the data of a single frame on a GPU took only several milliseconds. Moreover, the proposed method has been implemented in a 64-channel system that we built in-house to demonstrate the feasibility of the proposed algorithm in a real system. It was found that channel data from a 64-channel system can be transferred using the standard USB 3.0 interface in most practical imaging applications.

GERICOS: A Generic Framework for the Development of On-Board Software

NASA Astrophysics Data System (ADS)

Plasson, P.; Cuomo, C.; Gabriel, G.; Gauthier, N.; Gueguen, L.; Malac-Allain, L.

2016-08-01

This paper presents an overview of the GERICOS framework (GEneRIC Onboard Software), its architecture, its various layers and its future evolutions. The GERICOS framework, developed and qualified by LESIA, offers a set of generic, reusable and customizable software components for the rapid development of payload flight software. The GERICOS framework has a layered structure. The first layer (GERICOS::CORE) implements the concept of active objects and forms an abstraction layer over the top of real-time kernels. The second layer (GERICOS::BLOCKS) offers a set of reusable software components for building flight software based on generic solutions to recurrent functionalities. The third layer (GERICOS::DRIVERS) implements software drivers for several COTS IP cores of the LEON processor ecosystem.

Software verification plan for GCS. [guidance and control software

NASA Technical Reports Server (NTRS)

Dent, Leslie A.; Shagnea, Anita M.; Hayhurst, Kelly J.

1990-01-01

This verification plan is written as part of an experiment designed to study the fundamental characteristics of the software failure process. The experiment will be conducted using several implementations of software that were produced according to industry-standard guidelines, namely the Radio Technical Commission for Aeronautics RTCA/DO-178A guidelines, Software Consideration in Airborne Systems and Equipment Certification, for the development of flight software. This plan fulfills the DO-178A requirements for providing instructions on the testing of each implementation of software. The plan details the verification activities to be performed at each phase in the development process, contains a step by step description of the testing procedures, and discusses all of the tools used throughout the verification process.

FPGA-Based, Self-Checking, Fault-Tolerant Computers

NASA Technical Reports Server (NTRS)

Some, Raphael; Rennels, David

2004-01-01

A proposed computer architecture would exploit the capabilities of commercially available field-programmable gate arrays (FPGAs) to enable computers to detect and recover from bit errors. The main purpose of the proposed architecture is to enable fault-tolerant computing in the presence of single-event upsets (SEUs). [An SEU is a spurious bit flip (also called a soft error) caused by a single impact of ionizing radiation.] The architecture would also enable recovery from some soft errors caused by electrical transients and, to some extent, from intermittent and permanent (hard) errors caused by aging of electronic components. A typical FPGA of the current generation contains one or more complete processor cores, memories, and highspeed serial input/output (I/O) channels, making it possible to shrink a board-level processor node to a single integrated-circuit chip. Custom, highly efficient microcontrollers, general-purpose computers, custom I/O processors, and signal processors can be rapidly and efficiently implemented by use of FPGAs. Unfortunately, FPGAs are susceptible to SEUs. Prior efforts to mitigate the effects of SEUs have yielded solutions that degrade performance of the system and require support from external hardware and software. In comparison with other fault-tolerant- computing architectures (e.g., triple modular redundancy), the proposed architecture could be implemented with less circuitry and lower power demand. Moreover, the fault-tolerant computing functions would require only minimal support from circuitry outside the central processing units (CPUs) of computers, would not require any software support, and would be largely transparent to software and to other computer hardware. There would be two types of modules: a self-checking processor module and a memory system (see figure). The self-checking processor module would be implemented on a single FPGA and would be capable of detecting its own internal errors. It would contain two CPUs executing identical programs in lock step, with comparison of their outputs to detect errors. It would also contain various cache local memory circuits, communication circuits, and configurable special-purpose processors that would use self-checking checkers. (The basic principle of the self-checking checker method is to utilize logic circuitry that generates error signals whenever there is an error in either the checker or the circuit being checked.) The memory system would comprise a main memory and a hardware-controlled check-pointing system (CPS) based on a buffer memory denoted the recovery cache. The main memory would contain random-access memory (RAM) chips and FPGAs that would, in addition to everything else, implement double-error-detecting and single-error-correcting memory functions to enable recovery from single-bit errors.

Does This Really Work? The Keys to Implementing New Technology while Providing Evidence that Technology Is Successful

ERIC Educational Resources Information Center

Sawtelle, Sara

2008-01-01

Proving that technology works is not as simple as proving that a new vendor for art supplies is more cost effective. Technology effectiveness requires both the right software and the right implementation. Just having the software is not enough. Proper planning, training, leadership, support, pedagogy, and software use--along with many other…

Acquisition Handbook - Update. Comprehensive Approach to Reusable Defensive Software (CARDS)

DTIC Science & Technology

1994-03-25

designs, and implementation components (source code, test plans, procedures and results, and system/software documentation). This handbook provides a...activities where software components are acquired, evaluated, tested and sometimes modified. In addition to serving as a facility for the acquisition and...systems from such components [1]. Implementation components are at the lowest level and consist of: specifications; detailed designs; code, test

Training survey -- educational profile for Hanford HANDI 2000 project

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

Wilson, D.

Fluor Daniel Hanford, Inc. (FDH) is currently adopting streamlined business processes through integrated software solutions. Replacing the legacy software (current/replacement systems, attached) also avoids significant maintenance required to resolve Year 2000 issues. This initiative is being referred to as `HANDI 2000`. The software being implemented in the first phase of this project includes Indus International`s PASSPORT Software, Peoplesoft and Primavera P3 Software. The project, which encompasses all the system replacements that will occur, has been named `HANDI 2000.` The PASSPORT applications being implemented are Inventory Management, Purchasing, Contract Management, Accounts Payable, and MSDS (Material Safety Data Sheets).

Top Down Implementation Plan for system performance test software

NASA Technical Reports Server (NTRS)

Jacobson, G. N.; Spinak, A.

1982-01-01

The top down implementation plan used for the development of system performance test software during the Mark IV-A era is described. The plan is based upon the identification of the hierarchical relationship of the individual elements of the software design, the development of a sequence of functionally oriented demonstrable steps, the allocation of subroutines to the specific step where they are first required, and objective status reporting. The results are: determination of milestones, improved managerial visibility, better project control, and a successful software development.

San Antonio I Software Workshop Proceedings. DoD Software for the 1990s, Held in San Antonio, Texas on 28 January - 1 February 1991

DTIC Science & Technology

1991-12-01

management and engineering issues common to the military-industrial complex, - to learn from past experience, - to understand future software...prospective policy documents. - :Prepare a draft issue paper and presentation for the DAE. These items should address the key implementation issues with...respect to MCCR software metrics and establish a clear need for DAE support. Long Term Actions ( past 12-18 mcnths) ... Draft final implementation

Algorithm 971: An Implementation of a Randomized Algorithm for Principal Component Analysis

PubMed Central

LI, HUAMIN; LINDERMAN, GEORGE C.; SZLAM, ARTHUR; STANTON, KELLY P.; KLUGER, YUVAL; TYGERT, MARK

2017-01-01

Recent years have witnessed intense development of randomized methods for low-rank approximation. These methods target principal component analysis and the calculation of truncated singular value decompositions. The present article presents an essentially black-box, foolproof implementation for Mathworks’ MATLAB, a popular software platform for numerical computation. As illustrated via several tests, the randomized algorithms for low-rank approximation outperform or at least match the classical deterministic techniques (such as Lanczos iterations run to convergence) in basically all respects: accuracy, computational efficiency (both speed and memory usage), ease-of-use, parallelizability, and reliability. However, the classical procedures remain the methods of choice for estimating spectral norms and are far superior for calculating the least singular values and corresponding singular vectors (or singular subspaces). PMID:28983138

Discrete Fourier Transform Analysis in a Complex Vector Space

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2009-01-01

Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.

Mapping analysis and planning system for the John F. Kennedy Space Center

NASA Technical Reports Server (NTRS)

Hall, C. R.; Barkaszi, M. J.; Provancha, M. J.; Reddick, N. A.; Hinkle, C. R.; Engel, B. A.; Summerfield, B. R.

1994-01-01

Environmental management, impact assessment, research and monitoring are multidisciplinary activities which are ideally suited to incorporate a multi-media approach to environmental problem solving. Geographic information systems (GIS), simulation models, neural networks and expert-system software are some of the advancing technologies being used for data management, query, analysis and display. At the 140,000 acre John F. Kennedy Space Center, the Advanced Software Technology group has been supporting development and implementation of a program that integrates these and other rapidly evolving hardware and software capabilities into a comprehensive Mapping, Analysis and Planning System (MAPS) based in a workstation/local are network environment. An expert-system shell is being developed to link the various databases to guide users through the numerous stages of a facility siting and environmental assessment. The expert-system shell approach is appealing for its ease of data access by management-level decision makers while maintaining the involvement of the data specialists. This, as well as increased efficiency and accuracy in data analysis and report preparation, can benefit any organization involved in natural resources management.

Open release of the DCA++ project

NASA Astrophysics Data System (ADS)

Haehner, Urs; Solca, Raffaele; Staar, Peter; Alvarez, Gonzalo; Maier, Thomas; Summers, Michael; Schulthess, Thomas

We present the first open release of the DCA++ project, a highly scalable and efficient research code to solve quantum many-body problems with cutting edge quantum cluster algorithms. The implemented dynamical cluster approximation (DCA) and its DCA+ extension with a continuous self-energy capture nonlocal correlations in strongly correlated electron systems thereby allowing insight into high-Tc superconductivity. With the increasing heterogeneity of modern machines, DCA++ provides portable performance on conventional and emerging new architectures, such as hybrid CPU-GPU and Xeon Phi, sustaining multiple petaflops on ORNL's Titan and CSCS' Piz Daint. Moreover, we will describe how best practices in software engineering can be applied to make software development sustainable and scalable in a research group. Software testing and documentation not only prevent productivity collapse, but more importantly, they are necessary for correctness, credibility and reproducibility of scientific results. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) awarded by the INCITE program, and of the Swiss National Supercomputing Center. OLCF is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

Using CLIPS in the domain of knowledge-based massively parallel programming

NASA Technical Reports Server (NTRS)

Dvorak, Jiri J.

1994-01-01

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

Software Defined Networking (SDN) controlled all optical switching networks with multi-dimensional switching architecture

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Ji, Yuefeng; Zhang, Jie; Li, Hui; Xiong, Qianjin; Qiu, Shaofeng

2014-08-01

Ultrahigh throughout capacity requirement is challenging the current optical switching nodes with the fast development of data center networks. Pbit/s level all optical switching networks need to be deployed soon, which will cause the high complexity of node architecture. How to control the future network and node equipment together will become a new problem. An enhanced Software Defined Networking (eSDN) control architecture is proposed in the paper, which consists of Provider NOX (P-NOX) and Node NOX (N-NOX). With the cooperation of P-NOX and N-NOX, the flexible control of the entire network can be achieved. All optical switching network testbed has been experimentally demonstrated with efficient control of enhanced Software Defined Networking (eSDN). Pbit/s level all optical switching nodes in the testbed are implemented based on multi-dimensional switching architecture, i.e. multi-level and multi-planar. Due to the space and cost limitation, each optical switching node is only equipped with four input line boxes and four output line boxes respectively. Experimental results are given to verify the performance of our proposed control and switching architecture.

Point of care use of a personal digital assistant for patient consultation management: experience of an intravenous resource nurse team in a major Canadian teaching hospital.

PubMed

Bosma, Laine; Balen, Robert M; Davidson, Erin; Jewesson, Peter J

2003-01-01

The development and integration of a personal digital assistant (PDA)-based point-of-care database into an intravenous resource nurse (IVRN) consultation service for the purposes of consultation management and service characterization are described. The IVRN team provides a consultation service 7 days a week in this 1000-bed tertiary adult care teaching hospital. No simple, reliable method for documenting IVRN patient care activity and facilitating IVRN-initiated patient follow-up evaluation was available. Implementation of a PDA database with exportability of data to statistical analysis software was undertaken in July 2001. A Palm IIIXE PDA was purchased and a three-table, 13-field database was developed using HanDBase software. During the 7-month period of data collection, the IVRN team recorded 4868 consultations for 40 patient care areas. Full analysis of service characteristics was conducted using SPSS 10.0 software. Team members adopted the new technology with few problems, and the authors now can efficiently track and analyze the services provided by their IVRN team.

Development of Efficient Authoring Software for e-Learning Contents

NASA Astrophysics Data System (ADS)

Kozono, Kazutake; Teramoto, Akemi; Akiyama, Hidenori

The contents creation in e-Learning system becomes an important problem. The contents of e-Learning should include figure and voice media for a high-level educational effect. However, the use of figure and voice complicates the operation of authoring software considerably. A new authoring software, which can build e-Learning contents efficiently, has been developed to solve this problem. This paper reports development results of the authoring software.

Adapting iterative algorithms for solving large sparse linear systems for efficient use on the CDC CYBER 205

NASA Technical Reports Server (NTRS)

Kincaid, D. R.; Young, D. M.

1984-01-01

Adapting and designing mathematical software to achieve optimum performance on the CYBER 205 is discussed. Comments and observations are made in light of recent work done on modifying the ITPACK software package and on writing new software for vector supercomputers. The goal was to develop very efficient vector algorithms and software for solving large sparse linear systems using iterative methods.

Rapid Building Assessment Project

DTIC Science & Technology

2014-05-01

ongoing management of commercial energy efficiency. No other company offers all of these proven services on a seamless, integrated Software -as-a- Service ...FirstFuel has added a suite of additional Software -as-a- Service analytics capabilities to support the entire energy efficiency lifecycle, including...the client side. In this document, we refer to the service side software as “BUILDER” and the client software as “BuilderRED,” following the Army

The GenABEL Project for statistical genomics

PubMed Central

Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

Integrating environmental gap analysis with spatial conservation prioritization: a case study from Victoria, Australia.

PubMed

Sharafi, Seyedeh Mahdieh; Moilanen, Atte; White, Matt; Burgman, Mark

2012-12-15

Gap analysis is used to analyse reserve networks and their coverage of biodiversity, thus identifying gaps in biodiversity representation that may be filled by additional conservation measures. Gap analysis has been used to identify priorities for species and habitat types. When it is applied to identify gaps in the coverage of environmental variables, it embodies the assumption that combinations of environmental variables are effective surrogates for biodiversity attributes. The question remains of how to fill gaps in conservation systems efficiently. Conservation prioritization software can identify those areas outside existing conservation areas that contribute to the efficient covering of gaps in biodiversity features. We show how environmental gap analysis can be implemented using high-resolution information about environmental variables and ecosystem condition with the publicly available conservation prioritization software, Zonation. Our method is based on the conversion of combinations of environmental variables into biodiversity features. We also replicated the analysis by using Species Distribution Models (SDMs) as biodiversity features to evaluate the robustness and utility of our environment-based analysis. We apply the technique to a planning case study of the state of Victoria, Australia. Copyright © 2012 Elsevier Ltd. All rights reserved.

webpic: A flexible web application for collecting distance and count measurements from images

PubMed Central

2018-01-01

Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible. Improving the efficiency of these tasks, which allows for more high quality data to be collected in a shorter amount of time, is therefore a high priority. The open-source web application, webpic, implements common web languages and widely available libraries and productivity apps to streamline the process of collecting distance and count measurements from images. In this paper, I introduce the framework of webpic and demonstrate one readily available feature of this application, linear measurements, using fossil leaf specimens. This application fills the gap between workflows accomplishable by individuals through existing software and those accomplishable by large, unmoderated crowds. It demonstrates that flexible web languages can be used to streamline time-intensive research tasks without the use of specialized equipment or proprietary software and highlights the potential for web resources to facilitate data collection in research tasks and outreach activities with improved efficiency. PMID:29608592

Some useful innovations with TRASYS and SINDA-85

NASA Technical Reports Server (NTRS)

Amundsen, Ruth M.

1993-01-01

Several innovative methods were used to allow more efficient and accurate thermal analysis using SINDA-85 and TRASYS, including model integration and reduction, planetary surface calculations, and model animation. Integration with other modeling and analysis codes allows an analyst to import a geometry from a solid modeling or computer-aided design (CAD) software package, rather than building the geometry 'by hand.' This is more efficient as well as potentially more accurate. However, the use of solid modeling software often generates large analytical models. The problem of reducing large models was elegantly solved using the response of the transient derivative to a forcing step function. The thermal analysis of a lunar rover implemented two unusual features of the TRASYS/SINDA system. A little-known TRASYS routine SURFP calculates the solar heating of a rover on the lunar surface for several different rover positions and orientations. This is used not only to determine the rover temperatures, but also to automatically determine the power generated by the solar arrays. The animation of transient thermal results is an effective tool, especially in a vivid case such as the 14-day progress of the sun over the lunar rover. An animated color map on the solid model displays the progression of temperatures.

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

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

Nakhleh, Luay

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

An economic analysis for optimal distributed computing resources for mask synthesis and tape-out in production environment

NASA Astrophysics Data System (ADS)

Cork, Chris; Lugg, Robert; Chacko, Manoj; Levi, Shimon

2005-06-01

With the exponential increase in output database size due to the aggressive optical proximity correction (OPC) and resolution enhancement technique (RET) required for deep sub-wavelength process nodes, the CPU time required for mask tape-out continues to increase significantly. For integrated device manufacturers (IDMs), this can impact the time-to-market for their products where even a few days delay could have a huge commercial impact and loss of market window opportunity. For foundries, a shorter turnaround time provides a competitive advantage in their demanding market, too slow could mean customers looking elsewhere for these services; while a fast turnaround may even command a higher price. With FAB turnaround of a mature, plain-vanilla CMOS process of around 20-30 days, a delay of several days in mask tapeout would contribute a significant fraction to the total time to deliver prototypes. Unlike silicon processing, masks tape-out time can be decreased by simply purchasing extra computing resources and software licenses. Mask tape-out groups are taking advantage of the ever-decreasing hardware cost and increasing power of commodity processors. The significant distributability inherent in some commercial Mask Synthesis software can be leveraged to address this critical business issue. Different implementations have different fractions of the code that cannot be parallelized and this affects the efficiency with which it scales, as is described by Amdahl"s law. Very few are efficient enough to allow the effective use of 1000"s of processors, enabling run times to drop from days to only minutes. What follows is a cost aware methodology to quantify the scalability of this class of software, and thus act as a guide to estimating the optimal investment in terms of hardware and software licenses.

Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight

NASA Technical Reports Server (NTRS)

Huynh, An; Brain, Thomas A.; MacLean, John R.; Quiocho, Leslie J.

2016-01-01

During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software.

A new Scheme for ATLAS Trigger Simulation using Legacy Code

NASA Astrophysics Data System (ADS)

Galster, Gorm; Stelzer, Joerg; Wiedenmann, Werner

2014-06-01

Analyses at the LHC which search for rare physics processes or determine with high precision Standard Model parameters require accurate simulations of the detector response and the event selection processes. The accurate determination of the trigger response is crucial for the determination of overall selection efficiencies and signal sensitivities. For the generation and the reconstruction of simulated event data, the most recent software releases are usually used to ensure the best agreement between simulated data and real data. For the simulation of the trigger selection process, however, ideally the same software release that was deployed when the real data were taken should be used. This potentially requires running software dating many years back. Having a strategy for running old software in a modern environment thus becomes essential when data simulated for past years start to present a sizable fraction of the total. We examined the requirements and possibilities for such a simulation scheme within the ATLAS software framework and successfully implemented a proof-of-concept simulation chain. One of the greatest challenges was the choice of a data format which promises long term compatibility with old and new software releases. Over the time periods envisaged, data format incompatibilities are also likely to emerge in databases and other external support services. Software availability may become an issue, when e.g. the support for the underlying operating system might stop. In this paper we present the encountered problems and developed solutions, and discuss proposals for future development. Some ideas reach beyond the retrospective trigger simulation scheme in ATLAS as they also touch more generally aspects of data preservation.

Effective use of e-grading in the dental simulation clinic.

PubMed

Morrow, Jay A; Pulido, M Teresa; Smith, P Bradford; McDaniel, Thomas F; Willcox, Austin B

2014-06-01

The purpose of this article is to describe the development and implementation of a grading software system, accessible from any platform, that engages today's generation of students and replaces paper grading. Set up at one U.S. dental school in an all-access, anytime (24/7) web-based program accessed through tablets, the software allows for a comparison between students' self-grading and instructor grading. This comparison facilitates student-faculty interaction, promoting discussion and student learning. The software can also be used for practical examination grading in which blinded grading between instructors is possible. The data gathered can produce descriptive reports students can draw upon to encourage self-learning and guided learning, propelling students to a better understanding of critical principles as they progress through multiple psychomotor skill sets. Other reports generated by the software allow for instructor calibration, exporting of grades directly into the university grading report system, and visual analysis of trends within each class. In a post-course survey, students (56 percent response rate) and faculty (79 percent response rate) agreed that the electronic grading was more efficient and allowed more time for faculty-student interaction than the previous grading system, thus creating an environment more conducive to learning. Overall, the software has improved students' perception of enhanced kinetic skills, while facilitating administration of preclinical projects and practical examinations.

Identification of triacylglycerol using automated annotation of high resolution multistage mass spectral trees.

PubMed

Wang, Xiupin; Peng, Qingzhi; Li, Peiwu; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen; Zhang, Liangxiao

2016-10-12

High complexity of identification for non-target triacylglycerols (TAGs) is a major challenge in lipidomics analysis. To identify non-target TAGs, a powerful tool named accurate MS(n) spectrometry generating so-called ion trees is used. In this paper, we presented a technique for efficient structural elucidation of TAGs on MS(n) spectral trees produced by LTQ Orbitrap MS(n), which was implemented as an open source software package, or TIT. The TIT software was used to support automatic annotation of non-target TAGs on MS(n) ion trees from a self-built fragment ion database. This database includes 19108 simulate TAG molecules from a random combination of fatty acids and corresponding 500582 self-built multistage fragment ions (MS ≤ 3). Our software can identify TAGs using a "stage-by-stage elimination" strategy. By utilizing the MS(1) accurate mass and referenced RKMD, the TIT software can discriminate unique elemental composition candidates. The regiospecific isomers of fatty acyl chains will be distinguished using MS(2) and MS(3) fragment spectra. We applied the algorithm to the selection of 45 TAG standards and demonstrated that the molecular ions could be 100% correctly assigned. Therefore, the TIT software could be applied to TAG identification in complex biological samples such as mouse plasma extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

PubMed

Li, Wenyuan; Gong, Ke; Li, Qingjiao; Alber, Frank; Zhou, Xianghong Jasmine

2015-03-15

Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability-the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency-the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed-the parallel version can run very fast on multiple computing nodes with limited local memory. The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http://zhoulab.usc.edu/Hi-Corrector/. © The Author 2014. Published by Oxford University Press.

NASA Software Safety Standard

NASA Technical Reports Server (NTRS)

Rosenberg, Linda

1997-01-01

If software is a critical element in a safety critical system, it is imperative to implement a systematic approach to software safety as an integral part of the overall system safety programs. The NASA-STD-8719.13A, "NASA Software Safety Standard", describes the activities necessary to ensure that safety is designed into software that is acquired or developed by NASA, and that safety is maintained throughout the software life cycle. A PDF version, is available on the WWW from Lewis. A Guidebook that will assist in the implementation of the requirements in the Safety Standard is under development at the Lewis Research Center (LeRC). After completion, it will also be available on the WWW from Lewis.

Software development to implement the TxDOT culvert rating guide.

DOT National Transportation Integrated Search

2013-05-01

This implementation project created CULVLR: Culvert Load Rating, Version 1.0.0, a Windows-based : desktop application software package that automates the process by which Texas Department of Transportation : (TxDOT) engineers and their consultants ...

Digital echocardiography 2002: now is the time

NASA Technical Reports Server (NTRS)

Thomas, James D.; Greenberg, Neil L.; Garcia, Mario J.

2002-01-01

The ability to acquire echocardiographic images digitally, store and transfer these data using the DICOM standard, and routinely analyze examinations exists today and allows the implementation of a digital echocardiography laboratory. The purpose of this review article is to outline the critical components of a digital echocardiography laboratory, discuss general strategies for implementation, and put forth some of the pitfalls that we have encountered in our own implementation. The major components of the digital laboratory include (1) digital echocardiography machines with network output, (2) a switched high-speed network, (3) a high throughput server with abundant local storage, (4) a reliable low-cost archive, (5) software to manage information, and (6) support mechanisms for software and hardware. Implementation strategies can vary from a complete vendor solution providing all components (hardware, software, support), to a strategy similar to our own where standard computer and networking hardware are used with specialized software for management of image and measurement information.

Development and analysis of the Software Implemented Fault-Tolerance (SIFT) computer

NASA Technical Reports Server (NTRS)

Goldberg, J.; Kautz, W. H.; Melliar-Smith, P. M.; Green, M. W.; Levitt, K. N.; Schwartz, R. L.; Weinstock, C. B.

1984-01-01

SIFT (Software Implemented Fault Tolerance) is an experimental, fault-tolerant computer system designed to meet the extreme reliability requirements for safety-critical functions in advanced aircraft. Errors are masked by performing a majority voting operation over the results of identical computations, and faulty processors are removed from service by reassigning computations to the nonfaulty processors. This scheme has been implemented in a special architecture using a set of standard Bendix BDX930 processors, augmented by a special asynchronous-broadcast communication interface that provides direct, processor to processor communication among all processors. Fault isolation is accomplished in hardware; all other fault-tolerance functions, together with scheduling and synchronization are implemented exclusively by executive system software. The system reliability is predicted by a Markov model. Mathematical consistency of the system software with respect to the reliability model has been partially verified, using recently developed tools for machine-aided proof of program correctness.

Multiscale Modeling and Uncertainty Quantification for Nuclear Fuel Performance

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

Estep, Donald; El-Azab, Anter; Pernice, Michael

2017-03-23

In this project, we will address the challenges associated with constructing high fidelity multiscale models of nuclear fuel performance. We (*) propose a novel approach for coupling mesoscale and macroscale models, (*) devise efficient numerical methods for simulating the coupled system, and (*) devise and analyze effective numerical approaches for error and uncertainty quantification for the coupled multiscale system. As an integral part of the project, we will carry out analysis of the effects of upscaling and downscaling, investigate efficient methods for stochastic sensitivity analysis of the individual macroscale and mesoscale models, and carry out a posteriori error analysis formore » computed results. We will pursue development and implementation of solutions in software used at Idaho National Laboratories on models of interest to the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program.« less

Guidance and Control Software Project Data - Volume 3: Verification Documents

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J. (Editor)

2008-01-01

The Guidance and Control Software (GCS) project was the last in a series of software reliability studies conducted at Langley Research Center between 1977 and 1994. The technical results of the GCS project were recorded after the experiment was completed. Some of the support documentation produced as part of the experiment, however, is serving an unexpected role far beyond its original project context. Some of the software used as part of the GCS project was developed to conform to the RTCA/DO-178B software standard, "Software Considerations in Airborne Systems and Equipment Certification," used in the civil aviation industry. That standard requires extensive documentation throughout the software development life cycle, including plans, software requirements, design and source code, verification cases and results, and configuration management and quality control data. The project documentation that includes this information is open for public scrutiny without the legal or safety implications associated with comparable data from an avionics manufacturer. This public availability has afforded an opportunity to use the GCS project documents for DO-178B training. This report provides a brief overview of the GCS project, describes the 4-volume set of documents and the role they are playing in training, and includes the verification documents from the GCS project. Volume 3 contains four appendices: A. Software Verification Cases and Procedures for the Guidance and Control Software Project; B. Software Verification Results for the Pluto Implementation of the Guidance and Control Software; C. Review Records for the Pluto Implementation of the Guidance and Control Software; and D. Test Results Logs for the Pluto Implementation of the Guidance and Control Software.

RSA cryptography and multi prime RSA cryptography

NASA Astrophysics Data System (ADS)

Sani, Nur Atiqah Abdul; Kamarulhaili, Hailiza

2017-08-01

RSA cryptography is one of the most powerful and popular cryptosystem which is being applied until now. There is one variant of RSA cryptography named Multi Prime RSA (MPRSA) cryptography. MPRSA cryptography is the improved version of RSA cryptography. We only need to modify a few steps in key generation part and apply the Chinese Remainder Theorem (CRT) in the decryption part to get the MPRSA algorithm. The focus of this research is to compare between the standard RSA cryptography and MPRSA cryptography in a few aspects. The research shows that MPRSA cryptography is more efficient than the RSA cryptography. Time complexity using Mathematica software is also conducted and it is proven that MPRSA cryptography has shorter time taken. It also implies the computational time is less than RSA cryptography. Mathematica software version 9.0 and a laptop HP ProBook 4331s are used to check the timing and to implement both algorithms.

Test Methods for Robot Agility in Manufacturing

PubMed Central

Downs, Anthony; Harrison, William; Schlenoff, Craig

2017-01-01

Purpose The paper aims to define and describe test methods and metrics to assess industrial robot system agility in both simulation and in reality. Design/methodology/approach The paper describes test methods and associated quantitative and qualitative metrics for assessing robot system efficiency and effectiveness which can then be used for the assessment of system agility. Findings The paper describes how the test methods were implemented in a simulation environment and real world environment. It also shows how the metrics are measured and assessed as they would be in a future competition. Practical Implications The test methods described in this paper will push forward the state of the art in software agility for manufacturing robots, allowing small and medium manufacturers to better utilize robotic systems. Originality / value The paper fulfills the identified need for standard test methods to measure and allow for improvement in software agility for manufacturing robots. PMID:28203034

Simulation of Triple Oxidation Ditch Wastewater Treatment Process

NASA Astrophysics Data System (ADS)

Yang, Yue; Zhang, Jinsong; Liu, Lixiang; Hu, Yongfeng; Xu, Ziming

2010-11-01

This paper presented the modeling mechanism and method of a sewage treatment system. A triple oxidation ditch process of a WWTP was simulated based on activated sludge model ASM2D with GPS-X software. In order to identify the adequate model structure to be implemented into the GPS-X environment, the oxidation ditch was divided into several completely stirred tank reactors depended on the distribution of aeration devices and dissolved oxygen concentration. The removal efficiency of COD, ammonia nitrogen, total nitrogen, total phosphorus and SS were simulated by GPS-X software with influent quality data of this WWTP from June to August 2009, to investigate the differences between the simulated results and the actual results. The results showed that, the simulated values could well reflect the actual condition of the triple oxidation ditch process. Mathematical modeling method was appropriate in effluent quality predicting and process optimizing.

Electro-optic Mach-Zehnder Interferometer based Optical Digital Magnitude Comparator and 1's Complement Calculator

NASA Astrophysics Data System (ADS)

Kumar, Ajay; Raghuwanshi, Sanjeev Kumar

2016-06-01

The optical switching activity is one of the most essential phenomena in the optical domain. The electro-optic effect-based switching phenomena are applicable to generate some effective combinational and sequential logic circuits. The processing of digital computational technique in the optical domain includes some considerable advantages of optical communication technology, e.g. immunity to electro-magnetic interferences, compact size, signal security, parallel computing and larger bandwidth. The paper describes some efficient technique to implement single bit magnitude comparator and 1's complement calculator using the concepts of electro-optic effect. The proposed techniques are simulated on the MATLAB software. However, the suitability of the techniques is verified using the highly reliable Opti-BPM software. It is interesting to analyze the circuits in order to specify some optimized device parameter in order to optimize some performance affecting parameters, e.g. crosstalk, extinction ratio, signal losses through the curved and straight waveguide sections.

IsoCor: correcting MS data in isotope labeling experiments.

PubMed

Millard, Pierre; Letisse, Fabien; Sokol, Serguei; Portais, Jean-Charles

2012-05-01

Mass spectrometry (MS) is widely used for isotopic labeling studies of metabolism and other biological processes. Quantitative applications-e.g. metabolic flux analysis-require tools to correct the raw MS data for the contribution of all naturally abundant isotopes. IsoCor is a software that allows such correction to be applied to any chemical species. Hence it can be used to exploit any isotopic tracer, from well-known ((13)C, (15)N, (18)O, etc) to unusual ((57)Fe, (77)Se, etc) isotopes. It also provides new features-e.g. correction for the isotopic purity of the tracer-to improve the accuracy of quantitative isotopic studies, and implements an efficient algorithm to process large datasets. Its user-friendly interface makes isotope labeling experiments more accessible to a wider biological community. IsoCor is distributed under OpenSource license at http://metasys.insa-toulouse.fr/software/isocor/

An efficient approach to integrated MeV ion imaging.

PubMed

Nikbakht, T; Kakuee, O; Solé, V A; Vosuoghi, Y; Lamehi-Rachti, M

2018-03-01

An ionoluminescence (IL) spectral imaging system, besides the common MeV ion imaging facilities such as µ-PIXE and µ-RBS, is implemented at the Van de Graaff laboratory of Tehran. A versatile processing software is required to handle the large amount of data concurrently collected in µ-IL and common MeV ion imaging measurements through the respective methodologies. The open-source freeware PyMca, with image processing and multivariate analysis capabilities, is employed to simultaneously process common MeV ion imaging and µ-IL data. Herein, the program was adapted to support the OM_DAQ listmode data format. The appropriate performance of the µ-IL data acquisition system is confirmed through a case study. Moreover, the capabilities of the software for simultaneous analysis of µ-PIXE and µ-RBS experimental data are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

Applying Use Cases to Describe the Role of Standards in e-Health Information Systems

NASA Astrophysics Data System (ADS)

Chávez, Emma; Finnie, Gavin; Krishnan, Padmanabhan

Individual health records (IHRs) contain a person's lifetime records of their key health history and care within a health system (National E-Health Transition Authority, Retrieved Jan 12, 2009 from http://www.nehta.gov.au/coordinated-care/whats-in-iehr, 2004). This information can be processed and stored in different ways. The record should be available electronically to authorized health care providers and the individual anywhere, anytime, to support high-quality care. Many organizations provide a diversity of solutions for e-health and its services. Standards play an important role to enable these organizations to support information interchange and improve efficiency of health care delivery. However, there are numerous standards to choose from and not all of them are accessible to the software developer. This chapter proposes a framework to describe the e-health standards that can be used by software engineers to implement e-health information systems.

Multiscale Fatigue Life Prediction for Composite Panels

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Yarrington, Phillip W.; Arnold, Steven M.

2012-01-01

Fatigue life prediction capabilities have been incorporated into the HyperSizer Composite Analysis and Structural Sizing Software. The fatigue damage model is introduced at the fiber/matrix constituent scale through HyperSizer s coupling with NASA s MAC/GMC micromechanics software. This enables prediction of the micro scale damage progression throughout stiffened and sandwich panels as a function of cycles leading ultimately to simulated panel failure. The fatigue model implementation uses a cycle jumping technique such that, rather than applying a specified number of additional cycles, a specified local damage increment is specified and the number of additional cycles to reach this damage increment is calculated. In this way, the effect of stress redistribution due to damage-induced stiffness change is captured, but the fatigue simulations remain computationally efficient. The model is compared to experimental fatigue life data for two composite facesheet/foam core sandwich panels, demonstrating very good agreement.

Efficiency of jet grout columns and sand-recycled material mixtures for mitigating liquefaction damage

NASA Astrophysics Data System (ADS)

Kerem Ertek, M.; Demir, Gökhan; Köktan, Utku

2017-04-01

Liquefaction is an important seismic phenomena that has to be assessed and consequently makes it essential to take measures in order to reduce related hazards. There are several ways to assess liquefaction potential analytically and some constitutive models implemented in FEM softwares presenting cyclic behaviour of sand making it possible to observe shear strain or excess pore pressure ratio which are measures to hold a view about liquefaction occurrence. According to various studies in the literature, post-earthquake inspections show that the measures in terms of grouting, piled rafts and sand mixtures with different non-liquefiable materials reduce liquefaction related damage. This paper aims to provide a brief information about effectiveness of jet-grout columns and recycled material-sand mixtures against liquefaction by the help of numerical analyses performed with MIDAS GTS NX software with regard to generation of shear strains. Key words: liquefaction, numerical analyses, jet-grout, sand mixtures

Adaptive controller for volumetric display of neuroimaging studies

NASA Astrophysics Data System (ADS)

Bleiberg, Ben; Senseney, Justin; Caban, Jesus

2014-03-01

Volumetric display of medical images is an increasingly relevant method for examining an imaging acquisition as the prevalence of thin-slice imaging increases in clinical studies. Current mouse and keyboard implementations for volumetric control provide neither the sensitivity nor specificity required to manipulate a volumetric display for efficient reading in a clinical setting. Solutions to efficient volumetric manipulation provide more sensitivity by removing the binary nature of actions controlled by keyboard clicks, but specificity is lost because a single action may change display in several directions. When specificity is then further addressed by re-implementing hardware binary functions through the introduction of mode control, the result is a cumbersome interface that fails to achieve the revolutionary benefit required for adoption of a new technology. We address the specificity versus sensitivity problem of volumetric interfaces by providing adaptive positional awareness to the volumetric control device by manipulating communication between hardware driver and existing software methods for volumetric display of medical images. This creates a tethered effect for volumetric display, providing a smooth interface that improves on existing hardware approaches to volumetric scene manipulation.

Parallel software support for computational structural mechanics

NASA Technical Reports Server (NTRS)

Jordan, Harry F.

1987-01-01

The application of the parallel programming methodology known as the Force was conducted. Two application issues were addressed. The first involves the efficiency of the implementation and its completeness in terms of satisfying the needs of other researchers implementing parallel algorithms. Support for, and interaction with, other Computational Structural Mechanics (CSM) researchers using the Force was the main issue, but some independent investigation of the Barrier construct, which is extremely important to overall performance, was also undertaken. Another efficiency issue which was addressed was that of relaxing the strong synchronization condition imposed on the self-scheduled parallel DO loop. The Force was extended by the addition of logical conditions to the cases of a parallel case construct and by the inclusion of a self-scheduled version of this construct. The second issue involved applying the Force to the parallelization of finite element codes such as those found in the NICE/SPAR testbed system. One of the more difficult problems encountered is the determination of what information in COMMON blocks is actually used outside of a subroutine and when a subroutine uses a COMMON block merely as scratch storage for internal temporary results.

Implementing the Data Center Energy Productivity Metric in a High Performance Computing Data Center

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

Sego, Landon H.; Marquez, Andres; Rawson, Andrew

2013-06-30

As data centers proliferate in size and number, the improvement of their energy efficiency and productivity has become an economic and environmental imperative. Making these improvements requires metrics that are robust, interpretable, and practical. We discuss the properties of a number of the proposed metrics of energy efficiency and productivity. In particular, we focus on the Data Center Energy Productivity (DCeP) metric, which is the ratio of useful work produced by the data center to the energy consumed performing that work. We describe our approach for using DCeP as the principal outcome of a designed experiment using a highly instrumented,more » high-performance computing data center. We found that DCeP was successful in clearly distinguishing different operational states in the data center, thereby validating its utility as a metric for identifying configurations of hardware and software that would improve energy productivity. We also discuss some of the challenges and benefits associated with implementing the DCeP metric, and we examine the efficacy of the metric in making comparisons within a data center and between data centers.« less

The Effect of Pulse Shaping QPSK on Bandwidth Efficiency

NASA Technical Reports Server (NTRS)

Purba, Josua Bisuk Mubyarto; Horan, Shelia

1997-01-01

This research investigates the effect of pulse shaping QPSK on bandwidth efficiency over a non-linear channel. This investigation will include software simulations and the hardware implementation. Three kinds of filters: the 5th order Butterworth filter, the 3rd order Bessel filter and the Square Root Raised Cosine filter with a roll off factor (alpha) of 0.25,0.5 and 1, have been investigated as pulse shaping filters. Two different high power amplifiers, one a Traveling Wave Tube Amplifier (TWTA) and the other a Solid State Power Amplifier (SSPA) have been investigated in the hardware implementation. A significant improvement in the bandwidth utilization (rho) for the filtered data compared to unfiltered data through the non-linear channel is shown in the results. This method promises strong performance gains in a bandlimited channel when compared to unfiltered systems. This work was conducted at NMSU in the Center for Space Telemetering, and Telecommunications Systems in the Klipsch School of Electrical and Computer Engineering Department and is supported by a grant from the National Aeronautics and Space Administration (NASA) NAG5-1491.

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

ERIC Educational Resources Information Center

Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

2012-01-01

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

Using iKidTools™ Software Support Systems to Develop and Implement Self-Monitoring Interventions

ERIC Educational Resources Information Center

Patti, Angela L.; Miller, Kevin J.

2011-01-01

Educational teams often are faced with the task of developing and implementing Behavioral Intervention Plans (BIPs) for students who present challenging and/or disruptive behaviors. This article describes the steps used to develop and implement a self-monitoring BIP that incorporated an innovative software system, iKidTools™. An authentic case…

Implementation of an optimum profile guidance system on STOLAND

NASA Technical Reports Server (NTRS)

Flanagan, P. F.

1978-01-01

The implementation on the STOLAND airborne digital computer of an optimum profile guidance system for the augmentor wing jet STOL research aircraft is described. Major tasks were to implement the guidance and control logic to airborne computer software and to integrate the module with the existing STOLAND navigation, display, and autopilot routines. The optimum profile guidance system comprises an algorithm for synthesizing mimimum fuel trajectories for a wide range of starting positions in the terminal area and a control law for flying the aircraft automatically along the trajectory. The avionics software developed is described along with a FORTRAN program that was constructed to reflect the modular nature and algorthms implemented in the avionics software.

The impact of software quality characteristics on healthcare outcome: a literature review.

PubMed

Aghazadeh, Sakineh; Pirnejad, Habibollah; Moradkhani, Alireza; Aliev, Alvosat

2014-01-01

The aim of this study was to discover the effect of software quality characteristics on healthcare quality and efficiency indicators. Through a systematic literature review, we selected and analyzed 37 original research papers to investigate the impact of the software indicators (coming from the standard ISO 9126 quality characteristics and sub-characteristics) on some of healthcare important outcome indicators and finally ranked these software indicators. The results showed that the software characteristics usability, reliability and efficiency were mostly favored in the studies, indicating their importance. On the other hand, user satisfaction, quality of patient care, clinical workflow efficiency, providers' communication and information exchange, patient satisfaction and care costs were among the healthcare outcome indicators frequently evaluated in relation to the mentioned software characteristics. Regression Logistic Method was the most common assessment methodology, and Confirmatory Factor Analysis and Structural Equation Modeling were performed to test the structural model's fit. The software characteristics were considered to impact the healthcare outcome indicators through other intermediate factors (variables).

The energy audit process for universities accommodation in Malaysia: a preliminary study

NASA Astrophysics Data System (ADS)

Dzulkefli Muhammad, Hilmi

2017-05-01

The increase of energy consumption in the Malaysian Universities has raised national concerns due to the fact that its consumption increase government fiscal budget and at the same time contributes negative impacts towards the environment. The purpose of this research is to focus on the process of energy audit conducted in the Malaysian universities and to identify the significant practice that can improve energy consumption of the selected universities. The significant criteria in energy audit may be found by comparing the energy implementation process of selected Malaysian universities through the investigation of energy consumption behavior and the number of electrical appliances, equipment, machinery and buildings activities that have an impact on energy consumption that can improve energy-efficiency in building. The Energy Efficiency Index (EEI) will be used as an indicator and combined with the suggested application of HOMER software to obtain solution and possible improvement of energy consumption during energy audit implementation. A document analysis approach will also be obtained in order to identify the best practice through the selected energy documentations. The result of this research may be used as a guideline for other universities that consume high energy in order to help improving the implementation of energy audit process in their universities.

Radiology on handheld devices: image display, manipulation, and PACS integration issues.

PubMed

Raman, Bhargav; Raman, Raghav; Raman, Lalithakala; Beaulieu, Christopher F

2004-01-01

Handheld personal digital assistants (PDAs) have undergone continuous and substantial improvements in hardware and graphics capabilities, making them a compelling platform for novel developments in teleradiology. The latest PDAs have processor speeds of up to 400 MHz and storage capacities of up to 80 Gbytes with memory expansion methods. A Digital Imaging and Communications in Medicine (DICOM)-compliant, vendor-independent handheld image access system was developed in which a PDA server acts as the gateway between a picture archiving and communication system (PACS) and PDAs. The system is compatible with most currently available PDA models. It is capable of both wired and wireless transfer of images and includes custom PDA software and World Wide Web interfaces that implement a variety of basic image manipulation functions. Implementation of this system, which is currently undergoing debugging and beta testing, required optimization of the user interface to efficiently display images on smaller PDA screens. The PDA server manages user work lists and implements compression and security features to accelerate transfer speeds, protect patient information, and regulate access. Although some limitations remain, PDA-based teleradiology has the potential to increase the efficiency of the radiologic work flow, increasing productivity and improving communication with referring physicians and patients. Copyright RSNA, 2004

Utah's Regional/Urban ANSS Seismic Network---Strategies and Tools for Quality Performance

NASA Astrophysics Data System (ADS)

Burlacu, R.; Arabasz, W. J.; Pankow, K. L.; Pechmann, J. C.; Drobeck, D. L.; Moeinvaziri, A.; Roberson, P. M.; Rusho, J. A.

2007-05-01

The University of Utah's regional/urban seismic network (224 stations recorded: 39 broadband, 87 strong-motion, 98 short-period) has become a model for locally implementing the Advanced National Seismic System (ANSS) because of successes in integrating weak- and strong-motion recording and in developing an effective real-time earthquake information system. Early achievements included implementing ShakeMap, ShakeCast, point-to- multipoint digital telemetry, and an Earthworm Oracle database, as well as in-situ calibration of all broadband and strong-motion stations and submission of all data and metadata into the IRIS DMC. Regarding quality performance, our experience as a medium-size regional network affirms the fundamental importance of basics such as the following: for data acquisition, deliberate attention to high-quality field installations, signal quality, and computer operations; for operational efficiency, a consistent focus on professional project management and human resources; and for customer service, healthy partnerships---including constant interactions with emergency managers, engineers, public policy-makers, and other stakeholders as part of an effective state earthquake program. (Operational cost efficiencies almost invariably involve trade-offs between personnel costs and the quality of hardware and software.) Software tools that we currently rely on for quality performance include those developed by UUSS (e.g., SAC and shell scripts for estimating local magnitudes) and software developed by other organizations such as: USGS (Earthworm), University of Washington (interactive analysis software), ISTI (SeisNetWatch), and IRIS (PDCC, BUD tools). Although there are many pieces, there is little integration. One of the main challenges we face is the availability of a complete and coherent set of tools for automatic and post-processing to assist in achieving the goals/requirements set forth by ANSS. Taking our own network---and ANSS---to the next level will require standardized, well-designed, and supported software. Other advances in seismic network performance will come from diversified instrumentation. We have recently shown the utility of incorporating strong-motion data (even from soil sites) into the routine analysis of local seismicity, and have also collocated an acoustic array with a broadband seismic station (in collaboration with Southern Methodist University). For the latter experiment, the purpose of collocated seismic and infrasound sensors is to (1) further an understanding of the physics associated with the generation and the propagation of seismic and low-frequency acoustic energy from shallow sources and (2) explore the potential for blast discrimination and improved source location using seismic and infrasonic data in a synergetic way.

Systems Architecture for Fully Autonomous Space Missions

NASA Technical Reports Server (NTRS)

Esper, Jamie; Schnurr, R.; VanSteenberg, M.; Brumfield, Mark (Technical Monitor)

2002-01-01

The NASA Goddard Space Flight Center is working to develop a revolutionary new system architecture concept in support of fully autonomous missions. As part of GSFC's contribution to the New Millenium Program (NMP) Space Technology 7 Autonomy and on-Board Processing (ST7-A) Concept Definition Study, the system incorporates the latest commercial Internet and software development ideas and extends them into NASA ground and space segment architectures. The unique challenges facing the exploration of remote and inaccessible locales and the need to incorporate corresponding autonomy technologies within reasonable cost necessitate the re-thinking of traditional mission architectures. A measure of the resiliency of this architecture in its application to a broad range of future autonomy missions will depend on its effectiveness in leveraging from commercial tools developed for the personal computer and Internet markets. Specialized test stations and supporting software come to past as spacecraft take advantage of the extensive tools and research investments of billion-dollar commercial ventures. The projected improvements of the Internet and supporting infrastructure go hand-in-hand with market pressures that provide continuity in research. By taking advantage of consumer-oriented methods and processes, space-flight missions will continue to leverage on investments tailored to provide better services at reduced cost. The application of ground and space segment architectures each based on Local Area Networks (LAN), the use of personal computer-based operating systems, and the execution of activities and operations through a Wide Area Network (Internet) enable a revolution in spacecraft mission formulation, implementation, and flight operations. Hardware and software design, development, integration, test, and flight operations are all tied-in closely to a common thread that enables the smooth transitioning between program phases. The application of commercial software development techniques lays the foundation for delivery of product-oriented flight software modules and models. Software can then be readily applied to support the on-board autonomy required for mission self-management. An on-board intelligent system, based on advanced scripting languages, facilitates the mission autonomy required to offload ground system resources, and enables the spacecraft to manage itself safely through an efficient and effective process of reactive planning, science data acquisition, synthesis, and transmission to the ground. Autonomous ground systems in turn coordinate and support schedule contact times with the spacecraft. Specific autonomy software modules on-board include mission and science planners, instrument and subsystem control, and fault tolerance response software, all residing within a distributed computing environment supported through the flight LAN. Autonomy also requires the minimization of human intervention between users on the ground and the spacecraft, and hence calls for the elimination of the traditional operations control center as a funnel for data manipulation. Basic goal-oriented commands are sent directly from the user to the spacecraft through a distributed internet-based payload operations "center". The ensuing architecture calls for the use of spacecraft as point extensions on the Internet. This paper will detail the system architecture implementation chosen to enable cost-effective autonomous missions with applicability to a broad range of conditions. It will define the structure needed for implementation of such missions, including software and hardware infrastructures. The overall architecture is then laid out as a common thread in the mission life cycle from formulation through implementation and flight operations.