Beyond Molecular Codes: Simple Rules to Wire Complex Brains

PubMed Central

Hassan, Bassem A.; Hiesinger, P. Robin

2015-01-01

Summary Molecular codes, like postal zip codes, are generally considered a robust way to ensure the specificity of neuronal target selection. However, a code capable of unambiguously generating complex neural circuits is difficult to conceive. Here, we re-examine the notion of molecular codes in the light of developmental algorithms. We explore how molecules and mechanisms that have been considered part of a code may alternatively implement simple pattern formation rules sufficient to ensure wiring specificity in neural circuits. This analysis delineates a pattern-based framework for circuit construction that may contribute to our understanding of brain wiring. PMID:26451480

How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation

NASA Astrophysics Data System (ADS)

Giorgino, Toni

2018-07-01

The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation.

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

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

Saad, Tony; Sutherland, James C.

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

DOE PAGES

Saad, Tony; Sutherland, James C.

2016-05-04

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

MATIN: A Random Network Coding Based Framework for High Quality Peer-to-Peer Live Video Streaming

PubMed Central

Barekatain, Behrang; Khezrimotlagh, Dariush; Aizaini Maarof, Mohd; Ghaeini, Hamid Reza; Salleh, Shaharuddin; Quintana, Alfonso Ariza; Akbari, Behzad; Cabrera, Alicia Triviño

2013-01-01

In recent years, Random Network Coding (RNC) has emerged as a promising solution for efficient Peer-to-Peer (P2P) video multicasting over the Internet. This probably refers to this fact that RNC noticeably increases the error resiliency and throughput of the network. However, high transmission overhead arising from sending large coefficients vector as header has been the most important challenge of the RNC. Moreover, due to employing the Gauss-Jordan elimination method, considerable computational complexity can be imposed on peers in decoding the encoded blocks and checking linear dependency among the coefficients vectors. In order to address these challenges, this study introduces MATIN which is a random network coding based framework for efficient P2P video streaming. The MATIN includes a novel coefficients matrix generation method so that there is no linear dependency in the generated coefficients matrix. Using the proposed framework, each peer encapsulates one instead of n coefficients entries into the generated encoded packet which results in very low transmission overhead. It is also possible to obtain the inverted coefficients matrix using a bit number of simple arithmetic operations. In this regard, peers sustain very low computational complexities. As a result, the MATIN permits random network coding to be more efficient in P2P video streaming systems. The results obtained from simulation using OMNET++ show that it substantially outperforms the RNC which uses the Gauss-Jordan elimination method by providing better video quality on peers in terms of the four important performance metrics including video distortion, dependency distortion, End-to-End delay and Initial Startup delay. PMID:23940530

Open-source Framework for Storing and Manipulation of Plasma Chemical Reaction Data

NASA Astrophysics Data System (ADS)

Jenkins, T. G.; Averkin, S. N.; Cary, J. R.; Kruger, S. E.

2017-10-01

We present a new open-source framework for storage and manipulation of plasma chemical reaction data that has emerged from our in-house project MUNCHKIN. This framework consists of python scripts and C + + programs. It stores data in an SQL data base for fast retrieval and manipulation. For example, it is possible to fit cross-section data into most widely used analytical expressions, calculate reaction rates for Maxwellian distribution functions of colliding particles, and fit them into different analytical expressions. Another important feature of this framework is the ability to calculate transport properties based on the cross-section data and supplied distribution functions. In addition, this framework allows the export of chemical reaction descriptions in LaTeX format for ease of inclusion in scientific papers. With the help of this framework it is possible to generate corresponding VSim (Particle-In-Cell simulation code) and USim (unstructured multi-fluid code) input blocks with appropriate cross-sections.

An information theoretic approach to use high-fidelity codes to calibrate low-fidelity codes

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

Lewis, Allison, E-mail: lewis.allison10@gmail.com; Smith, Ralph; Williams, Brian

For many simulation models, it can be prohibitively expensive or physically infeasible to obtain a complete set of experimental data to calibrate model parameters. In such cases, one can alternatively employ validated higher-fidelity codes to generate simulated data, which can be used to calibrate the lower-fidelity code. In this paper, we employ an information-theoretic framework to determine the reduction in parameter uncertainty that is obtained by evaluating the high-fidelity code at a specific set of design conditions. These conditions are chosen sequentially, based on the amount of information that they contribute to the low-fidelity model parameters. The goal is tomore » employ Bayesian experimental design techniques to minimize the number of high-fidelity code evaluations required to accurately calibrate the low-fidelity model. We illustrate the performance of this framework using heat and diffusion examples, a 1-D kinetic neutron diffusion equation, and a particle transport model, and include initial results from the integration of the high-fidelity thermal-hydraulics code Hydra-TH with a low-fidelity exponential model for the friction correlation factor.« less

Faunus: An object oriented framework for molecular simulation

PubMed Central

Lund, Mikael; Trulsson, Martin; Persson, Björn

2008-01-01

Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

Global magnetosphere simulations using constrained-transport Hall-MHD with CWENO reconstruction

NASA Astrophysics Data System (ADS)

Lin, L.; Germaschewski, K.; Maynard, K. M.; Abbott, S.; Bhattacharjee, A.; Raeder, J.

2013-12-01

We present a new CWENO (Centrally-Weighted Essentially Non-Oscillatory) reconstruction based MHD solver for the OpenGGCM global magnetosphere code. The solver was built using libMRC, a library for creating efficient parallel PDE solvers on structured grids. The use of libMRC gives us access to its core functionality of providing an automated code generation framework which takes a user provided PDE right hand side in symbolic form to generate an efficient, computer architecture specific, parallel code. libMRC also supports block-structured adaptive mesh refinement and implicit-time stepping through integration with the PETSc library. We validate the new CWENO Hall-MHD solver against existing solvers both in standard test problems as well as in global magnetosphere simulations.

Use of Annotations for Component and Framework Interoperability

NASA Astrophysics Data System (ADS)

David, O.; Lloyd, W.; Carlson, J.; Leavesley, G. H.; Geter, F.

2009-12-01

The popular programming languages Java and C# provide annotations, a form of meta-data construct. Software frameworks for web integration, web services, database access, and unit testing now take advantage of annotations to reduce the complexity of APIs and the quantity of integration code between the application and framework infrastructure. Adopting annotation features in frameworks has been observed to lead to cleaner and leaner application code. The USDA Object Modeling System (OMS) version 3.0 fully embraces the annotation approach and additionally defines a meta-data standard for components and models. In version 3.0 framework/model integration previously accomplished using API calls is now achieved using descriptive annotations. This enables the framework to provide additional functionality non-invasively such as implicit multithreading, and auto-documenting capabilities while achieving a significant reduction in the size of the model source code. Using a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside of it. To study the effectiveness of an annotation based framework approach with other modeling frameworks, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A monthly water balance model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. In a next step, the PRMS model was implemented in OMS 3.0 and is currently being implemented for water supply forecasting in the western United States at the USDA NRCS National Water and Climate Center. PRMS is a component based modular precipitation-runoff model developed to evaluate the impacts of various combinations of precipitation, climate, and land use on streamflow and general basin hydrology. The new OMS 3.0 PRMS model source code is more concise and flexible as a result of using the new framework’s annotation based approach. The fully annotated components are now providing information directly for (i) model assembly and building, (ii) dataflow analysis for implicit multithreading, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks. As a prototype example, model code annotations were used to generate binding and mediation code to allow the use of OMS 3.0 model components within the OpenMI context.

LIBVERSIONINGCOMPILER: An easy-to-use library for dynamic generation and invocation of multiple code versions

NASA Astrophysics Data System (ADS)

Cherubin, S.; Agosta, G.

2018-01-01

We present LIBVERSIONINGCOMPILER, a C++ library designed to support the dynamic generation of multiple versions of the same compute kernel in a HPC scenario. It can be used to provide continuous optimization, code specialization based on the input data or on workload changes, or otherwise to dynamically adjust the application, without the burden of a full dynamic compiler. The library supports multiple underlying compilers but specifically targets the LLVM framework. We also provide examples of use, showing the overhead of the library, and providing guidelines for its efficient use.

Reynolds-averaged Navier-Stokes based ice accretion for aircraft wings

NASA Astrophysics Data System (ADS)

Lashkajani, Kazem Hasanzadeh

This thesis addresses one of the current issues in flight safety towards increasing icing simulation capabilities for prediction of complex 2D and 3D glaze ice shapes over aircraft surfaces. During the 1980's and 1990's, the field of aero-icing was established to support design and certification of aircraft flying in icing conditions. The multidisciplinary technologies used in such codes were: aerodynamics (panel method), droplet trajectory calculations (Lagrangian framework), thermodynamic module (Messinger model) and geometry module (ice accretion). These are embedded in a quasi-steady module to simulate the time-dependent ice accretion process (multi-step procedure). The objectives of the present research are to upgrade the aerodynamic module from Laplace to Reynolds-Average Navier-Stokes equations solver. The advantages are many. First, the physical model allows accounting for viscous effects in the aerodynamic module. Second, the solution of the aero-icing module directly provides the means for characterizing the aerodynamic effects of icing, such as loss of lift and increased drag. Third, the use of a finite volume approach to solving the Partial Differential Equations allows rigorous mesh and time convergence analysis. Finally, the approaches developed in 2D can be easily transposed to 3D problems. The research was performed in three major steps, each providing insights into the overall numerical approaches. The most important realization comes from the need to develop specific mesh generation algorithms to ensure feasible solutions in very complex multi-step aero-icing calculations. The contributions are presented in chronological order of their realization. First, a new framework for RANS based two-dimensional ice accretion code, CANICE2D-NS, is developed. A multi-block RANS code from U. of Liverpool (named PMB) is providing the aerodynamic field using the Spalart-Allmaras turbulence model. The ICEM-CFD commercial tool is used for the iced airfoil remeshing and field smoothing. The new coupling is fully automated and capable of multi-step ice accretion simulations via a quasi-steady approach. In addition, the framework allows for flow analysis and aerodynamic performance prediction of the iced airfoils. The convergence of the quasi-steady algorithm is verified and identifies the need for an order of magnitude increase in the number of multi-time steps in icing simulations to achieve solver independent solutions. Second, a Multi-Block Navier-Stokes code, NSMB, is coupled with the CANICE2D icing framework. Attention is paid to the roughness implementation of the ONERA roughness model within the Spalart-Allmaras turbulence model, and to the convergence of the steady and quasi-steady iterative procedure. Effects of uniform surface roughness in quasi-steady ice accretion simulation are analyzed through different validation test cases. The results of CANICE2D-NS show good agreement with experimental data both in terms of predicted ice shapes as well as aerodynamic analysis of predicted and experimental ice shapes. Third, an efficient single-block structured Navier-Stokes CFD code, NSCODE, is coupled with the CANICE2D-NS icing framework. Attention is paid to the roughness implementation of the Boeing model within the Spalart-Allmaras turbulence model, and to acceleration of the convergence of the steady and quasi-steady iterative procedures. Effects of uniform surface roughness in quasi-steady ice accretion simulation are analyzed through different validation test cases, including code to code comparisons with the same framework coupled with the NSMB Navier-Stokes solver. The efficiency of the J-multigrid approach to solve the flow equations on complex iced geometries is demonstrated. Since it was noted in all these calculations that the ICEM-CFD grid generation package produced a number of issues such as inefficient mesh quality and smoothing deficiencies (notably grid shocks), a fourth study proposes a new mesh generation algorithm. A PDE based multi-block structured grid generation code, NSGRID, is developed for this purpose. The study includes the developments of novel mesh generation algorithms over complex glaze ice shapes containing multi-curvature ice accretion geometries, such as single/double ice horns. The twofold approaches tackle surface geometry discretization as well as field mesh generation. An adaptive curvilinear curvature control algorithm is constructed solving a 1D elliptic PDE equation with periodic source terms. This method controls the arclength grid spacing so that high convex and concave curvature regions around ice horns are appropriately captured and is shown to effectively treat the grid shock problem. Then, a novel blended method is developed by defining combinations of source terms with 2D elliptic equations. The source terms include two common control functions, Sorenson and Spekreijse, and an additional third source term to improve orthogonality. This blended method is shown to be very effective for improving grid quality metrics for complex glaze ice meshes with RANS resolution. The performance in terms of residual reduction per non-linear iteration of several solution algorithms (Point-Jacobi, Gauss-Seidel, ADI, Point and Line SOR) are discussed within the context of a full Multi-grid operator. Details are given on the various formulations used in the linearization process. It is shown that the performance of the solution algorithm depends on the type of control function used. Finally, the algorithms are validated on standard complex experimental ice shapes, demonstrating the applicability of the methods. Finally, the automated framework of RANS based two-dimensional multi-step ice accretion, CANICE2D-NS is developed, coupled with a Multi-Block Navier-Stokes CFD code, NSCODE2D, a Multi-Block elliptic grid generation code, NSGRID2D, and a Multi-Block Eulerian droplet solver, NSDROP2D (developed at Polytechnique Montreal). The framework allows Lagrangian and Eulerian droplet computations within a chimera approach treating multi-elements geometries. The code was tested on public and confidential validation test cases including standard NATO cases. In addition, up to 10 times speedup is observed in the mesh generation procedure by using the implicit line SOR and ADI smoothers within a multigrid procedure. The results demonstrate the benefits and robustness of the new framework in predicting ice shapes and aerodynamic performance parameters.

FRANOPP: Framework for analysis and optimization problems user's guide

NASA Technical Reports Server (NTRS)

Riley, K. M.

1981-01-01

Framework for analysis and optimization problems (FRANOPP) is a software aid for the study and solution of design (optimization) problems which provides the driving program and plotting capability for a user generated programming system. In addition to FRANOPP, the programming system also contains the optimization code CONMIN, and two user supplied codes, one for analysis and one for output. With FRANOPP the user is provided with five options for studying a design problem. Three of the options utilize the plot capability and present an indepth study of the design problem. The study can be focused on a history of the optimization process or on the interaction of variables within the design problem.

ng: What next-generation languages can teach us about HENP frameworks in the manycore era

NASA Astrophysics Data System (ADS)

Binet, Sébastien

2011-12-01

Current High Energy and Nuclear Physics (HENP) frameworks were written before multicore systems became widely deployed. A 'single-thread' execution model naturally emerged from that environment, however, this no longer fits into the processing model on the dawn of the manycore era. Although previous work focused on minimizing the changes to be applied to the LHC frameworks (because of the data taking phase) while still trying to reap the benefits of the parallel-enhanced CPU architectures, this paper explores what new languages could bring to the design of the next-generation frameworks. Parallel programming is still in an intensive phase of R&D and no silver bullet exists despite the 30+ years of literature on the subject. Yet, several parallel programming styles have emerged: actors, message passing, communicating sequential processes, task-based programming, data flow programming, ... to name a few. We present the work of the prototyping of a next-generation framework in new and expressive languages (python and Go) to investigate how code clarity and robustness are affected and what are the downsides of using languages younger than FORTRAN/C/C++.

ANNarchy: a code generation approach to neural simulations on parallel hardware

PubMed Central

Vitay, Julien; Dinkelbach, Helge Ü.; Hamker, Fred H.

2015-01-01

Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957

Facial Expression Generation from Speaker's Emotional States in Daily Conversation

NASA Astrophysics Data System (ADS)

Mori, Hiroki; Ohshima, Koh

A framework for generating facial expressions from emotional states in daily conversation is described. It provides a mapping between emotional states and facial expressions, where the former is represented by vectors with psychologically-defined abstract dimensions, and the latter is coded by the Facial Action Coding System. In order to obtain the mapping, parallel data with rated emotional states and facial expressions were collected for utterances of a female speaker, and a neural network was trained with the data. The effectiveness of proposed method is verified by a subjective evaluation test. As the result, the Mean Opinion Score with respect to the suitability of generated facial expression was 3.86 for the speaker, which was close to that of hand-made facial expressions.

Analysis of Intelligent Transportation Systems Using Model-Driven Simulations.

PubMed

Fernández-Isabel, Alberto; Fuentes-Fernández, Rubén

2015-06-15

Intelligent Transportation Systems (ITSs) integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use.

Analysis of Intelligent Transportation Systems Using Model-Driven Simulations

PubMed Central

Fernández-Isabel, Alberto; Fuentes-Fernández, Rubén

2015-01-01

Intelligent Transportation Systems (ITSs) integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use. PMID:26083232

Linking theory with qualitative research through study of stroke caregiving families.

PubMed

Pierce, Linda L; Steiner, Victoria; Cervantez Thompson, Teresa L; Friedemann, Marie-Luise

2014-01-01

This theoretical article outlines the deliberate process of applying a qualitative data analysis method rooted in Friedemann's Framework of Systemic Organization through the study of a web-based education and support intervention for stroke caregiving families. Directed by Friedemann's framework, the analytic method involved developing, refining, and using a coding rubric to explore interactive patterns between caregivers and care recipients from this 3-month feasibility study using this education and support intervention. Specifically, data were gathered from the intervention's web-based discussion component between caregivers and the nurse specialist, as well as from telephone caregiver interviews. A theoretical framework guided the process of developing and refining this coding rubric for the purpose of organizing data; but, more importantly, guided the investigators' thought processes, allowing them to extract rich information from the data set, as well as synthesize this information to generate a broad understanding of the caring situation. © 2013 Association of Rehabilitation Nurses.

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

National Combustion Code, a Multidisciplinary Combustor Design System, Will Be Transferred to the Commercial Sector

NASA Technical Reports Server (NTRS)

Steele, Gynelle C.

1999-01-01

The NASA Lewis Research Center and Flow Parametrics will enter into an agreement to commercialize the National Combustion Code (NCC). This multidisciplinary combustor design system utilizes computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. This integrated system can facilitate and enhance various phases of the design and analysis process.

featsel: A framework for benchmarking of feature selection algorithms and cost functions

NASA Astrophysics Data System (ADS)

Reis, Marcelo S.; Estrela, Gustavo; Ferreira, Carlos Eduardo; Barrera, Junior

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and cost functions for benchmarking experiments. We also provide illustrative examples, in which featsel outperforms the popular Weka workbench in feature selection procedures on data sets from the UCI Machine Learning Repository.

A Model-Based Approach for Bridging Virtual and Physical Sensor Nodes in a Hybrid Simulation Framework

PubMed Central

Mozumdar, Mohammad; Song, Zhen Yu; Lavagno, Luciano; Sangiovanni-Vincentelli, Alberto L.

2014-01-01

The Model Based Design (MBD) approach is a popular trend to speed up application development of embedded systems, which uses high-level abstractions to capture functional requirements in an executable manner, and which automates implementation code generation. Wireless Sensor Networks (WSNs) are an emerging very promising application area for embedded systems. However, there is a lack of tools in this area, which would allow an application developer to model a WSN application by using high level abstractions, simulate it mapped to a multi-node scenario for functional analysis, and finally use the refined model to automatically generate code for different WSN platforms. Motivated by this idea, in this paper we present a hybrid simulation framework that not only follows the MBD approach for WSN application development, but also interconnects a simulated sub-network with a physical sub-network and then allows one to co-simulate them, which is also known as Hardware-In-the-Loop (HIL) simulation. PMID:24960083

GCS component development cycle

NASA Astrophysics Data System (ADS)

Rodríguez, Jose A.; Macias, Rosa; Molgo, Jordi; Guerra, Dailos; Pi, Marti

2012-09-01

The GTC1 is an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). First light was at 13/07/2007 and since them it is in the operation phase. The GTC control system (GCS) is a distributed object & component oriented system based on RT-CORBA8 and it is responsible for the management and operation of the telescope, including its instrumentation. GCS has used the Rational Unified process (RUP9) in its development. RUP is an iterative software development process framework. After analysing (use cases) and designing (UML10) any of GCS subsystems, an initial component description of its interface is obtained and from that information a component specification is written. In order to improve the code productivity, GCS has adopted the code generation to transform this component specification into the skeleton of component classes based on a software framework, called Device Component Framework. Using the GCS development tools, based on javadoc and gcc, in only one step, the component is generated, compiled and deployed to be tested for the first time through our GUI inspector. The main advantages of this approach are the following: It reduces the learning curve of new developers and the development error rate, allows a systematic use of design patterns in the development and software reuse, speeds up the deliverables of the software product and massively increase the timescale, design consistency and design quality, and eliminates the future refactoring process required for the code.

Anisotropic Resistivity Forward Modelling Using Automatic Generated Higher-order Finite Element Codes

NASA Astrophysics Data System (ADS)

Wang, W.; Liu, J.

2016-12-01

Forward modelling is the general way to obtain responses of geoelectrical structures. Field investigators might find it useful for planning surveys and choosing optimal electrode configurations with respect to their targets. During the past few decades much effort has been put into the development of numerical forward codes, such as integral equation method, finite difference method and finite element method. Nowadays, most researchers prefer the finite element method (FEM) for its flexible meshing scheme, which can handle models with complex geometry. Resistivity Modelling with commercial sofewares such as ANSYS and COMSOL is convenient, but like working with a black box. Modifying the existed codes or developing new codes is somehow a long period. We present a new way to obtain resistivity forward modelling codes quickly, which is based on the commercial sofeware FEPG (Finite element Program Generator). Just with several demanding scripts, FEPG could generate FORTRAN program framework which can easily be altered to adjust our targets. By supposing the electric potential is quadratic in each element of a two-layer model, we obtain quite accurate results with errors less than 1%, while more than 5% errors could appear by linear FE codes. The anisotropic half-space model is supposed to concern vertical distributed fractures. The measured apparent resistivities along the fractures are bigger than results from its orthogonal direction, which are opposite of the true resistivities. Interpretation could be misunderstood if this anisotropic paradox is ignored. The technique we used can obtain scientific codes in a short time. The generated powerful FORTRAN codes could reach accurate results by higher-order assumption and can handle anisotropy to make better interpretations. The method we used could be expand easily to other domain where FE codes are needed.

Time Resolved Phonon Spectroscopy, Version 1.0

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

Goett, Johnny; Zhu, Brian

TRPS code was developed for the project "Time Resolved Phonon Spectroscopy". Routines contained in this piece of software were specially created to model phonon generation and tracking within materials that interact with ionizing radiation, particularly applicable to the modeling of cryogenic radiation detectors for dark matter and neutrino research. These routines were created to link seamlessly with the open source Geant4 framework for the modeling of radiation transport in matter, with the explicit intent of open sourcing them for eventual integration into that code base.

SpecBit, DecayBit and PrecisionBit: GAMBIT modules for computing mass spectra, particle decay rates and precision observables

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Kvellestad, Anders; McKay, James; Putze, Antje; Rogan, Chris; Scott, Pat; Weniger, Christoph; White, Martin

2018-01-01

We present the GAMBIT modules SpecBit, DecayBit and PrecisionBit. Together they provide a new framework for linking publicly available spectrum generators, decay codes and other precision observable calculations in a physically and statistically consistent manner. This allows users to automatically run various combinations of existing codes as if they are a single package. The modular design allows software packages fulfilling the same role to be exchanged freely at runtime, with the results presented in a common format that can easily be passed to downstream dark matter, collider and flavour codes. These modules constitute an essential part of the broader GAMBIT framework, a major new software package for performing global fits. In this paper we present the observable calculations, data, and likelihood functions implemented in the three modules, as well as the conventions and assumptions used in interfacing them with external codes. We also present 3-BIT-HIT, a command-line utility for computing mass spectra, couplings, decays and precision observables in the MSSM, which shows how the three modules can easily be used independently of GAMBIT.

Development of a Next Generation Concurrent Framework for the ATLAS Experiment

NASA Astrophysics Data System (ADS)

Calafiura, P.; Lampl, W.; Leggett, C.; Malon, D.; Stewart, G.; Wynne, B.

2015-12-01

The ATLAS experiment has successfully used its Gaudi/Athena software framework for data taking and analysis during the first LHC run, with billions of events successfully processed. However, the design of Gaudi/Athena dates from early 2000 and the software and the physics code has been written using a single threaded, serial design. This programming model has increasing difficulty in exploiting the potential of current CPUs, which offer their best performance only through taking full advantage of multiple cores and wide vector registers. Future CPU evolution will intensify this trend, with core counts increasing and memory per core falling. With current memory consumption for 64 bit ATLAS reconstruction in a high luminosity environment approaching 4GB, it will become impossible to fully occupy all cores in a machine without exhausting available memory. However, since maximizing performance per watt will be a key metric, a mechanism must be found to use all cores as efficiently as possible. In this paper we report on our progress with a practical demonstration of the use of multithreading in the ATLAS reconstruction software, using the GaudiHive framework. We have expanded support to Calorimeter, Inner Detector, and Tracking code, discussing what changes were necessary in order to allow the serially designed ATLAS code to run, both to the framework and to the tools and algorithms used. We report on both the performance gains, and what general lessons were learned about the code patterns that had been employed in the software and which patterns were identified as particularly problematic for multi-threading. We also present our findings on implementing a hybrid multi-threaded / multi-process framework, to take advantage of the strengths of each type of concurrency, while avoiding some of their corresponding limitations.

TABULATED EQUIVALENT SDR FLAMELET (TESF) MODEFL

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

KUNDU, PRITHWISH; AMEEN, mUHSIN MOHAMMED; UNNIKRISHNAN, UMESH

The code consists of an implementation of a novel tabulated combustion model for non-premixed flames in CFD solvers. This novel technique/model is used to implement an unsteady flamelet tabulation without using progress variables for non-premixed flames. It also has the capability to include history effects which is unique within tabulated flamelet models. The flamelet table generation code can be run in parallel to generate tables with large chemistry mechanisms in relatively short wall clock times. The combustion model/code reads these tables. This framework can be coupled with any CFD solver with RANS as well as LES turbulence models. This frameworkmore » enables CFD solvers to run large chemistry mechanisms with large number of grids at relatively lower computational costs. Currently it has been coupled with the Converge CFD code and validated against available experimental data. This model can be used to simulate non-premixed combustion in a variety of applications like reciprocating engines, gas turbines and industrial burners operating over a wide range of fuels.« less

JEWEL 2.0.0: directions for use

NASA Astrophysics Data System (ADS)

Zapp, Korinna

2014-02-01

In this publication the first official release of the Jewel 2.0.0 code [The first version Jewel 1 (Zapp et al. in Eur Phys J C 60:617, 2009) could only treat elastic scattering explicitly and the code was never published, The code can be downloaded from the official Jewel homepage http://jewel.hepforge.org] is presented. Jewel is a Monte Carlo event generator simulating QCD jet evolution in heavy-ion collisions. It treats the interplay of QCD radiation and re-scattering in a medium with fully microscopic dynamics in a consistent perturbative framework with minimal assumptions. After a qualitative introduction into the physics of Jewel detailed information about the practical aspects of using the code is given. The code is available from the official Jewel homepage http://jewel.hepforge.org.

ControlShell - A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Ullman, Marc A.; Chen, Vincent W.

1991-01-01

ControlShell is designed to enable modular design and impplementation of real-time software. It is an object-oriented tool-set for real-time software system programming. It provides a series of execution and data interchange mechansims that form a framework for building real-time applications. These mechanisms allow a component-based approach to real-time software generation and mangement. By defining a set of interface specifications for intermodule interaction, ControlShell provides a common platform that is the basis for real-time code development and exchange.

From Pixels to Response Maps: Discriminative Image Filtering for Face Alignment in the Wild.

PubMed

Asthana, Akshay; Zafeiriou, Stefanos; Tzimiropoulos, Georgios; Cheng, Shiyang; Pantic, Maja

2015-06-01

We propose a face alignment framework that relies on the texture model generated by the responses of discriminatively trained part-based filters. Unlike standard texture models built from pixel intensities or responses generated by generic filters (e.g. Gabor), our framework has two important advantages. First, by virtue of discriminative training, invariance to external variations (like identity, pose, illumination and expression) is achieved. Second, we show that the responses generated by discriminatively trained filters (or patch-experts) are sparse and can be modeled using a very small number of parameters. As a result, the optimization methods based on the proposed texture model can better cope with unseen variations. We illustrate this point by formulating both part-based and holistic approaches for generic face alignment and show that our framework outperforms the state-of-the-art on multiple "wild" databases. The code and dataset annotations are available for research purposes from http://ibug.doc.ic.ac.uk/resources.

A framework for streamlining research workflow in neuroscience and psychology

PubMed Central

Kubilius, Jonas

2014-01-01

Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad-hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for a faster, more robust code development and collaboration for researchers. PMID:24478691

Numerical Propulsion System Simulation Architecture

NASA Technical Reports Server (NTRS)

Naiman, Cynthia G.

2004-01-01

The Numerical Propulsion System Simulation (NPSS) is a framework for performing analysis of complex systems. Because the NPSS was developed using the object-oriented paradigm, the resulting architecture is an extensible and flexible framework that is currently being used by a diverse set of participants in government, academia, and the aerospace industry. NPSS is being used by over 15 different institutions to support rockets, hypersonics, power and propulsion, fuel cells, ground based power, and aerospace. Full system-level simulations as well as subsystems may be modeled using NPSS. The NPSS architecture enables the coupling of analyses at various levels of detail, which is called numerical zooming. The middleware used to enable zooming and distributed simulations is the Common Object Request Broker Architecture (CORBA). The NPSS Developer's Kit offers tools for the developer to generate CORBA-based components and wrap codes. The Developer's Kit enables distributed multi-fidelity and multi-discipline simulations, preserves proprietary and legacy codes, and facilitates addition of customized codes. The platforms supported are PC, Linux, HP, Sun, and SGI.

A domain specific language for performance portable molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

Do-it-yourself networks: a novel method of generating weighted networks.

PubMed

Shanafelt, D W; Salau, K R; Baggio, J A

2017-11-01

Network theory is finding applications in the life and social sciences for ecology, epidemiology, finance and social-ecological systems. While there are methods to generate specific types of networks, the broad literature is focused on generating unweighted networks. In this paper, we present a framework for generating weighted networks that satisfy user-defined criteria. Each criterion hierarchically defines a feature of the network and, in doing so, complements existing algorithms in the literature. We use a general example of ecological species dispersal to illustrate the method and provide open-source code for academic purposes.

Parametric Model of an Aerospike Rocket Engine

NASA Technical Reports Server (NTRS)

Korte, J. J.

2000-01-01

A suite of computer codes was assembled to simulate the performance of an aerospike engine and to generate the engine input for the Program to Optimize Simulated Trajectories. First an engine simulator module was developed that predicts the aerospike engine performance for a given mixture ratio, power level, thrust vectoring level, and altitude. This module was then used to rapidly generate the aerospike engine performance tables for axial thrust, normal thrust, pitching moment, and specific thrust. Parametric engine geometry was defined for use with the engine simulator module. The parametric model was also integrated into the iSIGHTI multidisciplinary framework so that alternate designs could be determined. The computer codes were used to support in-house conceptual studies of reusable launch vehicle designs.

Parametric Model of an Aerospike Rocket Engine

NASA Technical Reports Server (NTRS)

Korte, J. J.

2000-01-01

A suite of computer codes was assembled to simulate the performance of an aerospike engine and to generate the engine input for the Program to Optimize Simulated Trajectories. First an engine simulator module was developed that predicts the aerospike engine performance for a given mixture ratio, power level, thrust vectoring level, and altitude. This module was then used to rapidly generate the aerospike engine performance tables for axial thrust, normal thrust, pitching moment, and specific thrust. Parametric engine geometry was defined for use with the engine simulator module. The parametric model was also integrated into the iSIGHT multidisciplinary framework so that alternate designs could be determined. The computer codes were used to support in-house conceptual studies of reusable launch vehicle designs.

2-Step scalar deadzone quantization for bitplane image coding.

PubMed

Auli-Llinas, Francesc

2013-12-01

Modern lossy image coding systems generate a quality progressive codestream that, truncated at increasing rates, produces an image with decreasing distortion. Quality progressivity is commonly provided by an embedded quantizer that employs uniform scalar deadzone quantization (USDQ) together with a bitplane coding strategy. This paper introduces a 2-step scalar deadzone quantization (2SDQ) scheme that achieves same coding performance as that of USDQ while reducing the coding passes and the emitted symbols of the bitplane coding engine. This serves to reduce the computational costs of the codec and/or to code high dynamic range images. The main insights behind 2SDQ are the use of two quantization step sizes that approximate wavelet coefficients with more or less precision depending on their density, and a rate-distortion optimization technique that adjusts the distortion decreases produced when coding 2SDQ indexes. The integration of 2SDQ in current codecs is straightforward. The applicability and efficiency of 2SDQ are demonstrated within the framework of JPEG2000.

Developing CORBA-Based Distributed Scientific Applications From Legacy Fortran Programs

NASA Technical Reports Server (NTRS)

Sang, Janche; Kim, Chan; Lopez, Isaac

2000-01-01

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

How to review 4 million lines of ATLAS code

NASA Astrophysics Data System (ADS)

Stewart, Graeme A.; Lampl, Walter; ATLAS Collaboration

2017-10-01

As the ATLAS Experiment prepares to move to a multi-threaded framework (AthenaMT) for Run3, we are faced with the problem of how to migrate 4 million lines of C++ source code. This code has been written over the past 15 years and has often been adapted, re-written or extended to the changing requirements and circumstances of LHC data taking. The code was developed by different authors, many of whom are no longer active, and under the deep assumption that processing ATLAS data would be done in a serial fashion. In order to understand the scale of the problem faced by the ATLAS software community, and to plan appropriately the significant efforts posed by the new AthenaMT framework, ATLAS embarked on a wide ranging review of our offline code, covering all areas of activity: event generation, simulation, trigger, reconstruction. We discuss the difficulties in even logistically organising such reviews in an already busy community, how to examine areas in sufficient depth to learn key areas in need of upgrade, yet also to finish the reviews in a timely fashion. We show how the reviews were organised and how the ouptuts were captured in a way that the sub-system communities could then tackle the problems uncovered on a realistic timeline. Further, we discuss how the review has inuenced the overall planning for the Run 3 ATLAS offline code.

MEMOPS: data modelling and automatic code generation.

PubMed

Fogh, Rasmus H; Boucher, Wayne; Ionides, John M C; Vranken, Wim F; Stevens, Tim J; Laue, Ernest D

2010-03-25

In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces--APIs--currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.

FireHose Streaming Benchmarks

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

Karl Anderson, Steve Plimpton

2015-01-27

The FireHose Streaming Benchmarks are a suite of stream-processing benchmarks defined to enable comparison of streaming software and hardware, both quantitatively vis-a-vis the rate at which they can process data, and qualitatively by judging the effort involved to implement and run the benchmarks. Each benchmark has two parts. The first is a generator which produces and outputs datums at a high rate in a specific format. The second is an analytic which reads the stream of datums and is required to perform a well-defined calculation on the collection of datums, typically to find anomalous datums that have been created inmore » the stream by the generator. The FireHose suite provides code for the generators, sample code for the analytics (which users are free to re-implement in their own custom frameworks), and a precise definition of each benchmark calculation.« less

A software framework for pipelined arithmetic algorithms in field programmable gate arrays

NASA Astrophysics Data System (ADS)

Kim, J. B.; Won, E.

2018-03-01

Pipelined algorithms implemented in field programmable gate arrays are extensively used for hardware triggers in the modern experimental high energy physics field and the complexity of such algorithms increases rapidly. For development of such hardware triggers, algorithms are developed in C++, ported to hardware description language for synthesizing firmware, and then ported back to C++ for simulating the firmware response down to the single bit level. We present a C++ software framework which automatically simulates and generates hardware description language code for pipelined arithmetic algorithms.

A conceptual framework to facilitate the mental health of student nurses working with persons with intellectual disabilities.

PubMed

van Rensburg, Elsie S Janse; Poggenpoel, Marie; Myburgh, Chris

2015-11-25

Student nurses (SNs) experience emotional discomfort during placement in the clinical psychiatric learning environment. This may negatively influence their mental health. Limited support is available to assist both SNs working with persons with intellectual disabilities and nurse educators during clinical accompaniment. This article aims to discuss the generation of this framework to enhance student support. A theory-generative, qualitative, exploratory, descriptive, contextual design was utilised to develop the framework by applying four steps. In step 1 concept analysis identified the central concept through field work. Data were collected from 13 SNs purposively selected from a specific higher educational institution in Gauteng through two focus group interviews, reflective journals, a reflective letter, naïve sketches, drawings and field notes and analysed with thematic coding. The central concept was identified from the results, supported by a literature review and defined by essential attributes. The central concept was classified through a survey list and demonstrated in a model case. In step 2 the central concepts were placed into relationships with each other. The conceptual framework was described and evaluated in step 3 and guidelines for implementation were described in step 4. The focus of this article will be on generating the conceptual framework. The central concept was 'the facilitation of engagement on a deeper emotional level of SNs'. The conceptual framework was described and evaluated. The conceptual framework can enhance the educational practices of nurse educators and can SN's practices of care for persons with intellectual disabilities.

Voxel2MCNP: a framework for modeling, simulation and evaluation of radiation transport scenarios for Monte Carlo codes.

PubMed

Pölz, Stefan; Laubersheimer, Sven; Eberhardt, Jakob S; Harrendorf, Marco A; Keck, Thomas; Benzler, Andreas; Breustedt, Bastian

2013-08-21

The basic idea of Voxel2MCNP is to provide a framework supporting users in modeling radiation transport scenarios using voxel phantoms and other geometric models, generating corresponding input for the Monte Carlo code MCNPX, and evaluating simulation output. Applications at Karlsruhe Institute of Technology are primarily whole and partial body counter calibration and calculation of dose conversion coefficients. A new generic data model describing data related to radiation transport, including phantom and detector geometries and their properties, sources, tallies and materials, has been developed. It is modular and generally independent of the targeted Monte Carlo code. The data model has been implemented as an XML-based file format to facilitate data exchange, and integrated with Voxel2MCNP to provide a common interface for modeling, visualization, and evaluation of data. Also, extensions to allow compatibility with several file formats, such as ENSDF for nuclear structure properties and radioactive decay data, SimpleGeo for solid geometry modeling, ImageJ for voxel lattices, and MCNPX's MCTAL for simulation results have been added. The framework is presented and discussed in this paper and example workflows for body counter calibration and calculation of dose conversion coefficients is given to illustrate its application.

A flexible data-driven comorbidity feature extraction framework.

PubMed

Sideris, Costas; Pourhomayoun, Mohammad; Kalantarian, Haik; Sarrafzadeh, Majid

2016-06-01

Disease and symptom diagnostic codes are a valuable resource for classifying and predicting patient outcomes. In this paper, we propose a novel methodology for utilizing disease diagnostic information in a predictive machine learning framework. Our methodology relies on a novel, clustering-based feature extraction framework using disease diagnostic information. To reduce the data dimensionality, we identify disease clusters using co-occurrence statistics. We optimize the number of generated clusters in the training set and then utilize these clusters as features to predict patient severity of condition and patient readmission risk. We build our clustering and feature extraction algorithm using the 2012 National Inpatient Sample (NIS), Healthcare Cost and Utilization Project (HCUP) which contains 7 million hospital discharge records and ICD-9-CM codes. The proposed framework is tested on Ronald Reagan UCLA Medical Center Electronic Health Records (EHR) from 3041 Congestive Heart Failure (CHF) patients and the UCI 130-US diabetes dataset that includes admissions from 69,980 diabetic patients. We compare our cluster-based feature set with the commonly used comorbidity frameworks including Charlson's index, Elixhauser's comorbidities and their variations. The proposed approach was shown to have significant gains between 10.7-22.1% in predictive accuracy for CHF severity of condition prediction and 4.65-5.75% in diabetes readmission prediction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spiral: Automated Computing for Linear Transforms

NASA Astrophysics Data System (ADS)

Püschel, Markus

2010-09-01

Writing fast software has become extraordinarily difficult. For optimal performance, programs and their underlying algorithms have to be adapted to take full advantage of the platform's parallelism, memory hierarchy, and available instruction set. To make things worse, the best implementations are often platform-dependent and platforms are constantly evolving, which quickly renders libraries obsolete. We present Spiral, a domain-specific program generation system for important functionality used in signal processing and communication including linear transforms, filters, and other functions. Spiral completely replaces the human programmer. For a desired function, Spiral generates alternative algorithms, optimizes them, compiles them into programs, and intelligently searches for the best match to the computing platform. The main idea behind Spiral is a mathematical, declarative, domain-specific framework to represent algorithms and the use of rewriting systems to generate and optimize algorithms at a high level of abstraction. Experimental results show that the code generated by Spiral competes with, and sometimes outperforms, the best available human-written code.

Composing Data Parallel Code for a SPARQL Graph Engine

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

Castellana, Vito G.; Tumeo, Antonino; Villa, Oreste

Big data analytics process large amount of data to extract knowledge from them. Semantic databases are big data applications that adopt the Resource Description Framework (RDF) to structure metadata through a graph-based representation. The graph based representation provides several benefits, such as the possibility to perform in memory processing with large amounts of parallelism. SPARQL is a language used to perform queries on RDF-structured data through graph matching. In this paper we present a tool that automatically translates SPARQL queries to parallel graph crawling and graph matching operations. The tool also supports complex SPARQL constructs, which requires more than basicmore » graph matching for their implementation. The tool generates parallel code annotated with OpenMP pragmas for x86 Shared-memory Multiprocessors (SMPs). With respect to commercial database systems such as Virtuoso, our approach reduces memory occupation due to join operations and provides higher performance. We show the scaling of the automatically generated graph-matching code on a 48-core SMP.« less

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2018-01-15

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in parallel tiled code implementing Nussinov's RNA folding. Experimental results, received on modern Intel multi-core processors, demonstrate that this code outperforms known closely related implementations when the length of RNA strands is bigger than 2500.

Topological order and memory time in marginally-self-correcting quantum memory

NASA Astrophysics Data System (ADS)

Siva, Karthik; Yoshida, Beni

2017-03-01

We examine two proposals for marginally-self-correcting quantum memory: the cubic code by Haah and the welded code by Michnicki. In particular, we prove explicitly that they are absent of topological order above zero temperature, as their Gibbs ensembles can be prepared via a short-depth quantum circuit from classical ensembles. Our proof technique naturally gives rise to the notion of free energy associated with excitations. Further, we develop a framework for an ergodic decomposition of Davies generators in CSS codes which enables formal reduction to simpler classical memory problems. We then show that memory time in the welded code is doubly exponential in inverse temperature via the Peierls argument. These results introduce further connections between thermal topological order and self-correction from the viewpoint of free energy and quantum circuit depth.

Development of Parallel Computing Framework to Enhance Radiation Transport Code Capabilities for Rare Isotope Beam Facility Design

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

Kostin, Mikhail; Mokhov, Nikolai; Niita, Koji

A parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. It is intended to be used with older radiation transport codes implemented in Fortran77, Fortran 90 or C. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was developed and tested in conjunction with the MARS15 code. It is possible to use it with other codes such as PHITS, FLUKA andmore » MCNP after certain adjustments. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility can be used in single process calculations as well as in the parallel regime. The framework corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

Flexible configuration-interaction shell-model many-body solver

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

Johnson, Calvin W.; Ormand, W. Erich; McElvain, Kenneth S.

BIGSTICK Is a flexible configuration-Interaction open-source shell-model code for the many-fermion problem In a shell model (occupation representation) framework. BIGSTICK can generate energy spectra, static and transition one-body densities, and expectation values of scalar operators. Using the built-in Lanczos algorithm one can compute transition probabflity distributions and decompose wave functions into components defined by group theory.

The Interaction between Interoceptive and Action States within a Framework of Predictive Coding

PubMed Central

Marshall, Amanda C.; Gentsch, Antje; Schütz-Bosbach, Simone

2018-01-01

The notion of predictive coding assumes that perception is an iterative process between prior knowledge and sensory feedback. To date, this perspective has been primarily applied to exteroceptive perception as well as action and its associated phenomenological experiences such as agency. More recently, this predictive, inferential framework has been theoretically extended to interoception. This idea postulates that subjective feeling states are generated by top–down inferences made about internal and external causes of interoceptive afferents. While the processing of motor signals for action control and the emergence of selfhood have been studied extensively, the contributions of interoceptive input and especially the potential interaction of motor and interoceptive signals remain largely unaddressed. Here, we argue for a specific functional relation between motor and interoceptive awareness. Specifically, we implicate interoceptive predictions in the generation of subjective motor-related feeling states. Furthermore, we propose a distinction between reflexive and pre-reflexive modes of agentic action control and suggest that interoceptive input may affect each differently. Finally, we advocate the necessity of continuous interoceptive input for conscious forms of agentic action control. We conclude by discussing further research contributions that would allow for a fuller understanding of the interaction between agency and interoceptive awareness. PMID:29515495

Galen: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

PubMed

Trombert-Paviot, B; Rodrigues, J M; Rogers, J E; Baud, R; van der Haring, E; Rassinoux, A M; Abrial, V; Clavel, L; Idir, H

1999-01-01

GALEN has developed a new generation of terminology tools based on a language independent concept reference model using a compositional formalism allowing computer processing and multiple reuses. During the 4th framework program project Galen-In-Use we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures (CCAM) in France. On one hand we contributed to a language independent knowledge repository for multicultural Europe. On the other hand we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW to process French professional medical language rubrics produced by the national colleges of surgeons into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation on one hand we generate controlled French natural language to support the finalization of the linguistic labels in relation with the meanings of the conceptual system structure. On the other hand the classification manager of third generation proves to be very powerful to retrieve the initial professional rubrics with different categories of concepts within a semantic network.

A Grassroots Remote Sensing Toolkit Using Live Coding, Smartphones, Kites and Lightweight Drones

PubMed Central

Anderson, K.; Griffiths, D.; DeBell, L.; Hancock, S.; Duffy, J. P.; Shutler, J. D.; Reinhardt, W. J.; Griffiths, A.

2016-01-01

This manuscript describes the development of an android-based smartphone application for capturing aerial photographs and spatial metadata automatically, for use in grassroots mapping applications. The aim of the project was to exploit the plethora of on-board sensors within modern smartphones (accelerometer, GPS, compass, camera) to generate ready-to-use spatial data from lightweight aerial platforms such as drones or kites. A visual coding ‘scheme blocks’ framework was used to build the application (‘app’), so that users could customise their own data capture tools in the field. The paper reports on the coding framework, then shows the results of test flights from kites and lightweight drones and finally shows how open-source geospatial toolkits were used to generate geographical information system (GIS)-ready GeoTIFF images from the metadata stored by the app. Two Android smartphones were used in testing–a high specification OnePlus One handset and a lower cost Acer Liquid Z3 handset, to test the operational limits of the app on phones with different sensor sets. We demonstrate that best results were obtained when the phone was attached to a stable single line kite or to a gliding drone. Results show that engine or motor vibrations from powered aircraft required dampening to ensure capture of high quality images. We demonstrate how the products generated from the open-source processing workflow are easily used in GIS. The app can be downloaded freely from the Google store by searching for ‘UAV toolkit’ (UAV toolkit 2016), and used wherever an Android smartphone and aerial platform are available to deliver rapid spatial data (e.g. in supporting decision-making in humanitarian disaster-relief zones, in teaching or for grassroots remote sensing and democratic mapping). PMID:27144310

A Grassroots Remote Sensing Toolkit Using Live Coding, Smartphones, Kites and Lightweight Drones.

PubMed

Anderson, K; Griffiths, D; DeBell, L; Hancock, S; Duffy, J P; Shutler, J D; Reinhardt, W J; Griffiths, A

2016-01-01

This manuscript describes the development of an android-based smartphone application for capturing aerial photographs and spatial metadata automatically, for use in grassroots mapping applications. The aim of the project was to exploit the plethora of on-board sensors within modern smartphones (accelerometer, GPS, compass, camera) to generate ready-to-use spatial data from lightweight aerial platforms such as drones or kites. A visual coding 'scheme blocks' framework was used to build the application ('app'), so that users could customise their own data capture tools in the field. The paper reports on the coding framework, then shows the results of test flights from kites and lightweight drones and finally shows how open-source geospatial toolkits were used to generate geographical information system (GIS)-ready GeoTIFF images from the metadata stored by the app. Two Android smartphones were used in testing-a high specification OnePlus One handset and a lower cost Acer Liquid Z3 handset, to test the operational limits of the app on phones with different sensor sets. We demonstrate that best results were obtained when the phone was attached to a stable single line kite or to a gliding drone. Results show that engine or motor vibrations from powered aircraft required dampening to ensure capture of high quality images. We demonstrate how the products generated from the open-source processing workflow are easily used in GIS. The app can be downloaded freely from the Google store by searching for 'UAV toolkit' (UAV toolkit 2016), and used wherever an Android smartphone and aerial platform are available to deliver rapid spatial data (e.g. in supporting decision-making in humanitarian disaster-relief zones, in teaching or for grassroots remote sensing and democratic mapping).

Dyadic brain modelling, mirror systems and the ontogenetic ritualization of ape gesture

PubMed Central

Arbib, Michael; Ganesh, Varsha; Gasser, Brad

2014-01-01

The paper introduces dyadic brain modelling, offering both a framework for modelling the brains of interacting agents and a general framework for simulating and visualizing the interactions generated when the brains (and the two bodies) are each coded up in computational detail. It models selected neural mechanisms in ape brains supportive of social interactions, including putative mirror neuron systems inspired by macaque neurophysiology but augmented by increased access to proprioceptive state. Simulation results for a reduced version of the model show ritualized gesture emerging from interactions between a simulated child and mother ape. PMID:24778382

Dyadic brain modelling, mirror systems and the ontogenetic ritualization of ape gesture.

PubMed

Arbib, Michael; Ganesh, Varsha; Gasser, Brad

2014-01-01

The paper introduces dyadic brain modelling, offering both a framework for modelling the brains of interacting agents and a general framework for simulating and visualizing the interactions generated when the brains (and the two bodies) are each coded up in computational detail. It models selected neural mechanisms in ape brains supportive of social interactions, including putative mirror neuron systems inspired by macaque neurophysiology but augmented by increased access to proprioceptive state. Simulation results for a reduced version of the model show ritualized gesture emerging from interactions between a simulated child and mother ape.

Flexible, secure agent development framework

DOEpatents

Goldsmith,; Steven, Y [Rochester, MN

2009-04-07

While an agent generator is generating an intelligent agent, it can also evaluate the data processing platform on which it is executing, in order to assess a risk factor associated with operation of the agent generator on the data processing platform. The agent generator can retrieve from a location external to the data processing platform an open site that is configurable by the user, and load the open site into an agent substrate, thereby creating a development agent with code development capabilities. While an intelligent agent is executing a functional program on a data processing platform, it can also evaluate the data processing platform to assess a risk factor associated with performing the data processing function on the data processing platform.

Production code control system for hydrodynamics simulations

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

Slone, D.M.

1997-08-18

We describe how the Production Code Control System (pCCS), written in Perl, has been used to control and monitor the execution of a large hydrodynamics simulation code in a production environment. We have been able to integrate new, disparate, and often independent, applications into the PCCS framework without the need to modify any of our existing application codes. Both users and code developers see a consistent interface to the simulation code and associated applications regardless of the physical platform, whether an MPP, SMP, server, or desktop workstation. We will also describe our use of Perl to develop a configuration managementmore » system for the simulation code, as well as a code usage database and report generator. We used Perl to write a backplane that allows us plug in preprocessors, the hydrocode, postprocessors, visualization tools, persistent storage requests, and other codes. We need only teach PCCS a minimal amount about any new tool or code to essentially plug it in and make it usable to the hydrocode. PCCS has made it easier to link together disparate codes, since using Perl has removed the need to learn the idiosyncrasies of system or RPC programming. The text handling in Perl makes it easy to teach PCCS about new codes, or changes to existing codes.« less

New Parallel computing framework for radiation transport codes

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

Kostin, M.A.; /Michigan State U., NSCL; Mokhov, N.V.

A new parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was integrated with the MARS15 code, and an effort is under way to deploy it in PHITS. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility canmore » be used in single process calculations as well as in the parallel regime. Several checkpoint files can be merged into one thus combining results of several calculations. The framework also corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

A Framework for Testing Scientific Software: A Case Study of Testing Amsterdam Discrete Dipole Approximation Software

NASA Astrophysics Data System (ADS)

Shao, Hongbing

Software testing with scientific software systems often suffers from test oracle problem, i.e., lack of test oracles. Amsterdam discrete dipole approximation code (ADDA) is a scientific software system that can be used to simulate light scattering of scatterers of various types. Testing of ADDA suffers from "test oracle problem". In this thesis work, I established a testing framework to test scientific software systems and evaluated this framework using ADDA as a case study. To test ADDA, I first used CMMIE code as the pseudo oracle to test ADDA in simulating light scattering of a homogeneous sphere scatterer. Comparable results were obtained between ADDA and CMMIE code. This validated ADDA for use with homogeneous sphere scatterers. Then I used experimental result obtained for light scattering of a homogeneous sphere to validate use of ADDA with sphere scatterers. ADDA produced light scattering simulation comparable to the experimentally measured result. This further validated the use of ADDA for simulating light scattering of sphere scatterers. Then I used metamorphic testing to generate test cases covering scatterers of various geometries, orientations, homogeneity or non-homogeneity. ADDA was tested under each of these test cases and all tests passed. The use of statistical analysis together with metamorphic testing is discussed as a future direction. In short, using ADDA as a case study, I established a testing framework, including use of pseudo oracles, experimental results and the metamorphic testing techniques to test scientific software systems that suffer from test oracle problems. Each of these techniques is necessary and contributes to the testing of the software under test.

Aerodynamic shape optimization of Airfoils in 2-D incompressible flow

NASA Astrophysics Data System (ADS)

Rangasamy, Srinivethan; Upadhyay, Harshal; Somasekaran, Sandeep; Raghunath, Sreekanth

2010-11-01

An optimization framework was developed for maximizing the region of 2-D airfoil immersed in laminar flow with enhanced aerodynamic performance. It uses genetic algorithm over a population of 125, across 1000 generations, to optimize the airfoil. On a stand-alone computer, a run takes about an hour to obtain a converged solution. The airfoil geometry was generated using two Bezier curves; one to represent the thickness and the other the camber of the airfoil. The airfoil profile was generated by adding and subtracting the thickness curve from the camber curve. The coefficient of lift and drag was computed using potential velocity distribution obtained from panel code, and boundary layer transition prediction code was used to predict the location of onset of transition. The objective function of a particular design is evaluated as the weighted-average of aerodynamic characteristics at various angles of attacks. Optimization was carried out for several objective functions and the airfoil designs obtained were analyzed.

A Mixed Methods Approach to Code Stakeholder Beliefs in Urban Water Governance

NASA Astrophysics Data System (ADS)

Bell, E. V.; Henry, A.; Pivo, G.

2017-12-01

What is a reliable way to code policies to represent belief systems? The Advocacy Coalition Framework posits that public policy may be viewed as manifestations of belief systems. Belief systems include both ontological beliefs about cause-and-effect relationships and policy effectiveness, as well as normative beliefs about appropriate policy instruments and the relative value of different outcomes. The idea that belief systems are embodied in public policy is important for urban water governance because it trains our focus on belief conflict; this can help us understand why many water-scarce cities do not adopt innovative technology despite available scientific information. To date, there has been very little research on systematic, rigorous methods to measure the belief system content of public policies. We address this by testing the relationship between beliefs and policy participation to develop an innovative coding framework. With a focus on urban water governance in Tucson, Arizona, we analyze grey literature on local water management. Mentioned policies are coded into a typology of common approaches identified in urban water governance literature, which include regulation, education, price and non-price incentives, green infrastructure and other types of technology. We then survey local water stakeholders about their perceptions of these policies. Urban water governance requires coordination of organizations from multiple sectors, and we cannot assume that belief development and policy participation occur in a vacuum. Thus, we use a generalized exponential random graph model to test the relationship between perceptions and policy participation in the Tucson water governance network. We measure policy perceptions for organizations by averaging across their respective, affiliated respondents and generating a belief distance matrix of coordinating network participants. Similarly, we generate a distance matrix of these actors based on the frequency of their participation in each of the aforementioned policy types. By linking these perceptions and policies, we develop a coding frame that can supplement future content analysis when survey methods are not viable.

Iterative channel decoding of FEC-based multiple-description codes.

PubMed

Chang, Seok-Ho; Cosman, Pamela C; Milstein, Laurence B

2012-03-01

Multiple description coding has been receiving attention as a robust transmission framework for multimedia services. This paper studies the iterative decoding of FEC-based multiple description codes. The proposed decoding algorithms take advantage of the error detection capability of Reed-Solomon (RS) erasure codes. The information of correctly decoded RS codewords is exploited to enhance the error correction capability of the Viterbi algorithm at the next iteration of decoding. In the proposed algorithm, an intradescription interleaver is synergistically combined with the iterative decoder. The interleaver does not affect the performance of noniterative decoding but greatly enhances the performance when the system is iteratively decoded. We also address the optimal allocation of RS parity symbols for unequal error protection. For the optimal allocation in iterative decoding, we derive mathematical equations from which the probability distributions of description erasures can be generated in a simple way. The performance of the algorithm is evaluated over an orthogonal frequency-division multiplexing system. The results show that the performance of the multiple description codes is significantly enhanced.

On forward inferences of fast and slow readers. An eye movement study

PubMed Central

Hawelka, Stefan; Schuster, Sarah; Gagl, Benjamin; Hutzler, Florian

2015-01-01

Unimpaired readers process words incredibly fast and hence it was assumed that top-down processing, such as predicting upcoming words, would be too slow to play an appreciable role in reading. This runs counter the major postulate of the predictive coding framework that our brain continually predicts probable upcoming sensory events. This means, it may generate predictions about the probable upcoming word during reading (dubbed forward inferences). Trying to asses these contradictory assumptions, we evaluated the effect of the predictability of words in sentences on eye movement control during silent reading. Participants were a group of fluent (i.e., fast) and a group of speed-impaired (i.e., slow) readers. The findings indicate that fast readers generate forward inferences, whereas speed-impaired readers do so to a reduced extent - indicating a significant role of predictive coding for fluent reading. PMID:25678030

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers.

PubMed

Monge, Aurélien; Arrault, Alban; Marot, Christophe; Morin-Allory, Luc

2006-08-01

The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, 'drug-like' and 'lead-like' properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million 'drug-like' molecules among which, more than one million are 'lead-like'. This study has been carried out using 'ScreeningAssistant', a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with 'in-house' scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. 'ScreeningAssistant' is freely available under the GPL license.

A Framework for Cloudy Model Optimization and Database Storage

NASA Astrophysics Data System (ADS)

Calvén, Emilia; Helton, Andrew; Sankrit, Ravi

2018-01-01

We present a framework for producing Cloudy photoionization models of the nebular emission from novae ejecta and storing a subset of the results in SQL database format for later usage. The database can be searched for models best fitting observed spectral line ratios. Additionally, the framework includes an optimization feature that can be used in tandem with the database to search for and improve on models by creating new Cloudy models while, varying the parameters. The database search and optimization can be used to explore the structures of nebulae by deriving their properties from the best-fit models. The goal is to provide the community with a large database of Cloudy photoionization models, generated from parameters reflecting conditions within novae ejecta, that can be easily fitted to observed spectral lines; either by directly accessing the database using the framework code or by usage of a website specifically made for this purpose.

NIRP Core Software Suite v. 1.0

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

Whitener, Dustin Heath; Folz, Wesley; Vo, Duong

The NIRP Core Software Suite is a core set of code that supports multiple applications. It includes miscellaneous base code for data objects, mathematic equations, and user interface components; and the framework includes several fully-developed software applications that exist as stand-alone tools to compliment other applications. The stand-alone tools are described below. Analyst Manager: An application to manage contact information for people (analysts) that use the software products. This information is often included in generated reports and may be used to identify the owners of calculations. Radionuclide Viewer: An application for viewing the DCFPAK radiological data. Compliments the Mixture Managermore » tool. Mixture Manager: An application to create and manage radionuclides mixtures that are commonly used in other applications. High Explosive Manager: An application to manage explosives and their properties. Chart Viewer: An application to view charts of data (e.g. meteorology charts). Other applications may use this framework to create charts specific to their data needs.« less

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA

PubMed Central

Djebali, Sarah; Delaplace, Franck; Crollius, Hugues Roest

2006-01-01

Background Accurate and automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance to efficiently exploit the large volume of assembled genome sequences available to the community. Automatic methods have always been considered less reliable than human expertise. This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified. We hypothesized that replicating the accuracy of human annotators in an automatic method could be achieved by formalizing the rules and decisions that they use, in a mathematical formalism. Results We have developed Exogean, a flexible framework based on directed acyclic colored multigraphs (DACMs) that can represent biological objects (for example, mRNA, ESTs, protein alignments, exons) and relationships between them. Graphs are analyzed to process the information according to rules that replicate those used by human annotators. Simple individual starting objects given as input to Exogean are thus combined and synthesized into complex objects such as protein coding transcripts. Conclusion We show here, in the context of the EGASP project, that Exogean is currently the method that best reproduces protein coding gene annotations from human experts, in terms of identifying at least one exact coding sequence per gene. We discuss current limitations of the method and several avenues for improvement. PMID:16925841

Beyond standard model calculations with Sherpa

DOE PAGES

Höche, Stefan; Kuttimalai, Silvan; Schumann, Steffen; ...

2015-03-24

We present a fully automated framework as part of the Sherpa event generator for the computation of tree-level cross sections in beyond Standard Model scenarios, making use of model information given in the Universal FeynRules Output format. Elementary vertices are implemented into C++ code automatically and provided to the matrix-element generator Comix at runtime. Widths and branching ratios for unstable particles are computed from the same building blocks. The corresponding decays are simulated with spin correlations. Parton showers, QED radiation and hadronization are added by Sherpa, providing a full simulation of arbitrary BSM processes at the hadron level.

Beyond standard model calculations with Sherpa.

PubMed

Höche, Stefan; Kuttimalai, Silvan; Schumann, Steffen; Siegert, Frank

We present a fully automated framework as part of the Sherpa event generator for the computation of tree-level cross sections in Beyond Standard Model scenarios, making use of model information given in the Universal FeynRules Output format. Elementary vertices are implemented into C++ code automatically and provided to the matrix-element generator Comix at runtime. Widths and branching ratios for unstable particles are computed from the same building blocks. The corresponding decays are simulated with spin correlations. Parton showers, QED radiation and hadronization are added by Sherpa, providing a full simulation of arbitrary BSM processes at the hadron level.

A Simulation and Modeling Framework for Space Situational Awareness

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

Olivier, S S

This paper describes the development and initial demonstration of a new, integrated modeling and simulation framework, encompassing the space situational awareness enterprise, for quantitatively assessing the benefit of specific sensor systems, technologies and data analysis techniques. The framework is based on a flexible, scalable architecture to enable efficient, physics-based simulation of the current SSA enterprise, and to accommodate future advancements in SSA systems. In particular, the code is designed to take advantage of massively parallel computer systems available, for example, at Lawrence Livermore National Laboratory. The details of the modeling and simulation framework are described, including hydrodynamic models of satellitemore » intercept and debris generation, orbital propagation algorithms, radar cross section calculations, optical brightness calculations, generic radar system models, generic optical system models, specific Space Surveillance Network models, object detection algorithms, orbit determination algorithms, and visualization tools. The use of this integrated simulation and modeling framework on a specific scenario involving space debris is demonstrated.« less

Prediction of Acoustic Loads Generated by Propulsion Systems

NASA Technical Reports Server (NTRS)

Perez, Linamaria; Allgood, Daniel C.

2011-01-01

NASA Stennis Space Center is one of the nation's premier facilities for conducting large-scale rocket engine testing. As liquid rocket engines vary in size, so do the acoustic loads that they produce. When these acoustic loads reach very high levels they may cause damages both to humans and to actual structures surrounding the testing area. To prevent these damages, prediction tools are used to estimate the spectral content and levels of the acoustics being generated by the rocket engine plumes and model their propagation through the surrounding atmosphere. Prior to the current work, two different acoustic prediction tools were being implemented at Stennis Space Center, each having their own advantages and disadvantages depending on the application. Therefore, a new prediction tool was created, using NASA SP-8072 handbook as a guide, which would replicate the same prediction methods as the previous codes, but eliminate any of the drawbacks the individual codes had. Aside from replicating the previous modeling capability in a single framework, additional modeling functions were added thereby expanding the current modeling capability. To verify that the new code could reproduce the same predictions as the previous codes, two verification test cases were defined. These verification test cases also served as validation cases as the predicted results were compared to actual test data.

Development and Evaluation of Vectorised and Multi-Core Event Reconstruction Algorithms within the CMS Software Framework

NASA Astrophysics Data System (ADS)

Hauth, T.; Innocente and, V.; Piparo, D.

2012-12-01

The processing of data acquired by the CMS detector at LHC is carried out with an object-oriented C++ software framework: CMSSW. With the increasing luminosity delivered by the LHC, the treatment of recorded data requires extraordinary large computing resources, also in terms of CPU usage. A possible solution to cope with this task is the exploitation of the features offered by the latest microprocessor architectures. Modern CPUs present several vector units, the capacity of which is growing steadily with the introduction of new processor generations. Moreover, an increasing number of cores per die is offered by the main vendors, even on consumer hardware. Most recent C++ compilers provide facilities to take advantage of such innovations, either by explicit statements in the programs sources or automatically adapting the generated machine instructions to the available hardware, without the need of modifying the existing code base. Programming techniques to implement reconstruction algorithms and optimised data structures are presented, that aim to scalable vectorization and parallelization of the calculations. One of their features is the usage of new language features of the C++11 standard. Portions of the CMSSW framework are illustrated which have been found to be especially profitable for the application of vectorization and multi-threading techniques. Specific utility components have been developed to help vectorization and parallelization. They can easily become part of a larger common library. To conclude, careful measurements are described, which show the execution speedups achieved via vectorised and multi-threaded code in the context of CMSSW.

A conceptual framework for evaluating impairments in myasthenia gravis.

PubMed

Barnett, Carolina; Bril, Vera; Kapral, Moira; Kulkarni, Abhaya; Davis, Aileen M

2014-01-01

Myasthenia gravis is characterized by weakness and fatigability of different muscle groups, including ocular, bulbar and the limbs. Therefore, a measure of disease severity at the impairment level in myasthenia needs to reflect all the relevant impairments, as well as their variations with activity and fatigue. We conducted a qualitative study of patients with myasthenia, to explore their experiences and related impairments, aimed at developing a conceptual framework of disease severity at the impairment level in myasthenia gravis. Twenty patients representing the spectrum of disease participated in semi-structured interviews. Interviews were recorded and the transcripts were analyzed by content analysis using an inductive approach with line-by-line open coding. Themes were generated from these codes. Two main themes were identified: the severity of the impairments and fatigability (i.e., triggering or worsening of an impairment with activity). The impairments were further classified within body regions (ocular, bulbar and axial/limbs). Fatigability was described as a phenomenon affecting the whole body but also affecting specific impairments, and was associated with fluctuation of the symptoms. Patients were concerned that clinical examination at a single point in time might not reflect their true clinical state due to fatigability and fluctuations in severity. This conceptual framework reflects the relevance of both severity and fatigability in understanding impairment-based disease severity in myasthenia. This framework could inform the development of impairment measures in myasthenia gravis.

Framework GRASP: routine library for optimize processing of aerosol remote sensing observation

NASA Astrophysics Data System (ADS)

Fuertes, David; Torres, Benjamin; Dubovik, Oleg; Litvinov, Pavel; Lapyonok, Tatyana; Ducos, Fabrice; Aspetsberger, Michael; Federspiel, Christian

The present the development of a Framework for the Generalized Retrieval of Aerosol and Surface Properties (GRASP) developed by Dubovik et al., (2011). The framework is a source code project that attempts to strengthen the value of the GRASP inversion algorithm by transforming it into a library that will be used later for a group of customized application modules. The functions of the independent modules include the managing of the configuration of the code execution, as well as preparation of the input and output. The framework provides a number of advantages in utilization of the code. First, it implements loading data to the core of the scientific code directly from memory without passing through intermediary files on disk. Second, the framework allows consecutive use of the inversion code without the re-initiation of the core routine when new input is received. These features are essential for optimizing performance of the data production in processing of large observation sets, such as satellite images by the GRASP. Furthermore, the framework is a very convenient tool for further development, because this open-source platform is easily extended for implementing new features. For example, it could accommodate loading of raw data directly onto the inversion code from a specific instrument not included in default settings of the software. Finally, it will be demonstrated that from the user point of view, the framework provides a flexible, powerful and informative configuration system.

GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

PubMed

Trombert-Paviot, B; Rodrigues, J M; Rogers, J E; Baud, R; van der Haring, E; Rassinoux, A M; Abrial, V; Clavel, L; Idir, H

2000-09-01

Generalised architecture for languages, encyclopedia and nomenclatures in medicine (GALEN) has developed a new generation of terminology tools based on a language independent model describing the semantics and allowing computer processing and multiple reuses as well as natural language understanding systems applications to facilitate the sharing and maintaining of consistent medical knowledge. During the European Union 4 Th. framework program project GALEN-IN-USE and later on within two contracts with the national health authorities we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures named CCAM in a minority language country, France. On one hand, we contributed to a language independent knowledge repository and multilingual semantic dictionaries for multicultural Europe. On the other hand, we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW (for classification workbench) to process French professional medical language rubrics produced by the national colleges of surgeons domain experts into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation, on one hand, we generate with the LNAT natural language generator controlled French natural language to support the finalization of the linguistic labels (first generation) in relation with the meanings of the conceptual system structure. On the other hand, the Claw classification manager proves to be very powerful to retrieve the initial domain experts rubrics list with different categories of concepts (second generation) within a semantic structured representation (third generation) bridge to the electronic patient record detailed terminology.

Integrated modelling framework for short pulse high energy density physics experiments

NASA Astrophysics Data System (ADS)

Sircombe, N. J.; Hughes, S. J.; Ramsay, M. G.

2016-03-01

Modelling experimental campaigns on the Orion laser at AWE, and developing a viable point-design for fast ignition (FI), calls for a multi-scale approach; a complete description of the problem would require an extensive range of physics which cannot realistically be included in a single code. For modelling the laser-plasma interaction (LPI) we need a fine mesh which can capture the dispersion of electromagnetic waves, and a kinetic model for each plasma species. In the dense material of the bulk target, away from the LPI region, collisional physics dominates. The transport of hot particles generated by the action of the laser is dependent on their slowing and stopping in the dense material and their need to draw a return current. These effects will heat the target, which in turn influences transport. On longer timescales, the hydrodynamic response of the target will begin to play a role as the pressure generated from isochoric heating begins to take effect. Recent effort at AWE [1] has focussed on the development of an integrated code suite based on: the particle in cell code EPOCH, to model LPI; the Monte-Carlo electron transport code THOR, to model the onward transport of hot electrons; and the radiation hydrodynamics code CORVUS, to model the hydrodynamic response of the target. We outline the methodology adopted, elucidate on the advantages of a robustly integrated code suite compared to a single code approach, demonstrate the integrated code suite's application to modelling the heating of buried layers on Orion, and assess the potential of such experiments for the validation of modelling capability in advance of more ambitious HEDP experiments, as a step towards a predictive modelling capability for FI.

Algorithm Building and Learning Programming Languages Using a New Educational Paradigm

NASA Astrophysics Data System (ADS)

Jain, Anshul K.; Singhal, Manik; Gupta, Manu Sheel

2011-08-01

This research paper presents a new concept of using a single tool to associate syntax of various programming languages, algorithms and basic coding techniques. A simple framework has been programmed in Python that helps students learn skills to develop algorithms, and implement them in various programming languages. The tool provides an innovative and a unified graphical user interface for development of multimedia objects, educational games and applications. It also aids collaborative learning amongst students and teachers through an integrated mechanism based on Remote Procedure Calls. The paper also elucidates an innovative method for code generation to enable students to learn the basics of programming languages using drag-n-drop methods for image objects.

Conversion of Component-Based Point Definition to VSP Model and Higher Order Meshing

NASA Technical Reports Server (NTRS)

Ordaz, Irian

2011-01-01

Vehicle Sketch Pad (VSP) has become a powerful conceptual and parametric geometry tool with numerous export capabilities for third-party analysis codes as well as robust surface meshing capabilities for computational fluid dynamics (CFD) analysis. However, a capability gap currently exists for reconstructing a fully parametric VSP model of a geometry generated by third-party software. A computer code called GEO2VSP has been developed to close this gap and to allow the integration of VSP into a closed-loop geometry design process with other third-party design tools. Furthermore, the automated CFD surface meshing capability of VSP are demonstrated for component-based point definition geometries in a conceptual analysis and design framework.

Study on a novel laser target detection system based on software radio technique

NASA Astrophysics Data System (ADS)

Song, Song; Deng, Jia-hao; Wang, Xue-tian; Gao, Zhen; Sun, Ji; Sun, Zhi-hui

2008-12-01

This paper presents that software radio technique is applied to laser target detection system with the pseudo-random code modulation. Based on the theory of software radio, the basic framework of the system, hardware platform, and the implementation of the software system are detailed. Also, the block diagram of the system, DSP circuit, block diagram of the pseudo-random code generator, and soft flow diagram of signal processing are designed. Experimental results have shown that the application of software radio technique provides a novel method to realize the modularization, miniaturization and intelligence of the laser target detection system, and the upgrade and improvement of the system will become simpler, more convenient, and cheaper.

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

PubMed

Haydarlou, Reza; Jacobsen, Annika; Bonzanni, Nicola; Feenstra, K Anton; Abeln, Sanne; Heringa, Jaap

2016-06-15

Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model. To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language. The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF CONTACT: j.heringa@vu.nl. © The Author 2016. Published by Oxford University Press.

Compiler-Driven Performance Optimization and Tuning for Multicore Architectures

DTIC Science & Technology

2015-04-10

develop a powerful system for auto-tuning of library routines and compute-intensive kernels, driven by the Pluto system for multicores that we are...kernels, driven by the Pluto system for multicores that we are developing. The work here is motivated by recent advances in two major areas of...automatic C-to-CUDA code generator using a polyhedral compiler transformation framework. We have used and adapted PLUTO (our state-of-the-art tool

Support for Systematic Code Reviews with the SCRUB Tool

NASA Technical Reports Server (NTRS)

Holzmann, Gerald J.

2010-01-01

SCRUB is a code review tool that supports both large, team-based software development efforts (e.g., for mission software) as well as individual tasks. The tool was developed at JPL to support a new, streamlined code review process that combines human-generated review reports with program-generated review reports from a customizable range of state-of-the-art source code analyzers. The leading commercial tools include Codesonar, Coverity, and Klocwork, each of which can achieve a reasonably low rate of false-positives in the warnings that they generate. The time required to analyze code with these tools can vary greatly. In each case, however, the tools produce results that would be difficult to realize with human code inspections alone. There is little overlap in the results produced by the different analyzers, and each analyzer used generally increases the effectiveness of the overall effort. The SCRUB tool allows all reports to be accessed through a single, uniform interface (see figure) that facilitates brows ing code and reports. Improvements over existing software include significant simplification, and leveraging of a range of commercial, static source code analyzers in a single, uniform framework. The tool runs as a small stand-alone application, avoiding the security problems related to tools based on Web browsers. A developer or reviewer, for instance, must have already obtained access rights to a code base before that code can be browsed and reviewed with the SCRUB tool. The tool cannot open any files or folders to which the user does not already have access. This means that the tool does not need to enforce or administer any additional security policies. The analysis results presented through the SCRUB tool s user interface are always computed off-line, given that, especially for larger projects, this computation can take longer than appropriate for interactive tool use. The recommended code review process that is supported by the SCRUB tool consists of three phases: Code Review, Developer Response, and Closeout Resolution. In the Code Review phase, all tool-based analysis reports are generated, and specific comments from expert code reviewers are entered into the SCRUB tool. In the second phase, Developer Response, the developer is asked to respond to each comment and tool-report that was produced, either agreeing or disagreeing to provide a fix that addresses the issue that was raised. In the third phase, Closeout Resolution, all disagreements are discussed in a meeting of all parties involved, and a resolution is made for all disagreements. The first two phases generally take one week each, and the third phase is concluded in a single closeout meeting.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model.

Adapting the coping in deliberation (CODE) framework: a multi-method approach in the context of familial ovarian cancer risk management.

PubMed

Witt, Jana; Elwyn, Glyn; Wood, Fiona; Rogers, Mark T; Menon, Usha; Brain, Kate

2014-11-01

To test whether the coping in deliberation (CODE) framework can be adapted to a specific preference-sensitive medical decision: risk-reducing bilateral salpingo-oophorectomy (RRSO) in women at increased risk of ovarian cancer. We performed a systematic literature search to identify issues important to women during deliberations about RRSO. Three focus groups with patients (most were pre-menopausal and untested for genetic mutations) and 11 interviews with health professionals were conducted to determine which issues mattered in the UK context. Data were used to adapt the generic CODE framework. The literature search yielded 49 relevant studies, which highlighted various issues and coping options important during deliberations, including mutation status, risks of surgery, family obligations, physician recommendation, peer support and reliable information sources. Consultations with UK stakeholders confirmed most of these factors as pertinent influences on deliberations. Questions in the generic framework were adapted to reflect the issues and coping options identified. The generic CODE framework was readily adapted to a specific preference-sensitive medical decision, showing that deliberations and coping are linked during deliberations about RRSO. Adapted versions of the CODE framework may be used to develop tailored decision support methods and materials in order to improve patient-centred care. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A new theory of development: the generation of complexity in ontogenesis.

PubMed

Barbieri, Marcello

2016-03-13

Today there is a very wide consensus on the idea that embryonic development is the result of a genetic programme and of epigenetic processes. Many models have been proposed in this theoretical framework to account for the various aspects of development, and virtually all of them have one thing in common: they do not acknowledge the presence of organic codes (codes between organic molecules) in ontogenesis. Here it is argued instead that embryonic development is a convergent increase in complexity that necessarily requires organic codes and organic memories, and a few examples of such codes are described. This is the code theory of development, a theory that was originally inspired by an algorithm that is capable of reconstructing structures from incomplete information, an algorithm that here is briefly summarized because it makes it intuitively appealing how a convergent increase in complexity can be achieved. The main thesis of the new theory is that the presence of organic codes in ontogenesis is not only a theoretical necessity but, first and foremost, an idea that can be tested and that has already been found to be in agreement with the evidence. © 2016 The Author(s).

RELAP-7 Closure Correlations

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

Zou, Ling; Berry, R. A.; Martineau, R. C.

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework, MOOSE (Multi-Physics Object Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s and TRACE’s capabilities and extends their analysis capabilities for all reactor system simulation scenarios. The RELAP-7 codemore » utilizes the well-posed 7-equation two-phase flow model for compressible two-phase flow. Closure models used in the TRACE code has been reviewed and selected to reflect the progress made during the past decades and provide a basis for the colure correlations implemented in the RELAP-7 code. This document provides a summary on the closure correlations that are currently implemented in the RELAP-7 code. The closure correlations include sub-grid models that describe interactions between the fluids and the flow channel, and interactions between the two phases.« less

PFLOTRAN: Reactive Flow & Transport Code for Use on Laptops to Leadership-Class Supercomputers

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

Hammond, Glenn E.; Lichtner, Peter C.; Lu, Chuan

PFLOTRAN, a next-generation reactive flow and transport code for modeling subsurface processes, has been designed from the ground up to run efficiently on machines ranging from leadership-class supercomputers to laptops. Based on an object-oriented design, the code is easily extensible to incorporate additional processes. It can interface seamlessly with Fortran 9X, C and C++ codes. Domain decomposition parallelism is employed, with the PETSc parallel framework used to manage parallel solvers, data structures and communication. Features of the code include a modular input file, implementation of high-performance I/O using parallel HDF5, ability to perform multiple realization simulations with multiple processors permore » realization in a seamless manner, and multiple modes for multiphase flow and multicomponent geochemical transport. Chemical reactions currently implemented in the code include homogeneous aqueous complexing reactions and heterogeneous mineral precipitation/dissolution, ion exchange, surface complexation and a multirate kinetic sorption model. PFLOTRAN has demonstrated petascale performance using 2{sup 17} processor cores with over 2 billion degrees of freedom. Accomplishments achieved to date include applications to the Hanford 300 Area and modeling CO{sub 2} sequestration in deep geologic formations.« less

Evaluation of the efficiency and fault density of software generated by code generators

NASA Technical Reports Server (NTRS)

Schreur, Barbara

1993-01-01

Flight computers and flight software are used for GN&C (guidance, navigation, and control), engine controllers, and avionics during missions. The software development requires the generation of a considerable amount of code. The engineers who generate the code make mistakes and the generation of a large body of code with high reliability requires considerable time. Computer-aided software engineering (CASE) tools are available which generates code automatically with inputs through graphical interfaces. These tools are referred to as code generators. In theory, code generators could write highly reliable code quickly and inexpensively. The various code generators offer different levels of reliability checking. Some check only the finished product while some allow checking of individual modules and combined sets of modules as well. Considering NASA's requirement for reliability, an in house manually generated code is needed. Furthermore, automatically generated code is reputed to be as efficient as the best manually generated code when executed. In house verification is warranted.

A Framework for Identifying and Classifying Undergraduate Student Proof Errors

ERIC Educational Resources Information Center

Strickland, S.; Rand, B.

2016-01-01

This paper describes a framework for identifying, classifying, and coding student proofs, modified from existing proof-grading rubrics. The framework includes 20 common errors, as well as categories for interpreting the severity of the error. The coding scheme is intended for use in a classroom context, for providing effective student feedback. In…

Interface Control Document for the EMPACT Module that Estimates Electric Power Transmission System Response to EMP-Caused Damage

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

Werley, Kenneth Alan; Mccown, Andrew William

The EPREP code is designed to evaluate the effects of an Electro-Magnetic Pulse (EMP) on the electric power transmission system. The EPREP code embodies an umbrella framework that allows a user to set up analysis conditions and to examine analysis results. The code links to three major physics/engineering modules. The first module describes the EM wave in space and time. The second module evaluates the damage caused by the wave on specific electric power (EP) transmission system components. The third module evaluates the consequence of the damaged network on its (reduced) ability to provide electric power to meet demand. Thismore » third module is the focus of the present paper. The EMPACT code serves as the third module. The EMPACT name denotes EMP effects on Alternating Current Transmission systems. The EMPACT algorithms compute electric power transmission network flow solutions under severely damaged network conditions. Initial solutions are often characterized by unacceptible network conditions including line overloads and bad voltages. The EMPACT code contains algorithms to adjust optimally network parameters to eliminate network problems while minimizing outages. System adjustments include automatically adjusting control equipment (generator V control, variable transformers, and variable shunts), as well as non-automatic control of generator power settings and minimal load shedding. The goal is to evaluate the minimal loss of customer load under equilibrium (steady-state) conditions during peak demand.« less

How Do Surgery Students Use Written Language to Say What They See? A Framework to Understand Medical Students' Written Evaluations of Their Teachers.

PubMed

Lim, David W; White, Jonathan S

2015-11-01

There remains debate regarding the value of the written comments that medical students are traditionally asked to provide to evaluate the teaching they receive. The purpose of this study was to examine written teaching evaluations to understand how medical students conceptualize teachers' behaviors and performance. All written comments collected from medical students about teachers in the two surgery clerkships at the University of Alberta in 2009-2010 and 2010-2011 were collated and anonymized. A grounded theory approach was used for analysis, with iterative reading and open coding to identify recurring themes. A framework capturing variations observed in the data was generated until data saturation was achieved. Domains and subdomains were named using an in situ coding approach. The conceptual framework contained three main domains: "Physician as Teacher," "Physician as Person," and "Physician as Physician." Under "Physician as Teacher," students commented on specific acts of teaching and subjective perceptions of an educator's teaching values. Under the "Physician as Physician" domain, students commented on elements of their educator's physicianship, including communication and collaborative skills, medical expertise, professionalism, and role modeling. Under "Physician as Person," students commented on how both positive and negative personality traits impacted their learning. This framework describes how medical students perceive their teachers and how they use written language to attach meaning to the behaviors they observe. Such a framework can be used to help students provide more constructive feedback to teachers and to assist in faculty development efforts aimed at improving teaching performance.

New virtual laboratories presenting advanced motion control concepts

NASA Astrophysics Data System (ADS)

Goubej, Martin; Krejčí, Alois; Reitinger, Jan

2015-11-01

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

Indirect Observation in Everyday Contexts: Concepts and Methodological Guidelines within a Mixed Methods Framework.

PubMed

Anguera, M Teresa; Portell, Mariona; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana

2018-01-01

Indirect observation is a recent concept in systematic observation. It largely involves analyzing textual material generated either indirectly from transcriptions of audio recordings of verbal behavior in natural settings (e.g., conversation, group discussions) or directly from narratives (e.g., letters of complaint, tweets, forum posts). It may also feature seemingly unobtrusive objects that can provide relevant insights into daily routines. All these materials constitute an extremely rich source of information for studying everyday life, and they are continuously growing with the burgeoning of new technologies for data recording, dissemination, and storage. Narratives are an excellent vehicle for studying everyday life, and quantitization is proposed as a means of integrating qualitative and quantitative elements. However, this analysis requires a structured system that enables researchers to analyze varying forms and sources of information objectively. In this paper, we present a methodological framework detailing the steps and decisions required to quantitatively analyze a set of data that was originally qualitative. We provide guidelines on study dimensions, text segmentation criteria, ad hoc observation instruments, data quality controls, and coding and preparation of text for quantitative analysis. The quality control stage is essential to ensure that the code matrices generated from the qualitative data are reliable. We provide examples of how an indirect observation study can produce data for quantitative analysis and also describe the different software tools available for the various stages of the process. The proposed method is framed within a specific mixed methods approach that involves collecting qualitative data and subsequently transforming these into matrices of codes (not frequencies) for quantitative analysis to detect underlying structures and behavioral patterns. The data collection and quality control procedures fully meet the requirement of flexibility and provide new perspectives on data integration in the study of biopsychosocial aspects in everyday contexts.

Examples of Linking Codes Within GeoFramework

NASA Astrophysics Data System (ADS)

Tan, E.; Choi, E.; Thoutireddy, P.; Aivazis, M.; Lavier, L.; Quenette, S.; Gurnis, M.

2003-12-01

Geological processes usually encompass a broad spectrum of length and time scales. Traditionally, a modeling code (solver) is written to solve a problem with specific length and time scales in mind. The utility of the solver beyond the designated purpose is usually limited. Furthermore, two distinct solvers, even if each can solve complementary parts of a new problem, are difficult to link together to solve the problem as a whole. For example, Lagrangian deformation model with visco-elastoplastic crust is used to study deformation near plate boundary. Ideally, the driving force of the deformation should be derived from underlying mantle convection, and it requires linking the Lagrangian deformation model with a Eulerian mantle convection model. As our understanding of geological processes evolves, the need of integrated modeling codes, which should reuse existing codes as much as possible, begins to surface. GeoFramework project addresses this need by developing a suite of reusable and re-combinable tools for the Earth science community. GeoFramework is based on and extends Pyre, a Python-based modeling framework, recently developed to link solid (Lagrangian) and fluid (Eulerian) models, as well as mesh generators, visualization packages, and databases, with one another for engineering applications. Under the framework, a solver is aware of the existence of other solvers and can interact with each other via exchanging information across adjacent boundary. A solver needs to conform a standard interface and provide its own implementation for exchanging boundary information. The framework also provides facilities to control the coordination between interacting solvers. We will show an example of linking two solvers within GeoFramework. CitcomS is a finite element code which solves for thermal convection within a 3D spherical shell. CitcomS can solve for problems either within a full spherical (global) domain or a restricted (regional) domain of a full sphere by using different meshers. We can embed a regional CitcomS solver within a global CitcomS solver. We not that linking instances of the same solver is conceptually equivalent to linking to different solvers. The global solver has a coarser grid and a longer stable time step than the regional solver. Therefore, a global-solver time step consists of several regional-solver time steps. The time-marching scheme is described below. First, the global solver is advanced one global-solver time step. Then, the regional solver is advanced for several regional-solver time steps until it catches up global solver. Within each regional-solver time step, the velocity field of the global solver is interpolated in time and then is imposed to the regional solver as boundary conditions. Finally, the temperature field of the regional solver is extrapolated in space and is fed back to the global. These two solvers are linked and synchronized by the time-marching scheme. An effort to embed a visco-elastoplastic representation of the crust within viscous mantle flow is underway.

EBR-II Static Neutronic Calculations by PHISICS / MCNP6 codes

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

Paolo Balestra; Carlo Parisi; Andrea Alfonsi

2016-02-01

The International Atomic Energy Agency (IAEA) launched a Coordinated Research Project (CRP) on the Shutdown Heat Removal Tests (SHRT) performed in the '80s at the Experimental fast Breeder Reactor EBR-II, USA. The scope of the CRP is to improve and validate the simulation tools for the study and the design of the liquid metal cooled fast reactors. Moreover, training of the next generation of fast reactor analysts is being also considered the other scope of the CRP. In this framework, a static neutronic model was developed, using state-of-the art neutron transport codes like SCALE/PHISICS (deterministic solution) and MCNP6 (stochastic solution).more » Comparison between both solutions is briefly illustrated in this summary.« less

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

Carothers, Christopher D.; Meredith, Jeremy S.; Blanco, Marc

Performance modeling of extreme-scale applications on accurate representations of potential architectures is critical for designing next generation supercomputing systems because it is impractical to construct prototype systems at scale with new network hardware in order to explore designs and policies. However, these simulations often rely on static application traces that can be difficult to work with because of their size and lack of flexibility to extend or scale up without rerunning the original application. To address this problem, we have created a new technique for generating scalable, flexible workloads from real applications, we have implemented a prototype, called Durango, thatmore » combines a proven analytical performance modeling language, Aspen, with the massively parallel HPC network modeling capabilities of the CODES framework.Our models are compact, parameterized and representative of real applications with computation events. They are not resource intensive to create and are portable across simulator environments. We demonstrate the utility of Durango by simulating the LULESH application in the CODES simulation environment on several topologies and show that Durango is practical to use for simulation without loss of fidelity, as quantified by simulation metrics. During our validation of Durango's generated communication model of LULESH, we found that the original LULESH miniapp code had a latent bug where the MPI_Waitall operation was used incorrectly. This finding underscores the potential need for a tool such as Durango, beyond its benefits for flexible workload generation and modeling.Additionally, we demonstrate the efficacy of Durango's direct integration approach, which links Aspen into CODES as part of the running network simulation model. Here, Aspen generates the application-level computation timing events, which in turn drive the start of a network communication phase. Results show that Durango's performance scales well when executing both torus and dragonfly network models on up to 4K Blue Gene/Q nodes using 32K MPI ranks, Durango also avoids the overheads and complexities associated with extreme-scale trace files.« less

Automated Kinematics Equations Generation and Constrained Motion Planning Resolution for Modular and Reconfigurable Robots

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

Pin, Francois G.; Love, Lonnie L.; Jung, David L.

2004-03-29

Contrary to the repetitive tasks performed by industrial robots, the tasks in most DOE missions such as environmental restoration or Decontamination and Decommissioning (D&D) can be characterized as ''batches-of-one'', in which robots must be capable of adapting to changes in constraints, tools, environment, criteria and configuration. No commercially available robot control code is suitable for use with such widely varying conditions. In this talk we present our development of a ''generic code'' to allow real time (at loop rate) robot behavior adaptation to changes in task objectives, tools, number and type of constraints, modes of controls or kinematics configuration. Wemore » present the analytical framework underlying our approach and detail the design of its two major modules for the automatic generation of the kinematics equations when the robot configuration or tools change and for the motion planning under time-varying constraints. Sample problems illustrating the capabilities of the developed system are presented.« less

Standardized mappings--a framework to combine different semantic mappers into a standardized web-API.

PubMed

Neuhaus, Philipp; Doods, Justin; Dugas, Martin

2015-01-01

Automatic coding of medical terms is an important, but highly complicated and laborious task. To compare and evaluate different strategies a framework with a standardized web-interface was created. Two UMLS mapping strategies are compared to demonstrate the interface. The framework is a Java Spring application running on a Tomcat application server. It accepts different parameters and returns results in JSON format. To demonstrate the framework, a list of medical data items was mapped by two different methods: similarity search in a large table of terminology codes versus search in a manually curated repository. These mappings were reviewed by a specialist. The evaluation shows that the framework is flexible (due to standardized interfaces like HTTP and JSON), performant and reliable. Accuracy of automatically assigned codes is limited (up to 40%). Combining different semantic mappers into a standardized Web-API is feasible. This framework can be easily enhanced due to its modular design.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model. PMID:25485311

Modeling ECCD/MHD coupling using NIMROD, GENRAY, and the Integrated Plasma Simulator

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Schnack, D. D.; Sovinec, C. R.; Hegna, C. C.; Callen, J. D.; Ebrahimi, F.; Kruger, S. E.; Carlsson, J.; Held, E. D.; Ji, J.-Y.; Harvey, R. W.; Smirnov, A. P.; Elwasif, W. R.

2009-11-01

We summarize ongoing theoretical/numerical work relevant to the development of a self--consistent framework for the inclusion of RF effects in fluid simulations; specifically, we consider the stabilization of resistive tearing modes in tokamak geometry by electron cyclotron current drive. In the fluid equations, ad hoc models for the RF--induced currents have previously been shown to shrink or altogether suppress the nonlinearly saturated magnetic islands generated by tearing modes; progress toward a self--consistent model is reported. The interfacing of the NIMROD [1] code with the GENRAY/CQL3D [2] codes (which calculate RF propagation and energy/momentum deposition) via the Integrated Plasma Simulator (IPS) framework [3] is explained, RF-induced rational surface motion and the equilibration of RF--induced currents over plasma flux surfaces are investigated, and the efficient reduction of saturated island widths through time modulation and spatial localization of the ECCD is explored. [1] Sovinec et al., JCP 195, 355 (2004) [2]www.compxco.com [3] Both the IPS development and the research presented here are part of the SWIM project. Funded by U.S. DoE.

Modeling of RF/MHD coupling using NIMROD, GENRAY, and the Integrated Plasma Simulator

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Schnack, D. D.; Sovinec, C. R.; Hegna, C. C.; Callen, J. D.; Ebrahimi, F.; Kruger, S. E.; Carlsson, J.; Held, E. D.; Ji, J.-Y.; Harvey, R. W.; Smirnov, A. P.

2009-05-01

We summarize ongoing theoretical/numerical work relevant to the development of a self--consistent framework for the inclusion of RF effects in fluid simulations; specifically considering resistive tearing mode stabilization in tokamak (DIII--D--like) geometry via ECCD. Relatively simple (though non--self--consistent) models for the RF--induced currents are incorporated into the fluid equations, markedly reducing the width of the nonlinearly saturated magnetic islands generated by tearing modes. We report our progress toward the self--consistent modeling of these RF--induced currents. The initial interfacing of the NIMROD* code with the GENRAY/CQL3D** codes (calculating RF propagation and energy/momentum deposition) via the Integrated Plasma Simulator (IPS) framework*** is explained, equilibration of RF--induced currents over the plasma flux surfaces is investigated, and studies exploring the efficient reduction of saturated island widths through time modulation and spatial localization of the ECCD are presented. *[Sovinec et al., JCP 195, 355 (2004)] **[www.compxco.com] ***[This research and the IPS development are both part of the SWIM project. Funded by U.S. DoE.

Tool for Generation of MAC/GMC Representative Unit Cell for CMC/PMC Analysis

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Pineda, Evan J.

2016-01-01

This document describes a recently developed analysis tool that enhances the resident capabilities of the Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) 4.0. This tool is especially useful in analyzing ceramic matrix composites (CMCs), where higher fidelity with improved accuracy of local response is needed. The tool, however, can be used for analyzing polymer matrix composites (PMCs) as well. MAC/GMC 4.0 is a composite material and laminate analysis software developed at NASA Glenn Research Center. The software package has been built around the concept of the generalized method of cells (GMC). The computer code is developed with a user friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermomechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The primary focus of the current effort is to provide a graphical user interface (GUI) capability that generates a number of different user-defined repeating unit cells (RUCs). In addition, the code has provisions for generation of a MAC/GMC-compatible input text file that can be merged with any MAC/GMC input file tailored to analyze composite materials. Although the primary intention was to address the three different constituents and phases that are usually present in CMCs-namely, fibers, matrix, and interphase-it can be easily modified to address two-phase polymer matrix composite (PMC) materials where an interphase is absent. Currently, the tool capability includes generation of RUCs for square packing, hexagonal packing, and random fiber packing as well as RUCs based on actual composite micrographs. All these options have the fibers modeled as having a circular cross-sectional area. In addition, a simplified version of RUC is provided where the fibers are treated as having a square cross section and are distributed randomly. This RUC facilitates a speedy analysis using the higher fidelity version of GMC known as HFGMC. The first four mentioned options above support uniform subcell discretization. The last one has variable subcell sizes due to the primary intention of keeping the RUC size to a minimum to gain the speed ups using the higher fidelity version of MAC. The code is implemented within the MATLAB (The Mathworks, Inc., Natick, MA) developmental framework; however, a standalone application that does not need a priori MATLAB installation is also created with the aid of the MATLAB compiler.

Automated Analysis of Stateflow Models

NASA Technical Reports Server (NTRS)

Bourbouh, Hamza; Garoche, Pierre-Loic; Garion, Christophe; Gurfinkel, Arie; Kahsaia, Temesghen; Thirioux, Xavier

2017-01-01

Stateflow is a widely used modeling framework for embedded and cyber physical systems where control software interacts with physical processes. In this work, we present a framework a fully automated safety verification technique for Stateflow models. Our approach is two-folded: (i) we faithfully compile Stateflow models into hierarchical state machines, and (ii) we use automated logic-based verification engine to decide the validity of safety properties. The starting point of our approach is a denotational semantics of State flow. We propose a compilation process using continuation-passing style (CPS) denotational semantics. Our compilation technique preserves the structural and modal behavior of the system. The overall approach is implemented as an open source toolbox that can be integrated into the existing Mathworks Simulink Stateflow modeling framework. We present preliminary experimental evaluations that illustrate the effectiveness of our approach in code generation and safety verification of industrial scale Stateflow models.

Pattern-based integer sample motion search strategies in the context of HEVC

NASA Astrophysics Data System (ADS)

Maier, Georg; Bross, Benjamin; Grois, Dan; Marpe, Detlev; Schwarz, Heiko; Veltkamp, Remco C.; Wiegand, Thomas

2015-09-01

The H.265/MPEG-H High Efficiency Video Coding (HEVC) standard provides a significant increase in coding efficiency compared to its predecessor, the H.264/MPEG-4 Advanced Video Coding (AVC) standard, which however comes at the cost of a high computational burden for a compliant encoder. Motion estimation (ME), which is a part of the inter-picture prediction process, typically consumes a high amount of computational resources, while significantly increasing the coding efficiency. In spite of the fact that both H.265/MPEG-H HEVC and H.264/MPEG-4 AVC standards allow processing motion information on a fractional sample level, the motion search algorithms based on the integer sample level remain to be an integral part of ME. In this paper, a flexible integer sample ME framework is proposed, thereby allowing to trade off significant reduction of ME computation time versus coding efficiency penalty in terms of bit rate overhead. As a result, through extensive experimentation, an integer sample ME algorithm that provides a good trade-off is derived, incorporating a combination and optimization of known predictive, pattern-based and early termination techniques. The proposed ME framework is implemented on a basis of the HEVC Test Model (HM) reference software, further being compared to the state-of-the-art fast search algorithm, which is a native part of HM. It is observed that for high resolution sequences, the integer sample ME process can be speed-up by factors varying from 3.2 to 7.6, resulting in the bit-rate overhead of 1.5% and 0.6% for Random Access (RA) and Low Delay P (LDP) configurations, respectively. In addition, the similar speed-up is observed for sequences with mainly Computer-Generated Imagery (CGI) content while trading off the bit rate overhead of up to 5.2%.

A CSP-Based Agent Modeling Framework for the Cougaar Agent-Based Architecture

NASA Technical Reports Server (NTRS)

Gracanin, Denis; Singh, H. Lally; Eltoweissy, Mohamed; Hinchey, Michael G.; Bohner, Shawn A.

2005-01-01

Cognitive Agent Architecture (Cougaar) is a Java-based architecture for large-scale distributed agent-based applications. A Cougaar agent is an autonomous software entity with behaviors that represent a real-world entity (e.g., a business process). A Cougaar-based Model Driven Architecture approach, currently under development, uses a description of system's functionality (requirements) to automatically implement the system in Cougaar. The Communicating Sequential Processes (CSP) formalism is used for the formal validation of the generated system. Two main agent components, a blackboard and a plugin, are modeled as CSP processes. A set of channels represents communications between the blackboard and individual plugins. The blackboard is represented as a CSP process that communicates with every agent in the collection. The developed CSP-based Cougaar modeling framework provides a starting point for a more complete formal verification of the automatically generated Cougaar code. Currently it is used to verify the behavior of an individual agent in terms of CSP properties and to analyze the corresponding Cougaar society.

IDGenerator: unique identifier generator for epidemiologic or clinical studies.

PubMed

Olden, Matthias; Holle, Rolf; Heid, Iris M; Stark, Klaus

2016-09-15

Creating study identifiers and assigning them to study participants is an important feature in epidemiologic studies, ensuring the consistency and privacy of the study data. The numbering system for identifiers needs to be random within certain number constraints, to carry extensions coding for organizational information, or to contain multiple layers of numbers per participant to diversify data access. Available software can generate globally-unique identifiers, but identifier-creating tools meeting the special needs of epidemiological studies are lacking. We have thus set out to develop a software program to generate IDs for epidemiological or clinical studies. Our software IDGenerator creates unique identifiers that not only carry a random identifier for a study participant, but also support the creation of structured IDs, where organizational information is coded into the ID directly. This may include study center (for multicenter-studies), study track (for studies with diversified study programs), or study visit (baseline, follow-up, regularly repeated visits). Our software can be used to add a check digit to the ID to minimize data entry errors. It facilitates the generation of IDs in batches and the creation of layered IDs (personal data ID, study data ID, temporary ID, external data ID) to ensure a high standard of data privacy. The software is supported by a user-friendly graphic interface that enables the generation of IDs in both standard text and barcode 128B format. Our software IDGenerator can create identifiers meeting the specific needs for epidemiologic or clinical studies to facilitate study organization and data privacy. IDGenerator is freeware under the GNU General Public License version 3; a Windows port and the source code can be downloaded at the Open Science Framework website: https://osf.io/urs2g/ .

An analysis of options available for developing a common laser ray tracing package for Ares and Kull code frameworks

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

Weeratunga, S K

Ares and Kull are mature code frameworks that support ALE hydrodynamics for a variety of HEDP applications at LLNL, using two widely different meshing approaches. While Ares is based on a 2-D/3-D block-structured mesh data base, Kull is designed to support unstructured, arbitrary polygonal/polyhedral meshes. In addition, both frameworks are capable of running applications on large, distributed-memory parallel machines. Currently, both these frameworks separately support assorted collections of physics packages related to HEDP, including one for the energy deposition by laser/ion-beam ray tracing. This study analyzes the options available for developing a common laser/ion-beam ray tracing package that can bemore » easily shared between these two code frameworks and concludes with a set of recommendations for its development.« less

Synthesizing Safety Conditions for Code Certification Using Meta-Level Programming

NASA Technical Reports Server (NTRS)

Eusterbrock, Jutta

2004-01-01

In code certification the code consumer publishes a safety policy and the code producer generates a proof that the produced code is in compliance with the published safety policy. In this paper, a novel viewpoint approach towards an implementational re-use oriented framework for code certification is taken. It adopts ingredients from Necula's approach for proof-carrying code, but in this work safety properties can be analyzed on a higher code level than assembly language instructions. It consists of three parts: (1) The specification language is extended to include generic pre-conditions that shall ensure safety at all states that can be reached during program execution. Actual safety requirements can be expressed by providing domain-specific definitions for the generic predicates which act as interface to the environment. (2) The Floyd-Hoare inductive assertion method is refined to obtain proof rules that allow the derivation of the proof obligations in terms of the generic safety predicates. (3) A meta-interpreter is designed and experimentally implemented that enables automatic synthesis of proof obligations for submitted programs by applying the modified Floyd-Hoare rules. The proof obligations have two separate conjuncts, one for functional correctness and another for the generic safety obligations. Proof of the generic obligations, having provided the actual safety definitions as context, ensures domain-specific safety of program execution in a particular environment and is simpler than full program verification.

Fortran interface layer of the framework for developing particle simulator FDPS

NASA Astrophysics Data System (ADS)

Namekata, Daisuke; Iwasawa, Masaki; Nitadori, Keigo; Tanikawa, Ataru; Muranushi, Takayuki; Wang, Long; Hosono, Natsuki; Nomura, Kentaro; Makino, Junichiro

2018-06-01

Numerical simulations based on particle methods have been widely used in various fields including astrophysics. To date, various versions of simulation software have been developed by individual researchers or research groups in each field, through a huge amount of time and effort, even though the numerical algorithms used are very similar. To improve the situation, we have developed a framework, called FDPS (Framework for Developing Particle Simulators), which enables researchers to develop massively parallel particle simulation codes for arbitrary particle methods easily. Until version 3.0, FDPS provided an API (application programming interface) for the C++ programming language only. This limitation comes from the fact that FDPS is developed using the template feature in C++, which is essential to support arbitrary data types of particle. However, there are many researchers who use Fortran to develop their codes. Thus, the previous versions of FDPS require such people to invest much time to learn C++. This is inefficient. To cope with this problem, we developed a Fortran interface layer in FDPS, which provides API for Fortran. In order to support arbitrary data types of particle in Fortran, we design the Fortran interface layer as follows. Based on a given derived data type in Fortran representing particle, a PYTHON script provided by us automatically generates a library that manipulates the C++ core part of FDPS. This library is seen as a Fortran module providing an API of FDPS from the Fortran side and uses C programs internally to interoperate Fortran with C++. In this way, we have overcome several technical issues when emulating a `template' in Fortran. Using the Fortran interface, users can develop all parts of their codes in Fortran. We show that the overhead of the Fortran interface part is sufficiently small and a code written in Fortran shows a performance practically identical to the one written in C++.

Development of an object-oriented ORIGEN for advanced nuclear fuel modeling applications

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

Skutnik, S.; Havloej, F.; Lago, D.

2013-07-01

The ORIGEN package serves as the core depletion and decay calculation module within the SCALE code system. A recent major re-factor to the ORIGEN code architecture as part of an overall modernization of the SCALE code system has both greatly enhanced its maintainability as well as afforded several new capabilities useful for incorporating depletion analysis into other code frameworks. This paper will present an overview of the improved ORIGEN code architecture (including the methods and data structures introduced) as well as current and potential future applications utilizing the new ORIGEN framework. (authors)

Numerical modeling of the fracture process in a three-unit all-ceramic fixed partial denture.

PubMed

Kou, Wen; Kou, Shaoquan; Liu, Hongyuan; Sjögren, Göran

2007-08-01

The main objectives were to examine the fracture mechanism and process of a ceramic fixed partial denture (FPD) framework under simulated mechanical loading using a recently developed numerical modeling code, the R-T(2D) code, and also to evaluate the suitability of R-T(2D) code as a tool for this purpose. Using the recently developed R-T(2D) code the fracture mechanism and process of a 3U yttria-tetragonal zirconia polycrystal ceramic (Y-TZP) FPD framework was simulated under static loading. In addition, the fracture pattern obtained using the numerical simulation was compared with the fracture pattern obtained in a previous laboratory test. The result revealed that the framework fracture pattern obtained using the numerical simulation agreed with that observed in a previous laboratory test. Quasi-photoelastic stress fringe pattern and acoustic emission showed that the fracture mechanism was tensile failure and that the crack started at the lower boundary of the framework. The fracture process could be followed both in step-by-step and step-in-step. Based on the findings in the current study, the R-T(2D) code seems suitable for use as a complement to other tests and clinical observations in studying stress distribution, fracture mechanism and fracture processes in ceramic FPD frameworks.

A Multi-Scale, Multi-Physics Optimization Framework for Additively Manufactured Structural Components

NASA Astrophysics Data System (ADS)

El-Wardany, Tahany; Lynch, Mathew; Gu, Wenjiong; Hsu, Arthur; Klecka, Michael; Nardi, Aaron; Viens, Daniel

This paper proposes an optimization framework enabling the integration of multi-scale / multi-physics simulation codes to perform structural optimization design for additively manufactured components. Cold spray was selected as the additive manufacturing (AM) process and its constraints were identified and included in the optimization scheme. The developed framework first utilizes topology optimization to maximize stiffness for conceptual design. The subsequent step applies shape optimization to refine the design for stress-life fatigue. The component weight was reduced by 20% while stresses were reduced by 75% and the rigidity was improved by 37%. The framework and analysis codes were implemented using Altair software as well as an in-house loading code. The optimized design was subsequently produced by the cold spray process.

Single block three-dimensional volume grids about complex aerodynamic vehicles

NASA Technical Reports Server (NTRS)

Alter, Stephen J.; Weilmuenster, K. James

1993-01-01

This paper presents an alternate approach for the generation of volumetric grids for supersonic and hypersonic flows about complex configurations. The method uses parametric two dimensional block face grid definition within the framework of GRIDGEN2D. The incorporation of face decomposition reduces complex surfaces to simple shapes. These simple shapes are combined to obtain the final face definition. The advantages of this method include the reduction of overall grid generation time through the use of vectorized computer code, the elimination of the need to generate matching block faces, and the implementation of simplified boundary conditions. A simple axisymmetric grid is used to illustrate this method. In addition, volume grids for two complex configurations, the Langley Lifting Body (HL-20) and the Space Shuttle Orbiter, are shown.

Translating expert system rules into Ada code with validation and verification

NASA Technical Reports Server (NTRS)

Becker, Lee; Duckworth, R. James; Green, Peter; Michalson, Bill; Gosselin, Dave; Nainani, Krishan; Pease, Adam

1991-01-01

The purpose of this ongoing research and development program is to develop software tools which enable the rapid development, upgrading, and maintenance of embedded real-time artificial intelligence systems. The goals of this phase of the research were to investigate the feasibility of developing software tools which automatically translate expert system rules into Ada code and develop methods for performing validation and verification testing of the resultant expert system. A prototype system was demonstrated which automatically translated rules from an Air Force expert system was demonstrated which detected errors in the execution of the resultant system. The method and prototype tools for converting AI representations into Ada code by converting the rules into Ada code modules and then linking them with an Activation Framework based run-time environment to form an executable load module are discussed. This method is based upon the use of Evidence Flow Graphs which are a data flow representation for intelligent systems. The development of prototype test generation and evaluation software which was used to test the resultant code is discussed. This testing was performed automatically using Monte-Carlo techniques based upon a constraint based description of the required performance for the system.

Development of structured ICD-10 and its application to computer-assisted ICD coding.

PubMed

Imai, Takeshi; Kajino, Masayuki; Sato, Megumi; Ohe, Kazuhiko

2010-01-01

This paper presents: (1) a framework of formal representation of ICD10, which functions as a bridge between ontological information and natural language expressions; and (2) a methodology to use formally described ICD10 for computer-assisted ICD coding. First, we analyzed and structurized the meanings of categories in 15 chapters of ICD10. Then we expanded the structured ICD10 (S-ICD10) by adding subordinate concepts and labels derived from Japanese Standard Disease Names. The information model to describe formal representation was refined repeatedly. The resultant model includes 74 types of semantic links. We also developed an ICD coding module based on S-ICD10 and a 'Coding Principle,' which achieved high accuracy (>70%) for four chapters. These results not only demonstrate the basic feasibility of our coding framework but might also inform the development of the information model for formal description framework in the ICD11 revision.

Livermore Compiler Analysis Loop Suite

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

Hornung, R. D.

2013-03-01

LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermoremore » Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

The InSAR Scientific Computing Environment

NASA Technical Reports Server (NTRS)

Rosen, Paul A.; Gurrola, Eric; Sacco, Gian Franco; Zebker, Howard

2012-01-01

We have developed a flexible and extensible Interferometric SAR (InSAR) Scientific Computing Environment (ISCE) for geodetic image processing. ISCE was designed from the ground up as a geophysics community tool for generating stacks of interferograms that lend themselves to various forms of time-series analysis, with attention paid to accuracy, extensibility, and modularity. The framework is python-based, with code elements rigorously componentized by separating input/output operations from the processing engines. This allows greater flexibility and extensibility in the data models, and creates algorithmic code that is less susceptible to unnecessary modification when new data types and sensors are available. In addition, the components support provenance and checkpointing to facilitate reprocessing and algorithm exploration. The algorithms, based on legacy processing codes, have been adapted to assume a common reference track approach for all images acquired from nearby orbits, simplifying and systematizing the geometry for time-series analysis. The framework is designed to easily allow user contributions, and is distributed for free use by researchers. ISCE can process data from the ALOS, ERS, EnviSAT, Cosmo-SkyMed, RadarSAT-1, RadarSAT-2, and TerraSAR-X platforms, starting from Level-0 or Level 1 as provided from the data source, and going as far as Level 3 geocoded deformation products. With its flexible design, it can be extended with raw/meta data parsers to enable it to work with radar data from other platforms

Coding conventions and principles for a National Land-Change Modeling Framework

USGS Publications Warehouse

Donato, David I.

2017-07-14

This report establishes specific rules for writing computer source code for use with the National Land-Change Modeling Framework (NLCMF). These specific rules consist of conventions and principles for writing code primarily in the C and C++ programming languages. Collectively, these coding conventions and coding principles create an NLCMF programming style. In addition to detailed naming conventions, this report provides general coding conventions and principles intended to facilitate the development of high-performance software implemented with code that is extensible, flexible, and interoperable. Conventions for developing modular code are explained in general terms and also enabled and demonstrated through the appended templates for C++ base source-code and header files. The NLCMF limited-extern approach to module structure, code inclusion, and cross-module access to data is both explained in the text and then illustrated through the module templates. Advice on the use of global variables is provided.

Distributed Adaptive Binary Quantization for Fast Nearest Neighbor Search.

PubMed

Xianglong Liu; Zhujin Li; Cheng Deng; Dacheng Tao

2017-11-01

Hashing has been proved an attractive technique for fast nearest neighbor search over big data. Compared with the projection based hashing methods, prototype-based ones own stronger power to generate discriminative binary codes for the data with complex intrinsic structure. However, existing prototype-based methods, such as spherical hashing and K-means hashing, still suffer from the ineffective coding that utilizes the complete binary codes in a hypercube. To address this problem, we propose an adaptive binary quantization (ABQ) method that learns a discriminative hash function with prototypes associated with small unique binary codes. Our alternating optimization adaptively discovers the prototype set and the code set of a varying size in an efficient way, which together robustly approximate the data relations. Our method can be naturally generalized to the product space for long hash codes, and enjoys the fast training linear to the number of the training data. We further devise a distributed framework for the large-scale learning, which can significantly speed up the training of ABQ in the distributed environment that has been widely deployed in many areas nowadays. The extensive experiments on four large-scale (up to 80 million) data sets demonstrate that our method significantly outperforms state-of-the-art hashing methods, with up to 58.84% performance gains relatively.

Generating Code Review Documentation for Auto-Generated Mission-Critical Software

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2009-01-01

Model-based design and automated code generation are increasingly used at NASA to produce actual flight code, particularly in the Guidance, Navigation, and Control domain. However, since code generators are typically not qualified, there is no guarantee that their output is correct, and consequently auto-generated code still needs to be fully tested and certified. We have thus developed AUTOCERT, a generator-independent plug-in that supports the certification of auto-generated code. AUTOCERT takes a set of mission safety requirements, and formally verifies that the autogenerated code satisfies these requirements. It generates a natural language report that explains why and how the code complies with the specified requirements. The report is hyper-linked to both the program and the verification conditions and thus provides a high-level structured argument containing tracing information for use in code reviews.

Semantic Segmentation of Indoor Point Clouds Using Convolutional Neural Network

NASA Astrophysics Data System (ADS)

Babacan, K.; Chen, L.; Sohn, G.

2017-11-01

As Building Information Modelling (BIM) thrives, geometry becomes no longer sufficient; an ever increasing variety of semantic information is needed to express an indoor model adequately. On the other hand, for the existing buildings, automatically generating semantically enriched BIM from point cloud data is in its infancy. The previous research to enhance the semantic content rely on frameworks in which some specific rules and/or features that are hand coded by specialists. These methods immanently lack generalization and easily break in different circumstances. On this account, a generalized framework is urgently needed to automatically and accurately generate semantic information. Therefore we propose to employ deep learning techniques for the semantic segmentation of point clouds into meaningful parts. More specifically, we build a volumetric data representation in order to efficiently generate the high number of training samples needed to initiate a convolutional neural network architecture. The feedforward propagation is used in such a way to perform the classification in voxel level for achieving semantic segmentation. The method is tested both for a mobile laser scanner point cloud, and a larger scale synthetically generated data. We also demonstrate a case study, in which our method can be effectively used to leverage the extraction of planar surfaces in challenging cluttered indoor environments.

Analytical Performance Modeling and Validation of Intel’s Xeon Phi Architecture

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

Chunduri, Sudheer; Balaprakash, Prasanna; Morozov, Vitali

Modeling the performance of scientific applications on emerging hardware plays a central role in achieving extreme-scale computing goals. Analytical models that capture the interaction between applications and hardware characteristics are attractive because even a reasonably accurate model can be useful for performance tuning before the hardware is made available. In this paper, we develop a hardware model for Intel’s second-generation Xeon Phi architecture code-named Knights Landing (KNL) for the SKOPE framework. We validate the KNL hardware model by projecting the performance of mini-benchmarks and application kernels. The results show that our KNL model can project the performance with prediction errorsmore » of 10% to 20%. The hardware model also provides informative recommendations for code transformations and tuning.« less

Fuel Performance Calculations for FeCrAl Cladding in BWRs

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

George, Nathan; Sweet, Ryan; Maldonado, G. Ivan

2015-01-01

This study expands upon previous neutronics analyses of the reactivity impact of alternate cladding concepts in boiling water reactor (BWR) cores and directs focus toward contrasting fuel performance characteristics of FeCrAl cladding against those of traditional Zircaloy. Using neutronics results from a modern version of the 3D nodal simulator NESTLE, linear power histories were generated and supplied to the BISON-CASL code for fuel performance evaluations. BISON-CASL (formerly Peregrine) expands on material libraries implemented in the BISON fuel performance code and the MOOSE framework by providing proprietary material data. By creating material libraries for Zircaloy and FeCrAl cladding, the thermomechanical behaviormore » of the fuel rod (e.g., strains, centerline fuel temperature, and time to gap closure) were investigated and contrasted.« less

An Object-Oriented Computer Code for Aircraft Engine Weight Estimation

NASA Technical Reports Server (NTRS)

Tong, Michael T.; Naylor, Bret A.

2009-01-01

Reliable engine-weight estimation at the conceptual design stage is critical to the development of new aircraft engines. It helps to identify the best engine concept amongst several candidates. At NASA Glenn Research Center (GRC), the Weight Analysis of Turbine Engines (WATE) computer code, originally developed by Boeing Aircraft, has been used to estimate the engine weight of various conceptual engine designs. The code, written in FORTRAN, was originally developed for NASA in 1979. Since then, substantial improvements have been made to the code to improve the weight calculations for most of the engine components. Most recently, to improve the maintainability and extensibility of WATE, the FORTRAN code has been converted into an object-oriented version. The conversion was done within the NASA's NPSS (Numerical Propulsion System Simulation) framework. This enables WATE to interact seamlessly with the thermodynamic cycle model which provides component flow data such as airflows, temperatures, and pressures, etc., that are required for sizing the components and weight calculations. The tighter integration between the NPSS and WATE would greatly enhance system-level analysis and optimization capabilities. It also would facilitate the enhancement of the WATE code for next-generation aircraft and space propulsion systems. In this paper, the architecture of the object-oriented WATE code (or WATE++) is described. Both the FORTRAN and object-oriented versions of the code are employed to compute the dimensions and weight of a 300-passenger aircraft engine (GE90 class). Both versions of the code produce essentially identical results as should be the case.

Certifying Auto-Generated Flight Code

NASA Technical Reports Server (NTRS)

Denney, Ewen

2008-01-01

Model-based design and automated code generation are being used increasingly at NASA. Many NASA projects now use MathWorks Simulink and Real-Time Workshop for at least some of their modeling and code development. However, there are substantial obstacles to more widespread adoption of code generators in safety-critical domains. Since code generators are typically not qualified, there is no guarantee that their output is correct, and consequently the generated code still needs to be fully tested and certified. Moreover, the regeneration of code can require complete recertification, which offsets many of the advantages of using a generator. Indeed, manual review of autocode can be more challenging than for hand-written code. Since the direct V&V of code generators is too laborious and complicated due to their complex (and often proprietary) nature, we have developed a generator plug-in to support the certification of the auto-generated code. Specifically, the AutoCert tool supports certification by formally verifying that the generated code is free of different safety violations, by constructing an independently verifiable certificate, and by explaining its analysis in a textual form suitable for code reviews. The generated documentation also contains substantial tracing information, allowing users to trace between model, code, documentation, and V&V artifacts. This enables missions to obtain assurance about the safety and reliability of the code without excessive manual V&V effort and, as a consequence, eases the acceptance of code generators in safety-critical contexts. The generation of explicit certificates and textual reports is particularly well-suited to supporting independent V&V. The primary contribution of this approach is the combination of human-friendly documentation with formal analysis. The key technical idea is to exploit the idiomatic nature of auto-generated code in order to automatically infer logical annotations. The annotation inference algorithm itself is generic, and parametrized with respect to a library of coding patterns that depend on the safety policies and the code generator. The patterns characterize the notions of definitions and uses that are specific to the given safety property. For example, for initialization safety, definitions correspond to variable initializations while uses are statements which read a variable, whereas for array bounds safety, definitions are the array declarations, while uses are statements which access an array variable. The inferred annotations are thus highly dependent on the actual program and the properties being proven. The annotations, themselves, need not be trusted, but are crucial to obtain the automatic formal verification of the safety properties without requiring access to the internals of the code generator. The approach has been applied to both in-house and commercial code generators, but is independent of the particular generator used. It is currently being adapted to flight code generated using MathWorks Real-Time Workshop, an automatic code generator that translates from Simulink/Stateflow models into embedded C code.

Can we Build on Social Movement Theories to Develop and Improve Community-Based Participatory Research? A Framework Synthesis Review.

PubMed

Tremblay, Marie-Claude; Martin, Debbie H; Macaulay, Ann C; Pluye, Pierre

2017-06-01

A long-standing challenge in community-based participatory research (CBPR) has been to anchor practice and evaluation in a relevant and comprehensive theoretical framework of community change. This study describes the development of a multidimensional conceptual framework that builds on social movement theories to identify key components of CBPR processes. Framework synthesis was used as a general literature search and analysis strategy. An initial conceptual framework was developed from the theoretical literature on social movement. A literature search performed to identify illustrative CBPR projects yielded 635 potentially relevant documents, from which eight projects (corresponding to 58 publications) were retained after record and full-text screening. Framework synthesis was used to code and organize data from these projects, ultimately providing a refined framework. The final conceptual framework maps key concepts of CBPR mobilization processes, such as the pivotal role of the partnership; resources and opportunities as necessary components feeding the partnership's development; the importance of framing processes; and a tight alignment between the cause (partnership's goal), the collective action strategy, and the system changes targeted. The revised framework provides a context-specific model to generate a new, innovative understanding of CBPR mobilization processes, drawing on existing theoretical foundations. © 2017 The Authors American Journal of Community Psychology published by Wiley Periodicals, Inc. on behalf of Society for Community Research and Action.

Barriers and Facilitators to Self-Directed Learning in Continuing Professional Development for Physicians in Canada: A Scoping Review.

PubMed

Jeong, Dahn; Presseau, Justin; ElChamaa, Rima; Naumann, Danielle N; Mascaro, Colin; Luconi, Francesca; Smith, Karen M; Kitto, Simon

2018-04-10

This scoping review explored the barriers and facilitators that influence engagement in and implementation of self-directed learning (SDL) in continuing professional development (CPD) for physicians in Canada. This review followed the six-stage scoping review framework of Arksey and O'Malley and of Daudt et al. In 2015, the authors searched eight online databases for English-language Canadian articles published January 2005-December 2015. To chart and analyze the data from the 17 included studies, they employed two-step analysis process of conventional content analysis followed by directed coding guided by the Theoretical Domains Framework (TDF). Conventional content analysis generated five categories of barriers and facilitators: individual, program, technological, environmental, and workplace/organizational. Directed coding guided by the TDF allowed analysis of barriers and facilitators to behavior change according to two key groups: physicians engaging in SDL and SDL developers designing and implementing SDL programs. Of the 318 total barriers and facilitators coded, 290 (91.2%) were coded for physicians and 28 (8.8%) for SDL developers. The majority (209; 65.7%) were coded in four key TDF domains: environmental context and resources, social influences, beliefs about consequences, and behavioral regulation. This scoping review identified five categories of barriers and facilitators in the literature and four key TDF domains where most factors related to behavior change of physicians and SDL developers regarding SDL programs in CPD were coded. There was a significant gap in the literature about factors that may contribute to SDL developers' capacity to design and implement SDL programs in CPD.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

TESS: A RELATIVISTIC HYDRODYNAMICS CODE ON A MOVING VORONOI MESH

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

Duffell, Paul C.; MacFadyen, Andrew I., E-mail: pcd233@nyu.edu, E-mail: macfadyen@nyu.edu

2011-12-01

We have generalized a method for the numerical solution of hyperbolic systems of equations using a dynamic Voronoi tessellation of the computational domain. The Voronoi tessellation is used to generate moving computational meshes for the solution of multidimensional systems of conservation laws in finite-volume form. The mesh-generating points are free to move with arbitrary velocity, with the choice of zero velocity resulting in an Eulerian formulation. Moving the points at the local fluid velocity makes the formulation effectively Lagrangian. We have written the TESS code to solve the equations of compressible hydrodynamics and magnetohydrodynamics for both relativistic and non-relativistic fluidsmore » on a dynamic Voronoi mesh. When run in Lagrangian mode, TESS is significantly less diffusive than fixed mesh codes and thus preserves contact discontinuities to high precision while also accurately capturing strong shock waves. TESS is written for Cartesian, spherical, and cylindrical coordinates and is modular so that auxiliary physics solvers are readily integrated into the TESS framework and so that this can be readily adapted to solve general systems of equations. We present results from a series of test problems to demonstrate the performance of TESS and to highlight some of the advantages of the dynamic tessellation method for solving challenging problems in astrophysical fluid dynamics.« less

ICAM (Conceptual Design for Computer-Integrated Manufacturing. Volume 2. Part 6. Task B - Establishment of the Factory of the Future Conceptual Framework Conceptual Framework Document, (MMR)

DTIC Science & Technology

1984-06-29

effort that requires hard copy documentation. As a result, there are generally numerous delays in providing current quality information. In the FoF...process have had fixed controls or were based on " hard -coded" information. A template, for example, is hard -coded information defining the shape of a...represents soft-coded control information. (Although manual handling of punch tapes still possess some of the limitations of " hard -coded" controls

Computer Simulation of the VASIMR Engine

NASA Technical Reports Server (NTRS)

Garrison, David

2005-01-01

The goal of this project is to develop a magneto-hydrodynamic (MHD) computer code for simulation of the VASIMR engine. This code is designed be easy to modify and use. We achieve this using the Cactus framework, a system originally developed for research in numerical relativity. Since its release, Cactus has become an extremely powerful and flexible open source framework. The development of the code will be done in stages, starting with a basic fluid dynamic simulation and working towards a more complex MHD code. Once developed, this code can be used by students and researchers in order to further test and improve the VASIMR engine.

Natural Language Interface for Safety Certification of Safety-Critical Software

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2011-01-01

Model-based design and automated code generation are being used increasingly at NASA. The trend is to move beyond simulation and prototyping to actual flight code, particularly in the guidance, navigation, and control domain. However, there are substantial obstacles to more widespread adoption of code generators in such safety-critical domains. Since code generators are typically not qualified, there is no guarantee that their output is correct, and consequently the generated code still needs to be fully tested and certified. The AutoCert generator plug-in supports the certification of automatically generated code by formally verifying that the generated code is free of different safety violations, by constructing an independently verifiable certificate, and by explaining its analysis in a textual form suitable for code reviews.

Dynamic state estimation based on Poisson spike trains—towards a theory of optimal encoding

NASA Astrophysics Data System (ADS)

Susemihl, Alex; Meir, Ron; Opper, Manfred

2013-03-01

Neurons in the nervous system convey information to higher brain regions by the generation of spike trains. An important question in the field of computational neuroscience is how these sensory neurons encode environmental information in a way which may be simply analyzed by subsequent systems. Many aspects of the form and function of the nervous system have been understood using the concepts of optimal population coding. Most studies, however, have neglected the aspect of temporal coding. Here we address this shortcoming through a filtering theory of inhomogeneous Poisson processes. We derive exact relations for the minimal mean squared error of the optimal Bayesian filter and, by optimizing the encoder, obtain optimal codes for populations of neurons. We also show that a class of non-Markovian, smooth stimuli are amenable to the same treatment, and provide results for the filtering and prediction error which hold for a general class of stochastic processes. This sets a sound mathematical framework for a population coding theory that takes temporal aspects into account. It also formalizes a number of studies which discussed temporal aspects of coding using time-window paradigms, by stating them in terms of correlation times and firing rates. We propose that this kind of analysis allows for a systematic study of temporal coding and will bring further insights into the nature of the neural code.

Hardware-efficient bosonic quantum error-correcting codes based on symmetry operators

NASA Astrophysics Data System (ADS)

Niu, Murphy Yuezhen; Chuang, Isaac L.; Shapiro, Jeffrey H.

2018-03-01

We establish a symmetry-operator framework for designing quantum error-correcting (QEC) codes based on fundamental properties of the underlying system dynamics. Based on this framework, we propose three hardware-efficient bosonic QEC codes that are suitable for χ(2 )-interaction based quantum computation in multimode Fock bases: the χ(2 ) parity-check code, the χ(2 ) embedded error-correcting code, and the χ(2 ) binomial code. All of these QEC codes detect photon-loss or photon-gain errors by means of photon-number parity measurements, and then correct them via χ(2 ) Hamiltonian evolutions and linear-optics transformations. Our symmetry-operator framework provides a systematic procedure for finding QEC codes that are not stabilizer codes, and it enables convenient extension of a given encoding to higher-dimensional qudit bases. The χ(2 ) binomial code is of special interest because, with m ≤N identified from channel monitoring, it can correct m -photon-loss errors, or m -photon-gain errors, or (m -1 )th -order dephasing errors using logical qudits that are encoded in O (N ) photons. In comparison, other bosonic QEC codes require O (N2) photons to correct the same degree of bosonic errors. Such improved photon efficiency underscores the additional error-correction power that can be provided by channel monitoring. We develop quantum Hamming bounds for photon-loss errors in the code subspaces associated with the χ(2 ) parity-check code and the χ(2 ) embedded error-correcting code, and we prove that these codes saturate their respective bounds. Our χ(2 ) QEC codes exhibit hardware efficiency in that they address the principal error mechanisms and exploit the available physical interactions of the underlying hardware, thus reducing the physical resources required for implementing their encoding, decoding, and error-correction operations, and their universal encoded-basis gate sets.

On Fusing Recursive Traversals of K-d Trees

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

Rajbhandari, Samyam; Kim, Jinsung; Krishnamoorthy, Sriram

Loop fusion is a key program transformation for data locality optimization that is implemented in production compilers. But optimizing compilers currently cannot exploit fusion opportunities across a set of recursive tree traversal computations with producer-consumer relationships. In this paper, we develop a compile-time approach to dependence characterization and program transformation to enable fusion across recursively specified traversals over k-ary trees. We present the FuseT source-to-source code transformation framework to automatically generate fused composite recursive operators from an input program containing a sequence of primitive recursive operators. We use our framework to implement fused operators for MADNESS, Multiresolution Adaptive Numerical Environmentmore » for Scientific Simulation. We show that locality optimization through fusion can offer more than an order of magnitude performance improvement.« less

Validation of High-Fidelity CFD/CAA Framework for Launch Vehicle Acoustic Environment Simulation against Scale Model Test Data

NASA Technical Reports Server (NTRS)

Liever, Peter A.; West, Jeffrey S.

2016-01-01

A hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) modeling framework has been developed for launch vehicle liftoff acoustic environment predictions. The framework couples the existing highly-scalable NASA production CFD code, Loci/CHEM, with a high-order accurate discontinuous Galerkin solver developed in the same production framework, Loci/THRUST, to accurately resolve and propagate acoustic physics across the entire launch environment. Time-accurate, Hybrid RANS/LES CFD modeling is applied for predicting the acoustic generation physics at the plume source, and a high-order accurate unstructured discontinuous Galerkin (DG) method is employed to propagate acoustic waves away from the source across large distances using high-order accurate schemes. The DG solver is capable of solving 2nd, 3rd, and 4th order Euler solutions for non-linear, conservative acoustic field propagation. Initial application testing and validation has been carried out against high resolution acoustic data from the Ares Scale Model Acoustic Test (ASMAT) series to evaluate the capabilities and production readiness of the CFD/CAA system to resolve the observed spectrum of acoustic frequency content. This paper presents results from this validation and outlines efforts to mature and improve the computational simulation framework.

Toward a first-principles integrated simulation of tokamak edge plasmas

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

Chang, C S; Klasky, Scott A; Cummings, Julian

2008-01-01

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary firstprinciples, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); andmore » (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles.« less

The Los Alamos suite of relativistic atomic physics codes

DOE PAGES

Fontes, C. J.; Zhang, H. L.; Jr, J. Abdallah; ...

2015-05-28

The Los Alamos SuitE of Relativistic (LASER) atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suitemore » can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions.« less

From Verified Models to Verifiable Code

NASA Technical Reports Server (NTRS)

Lensink, Leonard; Munoz, Cesar A.; Goodloe, Alwyn E.

2009-01-01

Declarative specifications of digital systems often contain parts that can be automatically translated into executable code. Automated code generation may reduce or eliminate the kinds of errors typically introduced through manual code writing. For this approach to be effective, the generated code should be reasonably efficient and, more importantly, verifiable. This paper presents a prototype code generator for the Prototype Verification System (PVS) that translates a subset of PVS functional specifications into an intermediate language and subsequently to multiple target programming languages. Several case studies are presented to illustrate the tool's functionality. The generated code can be analyzed by software verification tools such as verification condition generators, static analyzers, and software model-checkers to increase the confidence that the generated code is correct.

Software design and code generation for the engineering graphical user interface of the ASTRI SST-2M prototype for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Tanci, Claudio; Tosti, Gino; Antolini, Elisa; Gambini, Giorgio F.; Bruno, Pietro; Canestrari, Rodolfo; Conforti, Vito; Lombardi, Saverio; Russo, Federico; Sangiorgi, Pierluca; Scuderi, Salvatore

2016-08-01

ASTRI is an on-going project developed in the framework of the Cherenkov Telescope Array (CTA). An end- to-end prototype of a dual-mirror small-size telescope (SST-2M) has been installed at the INAF observing station on Mt. Etna, Italy. The next step is the development of the ASTRI mini-array composed of nine ASTRI SST-2M telescopes proposed to be installed at the CTA southern site. The ASTRI mini-array is a collaborative and international effort carried on by Italy, Brazil and South-Africa and led by the Italian National Institute of Astrophysics, INAF. To control the ASTRI telescopes, a specific ASTRI Mini-Array Software System (MASS) was designed using a scalable and distributed architecture to monitor all the hardware devices for the telescopes. Using code generation we built automatically from the ASTRI Interface Control Documents a set of communication libraries and extensive Graphical User Interfaces that provide full access to the capabilities offered by the telescope hardware subsystems for testing and maintenance. Leveraging these generated libraries and components we then implemented a human designed, integrated, Engineering GUI for MASS to perform the verification of the whole prototype and test shared services such as the alarms, configurations, control systems, and scientific on-line outcomes. In our experience the use of code generation dramatically reduced the amount of effort in development, integration and testing of the more basic software components and resulted in a fast software release life cycle. This approach could be valuable for the whole CTA project, characterized by a large diversity of hardware components.

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

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

Automation Framework for Flight Dynamics Products Generation

NASA Technical Reports Server (NTRS)

Wiegand, Robert E.; Esposito, Timothy C.; Watson, John S.; Jun, Linda; Shoan, Wendy; Matusow, Carla

2010-01-01

XFDS provides an easily adaptable automation platform. To date it has been used to support flight dynamics operations. It coordinates the execution of other applications such as Satellite TookKit, FreeFlyer, MATLAB, and Perl code. It provides a mechanism for passing messages among a collection of XFDS processes, and allows sending and receiving of GMSEC messages. A unified and consistent graphical user interface (GUI) is used for the various tools. Its automation configuration is stored in text files, and can be edited either directly or using the GUI.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

A generic framework for individual-based modelling and physical-biological interaction

PubMed Central

2018-01-01

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems. PMID:29351280

JACOB: an enterprise framework for computational chemistry.

PubMed

Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

2013-06-15

Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

Doing Better: Illuminating a Framework of Equitable Science Pedagogy through a Cross- Case Analysis of Urban High School Science Teachers

NASA Astrophysics Data System (ADS)

Sheth, Manali J.

Students of color are routinely asked to participate in science education that is less intellectually rich and self-affirming. Additionally, teachers have trouble embarking on professional growth related to issues of equity and diversity in science. The purpose of this dissertation research is to develop a multi-dimensional framework for equitable science pedagogy (ESP) through analyzing the efforts and struggles of high school science teachers. This study is grounded in a conceptual framework derived from scholarship in science education, multicultural education, critical science studies, and teacher learning. The following questions guide this research: 1) What visions and enactments emerge in teachers' practices towards equitable science pedagogy? 2) How are teachers' practice decisions towards ESP influenced by their personal theories of race/culture, science, and learning and sociocultural contexts? 3) Why are there consistencies and variances across teachers' practices? This study employs a qualitative multiple case study design with ethnographic data collection to explore the practices of three urban high school science teachers who were identified as being committed to nurturing the science learning of students of color. Data include over 120 hours of classroom observation, 60 hours of teacher interviews, and 500 teacher- and student-generated artifacts. Data analysis included coding teachers' practices using theory- and participant generated codes, construction of themes based on emergent patterns, and cross-case analysis. The affordances and limitations of the participants' pedagogical approaches inform the following framework for equitable science pedagogy: 1) Seeing race and culture and sharing responsibility for learning form foundational dimensions. Practices from the other three dimensions--- nurturing students' identities, re-centering students' epistemologies, and critiquing structural inequities---emerge from the foundation. As emergent practices, they are constituted by but not reduced to practices in the initial dimensions. 2) Ideas from the foundational dimensions are filtered through teachers' stances on science. Thus, teachers' practices in the emergent dimensions and the foundational dimensions are mediated by teachers' pedagogical ideas about science and school science. 3) Teachers' articulations of practice influence the possibility of on-going work towards equitable science pedagogy.

Visual coding of human bodies: perceptual aftereffects reveal norm-based, opponent coding of body identity.

PubMed

Rhodes, Gillian; Jeffery, Linda; Boeing, Alexandra; Calder, Andrew J

2013-04-01

Despite the discovery of body-selective neural areas in occipitotemporal cortex, little is known about how bodies are visually coded. We used perceptual adaptation to determine how body identity is coded. Brief exposure to a body (e.g., anti-Rose) biased perception toward an identity with opposite properties (Rose). Moreover, the size of this aftereffect increased with adaptor extremity, as predicted by norm-based, opponent coding of body identity. A size change between adapt and test bodies minimized the effects of low-level, retinotopic adaptation. These results demonstrate that body identity, like face identity, is opponent coded in higher-level vision. More generally, they show that a norm-based multidimensional framework, which is well established for face perception, may provide a powerful framework for understanding body perception.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

Methodology Development for Passive Component Reliability Modeling in a Multi-Physics Simulation Environment

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

Aldemir, Tunc; Denning, Richard; Catalyurek, Umit

Reduction in safety margin can be expected as passive structures and components undergo degradation with time. Limitations in the traditional probabilistic risk assessment (PRA) methodology constrain its value as an effective tool to address the impact of aging effects on risk and for quantifying the impact of aging management strategies in maintaining safety margins. A methodology has been developed to address multiple aging mechanisms involving large numbers of components (with possibly statistically dependent failures) within the PRA framework in a computationally feasible manner when the sequencing of events is conditioned on the physical conditions predicted in a simulation environment, suchmore » as the New Generation System Code (NGSC) concept. Both epistemic and aleatory uncertainties can be accounted for within the same phenomenological framework and maintenance can be accounted for in a coherent fashion. The framework accommodates the prospective impacts of various intervention strategies such as testing, maintenance, and refurbishment. The methodology is illustrated with several examples.« less

National Combustion Code: A Multidisciplinary Combustor Design System

NASA Technical Reports Server (NTRS)

Stubbs, Robert M.; Liu, Nan-Suey

1997-01-01

The Internal Fluid Mechanics Division conducts both basic research and technology, and system technology research for aerospace propulsion systems components. The research within the division, which is both computational and experimental, is aimed at improving fundamental understanding of flow physics in inlets, ducts, nozzles, turbomachinery, and combustors. This article and the following three articles highlight some of the work accomplished in 1996. A multidisciplinary combustor design system is critical for optimizing the combustor design process. Such a system should include sophisticated computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. The goal of the present effort is to develop some of the enabling technologies and to demonstrate their overall performance in an integrated system called the National Combustion Code.

Design and construction of a 2D metal organic framework with multiple cavities: a nonregular net with a paracyclophane that codes for multiply fused nodes.

PubMed

Papaefstathiou, Giannis S; Friscić, Tomislav; MacGillivray, Leonard R

2005-10-19

A metal organic framework with two different nodes (circle and square) and a structure related to one of the 20 known 2-uniform nets has been constructed using an organic building unit that codes for multiply fused nodes.

Indirect Observation in Everyday Contexts: Concepts and Methodological Guidelines within a Mixed Methods Framework

PubMed Central

Anguera, M. Teresa; Portell, Mariona; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana

2018-01-01

Indirect observation is a recent concept in systematic observation. It largely involves analyzing textual material generated either indirectly from transcriptions of audio recordings of verbal behavior in natural settings (e.g., conversation, group discussions) or directly from narratives (e.g., letters of complaint, tweets, forum posts). It may also feature seemingly unobtrusive objects that can provide relevant insights into daily routines. All these materials constitute an extremely rich source of information for studying everyday life, and they are continuously growing with the burgeoning of new technologies for data recording, dissemination, and storage. Narratives are an excellent vehicle for studying everyday life, and quantitization is proposed as a means of integrating qualitative and quantitative elements. However, this analysis requires a structured system that enables researchers to analyze varying forms and sources of information objectively. In this paper, we present a methodological framework detailing the steps and decisions required to quantitatively analyze a set of data that was originally qualitative. We provide guidelines on study dimensions, text segmentation criteria, ad hoc observation instruments, data quality controls, and coding and preparation of text for quantitative analysis. The quality control stage is essential to ensure that the code matrices generated from the qualitative data are reliable. We provide examples of how an indirect observation study can produce data for quantitative analysis and also describe the different software tools available for the various stages of the process. The proposed method is framed within a specific mixed methods approach that involves collecting qualitative data and subsequently transforming these into matrices of codes (not frequencies) for quantitative analysis to detect underlying structures and behavioral patterns. The data collection and quality control procedures fully meet the requirement of flexibility and provide new perspectives on data integration in the study of biopsychosocial aspects in everyday contexts. PMID:29441028

Transforming user needs into functional requirements for an antibiotic clinical decision support system: explicating content analysis for system design.

PubMed

Bright, T J

2013-01-01

Many informatics studies use content analysis to generate functional requirements for system development. Explication of this translational process from qualitative data to functional requirements can strengthen the understanding and scientific rigor when applying content analysis in informatics studies. To describe a user-centered approach transforming emergent themes derived from focus group data into functional requirements for informatics solutions and to illustrate these methods to the development of an antibiotic clinical decision support system (CDS). THE APPROACH CONSISTED OF FIVE STEPS: 1) identify unmet therapeutic planning information needs via Focus Group Study-I, 2) develop a coding framework of therapeutic planning themes to refine the domain scope to antibiotic therapeutic planning, 3) identify functional requirements of an antibiotic CDS system via Focus Group Study-II, 4) discover informatics solutions and functional requirements from coded data, and 5) determine the types of information needed to support the antibiotic CDS system and link with the identified informatics solutions and functional requirements. The coding framework for Focus Group Study-I revealed unmet therapeutic planning needs. Twelve subthemes emerged and were clustered into four themes; analysis indicated a need for an antibiotic CDS intervention. Focus Group Study-II included five types of information needs. Comments from the Barrier/Challenge to information access and Function/Feature themes produced three informatics solutions and 13 functional requirements of an antibiotic CDS system. Comments from the Patient, Institution, and Domain themes generated required data elements for each informatics solution. This study presents one example explicating content analysis of focus group data and the analysis process to functional requirements from narrative data. Illustration of this 5-step method was used to develop an antibiotic CDS system, resolving unmet antibiotic prescribing needs. As a reusable approach, these techniques can be refined and applied to resolve unmet information needs with informatics interventions in additional domains.

Transforming User Needs into Functional Requirements for an Antibiotic Clinical Decision Support System

PubMed Central

Bright, T.J.

2013-01-01

Summary Background Many informatics studies use content analysis to generate functional requirements for system development. Explication of this translational process from qualitative data to functional requirements can strengthen the understanding and scientific rigor when applying content analysis in informatics studies. Objective To describe a user-centered approach transforming emergent themes derived from focus group data into functional requirements for informatics solutions and to illustrate these methods to the development of an antibiotic clinical decision support system (CDS). Methods The approach consisted of five steps: 1) identify unmet therapeutic planning information needs via Focus Group Study-I, 2) develop a coding framework of therapeutic planning themes to refine the domain scope to antibiotic therapeutic planning, 3) identify functional requirements of an antibiotic CDS system via Focus Group Study-II, 4) discover informatics solutions and functional requirements from coded data, and 5) determine the types of information needed to support the antibiotic CDS system and link with the identified informatics solutions and functional requirements. Results The coding framework for Focus Group Study-I revealed unmet therapeutic planning needs. Twelve subthemes emerged and were clustered into four themes; analysis indicated a need for an antibiotic CDS intervention. Focus Group Study-II included five types of information needs. Comments from the Barrier/Challenge to information access and Function/Feature themes produced three informatics solutions and 13 functional requirements of an antibiotic CDS system. Comments from the Patient, Institution, and Domain themes generated required data elements for each informatics solution. Conclusion This study presents one example explicating content analysis of focus group data and the analysis process to functional requirements from narrative data. Illustration of this 5-step method was used to develop an antibiotic CDS system, resolving unmet antibiotic prescribing needs. As a reusable approach, these techniques can be refined and applied to resolve unmet information needs with informatics interventions in additional domains. PMID:24454586

CALCMIN - an EXCEL™ Visual Basic application for calculating mineral structural formulae from electron microprobe analyses

NASA Astrophysics Data System (ADS)

Brandelik, Andreas

2009-07-01

CALCMIN, an open source Visual Basic program, was implemented in EXCEL™. The program was primarily developed to support geoscientists in their routine task of calculating structural formulae of minerals on the basis of chemical analysis mainly obtained by electron microprobe (EMP) techniques. Calculation programs for various minerals are already included in the form of sub-routines. These routines are arranged in separate modules containing a minimum of code. The architecture of CALCMIN allows the user to easily develop new calculation routines or modify existing routines with little knowledge of programming techniques. By means of a simple mouse-click, the program automatically generates a rudimentary framework of code using the object model of the Visual Basic Editor (VBE). Within this framework simple commands and functions, which are provided by the program, can be used, for example, to perform various normalization procedures or to output the results of the computations. For the clarity of the code, element symbols are used as variables initialized by the program automatically. CALCMIN does not set any boundaries in complexity of the code used, resulting in a wide range of possible applications. Thus, matrix and optimization methods can be included, for instance, to determine end member contents for subsequent thermodynamic calculations. Diverse input procedures are provided, such as the automated read-in of output files created by the EMP. Furthermore, a subsequent filter routine enables the user to extract specific analyses in order to use them for a corresponding calculation routine. An event-driven, interactive operating mode was selected for easy application of the program. CALCMIN leads the user from the beginning to the end of the calculation process.

An Object-oriented Computer Code for Aircraft Engine Weight Estimation

NASA Technical Reports Server (NTRS)

Tong, Michael T.; Naylor, Bret A.

2008-01-01

Reliable engine-weight estimation at the conceptual design stage is critical to the development of new aircraft engines. It helps to identify the best engine concept amongst several candidates. At NASA Glenn (GRC), the Weight Analysis of Turbine Engines (WATE) computer code, originally developed by Boeing Aircraft, has been used to estimate the engine weight of various conceptual engine designs. The code, written in FORTRAN, was originally developed for NASA in 1979. Since then, substantial improvements have been made to the code to improve the weight calculations for most of the engine components. Most recently, to improve the maintainability and extensibility of WATE, the FORTRAN code has been converted into an object-oriented version. The conversion was done within the NASA s NPSS (Numerical Propulsion System Simulation) framework. This enables WATE to interact seamlessly with the thermodynamic cycle model which provides component flow data such as airflows, temperatures, and pressures, etc. that are required for sizing the components and weight calculations. The tighter integration between the NPSS and WATE would greatly enhance system-level analysis and optimization capabilities. It also would facilitate the enhancement of the WATE code for next-generation aircraft and space propulsion systems. In this paper, the architecture of the object-oriented WATE code (or WATE++) is described. Both the FORTRAN and object-oriented versions of the code are employed to compute the dimensions and weight of a 300- passenger aircraft engine (GE90 class). Both versions of the code produce essentially identical results as should be the case. Keywords: NASA, aircraft engine, weight, object-oriented

Computer programming for generating visual stimuli.

PubMed

Bukhari, Farhan; Kurylo, Daniel D

2008-02-01

Critical to vision research is the generation of visual displays with precise control over stimulus metrics. Generating stimuli often requires adapting commercial software or developing specialized software for specific research applications. In order to facilitate this process, we give here an overview that allows nonexpert users to generate and customize stimuli for vision research. We first give a review of relevant hardware and software considerations, to allow the selection of display hardware, operating system, programming language, and graphics packages most appropriate for specific research applications. We then describe the framework of a generic computer program that can be adapted for use with a broad range of experimental applications. Stimuli are generated in the context of trial events, allowing the display of text messages, the monitoring of subject responses and reaction times, and the inclusion of contingency algorithms. This approach allows direct control and management of computer-generated visual stimuli while utilizing the full capabilities of modern hardware and software systems. The flowchart and source code for the stimulus-generating program may be downloaded from www.psychonomic.org/archive.

Current Development Status of an Integrated Tool for Modeling Quasi-static Deformation in the Solid Earth

NASA Astrophysics Data System (ADS)

Williams, C. A.; Dicaprio, C.; Simons, M.

2003-12-01

With the advent of projects such as the Plate Boundary Observatory and future InSAR missions, spatially dense geodetic data of high quality will provide an increasingly detailed picture of the movement of the earth's surface. To interpret such information, powerful and easily accessible modeling tools are required. We are presently developing such a tool that we feel will meet many of the needs for evaluating quasi-static earth deformation. As a starting point, we begin with a modified version of the finite element code TECTON, which has been specifically designed to solve tectonic problems involving faulting and viscoelastic/plastic earth behavior. As our first priority, we are integrating the code into the GeoFramework, which is an extension of the Python-based Pyre modeling framework. The goal of this framework is to provide simplified user interfaces for powerful modeling codes, to provide easy access to utilities such as meshers and visualization tools, and to provide a tight integration between different modeling tools so they can interact with each other. The initial integration of the code into this framework is essentially complete, and a more thorough integration, where Python-based drivers control the entire solution, will be completed in the near future. We have an evolving set of priorities that we expect to solidify as we receive more input from the modeling community. Current priorities include the development of linear and quadratic tetrahedral elements, the development of a parallelized version of the code using the PETSc libraries, the addition of more complex rheologies, realistic fault friction models, adaptive time stepping, and spherical geometries. In this presentation we describe current progress toward our various priorities, briefly describe the structure of the code within the GeoFramework, and demonstrate some sample applications.

Leveraging the NLM map from SNOMED CT to ICD-10-CM to facilitate adoption of ICD-10-CM.

PubMed

Cartagena, F Phil; Schaeffer, Molly; Rifai, Dorothy; Doroshenko, Victoria; Goldberg, Howard S

2015-05-01

Develop and test web services to retrieve and identify the most precise ICD-10-CM code(s) for a given clinical encounter. Facilitate creation of user interfaces that 1) provide an initial shortlist of candidate codes, ideally visible on a single screen; and 2) enable code refinement. To satisfy our high-level use cases, the analysis and design process involved reviewing available maps and crosswalks, designing the rule adjudication framework, determining necessary metadata, retrieving related codes, and iteratively improving the code refinement algorithm. The Partners ICD-10-CM Search and Mapping Services (PI-10 Services) are SOAP web services written using Microsoft's.NET 4.0 Framework, Windows Communications Framework, and SQL Server 2012. The services cover 96% of the Partners problem list subset of SNOMED CT codes that map to ICD-10-CM codes and can return up to 76% of the 69,823 billable ICD-10-CM codes prior to creation of custom mapping rules. We consider ways to increase 1) the coverage ratio of the Partners problem list subset of SNOMED CT codes and 2) the upper bound of returnable ICD-10-CM codes by creating custom mapping rules. Future work will investigate the utility of the transitive closure of SNOMED CT codes and other methods to assist in custom rule creation and, ultimately, to provide more complete coverage of ICD-10-CM codes. ICD-10-CM will be easier for clinicians to manage if applications display short lists of candidate codes from which clinicians can subsequently select a code for further refinement. The PI-10 Services support ICD-10 migration by implementing this paradigm and enabling users to consistently and accurately find the best ICD-10-CM code(s) without translation from ICD-9-CM. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

HealthCyberMap: a semantic visual browser of medical Internet resources based on clinical codes and the human body metaphor.

PubMed

Kamel Boulos, Maged N; Roudsari, Abdul V; Carso N, Ewart R

2002-12-01

HealthCyberMap (HCM-http://healthcybermap.semanticweb.org) is a web-based service for healthcare professionals and librarians, patients and the public in general that aims at mapping parts of the health information resources in cyberspace in novel ways to improve their retrieval and navigation. HCM adopts a clinical metadata framework built upon a clinical coding ontology for the semantic indexing, classification and browsing of Internet health information resources. A resource metadata base holds information about selected resources. HCM then uses GIS (Geographic Information Systems) spatialization methods to generate interactive navigational cybermaps from the metadata base. These visual cybermaps are based on familiar medical metaphors. HCM cybermaps can be considered as semantically spatialized, ontology-based browsing views of the underlying resource metadata base. Using a clinical coding scheme as a metric for spatialization ('semantic distance') is unique to HCM and is very much suited for the semantic categorization and navigation of Internet health information resources. Clinical codes ensure reliable and unambiguous topical indexing of these resources. HCM also introduces a useful form of cyberspatial analysis for the detection of topical coverage gaps in the resource metadata base using choropleth (shaded) maps of human body systems.

Self-Supervised Video Hashing With Hierarchical Binary Auto-Encoder.

PubMed

Song, Jingkuan; Zhang, Hanwang; Li, Xiangpeng; Gao, Lianli; Wang, Meng; Hong, Richang

2018-07-01

Existing video hash functions are built on three isolated stages: frame pooling, relaxed learning, and binarization, which have not adequately explored the temporal order of video frames in a joint binary optimization model, resulting in severe information loss. In this paper, we propose a novel unsupervised video hashing framework dubbed self-supervised video hashing (SSVH), which is able to capture the temporal nature of videos in an end-to-end learning to hash fashion. We specifically address two central problems: 1) how to design an encoder-decoder architecture to generate binary codes for videos and 2) how to equip the binary codes with the ability of accurate video retrieval. We design a hierarchical binary auto-encoder to model the temporal dependencies in videos with multiple granularities, and embed the videos into binary codes with less computations than the stacked architecture. Then, we encourage the binary codes to simultaneously reconstruct the visual content and neighborhood structure of the videos. Experiments on two real-world data sets show that our SSVH method can significantly outperform the state-of-the-art methods and achieve the current best performance on the task of unsupervised video retrieval.

Micromechanics Analysis Code Post-Processing (MACPOST) User Guide. 1.0

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Comiskey, Michele D.; Bednarcyk, Brett A.

1999-01-01

As advanced composite materials have gained wider usage. the need for analytical models and computer codes to predict the thermomechanical deformation response of these materials has increased significantly. Recently, a micromechanics technique called the generalized method of cells (GMC) has been developed, which has the capability to fulfill this -oal. Tc provide a framework for GMC, the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) has been developed. As MAC/GMC has been updated, significant improvements have been made to the post-processing capabilities of the code. Through the MACPOST program, which operates directly within the MSC/PATRAN graphical pre- and post-processing package, a direct link between the analysis capabilities of MAC/GMC and the post-processing capabilities of MSC/PATRAN has been established. MACPOST has simplified the production, printing. and exportation of results for unit cells analyzed by MAC/GMC. MACPOST allows different micro-level quantities to be plotted quickly and easily in contour plots. In addition, meaningful data for X-Y plots can be examined. MACPOST thus serves as an important analysis and visualization tool for the macro- and micro-level data generated by MAC/GMC. This report serves as the user's manual for the MACPOST program.

Self-Supervised Video Hashing With Hierarchical Binary Auto-Encoder

NASA Astrophysics Data System (ADS)

Song, Jingkuan; Zhang, Hanwang; Li, Xiangpeng; Gao, Lianli; Wang, Meng; Hong, Richang

2018-07-01

Existing video hash functions are built on three isolated stages: frame pooling, relaxed learning, and binarization, which have not adequately explored the temporal order of video frames in a joint binary optimization model, resulting in severe information loss. In this paper, we propose a novel unsupervised video hashing framework dubbed Self-Supervised Video Hashing (SSVH), that is able to capture the temporal nature of videos in an end-to-end learning-to-hash fashion. We specifically address two central problems: 1) how to design an encoder-decoder architecture to generate binary codes for videos; and 2) how to equip the binary codes with the ability of accurate video retrieval. We design a hierarchical binary autoencoder to model the temporal dependencies in videos with multiple granularities, and embed the videos into binary codes with less computations than the stacked architecture. Then, we encourage the binary codes to simultaneously reconstruct the visual content and neighborhood structure of the videos. Experiments on two real-world datasets (FCVID and YFCC) show that our SSVH method can significantly outperform the state-of-the-art methods and achieve the currently best performance on the task of unsupervised video retrieval.

AN EXTENSION OF THE ATHENA++ CODE FRAMEWORK FOR GRMHD BASED ON ADVANCED RIEMANN SOLVERS AND STAGGERED-MESH CONSTRAINED TRANSPORT

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

White, Christopher J.; Stone, James M.; Gammie, Charles F.

2016-08-01

We present a new general relativistic magnetohydrodynamics (GRMHD) code integrated into the Athena++ framework. Improving upon the techniques used in most GRMHD codes, ours allows the use of advanced, less diffusive Riemann solvers, in particular HLLC and HLLD. We also employ a staggered-mesh constrained transport algorithm suited for curvilinear coordinate systems in order to maintain the divergence-free constraint of the magnetic field. Our code is designed to work with arbitrary stationary spacetimes in one, two, or three dimensions, and we demonstrate its reliability through a number of tests. We also report on its promising performance and scalability.

The predictive mind and the experience of visual art work

PubMed Central

Kesner, Ladislav

2014-01-01

Among the main challenges of the predictive brain/mind concept is how to link prediction at the neural level to prediction at the cognitive-psychological level and finding conceptually robust and empirically verifiable ways to harness this theoretical framework toward explaining higher-order mental and cognitive phenomena, including the subjective experience of aesthetic and symbolic forms. Building on the tentative prediction error account of visual art, this article extends the application of the predictive coding framework to the visual arts. It does so by linking this theoretical discussion to a subjective, phenomenological account of how a work of art is experienced. In order to engage more deeply with a work of art, viewers must be able to tune or adapt their prediction mechanism to recognize art as a specific class of objects whose ontological nature defies predictability, and they must be able to sustain a productive flow of predictions from low-level sensory, recognitional to abstract semantic, conceptual, and affective inferences. The affective component of the process of predictive error optimization that occurs when a viewer enters into dialog with a painting is constituted both by activating the affective affordances within the image and by the affective consequences of prediction error minimization itself. The predictive coding framework also has implications for the problem of the culturality of vision. A person’s mindset, which determines what top–down expectations and predictions are generated, is co-constituted by culture-relative skills and knowledge, which form hyperpriors that operate in the perception of art. PMID:25566111

Navigating the System: How Transgender Individuals Engage in Health Care Services.

PubMed

Roller, Cyndi Gale; Sedlak, Carol; Draucker, Claire Burke

2015-09-01

Transgender individuals (TIs) experience a number of healthcare disparities that result in compromised access to health care, placing them at high risk for poor health outcomes. Despite their unique health concerns, there is little known about how they engage in health care. The purpose of this grounded theory study was to construct a theoretical framework that depicts the process by which transgender individuals engage in health care. In this grounded theory study, data from interviews with 25 individuals who self-identified as transgender were used to develop a theoretical framework that depicts the process by which TIs engage in health care. Data analysis included open coding, category formation, and theoretical coding. Constant comparative analysis was used to facilitate theory generation. The central phenomenon of how TIs engage in health care was the core process of navigating the system. The core process involves four subprocesses: needing to move forward, doing due diligence, finding loopholes, and making it work. The theoretical framework of navigating the system can provide healthcare providers with a way to understand how TIs engage in health care as they move through the subprocesses of moving forward, doing due diligence, finding loopholes, and making it work in order to get their healthcare needs met. With a better understanding of the healthcare journeys of TIs, healthcare providers can provide better care for this population and advocate for change in policies that contribute to the health disparities TIs experience. © 2015 Sigma Theta Tau International.

The predictive mind and the experience of visual art work.

PubMed

Kesner, Ladislav

2014-01-01

Among the main challenges of the predictive brain/mind concept is how to link prediction at the neural level to prediction at the cognitive-psychological level and finding conceptually robust and empirically verifiable ways to harness this theoretical framework toward explaining higher-order mental and cognitive phenomena, including the subjective experience of aesthetic and symbolic forms. Building on the tentative prediction error account of visual art, this article extends the application of the predictive coding framework to the visual arts. It does so by linking this theoretical discussion to a subjective, phenomenological account of how a work of art is experienced. In order to engage more deeply with a work of art, viewers must be able to tune or adapt their prediction mechanism to recognize art as a specific class of objects whose ontological nature defies predictability, and they must be able to sustain a productive flow of predictions from low-level sensory, recognitional to abstract semantic, conceptual, and affective inferences. The affective component of the process of predictive error optimization that occurs when a viewer enters into dialog with a painting is constituted both by activating the affective affordances within the image and by the affective consequences of prediction error minimization itself. The predictive coding framework also has implications for the problem of the culturality of vision. A person's mindset, which determines what top-down expectations and predictions are generated, is co-constituted by culture-relative skills and knowledge, which form hyperpriors that operate in the perception of art.

An implementation framework for the feedback of individual research results and incidental findings in research.

PubMed

Thorogood, Adrian; Joly, Yann; Knoppers, Bartha Maria; Nilsson, Tommy; Metrakos, Peter; Lazaris, Anthoula; Salman, Ayat

2014-12-23

This article outlines procedures for the feedback of individual research data to participants. This feedback framework was developed in the context of a personalized medicine research project in Canada. Researchers in this domain have an ethical obligation to return individual research results and/or material incidental findings that are clinically significant, valid and actionable to participants. Communication of individual research data must proceed in an ethical and efficient manner. Feedback involves three procedural steps: assessing the health relevance of a finding, re-identifying the affected participant, and communicating the finding. Re-identification requires researchers to break the code in place to protect participant identities. Coding systems replace personal identifiers with a numerical code. Double coding systems provide added privacy protection by separating research data from personal identifying data with a third "linkage" database. A trusted and independent intermediary, the "keyholder", controls access to this linkage database. Procedural guidelines for the return of individual research results and incidental findings are lacking. This article outlines a procedural framework for the three steps of feedback: assessment, re-identification, and communication. This framework clarifies the roles of the researcher, Research Ethics Board, and keyholder in the process. The framework also addresses challenges posed by coding systems. Breaking the code involves privacy risks and should only be carried out in clearly defined circumstances. Where a double coding system is used, the keyholder plays an important role in balancing the benefits of individual feedback with the privacy risks of re-identification. Feedback policies should explicitly outline procedures for the assessment of findings, and the re-identification and contact of participants. The responsibilities of researchers, the Research Ethics Board, and the keyholder must be clearly defined. We provide general guidelines for keyholders involved in feedback. We also recommend that Research Ethics Boards should not be directly involved in the assessment of individual findings. Hospitals should instead establish formal, interdisciplinary clinical advisory committees to help researchers determine whether or not an uncertain finding should be returned.

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.

PubMed

Fleishman, Sarel J; Leaver-Fay, Andrew; Corn, Jacob E; Strauch, Eva-Maria; Khare, Sagar D; Koga, Nobuyasu; Ashworth, Justin; Murphy, Paul; Richter, Florian; Lemmon, Gordon; Meiler, Jens; Baker, David

2011-01-01

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins.

The brain, self and society: a social-neuroscience model of predictive processing.

PubMed

Kelly, Michael P; Kriznik, Natasha M; Kinmonth, Ann Louise; Fletcher, Paul C

2018-05-10

This paper presents a hypothesis about how social interactions shape and influence predictive processing in the brain. The paper integrates concepts from neuroscience and sociology where a gulf presently exists between the ways that each describe the same phenomenon - how the social world is engaged with by thinking humans. We combine the concepts of predictive processing models (also called predictive coding models in the neuroscience literature) with ideal types, typifications and social practice - concepts from the sociological literature. This generates a unified hypothetical framework integrating the social world and hypothesised brain processes. The hypothesis combines aspects of neuroscience and psychology with social theory to show how social behaviors may be "mapped" onto brain processes. It outlines a conceptual framework that connects the two disciplines and that may enable creative dialogue and potential future research.

A Hybrid Constraint Representation and Reasoning Framework

NASA Technical Reports Server (NTRS)

Golden, Keith; Pang, Wan-Lin

2003-01-01

This paper introduces JNET, a novel constraint representation and reasoning framework that supports procedural constraints and constraint attachments, providing a flexible way of integrating the constraint reasoner with a run- time software environment. Attachments in JNET are constraints over arbitrary Java objects, which are defined using Java code, at runtime, with no changes to the JNET source code.

Evaluating QR Code Case Studies Using a Mobile Learning Framework

ERIC Educational Resources Information Center

Rikala, Jenni

2014-01-01

The aim of this study was to evaluate the feasibility of Quick Response (QR) codes and mobile devices in the context of Finnish basic education. The feasibility was analyzed through a mobile learning framework, which includes the core characteristics of mobile learning. The study is part of a larger research where the aim is to develop a…

USEEIO Framework Demo

EPA Science Inventory

The code base for creating versions of the USEEIO model and USEEIO-like models is called the USEEIO Modeling Framework. The framework is built in a combination of R and Python languages.This demonstration provides a brief overview and introduction into the framework.

Interactive Exploration for Continuously Expanding Neuron Databases.

PubMed

Li, Zhongyu; Metaxas, Dimitris N; Lu, Aidong; Zhang, Shaoting

2017-02-15

This paper proposes a novel framework to help biologists explore and analyze neurons based on retrieval of data from neuron morphological databases. In recent years, the continuously expanding neuron databases provide a rich source of information to associate neuronal morphologies with their functional properties. We design a coarse-to-fine framework for efficient and effective data retrieval from large-scale neuron databases. In the coarse-level, for efficiency in large-scale, we employ a binary coding method to compress morphological features into binary codes of tens of bits. Short binary codes allow for real-time similarity searching in Hamming space. Because the neuron databases are continuously expanding, it is inefficient to re-train the binary coding model from scratch when adding new neurons. To solve this problem, we extend binary coding with online updating schemes, which only considers the newly added neurons and update the model on-the-fly, without accessing the whole neuron databases. In the fine-grained level, we introduce domain experts/users in the framework, which can give relevance feedback for the binary coding based retrieval results. This interactive strategy can improve the retrieval performance through re-ranking the above coarse results, where we design a new similarity measure and take the feedback into account. Our framework is validated on more than 17,000 neuron cells, showing promising retrieval accuracy and efficiency. Moreover, we demonstrate its use case in assisting biologists to identify and explore unknown neurons. Copyright © 2017 Elsevier Inc. All rights reserved.

Proceedings of the First NASA Formal Methods Symposium

NASA Technical Reports Server (NTRS)

Denney, Ewen (Editor); Giannakopoulou, Dimitra (Editor); Pasareanu, Corina S. (Editor)

2009-01-01

Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000.

Overview of the ArbiTER edge plasma eigenvalue code

NASA Astrophysics Data System (ADS)

Baver, Derek; Myra, James; Umansky, Maxim

2011-10-01

The Arbitrary Topology Equation Reader, or ArbiTER, is a flexible eigenvalue solver that is currently under development for plasma physics applications. The ArbiTER code builds on the equation parser framework of the existing 2DX code, extending it to include a topology parser. This will give the code the capability to model problems with complicated geometries (such as multiple X-points and scrape-off layers) or model equations with arbitrary numbers of dimensions (e.g. for kinetic analysis). In the equation parser framework, model equations are not included in the program's source code. Instead, an input file contains instructions for building a matrix from profile functions and elementary differential operators. The program then executes these instructions in a sequential manner. These instructions may also be translated into analytic form, thus giving the code transparency as well as flexibility. We will present an overview of how the ArbiTER code is to work, as well as preliminary results from early versions of this code. Work supported by the U.S. DOE.

Flexible Generation of Kalman Filter Code

NASA Technical Reports Server (NTRS)

Richardson, Julian; Wilson, Edward

2006-01-01

Domain-specific program synthesis can automatically generate high quality code in complex domains from succinct specifications, but the range of programs which can be generated by a given synthesis system is typically narrow. Obtaining code which falls outside this narrow scope necessitates either 1) extension of the code generator, which is usually very expensive, or 2) manual modification of the generated code, which is often difficult and which must be redone whenever changes are made to the program specification. In this paper, we describe adaptations and extensions of the AUTOFILTER Kalman filter synthesis system which greatly extend the range of programs which can be generated. Users augment the input specification with a specification of code fragments and how those fragments should interleave with or replace parts of the synthesized filter. This allows users to generate a much wider range of programs without their needing to modify the synthesis system or edit generated code. We demonstrate the usefulness of the approach by applying it to the synthesis of a complex state estimator which combines code from several Kalman filters with user-specified code. The work described in this paper allows the complex design decisions necessary for real-world applications to be reflected in the synthesized code. When executed on simulated input data, the generated state estimator was found to produce comparable estimates to those produced by a handcoded estimator

Support for User Interfaces for Distributed Systems

NASA Technical Reports Server (NTRS)

Eychaner, Glenn; Niessner, Albert

2005-01-01

An extensible Java(TradeMark) software framework supports the construction and operation of graphical user interfaces (GUIs) for distributed computing systems typified by ground control systems that send commands to, and receive telemetric data from, spacecraft. Heretofore, such GUIs have been custom built for each new system at considerable expense. In contrast, the present framework affords generic capabilities that can be shared by different distributed systems. Dynamic class loading, reflection, and other run-time capabilities of the Java language and JavaBeans component architecture enable the creation of a GUI for each new distributed computing system with a minimum of custom effort. By use of this framework, GUI components in control panels and menus can send commands to a particular distributed system with a minimum of system-specific code. The framework receives, decodes, processes, and displays telemetry data; custom telemetry data handling can be added for a particular system. The framework supports saving and later restoration of users configurations of control panels and telemetry displays with a minimum of effort in writing system-specific code. GUIs constructed within this framework can be deployed in any operating system with a Java run-time environment, without recompilation or code changes.

Reformation of Regulatory Technical Standards for Nuclear Power Generation Equipments in Japan

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

Mikio Kurihara; Masahiro Aoki; Yu Maruyama

2006-07-01

Comprehensive reformation of the regulatory system has been introduced in Japan in order to apply recent technical progress in a timely manner. 'The Technical Standards for Nuclear Power Generation Equipments', known as the Ordinance No.622) of the Ministry of International Trade and Industry, which is used for detailed design, construction and operating stage of Nuclear Power Plants, was being modified to performance specifications with the consensus codes and standards being used as prescriptive specifications, in order to facilitate prompt review of the Ordinance with response to technological innovation. The activities on modification were performed by the Nuclear and Industrial Safetymore » Agency (NISA), the regulatory body in Japan, with support of the Japan Nuclear Energy Safety Organization (JNES), a technical support organization. The revised Ordinance No.62 was issued on July 1, 2005 and is enforced from January 1 2006. During the period from the issuance to the enforcement, JNES carried out to prepare enforceable regulatory guide which complies with each provisions of the Ordinance No.62, and also made technical assessment to endorse the applicability of consensus codes and standards, in response to NISA's request. Some consensus codes and standards were re-assessed since they were already used in regulatory review of the construction plan submitted by licensee. Other consensus codes and standards were newly assessed for endorsement. In case that proper consensus code or standards were not prepared, details of regulatory requirements were described in the regulatory guide as immediate measures. At the same time, appropriate standards developing bodies were requested to prepare those consensus code or standards. Supplementary note which provides background information on the modification, applicable examples etc. was prepared for convenience to the users of the Ordinance No. 62. This paper shows the activities on modification and the results, following the NISA's presentation at ICONE-13 that introduced the framework of the performance specifications and the modification process of the Ordinance NO. 62. (authors)« less

Milk and social media: online communities and the International Code of Marketing of Breast-milk Substitutes.

PubMed

Abrahams, Sheryl W

2012-08-01

The advent of social networking sites and other online communities presents new opportunities and challenges for the promotion, protection, and support of breastfeeding. This study examines the presence of infant formula marketing on popular US social media sites, using the World Health Organization International Code of Marketing of Breast-milk Substitutes (the Code) as a framework. We examined to what extent each of 11 infant formula brands that are widely available in the US had established a social media presence in popular social media venues likely to be visited by expectant parents and families with young children. We then examined current marketing practices, using the Code as a basis for ethical marketing. Infant formula manufacturers have established a social media presence primarily through Facebook pages, interactive features on their own Web sites, mobile apps for new and expecting parents, YouTube videos, sponsored reviews on parenting blogs, and other financial relationships with parenting blogs. Violations of the Code as well as promotional practices unforeseen by the Code were identified. These practices included enabling user-generated content that promotes the use of infant formula, financial relationships between manufacturers and bloggers, and creation of mobile apps for use by parents. An additional concern identified for Code enforcement is lack of transparency in social media-based marketing. The use of social media for formula marketing may demand new strategies for monitoring and enforcing the Code in light of emerging challenges, including suggested content for upcoming consideration for World Health Assembly resolutions.

A Verification-Driven Approach to Traceability and Documentation for Auto-Generated Mathematical Software

NASA Technical Reports Server (NTRS)

Denney, Ewen W.; Fischer, Bernd

2009-01-01

Model-based development and automated code generation are increasingly used for production code in safety-critical applications, but since code generators are typically not qualified, the generated code must still be fully tested, reviewed, and certified. This is particularly arduous for mathematical and control engineering software which requires reviewers to trace subtle details of textbook formulas and algorithms to the code, and to match requirements (e.g., physical units or coordinate frames) not represented explicitly in models or code. Both tasks are complicated by the often opaque nature of auto-generated code. We address these problems by developing a verification-driven approach to traceability and documentation. We apply the AUTOCERT verification system to identify and then verify mathematical concepts in the code, based on a mathematical domain theory, and then use these verified traceability links between concepts, code, and verification conditions to construct a natural language report that provides a high-level structured argument explaining why and how the code uses the assumptions and complies with the requirements. We have applied our approach to generate review documents for several sub-systems of NASA s Project Constellation.

ESTEST: A Framework for the Verification and Validation of Electronic Structure Codes

NASA Astrophysics Data System (ADS)

Yuan, Gary; Gygi, Francois

2011-03-01

ESTEST is a verification and validation (V& V) framework for electronic structure codes that supports Qbox, Quantum Espresso, ABINIT, the Exciting Code and plans support for many more. We discuss various approaches to the electronic structure V& V problem implemented in ESTEST, that are related to parsing, formats, data management, search, comparison and analyses. Additionally, an early experiment in the distribution of V& V ESTEST servers among the electronic structure community will be presented. Supported by NSF-OCI 0749217 and DOE FC02-06ER25777.

Flexible patient information search and retrieval framework: pilot implementation

NASA Astrophysics Data System (ADS)

Erdal, Selnur; Catalyurek, Umit V.; Saltz, Joel; Kamal, Jyoti; Gurcan, Metin N.

2007-03-01

Medical centers collect and store significant amount of valuable data pertaining to patients' visit in the form of medical free-text. In addition, standardized diagnosis codes (International Classification of Diseases, Ninth Revision, Clinical Modification: ICD9-CM) related to those dictated reports are usually available. In this work, we have created a framework where image searches could be initiated through a combination of free-text reports as well as ICD9 codes. This framework enables more comprehensive search on existing large sets of patient data in a systematic way. The free text search is enriched by computer-aided inclusion of additional search terms enhanced by a thesaurus. This combination of enriched search allows users to access to a larger set of relevant results from a patient-centric PACS in a simpler way. Therefore, such framework is of particular use in tasks such as gathering images for desired patient populations, building disease models, and so on. As the motivating application of our framework, we implemented a search engine. This search engine processed two years of patient data from the OSU Medical Center's Information Warehouse and identified lung nodule location information using a combination of UMLS Meta-Thesaurus enhanced text report searches along with ICD9 code searches on patients that have been discharged. Five different queries with various ICD9 codes involving lung cancer were carried out on 172552 cases. Each search was completed under a minute on average per ICD9 code and the inclusion of UMLS thesaurus increased the number of relevant cases by 45% on average.

A climate robust integrated modelling framework for regional impact assessment of climate change

NASA Astrophysics Data System (ADS)

Janssen, Gijs; Bakker, Alexander; van Ek, Remco; Groot, Annemarie; Kroes, Joop; Kuiper, Marijn; Schipper, Peter; van Walsum, Paul; Wamelink, Wieger; Mol, Janet

2013-04-01

Decision making towards climate proofing the water management of regional catchments can benefit greatly from the availability of a climate robust integrated modelling framework, capable of a consistent assessment of climate change impacts on the various interests present in the catchments. In the Netherlands, much effort has been devoted to developing state-of-the-art regional dynamic groundwater models with a very high spatial resolution (25x25 m2). Still, these models are not completely satisfactory to decision makers because the modelling concepts do not take into account feedbacks between meteorology, vegetation/crop growth, and hydrology. This introduces uncertainties in forecasting the effects of climate change on groundwater, surface water, agricultural yields, and development of groundwater dependent terrestrial ecosystems. These uncertainties add to the uncertainties about the predictions on climate change itself. In order to create an integrated, climate robust modelling framework, we coupled existing model codes on hydrology, agriculture and nature that are currently in use at the different research institutes in the Netherlands. The modelling framework consists of the model codes MODFLOW (groundwater flow), MetaSWAP (vadose zone), WOFOST (crop growth), SMART2-SUMO2 (soil-vegetation) and NTM3 (nature valuation). MODFLOW, MetaSWAP and WOFOST are coupled online (i.e. exchange information on time step basis). Thus, changes in meteorology and CO2-concentrations affect crop growth and feedbacks between crop growth, vadose zone water movement and groundwater recharge are accounted for. The model chain WOFOST-MetaSWAP-MODFLOW generates hydrological input for the ecological prediction model combination SMART2-SUMO2-NTM3. The modelling framework was used to support the regional water management decision making process in the 267 km2 Baakse Beek-Veengoot catchment in the east of the Netherlands. Computations were performed for regionalized 30-year climate change scenarios developed by KNMI for precipitation and reference evapotranspiration according to Penman-Monteith. Special focus in the project was on the role of uncertainty. How valid is the information that is generated by this modelling framework? What are the most important uncertainties of the input data, how do they affect the results of the model chain and how can the uncertainties of the data, results, and model concepts be quantified and communicated? Besides these technical issues, an important part of the study was devoted to the perception of stakeholders. Stakeholder analysis and additional working sessions yielded insight into how the models, their results and the uncertainties are perceived, how the modelling framework and results connect to the stakeholders' information demands and what kind of additional information is needed for adequate support on decision making.

A Systematic Approach for Quantitative Analysis of Multidisciplinary Design Optimization Framework

NASA Astrophysics Data System (ADS)

Kim, Sangho; Park, Jungkeun; Lee, Jeong-Oog; Lee, Jae-Woo

An efficient Multidisciplinary Design and Optimization (MDO) framework for an aerospace engineering system should use and integrate distributed resources such as various analysis codes, optimization codes, Computer Aided Design (CAD) tools, Data Base Management Systems (DBMS), etc. in a heterogeneous environment, and need to provide user-friendly graphical user interfaces. In this paper, we propose a systematic approach for determining a reference MDO framework and for evaluating MDO frameworks. The proposed approach incorporates two well-known methods, Analytic Hierarchy Process (AHP) and Quality Function Deployment (QFD), in order to provide a quantitative analysis of the qualitative criteria of MDO frameworks. Identification and hierarchy of the framework requirements and the corresponding solutions for the reference MDO frameworks, the general one and the aircraft oriented one were carefully investigated. The reference frameworks were also quantitatively identified using AHP and QFD. An assessment of three in-house frameworks was then performed. The results produced clear and useful guidelines for improvement of the in-house MDO frameworks and showed the feasibility of the proposed approach for evaluating an MDO framework without a human interference.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

A Framework to Manage Information Models

NASA Astrophysics Data System (ADS)

Hughes, J. S.; King, T.; Crichton, D.; Walker, R.; Roberts, A.; Thieman, J.

2008-05-01

The Information Model is the foundation on which an Information System is built. It defines the entities to be processed, their attributes, and the relationships that add meaning. The development and subsequent management of the Information Model is the single most significant factor for the development of a successful information system. A framework of tools has been developed that supports the management of an information model with the rigor typically afforded to software development. This framework provides for evolutionary and collaborative development independent of system implementation choices. Once captured, the modeling information can be exported to common languages for the generation of documentation, application databases, and software code that supports both traditional and semantic web applications. This framework is being successfully used for several science information modeling projects including those for the Planetary Data System (PDS), the International Planetary Data Alliance (IPDA), the National Cancer Institute's Early Detection Research Network (EDRN), and several Consultative Committee for Space Data Systems (CCSDS) projects. The objective of the Space Physics Archive Search and Exchange (SPASE) program is to promote collaboration and coordination of archiving activity for the Space Plasma Physics community and ensure the compatibility of the architectures used for a global distributed system and the individual data centers. Over the past several years, the SPASE data model working group has made great progress in developing the SPASE Data Model and supporting artifacts including a data dictionary, XML Schema, and two ontologies. The authors have captured the SPASE Information Model in this framework. This allows the generation of documentation that presents the SPASE Information Model in object-oriented notation including UML class diagrams and class hierarchies. The modeling information can also be exported to semantic web languages such as OWL and RDF and written to XML Metadata Interchange (XMI) files for import into UML tools.

Decoding the "CoDe": A Framework for Conceptualizing and Designing Help Options in Computer-Based Second Language Listening

ERIC Educational Resources Information Center

Cardenas-Claros, Monica Stella; Gruba, Paul A.

2013-01-01

This paper proposes a theoretical framework for the conceptualization and design of help options in computer-based second language (L2) listening. Based on four empirical studies, it aims at clarifying both conceptualization and design (CoDe) components. The elements of conceptualization consist of a novel four-part classification of help options:…

Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

Toward a computational framework for cognitive biology: Unifying approaches from cognitive neuroscience and comparative cognition

NASA Astrophysics Data System (ADS)

Fitch, W. Tecumseh

2014-09-01

Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a neurally-grounded framework for theoretical cognitive science is within reach that can move beyond polarized debates and provide a more adequate theoretical future for cognitive biology.

Toward a computational framework for cognitive biology: unifying approaches from cognitive neuroscience and comparative cognition.

PubMed

Fitch, W Tecumseh

2014-09-01

Progress in understanding cognition requires a quantitative, theoretical framework, grounded in the other natural sciences and able to bridge between implementational, algorithmic and computational levels of explanation. I review recent results in neuroscience and cognitive biology that, when combined, provide key components of such an improved conceptual framework for contemporary cognitive science. Starting at the neuronal level, I first discuss the contemporary realization that single neurons are powerful tree-shaped computers, which implies a reorientation of computational models of learning and plasticity to a lower, cellular, level. I then turn to predictive systems theory (predictive coding and prediction-based learning) which provides a powerful formal framework for understanding brain function at a more global level. Although most formal models concerning predictive coding are framed in associationist terms, I argue that modern data necessitate a reinterpretation of such models in cognitive terms: as model-based predictive systems. Finally, I review the role of the theory of computation and formal language theory in the recent explosion of comparative biological research attempting to isolate and explore how different species differ in their cognitive capacities. Experiments to date strongly suggest that there is an important difference between humans and most other species, best characterized cognitively as a propensity by our species to infer tree structures from sequential data. Computationally, this capacity entails generative capacities above the regular (finite-state) level; implementationally, it requires some neural equivalent of a push-down stack. I dub this unusual human propensity "dendrophilia", and make a number of concrete suggestions about how such a system may be implemented in the human brain, about how and why it evolved, and what this implies for models of language acquisition. I conclude that, although much remains to be done, a neurally-grounded framework for theoretical cognitive science is within reach that can move beyond polarized debates and provide a more adequate theoretical future for cognitive biology. Copyright © 2014. Published by Elsevier B.V.

The navigation toolkit

NASA Technical Reports Server (NTRS)

Rich, William F.; Strom, Stephen W.

1994-01-01

This report summarizes the experience of the authors in managing, designing, and implementing an object-oriented applications framework for orbital navigation analysis for the Flight Design and Dynamics Department of the Rockwell Space Operations Company in Houston, in support of the Mission Operations Directorate of NASA's Johnson Space Center. The 8 person year project spanned 1.5 years and produced 30,000 lines of C++ code, replacing 150,000 lines of Fortran/C. We believe that our experience is important because it represents a 'second project' experience and generated real production-quality code - it was not a pilot. The project successfully demonstrated the use of 'continuous development' or rapid prototyping techniques. Use of formal methods and executable models contributed to the quality of the code. Keys to the success of the project were a strong architectural vision and highly skilled workers. This report focuses on process and methodology, and not on a detailed design description of the product. But the true importance of the object-oriented paradigm is its liberation of the developer to focus on the problem rather than the means used to solve the problem.

Validation of High-Fidelity CFD/CAA Framework for Launch Vehicle Acoustic Environment Simulation against Scale Model Test Data

NASA Technical Reports Server (NTRS)

Liever, Peter A.; West, Jeffrey S.; Harris, Robert E.

2016-01-01

A hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) modeling framework has been developed for launch vehicle liftoff acoustic environment predictions. The framework couples the existing highly-scalable NASA production CFD code, Loci/CHEM, with a high-order accurate Discontinuous Galerkin solver developed in the same production framework, Loci/THRUST, to accurately resolve and propagate acoustic physics across the entire launch environment. Time-accurate, Hybrid RANS/LES CFD modeling is applied for predicting the acoustic generation physics at the plume source, and a high-order accurate unstructured mesh Discontinuous Galerkin (DG) method is employed to propagate acoustic waves away from the source across large distances using high-order accurate schemes. The DG solver is capable of solving 2nd, 3rd, and 4th order Euler solutions for non-linear, conservative acoustic field propagation. Initial application testing and validation has been carried out against high resolution acoustic data from the Ares Scale Model Acoustic Test (ASMAT) series to evaluate the capabilities and production readiness of the CFD/CAA system to resolve the observed spectrum of acoustic frequency content. This paper presents results from this validation and outlines efforts to mature and improve the computational simulation framework.

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

Dillon, Heather E.; Antonopoulos, Chrissi A.; Solana, Amy E.

As the model energy codes are improved to reach efficiency levels 50 percent greater than current codes, use of on-site renewable energy generation is likely to become a code requirement. This requirement will be needed because traditional mechanisms for code improvement, including envelope, mechanical and lighting, have been pressed to the end of reasonable limits. Research has been conducted to determine the mechanism for implementing this requirement (Kaufman 2011). Kaufmann et al. determined that the most appropriate way to structure an on-site renewable requirement for commercial buildings is to define the requirement in terms of an installed power density permore » unit of roof area. This provides a mechanism that is suitable for the installation of photovoltaic (PV) systems on future buildings to offset electricity and reduce the total building energy load. Kaufmann et al. suggested that an appropriate maximum for the requirement in the commercial sector would be 4 W/ft{sup 2} of roof area or 0.5 W/ft{sup 2} of conditioned floor area. As with all code requirements, there must be an alternative compliance path for buildings that may not reasonably meet the renewables requirement. This might include conditions like shading (which makes rooftop PV arrays less effective), unusual architecture, undesirable roof pitch, unsuitable building orientation, or other issues. In the short term, alternative compliance paths including high performance mechanical equipment, dramatic envelope changes, or controls changes may be feasible. These options may be less expensive than many renewable systems, which will require careful balance of energy measures when setting the code requirement levels. As the stringency of the code continues to increase however, efficiency trade-offs will be maximized, requiring alternative compliance options to be focused solely on renewable electricity trade-offs or equivalent programs. One alternate compliance path includes purchase of Renewable Energy Credits (RECs). Each REC represents a specified amount of renewable electricity production and provides an offset of environmental externalities associated with non-renewable electricity production. The purpose of this paper is to explore the possible issues with RECs and comparable alternative compliance options. Existing codes have been examined to determine energy equivalence between the energy generation requirement and the RECs alternative over the life of the building. The price equivalence of the requirement and the alternative are determined to consider the economic drivers for a market decision. This research includes case studies that review how the few existing codes have incorporated RECs and some of the issues inherent with REC markets. Section 1 of the report reviews compliance options including RECs, green energy purchase programs, shared solar agreements and leases, and other options. Section 2 provides detailed case studies on codes that include RECs and community based alternative compliance methods. The methods the existing code requirements structure alternative compliance options like RECs are the focus of the case studies. Section 3 explores the possible structure of the renewable energy generation requirement in the context of energy and price equivalence. The price of RECs have shown high variation by market and over time which makes it critical to for code language to be updated frequently for a renewable energy generation requirement or the requirement will not remain price-equivalent over time. Section 4 of the report provides a maximum case estimate for impact to the PV market and the REC market based on the Kaufmann et al. proposed requirement levels. If all new buildings in the commercial sector complied with the requirement to install rooftop PV arrays, nearly 4,700 MW of solar would be installed in 2012, a major increase from EIA estimates of 640 MW of solar generation capacity installed in 2009. The residential sector could contribute roughly an additional 2,300 MW based on the same code requirement levels of 4 W/ft{sup 2} of roof area. Section 5 of the report provides a basic framework for draft code language recommendations based on the analysis of the alternative compliance levels.« less

FEDEF: A High Level Architecture Federate Development Framework

DTIC Science & Technology

2010-09-01

require code changes for operability between HLA specifications. Configuration of federate requirements such as publications, subscriptions, time ... management , and management protocol should occur outside of federate source code, allowing for federate reusability without code modification and re

Evaluating a Control System Architecture Based on a Formally Derived AOCS Model

NASA Astrophysics Data System (ADS)

Ilic, Dubravka; Latvala, Timo; Varpaaniemi, Kimmo; Vaisanen, Pauli; Troubitsyna, Elena; Laibinis, Linas

2010-08-01

Attitude & Orbit Control System (AOCS) refers to a wider class of control systems which are used to determine and control the attitude of the spacecraft while in orbit, based on the information obtained from various sensors. In this paper, we propose an approach to evaluate a typical (yet somewhat simplified) AOCS architecture using formal development - based on the Event-B method. As a starting point, an Ada specification of the AOCS is translated into a formal specification and further refined to incorporate all the details of its original source code specification. This way we are able not only to evaluate the Ada specification by expressing and verifying specific system properties in our formal models, but also to determine how well the chosen modelling framework copes with the level of detail required for an actual implementation and code generation from the derived models.

Methods for simulation-based analysis of fluid-structure interaction.

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

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Normalization is a general neural mechanism for context-dependent decision making

PubMed Central

Louie, Kenway; Khaw, Mel W.; Glimcher, Paul W.

2013-01-01

Understanding the neural code is critical to linking brain and behavior. In sensory systems, divisive normalization seems to be a canonical neural computation, observed in areas ranging from retina to cortex and mediating processes including contrast adaptation, surround suppression, visual attention, and multisensory integration. Recent electrophysiological studies have extended these insights beyond the sensory domain, demonstrating an analogous algorithm for the value signals that guide decision making, but the effects of normalization on choice behavior are unknown. Here, we show that choice models using normalization generate significant (and classically irrational) choice phenomena driven by either the value or number of alternative options. In value-guided choice experiments, both monkey and human choosers show novel context-dependent behavior consistent with normalization. These findings suggest that the neural mechanism of value coding critically influences stochastic choice behavior and provide a generalizable quantitative framework for examining context effects in decision making. PMID:23530203

Evolution of the ATLAS Software Framework towards Concurrency

NASA Astrophysics Data System (ADS)

Jones, R. W. L.; Stewart, G. A.; Leggett, C.; Wynne, B. M.

2015-05-01

The ATLAS experiment has successfully used its Gaudi/Athena software framework for data taking and analysis during the first LHC run, with billions of events successfully processed. However, the design of Gaudi/Athena dates from early 2000 and the software and the physics code has been written using a single threaded, serial design. This programming model has increasing difficulty in exploiting the potential of current CPUs, which offer their best performance only through taking full advantage of multiple cores and wide vector registers. Future CPU evolution will intensify this trend, with core counts increasing and memory per core falling. Maximising performance per watt will be a key metric, so all of these cores must be used as efficiently as possible. In order to address the deficiencies of the current framework, ATLAS has embarked upon two projects: first, a practical demonstration of the use of multi-threading in our reconstruction software, using the GaudiHive framework; second, an exercise to gather requirements for an updated framework, going back to the first principles of how event processing occurs. In this paper we report on both these aspects of our work. For the hive based demonstrators, we discuss what changes were necessary in order to allow the serially designed ATLAS code to run, both to the framework and to the tools and algorithms used. We report on what general lessons were learned about the code patterns that had been employed in the software and which patterns were identified as particularly problematic for multi-threading. These lessons were fed into our considerations of a new framework and we present preliminary conclusions on this work. In particular we identify areas where the framework can be simplified in order to aid the implementation of a concurrent event processing scheme. Finally, we discuss the practical difficulties involved in migrating a large established code base to a multi-threaded framework and how this can be achieved for LHC Run 3.

CARGO: effective format-free compressed storage of genomic information

PubMed Central

Roguski, Łukasz; Ribeca, Paolo

2016-01-01

The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats, sometimes inheriting from them suboptimal design choices; this hinders flexible and effective data sharing. Here, we present CARGO (Compressed ARchiving for GenOmics), a high-level framework to automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of our approach to FASTQ and SAM archives require a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors and scale well to multi-TB datasets. All CARGO software components can be freely downloaded for academic and non-commercial use from http://bio-cargo.sourceforge.net. PMID:27131376

RELAP-7 Level 2 Milestone Report: Demonstration of a Steady State Single Phase PWR Simulation with RELAP-7

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

David Andrs; Ray Berry; Derek Gaston

The document contains the simulation results of a steady state model PWR problem with the RELAP-7 code. The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on INL's modern scientific software development framework - MOOSE (Multi-Physics Object-Oriented Simulation Environment). This report summarizes the initial results of simulating a model steady-state single phase PWR problem using the current version of the RELAP-7 code. The major purpose of this demonstration simulation is to show that RELAP-7 code can be rapidly developed to simulate single-phase reactor problems. RELAP-7more » is a new project started on October 1st, 2011. It will become the main reactor systems simulation toolkit for RISMC (Risk Informed Safety Margin Characterization) and the next generation tool in the RELAP reactor safety/systems analysis application series (the replacement for RELAP5). The key to the success of RELAP-7 is the simultaneous advancement of physical models, numerical methods, and software design while maintaining a solid user perspective. Physical models include both PDEs (Partial Differential Equations) and ODEs (Ordinary Differential Equations) and experimental based closure models. RELAP-7 will eventually utilize well posed governing equations for multiphase flow, which can be strictly verified. Closure models used in RELAP5 and newly developed models will be reviewed and selected to reflect the progress made during the past three decades. RELAP-7 uses modern numerical methods, which allow implicit time integration, higher order schemes in both time and space, and strongly coupled multi-physics simulations. RELAP-7 is written with object oriented programming language C++. Its development follows modern software design paradigms. The code is easy to read, develop, maintain, and couple with other codes. Most importantly, the modern software design allows the RELAP-7 code to evolve with time. RELAP-7 is a MOOSE-based application. MOOSE (Multiphysics Object-Oriented Simulation Environment) is a framework for solving computational engineering problems in a well-planned, managed, and coordinated way. By leveraging millions of lines of open source software packages, such as PETSC (a nonlinear solver developed at Argonne National Laboratory) and LibMesh (a Finite Element Analysis package developed at University of Texas), MOOSE significantly reduces the expense and time required to develop new applications. Numerical integration methods and mesh management for parallel computation are provided by MOOSE. Therefore RELAP-7 code developers only need to focus on physics and user experiences. By using the MOOSE development environment, RELAP-7 code is developed by following the same modern software design paradigms used for other MOOSE development efforts. There are currently over 20 different MOOSE based applications ranging from 3-D transient neutron transport, detailed 3-D transient fuel performance analysis, to long-term material aging. Multi-physics and multiple dimensional analyses capabilities can be obtained by coupling RELAP-7 and other MOOSE based applications and by leveraging with capabilities developed by other DOE programs. This allows restricting the focus of RELAP-7 to systems analysis-type simulations and gives priority to retain and significantly extend RELAP5's capabilities.« less

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

A unified framework of unsupervised subjective optimized bit allocation for multiple video object coding

NASA Astrophysics Data System (ADS)

Chen, Zhenzhong; Han, Junwei; Ngan, King Ngi

2005-10-01

MPEG-4 treats a scene as a composition of several objects or so-called video object planes (VOPs) that are separately encoded and decoded. Such a flexible video coding framework makes it possible to code different video object with different distortion scale. It is necessary to analyze the priority of the video objects according to its semantic importance, intrinsic properties and psycho-visual characteristics such that the bit budget can be distributed properly to video objects to improve the perceptual quality of the compressed video. This paper aims to provide an automatic video object priority definition method based on object-level visual attention model and further propose an optimization framework for video object bit allocation. One significant contribution of this work is that the human visual system characteristics are incorporated into the video coding optimization process. Another advantage is that the priority of the video object can be obtained automatically instead of fixing weighting factors before encoding or relying on the user interactivity. To evaluate the performance of the proposed approach, we compare it with traditional verification model bit allocation and the optimal multiple video object bit allocation algorithms. Comparing with traditional bit allocation algorithms, the objective quality of the object with higher priority is significantly improved under this framework. These results demonstrate the usefulness of this unsupervised subjective quality lifting framework.

Eddy current-nulled convex optimized diffusion encoding (EN-CODE) for distortion-free diffusion tensor imaging with short echo times.

PubMed

Aliotta, Eric; Moulin, Kévin; Ennis, Daniel B

2018-02-01

To design and evaluate eddy current-nulled convex optimized diffusion encoding (EN-CODE) gradient waveforms for efficient diffusion tensor imaging (DTI) that is free of eddy current-induced image distortions. The EN-CODE framework was used to generate diffusion-encoding waveforms that are eddy current-compensated. The EN-CODE DTI waveform was compared with the existing eddy current-nulled twice refocused spin echo (TRSE) sequence as well as monopolar (MONO) and non-eddy current-compensated CODE in terms of echo time (TE) and image distortions. Comparisons were made in simulations, phantom experiments, and neuro imaging in 10 healthy volunteers. The EN-CODE sequence achieved eddy current compensation with a significantly shorter TE than TRSE (78 versus 96 ms) and a slightly shorter TE than MONO (78 versus 80 ms). Intravoxel signal variance was lower in phantoms with EN-CODE than with MONO (13.6 ± 11.6 versus 37.4 ± 25.8) and not different from TRSE (15.1 ± 11.6), indicating good robustness to eddy current-induced image distortions. Mean fractional anisotropy values in brain edges were also significantly lower with EN-CODE than with MONO (0.16 ± 0.01 versus 0.24 ± 0.02, P < 1 x 10 -5 ) and not different from TRSE (0.16 ± 0.01 versus 0.16 ± 0.01, P = nonsignificant). The EN-CODE sequence eliminated eddy current-induced image distortions in DTI with a TE comparable to MONO and substantially shorter than TRSE. Magn Reson Med 79:663-672, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Python package for model STructure ANalysis (pySTAN)

NASA Astrophysics Data System (ADS)

Van Hoey, Stijn; van der Kwast, Johannes; Nopens, Ingmar; Seuntjens, Piet

2013-04-01

The selection and identification of a suitable hydrological model structure is more than fitting parameters of a model structure to reproduce a measured hydrograph. The procedure is highly dependent on various criteria, i.e. the modelling objective, the characteristics and the scale of the system under investigation as well as the available data. Rigorous analysis of the candidate model structures is needed to support and objectify the selection of the most appropriate structure for a specific case (or eventually justify the use of a proposed ensemble of structures). This holds both in the situation of choosing between a limited set of different structures as well as in the framework of flexible model structures with interchangeable components. Many different methods to evaluate and analyse model structures exist. This leads to a sprawl of available methods, all characterized by different assumptions, changing conditions of application and various code implementations. Methods typically focus on optimization, sensitivity analysis or uncertainty analysis, with backgrounds from optimization, machine-learning or statistics amongst others. These methods also need an evaluation metric (objective function) to compare the model outcome with some observed data. However, for current methods described in literature, implementations are not always transparent and reproducible (if available at all). No standard procedures exist to share code and the popularity (and amount of applications) of the methods is sometimes more dependent on the availability than the merits of the method. Moreover, new implementations of existing methods are difficult to verify and the different theoretical backgrounds make it difficult for environmental scientists to decide about the usefulness of a specific method. A common and open framework with a large set of methods can support users in deciding about the most appropriate method. Hence, it enables to simultaneously apply and compare different methods on a fair basis. We developed and present pySTAN (python framework for STructure Analysis), a python package containing a set of functions for model structure evaluation to provide the analysis of (hydrological) model structures. A selected set of algorithms for optimization, uncertainty and sensitivity analysis is currently available, together with a set of evaluation (objective) functions and input distributions to sample from. The methods are implemented model-independent and the python language provides the wrapper functions to apply administer external model codes. Different objective functions can be considered simultaneously with both statistical metrics and more hydrology specific metrics. By using so-called reStructuredText (sphinx documentation generator) and Python documentation strings (docstrings), the generation of manual pages is semi-automated and a specific environment is available to enhance both the readability and transparency of the code. It thereby enables a larger group of users to apply and compare these methods and to extend the functionalities.

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

David, O.

2011-12-01

Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside. While providing all those capabilities, a significant reduction in the size of the model source code was achieved. To support the benefit of annotations for a modeler, studies were conducted to evaluate the effectiveness of an annotation based framework approach with other modeling frameworks and libraries, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A typical hydrological model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks.

Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex

PubMed Central

Procyk, Emmanuel; Dominey, Peter Ford

2016-01-01

Primates display a remarkable ability to adapt to novel situations. Determining what is most pertinent in these situations is not always possible based only on the current sensory inputs, and often also depends on recent inputs and behavioral outputs that contribute to internal states. Thus, one can ask how cortical dynamics generate representations of these complex situations. It has been observed that mixed selectivity in cortical neurons contributes to represent diverse situations defined by a combination of the current stimuli, and that mixed selectivity is readily obtained in randomly connected recurrent networks. In this context, these reservoir networks reproduce the highly recurrent nature of local cortical connectivity. Recombining present and past inputs, random recurrent networks from the reservoir computing framework generate mixed selectivity which provides pre-coded representations of an essentially universal set of contexts. These representations can then be selectively amplified through learning to solve the task at hand. We thus explored their representational power and dynamical properties after training a reservoir to perform a complex cognitive task initially developed for monkeys. The reservoir model inherently displayed a dynamic form of mixed selectivity, key to the representation of the behavioral context over time. The pre-coded representation of context was amplified by training a feedback neuron to explicitly represent this context, thereby reproducing the effect of learning and allowing the model to perform more robustly. This second version of the model demonstrates how a hybrid dynamical regime combining spatio-temporal processing of reservoirs, and input driven attracting dynamics generated by the feedback neuron, can be used to solve a complex cognitive task. We compared reservoir activity to neural activity of dorsal anterior cingulate cortex of monkeys which revealed similar network dynamics. We argue that reservoir computing is a pertinent framework to model local cortical dynamics and their contribution to higher cognitive function. PMID:27286251

Near-Field to Far-Field Uncertainty Propagation and Quantification of Ground Motions Generated by the Source Physics Experiments (SPE)

NASA Astrophysics Data System (ADS)

Antoun, T.; Ezzedine, S. M.; Vorobiev, O.; Pitarka, A.; Hurley, R.; Hirakawa, E. T.; Glenn, L.; Walter, W. R.

2016-12-01

LLNL has developed a framework for uncertainty propagation and quantification using HPC numerical codes to simulate end-to-end, from source to receivers, the ground motions observed during the Source Physics Experiments (SPE) conducted in fractured granitic rock at the Nevada National Security Site (NNSS). SPE includes six underground chemical explosions designed with different yields initiated at different depths. To date we have successfully applied this framework to explain the near-field shear motions observed in the vicinity of SPE3 thru SPE5. However, systematic uncertainty propagation to the far-field seismic receiver has not been addressed yet. In the current study, we used a coupling between the non-linear inelastic hydrodynamic regime in the near-field and the seismic elastic regime in the far-field to conduct the analysis. Several realizations of the stochastic discrete fracture network were generated conditional to the observed sparse data. These realizations were then used to calculate the ground motions generated from the SPE shots up to the elastic radius. The latter serves as the handshake interface for the far-field simulations. By creating several realizations of near-field responses one can embed those sources into the far-field elastic wave code and further the uncertainty propagation to the receivers. We will present a full assessment from end-to-end for the near- and far-field measurements. Separate analyses of the effect of the different conceptual geological models are also carried over using a nested Monte Carlo scheme. We compare the observed frequency content at several gages with the simulated ones. We conclude that both regions experience different sampling of frequencies: small features are relevant to near-field simulations while larger feature are more dominant at the far-field. We finally rank the primary sensitive parameters for both regions to drive and refine the field characterization data collection.

Task representation in individual and joint settings

PubMed Central

Prinz, Wolfgang

2015-01-01

This paper outlines a framework for task representation and discusses applications to interference tasks in individual and joint settings. The framework is derived from the Theory of Event Coding (TEC). This theory regards task sets as transient assemblies of event codes in which stimulus and response codes interact and shape each other in particular ways. On the one hand, stimulus and response codes compete with each other within their respective subsets (horizontal interactions). On the other hand, stimulus and response code cooperate with each other (vertical interactions). Code interactions instantiating competition and cooperation apply to two time scales: on-line performance (i.e., doing the task) and off-line implementation (i.e., setting the task). Interference arises when stimulus and response codes overlap in features that are irrelevant for stimulus identification, but relevant for response selection. To resolve this dilemma, the feature profiles of event codes may become restructured in various ways. The framework is applied to three kinds of interference paradigms. Special emphasis is given to joint settings where tasks are shared between two participants. Major conclusions derived from these applications include: (1) Response competition is the chief driver of interference. Likewise, different modes of response competition give rise to different patterns of interference; (2) The type of features in which stimulus and response codes overlap is also a crucial factor. Different types of such features give likewise rise to different patterns of interference; and (3) Task sets for joint settings conflate intraindividual conflicts between responses (what), with interindividual conflicts between responding agents (whom). Features of response codes may, therefore, not only address responses, but also responding agents (both physically and socially). PMID:26029085

Joint reconstruction of dynamic PET activity and kinetic parametric images using total variation constrained dictionary sparse coding

NASA Astrophysics Data System (ADS)

Yu, Haiqing; Chen, Shuhang; Chen, Yunmei; Liu, Huafeng

2017-05-01

Dynamic positron emission tomography (PET) is capable of providing both spatial and temporal information of radio tracers in vivo. In this paper, we present a novel joint estimation framework to reconstruct temporal sequences of dynamic PET images and the coefficients characterizing the system impulse response function, from which the associated parametric images of the system macro parameters for tracer kinetics can be estimated. The proposed algorithm, which combines statistical data measurement and tracer kinetic models, integrates a dictionary sparse coding (DSC) into a total variational minimization based algorithm for simultaneous reconstruction of the activity distribution and parametric map from measured emission sinograms. DSC, based on the compartmental theory, provides biologically meaningful regularization, and total variation regularization is incorporated to provide edge-preserving guidance. We rely on techniques from minimization algorithms (the alternating direction method of multipliers) to first generate the estimated activity distributions with sub-optimal kinetic parameter estimates, and then recover the parametric maps given these activity estimates. These coupled iterative steps are repeated as necessary until convergence. Experiments with synthetic, Monte Carlo generated data, and real patient data have been conducted, and the results are very promising.

Validation and Verification of LADEE Models and Software

NASA Technical Reports Server (NTRS)

Gundy-Burlet, Karen

2013-01-01

The Lunar Atmosphere Dust Environment Explorer (LADEE) mission will orbit the moon in order to measure the density, composition and time variability of the lunar dust environment. The ground-side and onboard flight software for the mission is being developed using a Model-Based Software methodology. In this technique, models of the spacecraft and flight software are developed in a graphical dynamics modeling package. Flight Software requirements are prototyped and refined using the simulated models. After the model is shown to work as desired in this simulation framework, C-code software is automatically generated from the models. The generated software is then tested in real time Processor-in-the-Loop and Hardware-in-the-Loop test beds. Travelling Road Show test beds were used for early integration tests with payloads and other subsystems. Traditional techniques for verifying computational sciences models are used to characterize the spacecraft simulation. A lightweight set of formal methods analysis, static analysis, formal inspection and code coverage analyses are utilized to further reduce defects in the onboard flight software artifacts. These techniques are applied early and often in the development process, iteratively increasing the capabilities of the software and the fidelity of the vehicle models and test beds.

Action understanding and active inference

PubMed Central

Mattout, Jérémie; Kilner, James

2012-01-01

We have suggested that the mirror-neuron system might be usefully understood as implementing Bayes-optimal perception of actions emitted by oneself or others. To substantiate this claim, we present neuronal simulations that show the same representations can prescribe motor behavior and encode motor intentions during action–observation. These simulations are based on the free-energy formulation of active inference, which is formally related to predictive coding. In this scheme, (generalised) states of the world are represented as trajectories. When these states include motor trajectories they implicitly entail intentions (future motor states). Optimizing the representation of these intentions enables predictive coding in a prospective sense. Crucially, the same generative models used to make predictions can be deployed to predict the actions of self or others by simply changing the bias or precision (i.e. attention) afforded to proprioceptive signals. We illustrate these points using simulations of handwriting to illustrate neuronally plausible generation and recognition of itinerant (wandering) motor trajectories. We then use the same simulations to produce synthetic electrophysiological responses to violations of intentional expectations. Our results affirm that a Bayes-optimal approach provides a principled framework, which accommodates current thinking about the mirror-neuron system. Furthermore, it endorses the general formulation of action as active inference. PMID:21327826

Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey

NASA Astrophysics Data System (ADS)

Guillemot, Christine; Siohan, Pierre

2005-12-01

Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.

Compressive Sampling based Image Coding for Resource-deficient Visual Communication.

PubMed

Liu, Xianming; Zhai, Deming; Zhou, Jiantao; Zhang, Xinfeng; Zhao, Debin; Gao, Wen

2016-04-14

In this paper, a new compressive sampling based image coding scheme is developed to achieve competitive coding efficiency at lower encoder computational complexity, while supporting error resilience. This technique is particularly suitable for visual communication with resource-deficient devices. At the encoder, compact image representation is produced, which is a polyphase down-sampled version of the input image; but the conventional low-pass filter prior to down-sampling is replaced by a local random binary convolution kernel. The pixels of the resulting down-sampled pre-filtered image are local random measurements and placed in the original spatial configuration. The advantages of local random measurements are two folds: 1) preserve high-frequency image features that are otherwise discarded by low-pass filtering; 2) remain a conventional image and can therefore be coded by any standardized codec to remove statistical redundancy of larger scales. Moreover, measurements generated by different kernels can be considered as multiple descriptions of the original image and therefore the proposed scheme has the advantage of multiple description coding. At the decoder, a unified sparsity-based soft-decoding technique is developed to recover the original image from received measurements in a framework of compressive sensing. Experimental results demonstrate that the proposed scheme is competitive compared with existing methods, with a unique strength of recovering fine details and sharp edges at low bit-rates.

Estimates of tsunami damage for Russian coast of the Black Sea

NASA Astrophysics Data System (ADS)

Zaytsev, Andrey; Yalciner, Ahmet; Pelinovsky, Efim

2010-05-01

The historic database of tsunamis in the Black Sea contains 20 - 30 events with different level of validity, and at least six events occurred in 20th century. Numerical modeling of the last historic events is performed in the framework of shallow-water theory with use of code NAMI-DANCE. The computed tide-gauge records in Russian coastal locations are in good agreement with instrumental data for the 1939 and 1966 tsunamis. The tsunami of the landslide origin occurred in Sochi in 1970 is modeled in the framework of the two-layer model realized in TUNAMI. Also, some hypothetic tsunamis generated in the open part of the Black Sea are computed and the distribution of the tsunami height along the Russian and Turkish coast ais found. In particular, the tsunami amplification near Sochi is highest to compare with other coastal locations on the Russian coast of Black Sea.

Supporting metabolomics with adaptable software: design architectures for the end-user.

PubMed

Sarpe, Vladimir; Schriemer, David C

2017-02-01

Large and disparate sets of LC-MS data are generated by modern metabolomics profiling initiatives, and while useful software tools are available to annotate and quantify compounds, the field requires continued software development in order to sustain methodological innovation. Advances in software development practices allow for a new paradigm in tool development for metabolomics, where increasingly the end-user can develop or redeploy utilities ranging from simple algorithms to complex workflows. Resources that provide an organized framework for development are described and illustrated with LC-MS processing packages that have leveraged their design tools. Full access to these resources depends in part on coding experience, but the emergence of workflow builders and pluggable frameworks strongly reduces the skill level required. Developers in the metabolomics community are encouraged to use these resources and design content for uptake and reuse. Copyright © 2016 Elsevier Ltd. All rights reserved.

Auto Code Generation for Simulink-Based Attitude Determination Control System

NASA Technical Reports Server (NTRS)

MolinaFraticelli, Jose Carlos

2012-01-01

This paper details the work done to auto generate C code from a Simulink-Based Attitude Determination Control System (ADCS) to be used in target platforms. NASA Marshall Engineers have developed an ADCS Simulink simulation to be used as a component for the flight software of a satellite. This generated code can be used for carrying out Hardware in the loop testing of components for a satellite in a convenient manner with easily tunable parameters. Due to the nature of the embedded hardware components such as microcontrollers, this simulation code cannot be used directly, as it is, on the target platform and must first be converted into C code; this process is known as auto code generation. In order to generate C code from this simulation; it must be modified to follow specific standards set in place by the auto code generation process. Some of these modifications include changing certain simulation models into their atomic representations which can bring new complications into the simulation. The execution order of these models can change based on these modifications. Great care must be taken in order to maintain a working simulation that can also be used for auto code generation. After modifying the ADCS simulation for the auto code generation process, it is shown that the difference between the output data of the former and that of the latter is between acceptable bounds. Thus, it can be said that the process is a success since all the output requirements are met. Based on these results, it can be argued that this generated C code can be effectively used by any desired platform as long as it follows the specific memory requirements established in the Simulink Model.

Fault trees for decision making in systems analysis

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

Lambert, Howard E.

1975-10-09

The application of fault tree analysis (FTA) to system safety and reliability is presented within the framework of system safety analysis. The concepts and techniques involved in manual and automated fault tree construction are described and their differences noted. The theory of mathematical reliability pertinent to FTA is presented with emphasis on engineering applications. An outline of the quantitative reliability techniques of the Reactor Safety Study is given. Concepts of probabilistic importance are presented within the fault tree framework and applied to the areas of system design, diagnosis and simulation. The computer code IMPORTANCE ranks basic events and cut setsmore » according to a sensitivity analysis. A useful feature of the IMPORTANCE code is that it can accept relative failure data as input. The output of the IMPORTANCE code can assist an analyst in finding weaknesses in system design and operation, suggest the most optimal course of system upgrade, and determine the optimal location of sensors within a system. A general simulation model of system failure in terms of fault tree logic is described. The model is intended for efficient diagnosis of the causes of system failure in the event of a system breakdown. It can also be used to assist an operator in making decisions under a time constraint regarding the future course of operations. The model is well suited for computer implementation. New results incorporated in the simulation model include an algorithm to generate repair checklists on the basis of fault tree logic and a one-step-ahead optimization procedure that minimizes the expected time to diagnose system failure.« less

The UPSF code: a metaprogramming-based high-performance automatically parallelized plasma simulation framework

NASA Astrophysics Data System (ADS)

Gao, Xiatian; Wang, Xiaogang; Jiang, Binhao

2017-10-01

UPSF (Universal Plasma Simulation Framework) is a new plasma simulation code designed for maximum flexibility by using edge-cutting techniques supported by C++17 standard. Through use of metaprogramming technique, UPSF provides arbitrary dimensional data structures and methods to support various kinds of plasma simulation models, like, Vlasov, particle in cell (PIC), fluid, Fokker-Planck, and their variants and hybrid methods. Through C++ metaprogramming technique, a single code can be used to arbitrary dimensional systems with no loss of performance. UPSF can also automatically parallelize the distributed data structure and accelerate matrix and tensor operations by BLAS. A three-dimensional particle in cell code is developed based on UPSF. Two test cases, Landau damping and Weibel instability for electrostatic and electromagnetic situation respectively, are presented to show the validation and performance of the UPSF code.

Coding Teaching for Simultaneity and Connections: Examining Teachers' Part-Whole Additive Relations Instruction

ERIC Educational Resources Information Center

Ekdahl, Anna-Lena; Venkat, Hamsa; Runesson, Ulla

2016-01-01

In this article, we present a coding framework based on simultaneity and connections. The coding focuses on microlevel attention to three aspects of simultaneity and connections: between representations, within examples, and between examples. Criteria for coding that we viewed as mathematically important within part-whole additive relations…

Using GTO-Velo to Facilitate Communication and Sharing of Simulation Results in Support of the Geothermal Technologies Office Code Comparison Study

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

White, Signe K.; Purohit, Sumit; Boyd, Lauren W.

The Geothermal Technologies Office Code Comparison Study (GTO-CCS) aims to support the DOE Geothermal Technologies Office in organizing and executing a model comparison activity. This project is directed at testing, diagnosing differences, and demonstrating modeling capabilities of a worldwide collection of numerical simulators for evaluating geothermal technologies. Teams of researchers are collaborating in this code comparison effort, and it is important to be able to share results in a forum where technical discussions can easily take place without requiring teams to travel to a common location. Pacific Northwest National Laboratory has developed an open-source, flexible framework called Velo that providesmore » a knowledge management infrastructure and tools to support modeling and simulation for a variety of types of projects in a number of scientific domains. GTO-Velo is a customized version of the Velo Framework that is being used as the collaborative tool in support of the GTO-CCS project. Velo is designed around a novel integration of a collaborative Web-based environment and a scalable enterprise Content Management System (CMS). The underlying framework provides a flexible and unstructured data storage system that allows for easy upload of files that can be in any format. Data files are organized in hierarchical folders and each folder and each file has a corresponding wiki page for metadata. The user interacts with Velo through a web browser based wiki technology, providing the benefit of familiarity and ease of use. High-level folders have been defined in GTO-Velo for the benchmark problem descriptions, descriptions of simulator/code capabilities, a project notebook, and folders for participating teams. Each team has a subfolder with write access limited only to the team members, where they can upload their simulation results. The GTO-CCS participants are charged with defining the benchmark problems for the study, and as each GTO-CCS Benchmark problem is defined, the problem creator can provide a description using a template on the metadata page corresponding to the benchmark problem folder. Project documents, references and videos of the weekly online meetings are shared via GTO-Velo. A results comparison tool allows users to plot their uploaded simulation results on the fly, along with those of other teams, to facilitate weekly discussions of the benchmark problem results being generated by the teams. GTO-Velo is an invaluable tool providing the project coordinators and team members with a framework for collaboration among geographically dispersed organizations.« less

Using bio.tools to generate and annotate workbench tool descriptions

PubMed Central

Hillion, Kenzo-Hugo; Kuzmin, Ivan; Khodak, Anton; Rasche, Eric; Crusoe, Michael; Peterson, Hedi; Ison, Jon; Ménager, Hervé

2017-01-01

Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata. PMID:29333231

One-way quantum repeaters with quantum Reed-Solomon codes

NASA Astrophysics Data System (ADS)

Muralidharan, Sreraman; Zou, Chang-Ling; Li, Linshu; Jiang, Liang

2018-05-01

We show that quantum Reed-Solomon codes constructed from classical Reed-Solomon codes can approach the capacity on the quantum erasure channel of d -level systems for large dimension d . We study the performance of one-way quantum repeaters with these codes and obtain a significant improvement in key generation rate compared to previously investigated encoding schemes with quantum parity codes and quantum polynomial codes. We also compare the three generations of quantum repeaters using quantum Reed-Solomon codes and identify parameter regimes where each generation performs the best.

Internal Wave Generation by Convection

NASA Astrophysics Data System (ADS)

Lecoanet, Daniel Michael

In nature, it is not unusual to find stably stratified fluid adjacent to convectively unstable fluid. This can occur in the Earth's atmosphere, where the troposphere is convective and the stratosphere is stably stratified; in lakes, where surface solar heating can drive convection above stably stratified fresh water; in the oceans, where geothermal heating can drive convection near the ocean floor, but the water above is stably stratified due to salinity gradients; possible in the Earth's liquid core, where gradients in thermal conductivity and composition diffusivities maybe lead to different layers of stable or unstable liquid metal; and, in stars, as most stars contain at least one convective and at least one radiative (stably stratified) zone. Internal waves propagate in stably stratified fluids. The characterization of the internal waves generated by convection is an open problem in geophysical and astrophysical fluid dynamics. Internal waves can play a dynamically important role via nonlocal transport. Momentum transport by convectively excited internal waves is thought to generate the quasi-biennial oscillation of zonal wind in the equatorial stratosphere, an important physical phenomenon used to calibrate global climate models. Angular momentum transport by convectively excited internal waves may play a crucial role in setting the initial rotation rates of neutron stars. In the last year of life of a massive star, convectively excited internal waves may transport even energy to the surface layers to unbind them, launching a wind. In each of these cases, internal waves are able to transport some quantity--momentum, angular momentum, energy--across large, stable buoyancy gradients. Thus, internal waves represent an important, if unusual, transport mechanism. This thesis advances our understanding of internal wave generation by convection. Chapter 2 provides an underlying theoretical framework to study this problem. It describes a detailed calculation of the internal gravity wave spectrum, using the Lighthill theory of wave excitation by turbulence. We use a Green's function approach, in which we convolve a convective source term with the Green's function of different internal gravity waves. The remainder of the thesis is a circuitous attempt to verify these analytical predictions. I test the predictions of Chapter 2 via numerical simulation. The first step is to identify a code suitable for this study. I helped develop the Dedalus code framework to study internal wave generation by convection. Dedalus can solve many different partial differential equations using the pseudo-spectral numerical method. In Chapter 3, I demonstrate Dedalus' ability to solve different equations used to model convection in astrophysics. I consider both the propagation and damping of internal waves, and the properties of low Rayleigh number convective steady states, in six different equation sets used in the astrophysics literature. This shows that Dedalus can be used to solve the equations of interest. Next, in Chapter 4, I verify the high accuracy of Dedalus by comparing it to the popular astrophysics code Athena in a standard Kelvin-Helmholtz instability test problem. Dedalus performs admirably in comparison to Athena, and provides a high standard for other codes solving the fully compressible Navier-Stokes equations. Chapter 5 demonstrates that Dedalus can simulate convective adjacent to a stably stratified region, by studying convective mixing near carbon flames. The convective overshoot and mixing is well-resolved, and is able to generate internal waves. Confident in Dedalus' ability to study the problem at hand, Chapter 6 describes simulations inspired by water experiments of internal wave generation by convection. The experiments exploit water's unusual property that its density maximum is at 4°C, rather than at 0°C. We use a similar equation of state in Dedalus, and study internal gravity waves generation by convection in a water-like fluid. We test two models of wave generation: bulk excitation (equivalent to the Lighthill theory described in Chapter 2), and surface excitation. We find the bulk excitation model accurately reproduces the waves generated in the simulations, validating the calculations of Chapter 2.

Ada Integrated Environment III Computer Program Development Specification. Volume III. Ada Optimizing Compiler.

DTIC Science & Technology

1981-12-01

file.library-unit{.subunit).SYMAP Statement Map: library-file. library-unit.subunit).SMAP Type Map: 1 ibrary.fi le. 1 ibrary-unit{.subunit). TMAP The library...generator SYMAP Symbol Map code generator SMAP Updated Statement Map code generator TMAP Type Map code generator A.3.5 The PUNIT Command The P UNIT...Core.Stmtmap) NAME Tmap (Core.Typemap) END Example A-3 Compiler Command Stream for the Code Generator Texas Instruments A-5 Ada Optimizing Compiler

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

Random sampling of elementary flux modes in large-scale metabolic networks.

PubMed

Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

2012-09-15

The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

Computing with scale-invariant neural representations

NASA Astrophysics Data System (ADS)

Howard, Marc; Shankar, Karthik

The Weber-Fechner law is perhaps the oldest quantitative relationship in psychology. Consider the problem of the brain representing a function f (x) . Different neurons have receptive fields that support different parts of the range, such that the ith neuron has a receptive field at xi. Weber-Fechner scaling refers to the finding that the width of the receptive field scales with xi as does the difference between the centers of adjacent receptive fields. Weber-Fechner scaling is exponentially resource-conserving. Neurophysiological evidence suggests that neural representations obey Weber-Fechner scaling in the visual system and perhaps other systems as well. We describe an optimality constraint that is solved by Weber-Fechner scaling, providing an information-theoretic rationale for this principle of neural coding. Weber-Fechner scaling can be generated within a mathematical framework using the Laplace transform. Within this framework, simple computations such as translation, correlation and cross-correlation can be accomplished. This framework can in principle be extended to provide a general computational language for brain-inspired cognitive computation on scale-invariant representations. Supported by NSF PHY 1444389 and the BU Initiative for the Physics and Mathematics of Neural Systems,.

MELCOR computer code manuals

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

Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.

1995-03-01

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, andmore » combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.« less

DynamiX, numerical tool for design of next-generation x-ray telescopes.

PubMed

Chauvin, Maxime; Roques, Jean-Pierre

2010-07-20

We present a new code aimed at the simulation of grazing-incidence x-ray telescopes subject to deformations and demonstrate its ability with two test cases: the Simbol-X and the International X-ray Observatory (IXO) missions. The code, based on Monte Carlo ray tracing, computes the full photon trajectories up to the detector plane, accounting for the x-ray interactions and for the telescope motion and deformation. The simulation produces images and spectra for any telescope configuration using Wolter I mirrors and semiconductor detectors. This numerical tool allows us to study the telescope performance in terms of angular resolution, effective area, and detector efficiency, accounting for the telescope behavior. We have implemented an image reconstruction method based on the measurement of the detector drifts by an optical sensor metrology. Using an accurate metrology, this method allows us to recover the loss of angular resolution induced by the telescope instability. In the framework of the Simbol-X mission, this code was used to study the impacts of the parameters on the telescope performance. In this paper we present detailed performance analysis of Simbol-X, taking into account the satellite motions and the image reconstruction. To illustrate the versatility of the code, we present an additional performance analysis with a particular configuration of IXO.

Mixed messages: An evaluation of NHS Trust Social Media policies in the North West of England.

PubMed

Scragg, B; Shaikh, S; Robinson, L; Mercer, C

2017-08-01

Despite National Health Service (NHS) information strategy promoting the use of Social Media (SoMe) to encourage greater engagement between service users and providers, a team investigating online SoMe interaction between breast screening practitioners and clients found that practitioners alleged discouragement from employers' policies. This study aimed to investigate whether this barrier was genuine, and illuminate whether local policy differed from national strategy. The study used a qualitative grounded theory approach to generate a theory. Nine policies from the North West of England were analysed. A framework was derived from the data, and an analysis of policy tone followed by a detailed coding of policy content was undertaken. Comparative analysis continued by reviewing the literature, and a condensed framework revealed five broad categories that policies addressed. The analysis revealed the policies varied in content, but not in tone, which was mostly discouraging. Coding the content revealed that the most frequently addressed point was that of protecting the employers' reputation, and after further analysis, the resultant condensed framework showed that policies were imbalanced and heavily skewed towards Security, Conduct & Behaviour and Reputation. Practitioners within breast screening services are discouraged by overly prohibitive and prescriptive SoMe policies; with these varying tremendously in comprehensiveness, but with a narrow focus on security and employers reputation; in contrast with national strategy. Recommendations are that policy revision is undertaken with consultation by more than one stakeholder, and SoMe training is offered for all members of NHS staff. Copyright © 2017 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

Synthesizing Certified Code

NASA Technical Reports Server (NTRS)

Whalen, Michael; Schumann, Johann; Fischer, Bernd

2002-01-01

Code certification is a lightweight approach to demonstrate software quality on a formal level. Its basic idea is to require producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates which can be checked independently. Since code certification uses the same underlying technology as program verification, it also requires many detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding theses annotations to the code is time-consuming and error-prone. We address this problem by combining code certification with automatic program synthesis. We propose an approach to generate simultaneously, from a high-level specification, code and all annotations required to certify generated code. Here, we describe a certification extension of AUTOBAYES, a synthesis tool which automatically generates complex data analysis programs from compact specifications. AUTOBAYES contains sufficient high-level domain knowledge to generate detailed annotations. This allows us to use a general-purpose verification condition generator to produce a set of proof obligations in first-order logic. The obligations are then discharged using the automated theorem E-SETHEO. We demonstrate our approach by certifying operator safety for a generated iterative data classification program without manual annotation of the code.

Automated Concurrent Blackboard System Generation in C++

NASA Technical Reports Server (NTRS)

Kaplan, J. A.; McManus, J. W.; Bynum, W. L.

1999-01-01

In his 1992 Ph.D. thesis, "Design and Analysis Techniques for Concurrent Blackboard Systems", John McManus defined several performance metrics for concurrent blackboard systems and developed a suite of tools for creating and analyzing such systems. These tools allow a user to analyze a concurrent blackboard system design and predict the performance of the system before any code is written. The design can be modified until simulated performance is satisfactory. Then, the code generator can be invoked to generate automatically all of the code required for the concurrent blackboard system except for the code implementing the functionality of each knowledge source. We have completed the port of the source code generator and a simulator for a concurrent blackboard system. The source code generator generates the necessary C++ source code to implement the concurrent blackboard system using Parallel Virtual Machine (PVM) running on a heterogeneous network of UNIX(trademark) workstations. The concurrent blackboard simulator uses the blackboard specification file to predict the performance of the concurrent blackboard design. The only part of the source code for the concurrent blackboard system that the user must supply is the code implementing the functionality of the knowledge sources.

Automatic Certification of Kalman Filters for Reliable Code Generation

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd; Schumann, Johann; Richardson, Julian

2005-01-01

AUTOFILTER is a tool for automatically deriving Kalman filter code from high-level declarative specifications of state estimation problems. It can generate code with a range of algorithmic characteristics and for several target platforms. The tool has been designed with reliability of the generated code in mind and is able to automatically certify that the code it generates is free from various error classes. Since documentation is an important part of software assurance, AUTOFILTER can also automatically generate various human-readable documents, containing both design and safety related information. We discuss how these features address software assurance standards such as DO-178B.

A framework for characterizing eHealth literacy demands and barriers.

PubMed

Chan, Connie V; Kaufman, David R

2011-11-17

Consumer eHealth interventions are of a growing importance in the individual management of health and health behaviors. However, a range of access, resources, and skills barriers prevent health care consumers from fully engaging in and benefiting from the spectrum of eHealth interventions. Consumers may engage in a range of eHealth tasks, such as participating in health discussion forums and entering information into a personal health record. eHealth literacy names a set of skills and knowledge that are essential for productive interactions with technology-based health tools, such as proficiency in information retrieval strategies, and communicating health concepts effectively. We propose a theoretical and methodological framework for characterizing complexity of eHealth tasks, which can be used to diagnose and describe literacy barriers and inform the development of solution strategies. We adapted and integrated two existing theoretical models relevant to the analysis of eHealth literacy into a single framework to systematically categorize and describe task demands and user performance on tasks needed by health care consumers in the information age. The method derived from the framework is applied to (1) code task demands using a cognitive task analysis, and (2) code user performance on tasks. The framework and method are applied to the analysis of a Web-based consumer eHealth task with information-seeking and decision-making demands. We present the results from the in-depth analysis of the task performance of a single user as well as of 20 users on the same task to illustrate both the detailed analysis and the aggregate measures obtained and potential analyses that can be performed using this method. The analysis shows that the framework can be used to classify task demands as well as the barriers encountered in user performance of the tasks. Our approach can be used to (1) characterize the challenges confronted by participants in performing the tasks, (2) determine the extent to which application of the framework to the cognitive task analysis can predict and explain the problems encountered by participants, and (3) inform revisions to the framework to increase accuracy of predictions. The results of this illustrative application suggest that the framework is useful for characterizing task complexity and for diagnosing and explaining barriers encountered in task completion. The framework and analytic approach can be a potentially powerful generative research platform to inform development of rigorous eHealth examination and design instruments, such as to assess eHealth competence, to design and evaluate consumer eHealth tools, and to develop an eHealth curriculum.

A Framework for Characterizing eHealth Literacy Demands and Barriers

PubMed Central

Chan, Connie V

2011-01-01

Background Consumer eHealth interventions are of a growing importance in the individual management of health and health behaviors. However, a range of access, resources, and skills barriers prevent health care consumers from fully engaging in and benefiting from the spectrum of eHealth interventions. Consumers may engage in a range of eHealth tasks, such as participating in health discussion forums and entering information into a personal health record. eHealth literacy names a set of skills and knowledge that are essential for productive interactions with technology-based health tools, such as proficiency in information retrieval strategies, and communicating health concepts effectively. Objective We propose a theoretical and methodological framework for characterizing complexity of eHealth tasks, which can be used to diagnose and describe literacy barriers and inform the development of solution strategies. Methods We adapted and integrated two existing theoretical models relevant to the analysis of eHealth literacy into a single framework to systematically categorize and describe task demands and user performance on tasks needed by health care consumers in the information age. The method derived from the framework is applied to (1) code task demands using a cognitive task analysis, and (2) code user performance on tasks. The framework and method are applied to the analysis of a Web-based consumer eHealth task with information-seeking and decision-making demands. We present the results from the in-depth analysis of the task performance of a single user as well as of 20 users on the same task to illustrate both the detailed analysis and the aggregate measures obtained and potential analyses that can be performed using this method. Results The analysis shows that the framework can be used to classify task demands as well as the barriers encountered in user performance of the tasks. Our approach can be used to (1) characterize the challenges confronted by participants in performing the tasks, (2) determine the extent to which application of the framework to the cognitive task analysis can predict and explain the problems encountered by participants, and (3) inform revisions to the framework to increase accuracy of predictions. Conclusions The results of this illustrative application suggest that the framework is useful for characterizing task complexity and for diagnosing and explaining barriers encountered in task completion. The framework and analytic approach can be a potentially powerful generative research platform to inform development of rigorous eHealth examination and design instruments, such as to assess eHealth competence, to design and evaluate consumer eHealth tools, and to develop an eHealth curriculum. PMID:22094891

Toward a Neuroscientific Understanding of Play: A Dimensional Coding Framework for Analyzing Infant–Adult Play Patterns

PubMed Central

Neale, Dave; Clackson, Kaili; Georgieva, Stanimira; Dedetas, Hatice; Scarpate, Melissa; Wass, Sam; Leong, Victoria

2018-01-01

Play during early life is a ubiquitous activity, and an individual’s propensity for play is positively related to cognitive development and emotional well-being. Play behavior (which may be solitary or shared with a social partner) is diverse and multi-faceted. A challenge for current research is to converge on a common definition and measurement system for play – whether examined at a behavioral, cognitive or neurological level. Combining these different approaches in a multimodal analysis could yield significant advances in understanding the neurocognitive mechanisms of play, and provide the basis for developing biologically grounded play models. However, there is currently no integrated framework for conducting a multimodal analysis of play that spans brain, cognition and behavior. The proposed coding framework uses grounded and observable behaviors along three dimensions (sensorimotor, cognitive and socio-emotional), to compute inferences about playful behavior in a social context, and related social interactional states. Here, we illustrate the sensitivity and utility of the proposed coding framework using two contrasting dyadic corpora (N = 5) of mother-infant object-oriented interactions during experimental conditions that were either non-conducive (Condition 1) or conducive (Condition 2) to the emergence of playful behavior. We find that the framework accurately identifies the modal form of social interaction as being either non-playful (Condition 1) or playful (Condition 2), and further provides useful insights about differences in the quality of social interaction and temporal synchronicity within the dyad. It is intended that this fine-grained coding of play behavior will be easily assimilated with, and inform, future analysis of neural data that is also collected during adult–infant play. In conclusion, here, we present a novel framework for analyzing the continuous time-evolution of adult–infant play patterns, underpinned by biologically informed state coding along sensorimotor, cognitive and socio-emotional dimensions. We expect that the proposed framework will have wide utility amongst researchers wishing to employ an integrated, multimodal approach to the study of play, and lead toward a greater understanding of the neuroscientific basis of play. It may also yield insights into a new biologically grounded taxonomy of play interactions. PMID:29618994

Toward a Neuroscientific Understanding of Play: A Dimensional Coding Framework for Analyzing Infant-Adult Play Patterns.

PubMed

Neale, Dave; Clackson, Kaili; Georgieva, Stanimira; Dedetas, Hatice; Scarpate, Melissa; Wass, Sam; Leong, Victoria

2018-01-01

Play during early life is a ubiquitous activity, and an individual's propensity for play is positively related to cognitive development and emotional well-being. Play behavior (which may be solitary or shared with a social partner) is diverse and multi-faceted. A challenge for current research is to converge on a common definition and measurement system for play - whether examined at a behavioral, cognitive or neurological level. Combining these different approaches in a multimodal analysis could yield significant advances in understanding the neurocognitive mechanisms of play, and provide the basis for developing biologically grounded play models. However, there is currently no integrated framework for conducting a multimodal analysis of play that spans brain, cognition and behavior. The proposed coding framework uses grounded and observable behaviors along three dimensions (sensorimotor, cognitive and socio-emotional), to compute inferences about playful behavior in a social context, and related social interactional states. Here, we illustrate the sensitivity and utility of the proposed coding framework using two contrasting dyadic corpora ( N = 5) of mother-infant object-oriented interactions during experimental conditions that were either non-conducive (Condition 1) or conducive (Condition 2) to the emergence of playful behavior. We find that the framework accurately identifies the modal form of social interaction as being either non-playful (Condition 1) or playful (Condition 2), and further provides useful insights about differences in the quality of social interaction and temporal synchronicity within the dyad. It is intended that this fine-grained coding of play behavior will be easily assimilated with, and inform, future analysis of neural data that is also collected during adult-infant play. In conclusion, here, we present a novel framework for analyzing the continuous time-evolution of adult-infant play patterns, underpinned by biologically informed state coding along sensorimotor, cognitive and socio-emotional dimensions. We expect that the proposed framework will have wide utility amongst researchers wishing to employ an integrated, multimodal approach to the study of play, and lead toward a greater understanding of the neuroscientific basis of play. It may also yield insights into a new biologically grounded taxonomy of play interactions.

Echo™ User Manual

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

Harvey, Dustin Yewell

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reportingmore » and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.« less

Audit of Clinical Coding of Major Head and Neck Operations

PubMed Central

Mitra, Indu; Malik, Tass; Homer, Jarrod J; Loughran, Sean

2009-01-01

INTRODUCTION Within the NHS, operations are coded using the Office of Population Censuses and Surveys (OPCS) classification system. These codes, together with diagnostic codes, are used to generate Healthcare Resource Group (HRG) codes, which correlate to a payment bracket. The aim of this study was to determine whether allocated procedure codes for major head and neck operations were correct and reflective of the work undertaken. HRG codes generated were assessed to determine accuracy of remuneration. PATIENTS AND METHODS The coding of consecutive major head and neck operations undertaken in a tertiary referral centre over a retrospective 3-month period were assessed. Procedure codes were initially ascribed by professional hospital coders. Operations were then recoded by the surgical trainee in liaison with the head of clinical coding. The initial and revised procedure codes were compared and used to generate HRG codes, to determine whether the payment banding had altered. RESULTS A total of 34 cases were reviewed. The number of procedure codes generated initially by the clinical coders was 99, whereas the revised codes generated 146. Of the original codes, 47 of 99 (47.4%) were incorrect. In 19 of the 34 cases reviewed (55.9%), the HRG code remained unchanged, thus resulting in the correct payment. Six cases were never coded, equating to £15,300 loss of payment. CONCLUSIONS These results highlight the inadequacy of this system to reward hospitals for the work carried out within the NHS in a fair and consistent manner. The current coding system was found to be complicated, ambiguous and inaccurate, resulting in loss of remuneration. PMID:19220944

Incorporating Manual and Autonomous Code Generation

NASA Technical Reports Server (NTRS)

McComas, David

1998-01-01

Code can be generated manually or using code-generated software tools, but how do you interpret the two? This article looks at a design methodology that combines object-oriented design with autonomic code generation for attitude control flight software. Recent improvements in space flight computers are allowing software engineers to spend more time engineering the applications software. The application developed was the attitude control flight software for an astronomical satellite called the Microwave Anisotropy Probe (MAP). The MAP flight system is being designed, developed, and integrated at NASA's Goddard Space Flight Center. The MAP controls engineers are using Integrated Systems Inc.'s MATRIXx for their controls analysis. In addition to providing a graphical analysis for an environment, MATRIXx includes an autonomic code generation facility called AutoCode. This article examines the forces that shaped the final design and describes three highlights of the design process: (1) Defining the manual to autonomic code interface; (2) Applying object-oriented design to the manual flight code; (3) Implementing the object-oriented design in C.

Gene-Auto: Automatic Software Code Generation for Real-Time Embedded Systems

NASA Astrophysics Data System (ADS)

Rugina, A.-E.; Thomas, D.; Olive, X.; Veran, G.

2008-08-01

This paper gives an overview of the Gene-Auto ITEA European project, which aims at building a qualified C code generator from mathematical models under Matlab-Simulink and Scilab-Scicos. The project is driven by major European industry partners, active in the real-time embedded systems domains. The Gene- Auto code generator will significantly improve the current development processes in such domains by shortening the time to market and by guaranteeing the quality of the generated code through the use of formal methods. The first version of the Gene-Auto code generator has already been released and has gone thought a validation phase on real-life case studies defined by each project partner. The validation results are taken into account in the implementation of the second version of the code generator. The partners aim at introducing the Gene-Auto results into industrial development by 2010.

Protecting quantum memories using coherent parity check codes

NASA Astrophysics Data System (ADS)

Roffe, Joschka; Headley, David; Chancellor, Nicholas; Horsman, Dominic; Kendon, Viv

2018-07-01

Coherent parity check (CPC) codes are a new framework for the construction of quantum error correction codes that encode multiple qubits per logical block. CPC codes have a canonical structure involving successive rounds of bit and phase parity checks, supplemented by cross-checks to fix the code distance. In this paper, we provide a detailed introduction to CPC codes using conventional quantum circuit notation. We demonstrate the implementation of a CPC code on real hardware, by designing a [[4, 2, 2

A generic biogeochemical module for Earth system models: Next Generation BioGeoChemical Module (NGBGC), version 1.0

NASA Astrophysics Data System (ADS)

Fang, Y.; Huang, M.; Liu, C.; Li, H.; Leung, L. R.

2013-11-01

Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the atmosphere, influencing global climate changes. Integration of these processes into Earth system models (e.g., community land models (CLMs)), however, currently faces three major challenges: (1) extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, (2) computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and (3) various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not impossible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module, Next Generation BioGeoChemical Module (NGBGC), version 1.0, with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter, and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into CLM. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of terrestrial ecosystems. The method presented here could in theory be applied to simulate biogeochemical cycles in other Earth system models.

Phase-coded microwave signal generation based on a single electro-optical modulator and its application in accurate distance measurement.

PubMed

Zhang, Fangzheng; Ge, Xiaozhong; Gao, Bindong; Pan, Shilong

2015-08-24

A novel scheme for photonic generation of a phase-coded microwave signal is proposed and its application in one-dimension distance measurement is demonstrated. The proposed signal generator has a simple and compact structure based on a single dual-polarization modulator. Besides, the generated phase-coded signal is stable and free from the DC and low-frequency backgrounds. An experiment is carried out. A 2 Gb/s phase-coded signal at 20 GHz is successfully generated, and the recovered phase information agrees well with the input 13-bit Barker code. To further investigate the performance of the proposed signal generator, its application in one-dimension distance measurement is demonstrated. The measurement accuracy is less than 1.7 centimeters within a measurement range of ~2 meters. The experimental results can verify the feasibility of the proposed phase-coded microwave signal generator and also provide strong evidence to support its practical applications.

Histone modifications controlling native and induced neural stem cell identity.

PubMed

Broccoli, Vania; Colasante, Gaia; Sessa, Alessandro; Rubio, Alicia

2015-10-01

During development, neural progenitor cells (NPCs) that are capable of self-renewing maintain a proliferative cellular pool while generating all differentiated neural cell components. Although the genetic network of transcription factors (TFs) required for neural specification has been well characterized, the unique set of histone modifications that accompanies this process has only recently started to be investigated. In vitro neural differentiation of pluripotent stem cells is emerging as a powerful system to examine epigenetic programs. Deciphering the histone code and how it shapes the chromatin environment will reveal the intimate link between epigenetic changes and mechanisms for neural fate determination in the developing nervous system. Furthermore, it will offer a molecular framework for a stringent comparison between native and induced neural stem cells (iNSCs) generated by direct neural cell conversion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

PubMed

Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J; Becker, Peter B; Marr, Carsten

2016-01-27

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity. Copyright © 2016 Elsevier Inc. All rights reserved.

New GOES satellite synchronized time code generation

NASA Technical Reports Server (NTRS)

Fossler, D. E.; Olson, R. K.

1984-01-01

The TRAK Systems' GOES Satellite Synchronized Time Code Generator is described. TRAK Systems has developed this timing instrument to supply improved accuracy over most existing GOES receiver clocks. A classical time code generator is integrated with a GOES receiver.

Improving Fidelity of Launch Vehicle Liftoff Acoustic Simulations

NASA Technical Reports Server (NTRS)

Liever, Peter; West, Jeff

2016-01-01

Launch vehicles experience high acoustic loads during ignition and liftoff affected by the interaction of rocket plume generated acoustic waves with launch pad structures. Application of highly parallelized Computational Fluid Dynamics (CFD) analysis tools optimized for application on the NAS computer systems such as the Loci/CHEM program now enable simulation of time-accurate, turbulent, multi-species plume formation and interaction with launch pad geometry and capture the generation of acoustic noise at the source regions in the plume shear layers and impingement regions. These CFD solvers are robust in capturing the acoustic fluctuations, but they are too dissipative to accurately resolve the propagation of the acoustic waves throughout the launch environment domain along the vehicle. A hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) modeling framework has been developed to improve such liftoff acoustic environment predictions. The framework combines the existing highly-scalable NASA production CFD code, Loci/CHEM, with a high-order accurate discontinuous Galerkin (DG) solver, Loci/THRUST, developed in the same computational framework. Loci/THRUST employs a low dissipation, high-order, unstructured DG method to accurately propagate acoustic waves away from the source regions across large distances. The DG solver is currently capable of solving up to 4th order solutions for non-linear, conservative acoustic field propagation. Higher order boundary conditions are implemented to accurately model the reflection and refraction of acoustic waves on launch pad components. The DG solver accepts generalized unstructured meshes, enabling efficient application of common mesh generation tools for CHEM and THRUST simulations. The DG solution is coupled with the CFD solution at interface boundaries placed near the CFD acoustic source regions. Both simulations are executed simultaneously with coordinated boundary condition data exchange.

Component Framework for Loosely Coupled High Performance Integrated Plasma Simulations

NASA Astrophysics Data System (ADS)

Elwasif, W. R.; Bernholdt, D. E.; Shet, A. G.; Batchelor, D. B.; Foley, S.

2010-11-01

We present the design and implementation of a component-based simulation framework for the execution of coupled time-dependent plasma modeling codes. The Integrated Plasma Simulator (IPS) provides a flexible lightweight component model that streamlines the integration of stand alone codes into coupled simulations. Standalone codes are adapted to the IPS component interface specification using a thin wrapping layer implemented in the Python programming language. The framework provides services for inter-component method invocation, configuration, task, and data management, asynchronous event management, simulation monitoring, and checkpoint/restart capabilities. Services are invoked, as needed, by the computational components to coordinate the execution of different aspects of coupled simulations on Massive parallel Processing (MPP) machines. A common plasma state layer serves as the foundation for inter-component, file-based data exchange. The IPS design principles, implementation details, and execution model will be presented, along with an overview of several use cases.

Development of an Object-Oriented Turbomachinery Analysis Code within the NPSS Framework

NASA Technical Reports Server (NTRS)

Jones, Scott M.

2014-01-01

During the preliminary or conceptual design phase of an aircraft engine, the turbomachinery designer has a need to estimate the effects of a large number of design parameters such as flow size, stage count, blade count, radial position, etc. on the weight and efficiency of a turbomachine. Computer codes are invariably used to perform this task however, such codes are often very old, written in outdated languages with arcane input files, and rarely adaptable to new architectures or unconventional layouts. Given the need to perform these kinds of preliminary design trades, a modern 2-D turbomachinery design and analysis code has been written using the Numerical Propulsion System Simulation (NPSS) framework. This paper discusses the development of the governing equations and the structure of the primary objects used in OTAC.

Theory of Mind: A Neural Prediction Problem

PubMed Central

Koster-Hale, Jorie; Saxe, Rebecca

2014-01-01

Predictive coding posits that neural systems make forward-looking predictions about incoming information. Neural signals contain information not about the currently perceived stimulus, but about the difference between the observed and the predicted stimulus. We propose to extend the predictive coding framework from high-level sensory processing to the more abstract domain of theory of mind; that is, to inferences about others’ goals, thoughts, and personalities. We review evidence that, across brain regions, neural responses to depictions of human behavior, from biological motion to trait descriptions, exhibit a key signature of predictive coding: reduced activity to predictable stimuli. We discuss how future experiments could distinguish predictive coding from alternative explanations of this response profile. This framework may provide an important new window on the neural computations underlying theory of mind. PMID:24012000

Applications of Coding in Network Communications

ERIC Educational Resources Information Center

Chang, Christopher SungWook

2012-01-01

This thesis uses the tool of network coding to investigate fast peer-to-peer file distribution, anonymous communication, robust network construction under uncertainty, and prioritized transmission. In a peer-to-peer file distribution system, we use a linear optimization approach to show that the network coding framework significantly simplifies…

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling

PubMed Central

Punzalan, Florencio Rusty; Kunieda, Yoshitoshi; Amano, Akira

2015-01-01

Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to generate code for physiological simulations and provides a tool for studying cardiac electrophysiology. PMID:26356082

Patients' perceptions and experiences of cardiovascular disease and diabetes prevention programmes: A systematic review and framework synthesis using the Theoretical Domains Framework.

PubMed

Shaw, Rachel L; Holland, Carol; Pattison, Helen M; Cooke, Richard

2016-05-01

This review provides a worked example of 'best fit' framework synthesis using the Theoretical Domains Framework (TDF) of health psychology theories as an a priori framework in the synthesis of qualitative evidence. Framework synthesis works best with 'policy urgent' questions. The review question selected was: what are patients' experiences of prevention programmes for cardiovascular disease (CVD) and diabetes? The significance of these conditions is clear: CVD claims more deaths worldwide than any other; diabetes is a risk factor for CVD and leading cause of death. A systematic review and framework synthesis were conducted. This novel method for synthesizing qualitative evidence aims to make health psychology theory accessible to implementation science and advance the application of qualitative research findings in evidence-based healthcare. Findings from 14 original studies were coded deductively into the TDF and subsequently an inductive thematic analysis was conducted. Synthesized findings produced six themes relating to: knowledge, beliefs, cues to (in)action, social influences, role and identity, and context. A conceptual model was generated illustrating combinations of factors that produce cues to (in)action. This model demonstrated interrelationships between individual (beliefs and knowledge) and societal (social influences, role and identity, context) factors. Several intervention points were highlighted where factors could be manipulated to produce favourable cues to action. However, a lack of transparency of behavioural components of published interventions needs to be corrected and further evaluations of acceptability in relation to patient experience are required. Further work is needed to test the comprehensiveness of the TDF as an a priori framework for 'policy urgent' questions using 'best fit' framework synthesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Method and apparatus for determining position using global positioning satellites

NASA Technical Reports Server (NTRS)

Ward, John (Inventor); Ward, William S. (Inventor)

1998-01-01

A global positioning satellite receiver having an antenna for receiving a L1 signal from a satellite. The L1 signal is processed by a preamplifier stage including a band pass filter and a low noise amplifier and output as a radio frequency (RF) signal. A mixer receives and de-spreads the RF signal in response to a pseudo-random noise code, i.e., Gold code, generated by an internal pseudo-random noise code generator. A microprocessor enters a code tracking loop, such that during the code tracking loop, it addresses the pseudo-random code generator to cause the pseudo-random code generator to sequentially output pseudo-random codes corresponding to satellite codes used to spread the L1 signal, until correlation occurs. When an output of the mixer is indicative of the occurrence of correlation between the RF signal and the generated pseudo-random codes, the microprocessor enters an operational state which slows the receiver code sequence to stay locked with the satellite code sequence. The output of the mixer is provided to a detector which, in turn, controls certain routines of the microprocessor. The microprocessor will output pseudo range information according to an interrupt routine in response detection of correlation. The pseudo range information is to be telemetered to a ground station which determines the position of the global positioning satellite receiver.

Novel Integration of Frame Rate Up Conversion and HEVC Coding Based on Rate-Distortion Optimization.

PubMed

Guo Lu; Xiaoyun Zhang; Li Chen; Zhiyong Gao

2018-02-01

Frame rate up conversion (FRUC) can improve the visual quality by interpolating new intermediate frames. However, high frame rate videos by FRUC are confronted with more bitrate consumption or annoying artifacts of interpolated frames. In this paper, a novel integration framework of FRUC and high efficiency video coding (HEVC) is proposed based on rate-distortion optimization, and the interpolated frames can be reconstructed at encoder side with low bitrate cost and high visual quality. First, joint motion estimation (JME) algorithm is proposed to obtain robust motion vectors, which are shared between FRUC and video coding. What's more, JME is embedded into the coding loop and employs the original motion search strategy in HEVC coding. Then, the frame interpolation is formulated as a rate-distortion optimization problem, where both the coding bitrate consumption and visual quality are taken into account. Due to the absence of original frames, the distortion model for interpolated frames is established according to the motion vector reliability and coding quantization error. Experimental results demonstrate that the proposed framework can achieve 21% ~ 42% reduction in BDBR, when compared with the traditional methods of FRUC cascaded with coding.

Pinoleville Pomo Nation Tribal Green Building Code

EPA Pesticide Factsheets

The Pinoleville Pomo Nation (PPN) worked with the U.S. Environmental Protection Agency (EPA) and the Development Center for Appropriate Technology (DCAT) to create this framework for tribal building codes.

Automated apparatus and method of generating native code for a stitching machine

NASA Technical Reports Server (NTRS)

Miller, Jeffrey L. (Inventor)

2000-01-01

A computer system automatically generates CNC code for a stitching machine. The computer determines the locations of a present stitching point and a next stitching point. If a constraint is not found between the present stitching point and the next stitching point, the computer generates code for making a stitch at the next stitching point. If a constraint is found, the computer generates code for changing a condition (e.g., direction) of the stitching machine's stitching head.

MetaJC++: A flexible and automatic program transformation technique using meta framework

NASA Astrophysics Data System (ADS)

Beevi, Nadera S.; Reghu, M.; Chitraprasad, D.; Vinodchandra, S. S.

2014-09-01

Compiler is a tool to translate abstract code containing natural language terms to machine code. Meta compilers are available to compile more than one languages. We have developed a meta framework intends to combine two dissimilar programming languages, namely C++ and Java to provide a flexible object oriented programming platform for the user. Suitable constructs from both the languages have been combined, thereby forming a new and stronger Meta-Language. The framework is developed using the compiler writing tools, Flex and Yacc to design the front end of the compiler. The lexer and parser have been developed to accommodate the complete keyword set and syntax set of both the languages. Two intermediate representations have been used in between the translation of the source program to machine code. Abstract Syntax Tree has been used as a high level intermediate representation that preserves the hierarchical properties of the source program. A new machine-independent stack-based byte-code has also been devised to act as a low level intermediate representation. The byte-code is essentially organised into an output class file that can be used to produce an interpreted output. The results especially in the spheres of providing C++ concepts in Java have given an insight regarding the potential strong features of the resultant meta-language.

HELAC-Onia 2.0: An upgraded matrix-element and event generator for heavy quarkonium physics

NASA Astrophysics Data System (ADS)

Shao, Hua-Sheng

2016-01-01

We present an upgraded version (denoted as version 2.0) of the program HELAC-ONIA for the automated computation of heavy-quarkonium helicity amplitudes within non-relativistic QCD framework. The new code has been designed to include many new and useful features for practical phenomenological simulations. It is designed for job submissions under cluster environment for parallel computations via PYTHON scripts. We have interfaced HELAC-ONIA to the parton shower Monte Carlo programs PYTHIA 8 and QEDPS to take into account the parton-shower effects. Moreover, the decay module guarantees that the program can perform the spin-entangled (cascade-)decay of heavy quarkonium after its generation. We have also implemented a reweighting method to automatically estimate the uncertainties from renormalization and/or factorization scales as well as parton-distribution functions to weighted or unweighted events. A further update is the possibility to generate one-dimensional or two-dimensional plots encoded in the analysis files on the fly. Some dedicated examples are given at the end of the writeup.

Fast and accurate mock catalogue generation for low-mass galaxies

NASA Astrophysics Data System (ADS)

Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

2016-06-01

We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

ESAS Deliverable PS 1.1.2.3: Customer Survey on Code Generations in Safety-Critical Applications

NASA Technical Reports Server (NTRS)

Schumann, Johann; Denney, Ewen

2006-01-01

Automated code generators (ACG) are tools that convert a (higher-level) model of a software (sub-)system into executable code without the necessity for a developer to actually implement the code. Although both commercially supported and in-house tools have been used in many industrial applications, little data exists on how these tools are used in safety-critical domains (e.g., spacecraft, aircraft, automotive, nuclear). The aims of the survey, therefore, were threefold: 1) to determine if code generation is primarily used as a tool for prototyping, including design exploration and simulation, or for fiight/production code; 2) to determine the verification issues with code generators relating, in particular, to qualification and certification in safety-critical domains; and 3) to determine perceived gaps in functionality of existing tools.

Mechanic: The MPI/HDF code framework for dynamical astronomy

NASA Astrophysics Data System (ADS)

Słonina, Mariusz; Goździewski, Krzysztof; Migaszewski, Cezary

2015-01-01

We introduce the Mechanic, a new open-source code framework. It is designed to reduce the development effort of scientific applications by providing unified API (Application Programming Interface) for configuration, data storage and task management. The communication layer is based on the well-established Message Passing Interface (MPI) standard, which is widely used on variety of parallel computers and CPU-clusters. The data storage is performed within the Hierarchical Data Format (HDF5). The design of the code follows core-module approach which allows to reduce the user’s codebase and makes it portable for single- and multi-CPU environments. The framework may be used in a local user’s environment, without administrative access to the cluster, under the PBS or Slurm job schedulers. It may become a helper tool for a wide range of astronomical applications, particularly focused on processing large data sets, such as dynamical studies of long-term orbital evolution of planetary systems with Monte Carlo methods, dynamical maps or evolutionary algorithms. It has been already applied in numerical experiments conducted for Kepler-11 (Migaszewski et al., 2012) and νOctantis planetary systems (Goździewski et al., 2013). In this paper we describe the basics of the framework, including code listings for the implementation of a sample user’s module. The code is illustrated on a model Hamiltonian introduced by (Froeschlé et al., 2000) presenting the Arnold diffusion. The Arnold web is shown with the help of the MEGNO (Mean Exponential Growth of Nearby Orbits) fast indicator (Goździewski et al., 2008a) applied onto symplectic SABAn integrators family (Laskar and Robutel, 2001).

A Bayesian framework for knowledge attribution: evidence from semantic integration.

PubMed

Powell, Derek; Horne, Zachary; Pinillos, N Ángel; Holyoak, Keith J

2015-06-01

We propose a Bayesian framework for the attribution of knowledge, and apply this framework to generate novel predictions about knowledge attribution for different types of "Gettier cases", in which an agent is led to a justified true belief yet has made erroneous assumptions. We tested these predictions using a paradigm based on semantic integration. We coded the frequencies with which participants falsely recalled the word "thought" as "knew" (or a near synonym), yielding an implicit measure of conceptual activation. Our experiments confirmed the predictions of our Bayesian account of knowledge attribution across three experiments. We found that Gettier cases due to counterfeit objects were not treated as knowledge (Experiment 1), but those due to intentionally-replaced evidence were (Experiment 2). Our findings are not well explained by an alternative account focused only on luck, because accidentally-replaced evidence activated the knowledge concept more strongly than did similar false belief cases (Experiment 3). We observed a consistent pattern of results across a number of different vignettes that varied the quality and type of evidence available to agents, the relative stakes involved, and surface details of content. Accordingly, the present findings establish basic phenomena surrounding people's knowledge attributions in Gettier cases, and provide explanations of these phenomena within a Bayesian framework. Copyright © 2015 Elsevier B.V. All rights reserved.

ASaiM: a Galaxy-based framework to analyze microbiota data.

PubMed

Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

2018-05-22

New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.

Models and Frameworks: A Synergistic Association for Developing Component-Based Applications

PubMed Central

Sánchez-Ledesma, Francisco; Sánchez, Pedro; Pastor, Juan A.; Álvarez, Bárbara

2014-01-01

The use of frameworks and components has been shown to be effective in improving software productivity and quality. However, the results in terms of reuse and standardization show a dearth of portability either of designs or of component-based implementations. This paper, which is based on the model driven software development paradigm, presents an approach that separates the description of component-based applications from their possible implementations for different platforms. This separation is supported by automatic integration of the code obtained from the input models into frameworks implemented using object-oriented technology. Thus, the approach combines the benefits of modeling applications from a higher level of abstraction than objects, with the higher levels of code reuse provided by frameworks. In order to illustrate the benefits of the proposed approach, two representative case studies that use both an existing framework and an ad hoc framework, are described. Finally, our approach is compared with other alternatives in terms of the cost of software development. PMID:25147858

Models and frameworks: a synergistic association for developing component-based applications.

PubMed

Alonso, Diego; Sánchez-Ledesma, Francisco; Sánchez, Pedro; Pastor, Juan A; Álvarez, Bárbara

2014-01-01

The use of frameworks and components has been shown to be effective in improving software productivity and quality. However, the results in terms of reuse and standardization show a dearth of portability either of designs or of component-based implementations. This paper, which is based on the model driven software development paradigm, presents an approach that separates the description of component-based applications from their possible implementations for different platforms. This separation is supported by automatic integration of the code obtained from the input models into frameworks implemented using object-oriented technology. Thus, the approach combines the benefits of modeling applications from a higher level of abstraction than objects, with the higher levels of code reuse provided by frameworks. In order to illustrate the benefits of the proposed approach, two representative case studies that use both an existing framework and an ad hoc framework, are described. Finally, our approach is compared with other alternatives in terms of the cost of software development.

Bit Error Probability for Maximum Likelihood Decoding of Linear Block Codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Fossorier, Marc P. C.; Rhee, Dojun

1996-01-01

In this paper, the bit error probability P(sub b) for maximum likelihood decoding of binary linear codes is investigated. The contribution of each information bit to P(sub b) is considered. For randomly generated codes, it is shown that the conventional approximation at high SNR P(sub b) is approximately equal to (d(sub H)/N)P(sub s), where P(sub s) represents the block error probability, holds for systematic encoding only. Also systematic encoding provides the minimum P(sub b) when the inverse mapping corresponding to the generator matrix of the code is used to retrieve the information sequence. The bit error performances corresponding to other generator matrix forms are also evaluated. Although derived for codes with a generator matrix randomly generated, these results are shown to provide good approximations for codes used in practice. Finally, for decoding methods which require a generator matrix with a particular structure such as trellis decoding or algebraic-based soft decision decoding, equivalent schemes that reduce the bit error probability are discussed.

In the Rearview Mirror: Social Skill Development in Deaf Youth, 1990-2015.

PubMed

Cawthon, Stephanie W; Fink, Bentley; Schoffstall, Sarah; Wendel, Erica

2018-01-01

Social skills are a vehicle by which individuals negotiate important relationships. The present article presents historical data on how social skills in deaf students were conceptualized and studied empirically during the period 1990-2015. Using a structured literature review approach, the researchers coded 266 articles for theoretical frameworks used and constructs studied. The vast majority of articles did not explicitly align with a specific theoretical framework. Of the 37 that did, most focused on socioemotional and cognitive frameworks, while a minority drew from frameworks focusing on attitudes, developmental theories, or ecological systems theory. In addition, 315 social-skill constructs were coded across the data set; the majority focused on socioemotional functioning. Trends in findings across the past quarter century and implications for research and practice are examined.

Avenue for integrating geoethics into the working world.

NASA Astrophysics Data System (ADS)

Boon, Jan

2017-04-01

GeoEthics is a young field and is taking shape through events such as the International Declaration on GeoEthics (2011) and conference sessions held since 2013 (http://www.geoethics.org/events). Many of these focused on the geoscience community and had an academic or educational focus. While interest in the subject is growing, the number of participants is still low as compared to that of other geoscience disciplines. The author has found it difficult to generate interest in the formal inclusion of geoethics and the related fields of social and environmental responsibility into university geoscience curricula. This paper proposes to link geoethics to the huge effort that has been under way over the past decade and a half in the extractive industries to develop industry-wide codes that facilitate and structure the introduction of social and environmental responsibility into company operations. All of these codes contain specific references to ethics. The paper builds on two well-developed codes: "e3 Plus - A Framework or Responsible Exploration" (Prospectors and Developers Association of Canada) and "Towards Sustainable Mining" (Mining Association of Canada) to propose an overall practical reference frame for geoethics that may facilitate the transfer of geoethicists' work into daily practice in the extractive industries.

SENR /NRPy + : Numerical relativity in singular curvilinear coordinate systems

NASA Astrophysics Data System (ADS)

Ruchlin, Ian; Etienne, Zachariah B.; Baumgarte, Thomas W.

2018-03-01

We report on a new open-source, user-friendly numerical relativity code package called SENR /NRPy + . Our code extends previous implementations of the BSSN reference-metric formulation to a much broader class of curvilinear coordinate systems, making it ideally suited to modeling physical configurations with approximate or exact symmetries. In the context of modeling black hole dynamics, it is orders of magnitude more efficient than other widely used open-source numerical relativity codes. NRPy + provides a Python-based interface in which equations are written in natural tensorial form and output at arbitrary finite difference order as highly efficient C code, putting complex tensorial equations at the scientist's fingertips without the need for an expensive software license. SENR provides the algorithmic framework that combines the C codes generated by NRPy + into a functioning numerical relativity code. We validate against two other established, state-of-the-art codes, and achieve excellent agreement. For the first time—in the context of moving puncture black hole evolutions—we demonstrate nearly exponential convergence of constraint violation and gravitational waveform errors to zero as the order of spatial finite difference derivatives is increased, while fixing the numerical grids at moderate resolution in a singular coordinate system. Such behavior outside the horizons is remarkable, as numerical errors do not converge to zero near punctures, and all points along the polar axis are coordinate singularities. The formulation addresses such coordinate singularities via cell-centered grids and a simple change of basis that analytically regularizes tensor components with respect to the coordinates. Future plans include extending this formulation to allow dynamical coordinate grids and bispherical-like distribution of points to efficiently capture orbiting compact binary dynamics.

FRAGS: estimation of coding sequence substitution rates from fragmentary data

PubMed Central

Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

2004-01-01

Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

Strategies for Managing a Multigenerational Workforce

NASA Astrophysics Data System (ADS)

Iden, Ronald

The multigenerational workforce presents a critical challenge for business managers, and each generation has different expectations. A human resource management study of organizations with more than 500 employees reported 58% of the managers experiencing conflict between younger and older workers. The purpose of this single case study was to explore the multigenerational strategies used by 3 managers from a Franklin County, Ohio manufacturing facility with a population size of 6 participants. The conceptual framework for this study was built upon generational theory and cohort group theory. The data were collected through face-to-face semistructured interviews, company documents, and a reflexive journal. Member checking was completed to strengthen the credibility and trustworthiness of the interpretation of participants' responses. A modified van Kaam method enabled separation of themes following the coding of data. Four themes emerged from the data: (a) required multigenerational managerial skills, (b) generational cohort differences, (c) most effective multigenerational management strategies, and (d) least effective multigenerational management strategies. Findings from this study may contribute to social change through better understanding, acceptance, and appreciation of the primary generations in the workforce, and, in turn, improve community relationships.

Friendly Extensible Transfer Tool Beta Version

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

Collins, William P.; Gutierrez, Kenneth M.; McRee, Susan R.

2016-04-15

Often data transfer software is designed to meet specific requirements or apply to specific environments. Frequently, this requires source code integration for added functionality. An extensible data transfer framework is needed to more easily incorporate new capabilities, in modular fashion. Using FrETT framework, functionality may be incorporated (in many cases without need of source code) to handle new platform capabilities: I/O methods (e.g., platform specific data access), network transport methods, data processing (e.g., data compression.).

Python scripting in the nengo simulator.

PubMed

Stewart, Terrence C; Tripp, Bryan; Eliasmith, Chris

2009-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models.

Python Scripting in the Nengo Simulator

PubMed Central

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models. PMID:19352442

Layered compression for high-precision depth data.

PubMed

Miao, Dan; Fu, Jingjing; Lu, Yan; Li, Shipeng; Chen, Chang Wen

2015-12-01

With the development of depth data acquisition technologies, access to high-precision depth with more than 8-b depths has become much easier and determining how to efficiently represent and compress high-precision depth is essential for practical depth storage and transmission systems. In this paper, we propose a layered high-precision depth compression framework based on an 8-b image/video encoder to achieve efficient compression with low complexity. Within this framework, considering the characteristics of the high-precision depth, a depth map is partitioned into two layers: 1) the most significant bits (MSBs) layer and 2) the least significant bits (LSBs) layer. The MSBs layer provides rough depth value distribution, while the LSBs layer records the details of the depth value variation. For the MSBs layer, an error-controllable pixel domain encoding scheme is proposed to exploit the data correlation of the general depth information with sharp edges and to guarantee the data format of LSBs layer is 8 b after taking the quantization error from MSBs layer. For the LSBs layer, standard 8-b image/video codec is leveraged to perform the compression. The experimental results demonstrate that the proposed coding scheme can achieve real-time depth compression with satisfactory reconstruction quality. Moreover, the compressed depth data generated from this scheme can achieve better performance in view synthesis and gesture recognition applications compared with the conventional coding schemes because of the error control algorithm.

Assessment of chemistry models for compressible reacting flows

NASA Astrophysics Data System (ADS)

Lapointe, Simon; Blanquart, Guillaume

2014-11-01

Recent technological advances in propulsion and power devices and renewed interest in the development of next generation supersonic and hypersonic vehicles have increased the need for detailed understanding of turbulence-combustion interactions in compressible reacting flows. In numerical simulations of such flows, accurate modeling of the fuel chemistry is a critical component of capturing the relevant physics. Various chemical models are currently being used in reacting flow simulations. However, the differences between these models and their impacts on the fluid dynamics in the context of compressible flows are not well understood. In the present work, a numerical code is developed to solve the fully coupled compressible conservation equations for reacting flows. The finite volume code is based on the theoretical and numerical framework developed by Oefelein (Prog. Aero. Sci. 42 (2006) 2-37) and employs an all-Mach-number formulation with dual time-stepping and preconditioning. The numerical approach is tested on turbulent premixed flames at high Karlovitz numbers. Different chemical models of varying complexity and computational cost are used and their effects are compared.

Neuronal cell fate specification by the molecular convergence of different spatio-temporal cues on a common initiator terminal selector gene

PubMed Central

Stratmann, Johannes

2017-01-01

The extensive genetic regulatory flows underlying specification of different neuronal subtypes are not well understood at the molecular level. The Nplp1 neuropeptide neurons in the developing Drosophila nerve cord belong to two sub-classes; Tv1 and dAp neurons, generated by two distinct progenitors. Nplp1 neurons are specified by spatial cues; the Hox homeotic network and GATA factor grn, and temporal cues; the hb -> Kr -> Pdm -> cas -> grh temporal cascade. These spatio-temporal cues combine into two distinct codes; one for Tv1 and one for dAp neurons that activate a common terminal selector feedforward cascade of col -> ap/eya -> dimm -> Nplp1. Here, we molecularly decode the specification of Nplp1 neurons, and find that the cis-regulatory organization of col functions as an integratory node for the different spatio-temporal combinatorial codes. These findings may provide a logical framework for addressing spatio-temporal control of neuronal sub-type specification in other systems. PMID:28414802

Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia;

Fisher Matrix Preloaded — FISHER4CAST

NASA Astrophysics Data System (ADS)

Bassett, Bruce A.; Fantaye, Yabebal; Hlozek, Renée; Kotze, Jacques

The Fisher Matrix is the backbone of modern cosmological forecasting. We describe the Fisher4Cast software: A general-purpose, easy-to-use, Fisher Matrix framework. It is open source, rigorously designed and tested and includes a Graphical User Interface (GUI) with automated LATEX file creation capability and point-and-click Fisher ellipse generation. Fisher4Cast was designed for ease of extension and, although written in Matlab, is easily portable to open-source alternatives such as Octave and Scilab. Here we use Fisher4Cast to present new 3D and 4D visualizations of the forecasting landscape and to investigate the effects of growth and curvature on future cosmological surveys. Early releases have been available at since mid-2008. The current release of the code is Version 2.2 which is described here. For ease of reference a Quick Start guide and the code used to produce the figures in this paper are included, in the hope that it will be useful to the cosmology and wider scientific communities.

Robust Joint Graph Sparse Coding for Unsupervised Spectral Feature Selection.

PubMed

Zhu, Xiaofeng; Li, Xuelong; Zhang, Shichao; Ju, Chunhua; Wu, Xindong

2017-06-01

In this paper, we propose a new unsupervised spectral feature selection model by embedding a graph regularizer into the framework of joint sparse regression for preserving the local structures of data. To do this, we first extract the bases of training data by previous dictionary learning methods and, then, map original data into the basis space to generate their new representations, by proposing a novel joint graph sparse coding (JGSC) model. In JGSC, we first formulate its objective function by simultaneously taking subspace learning and joint sparse regression into account, then, design a new optimization solution to solve the resulting objective function, and further prove the convergence of the proposed solution. Furthermore, we extend JGSC to a robust JGSC (RJGSC) via replacing the least square loss function with a robust loss function, for achieving the same goals and also avoiding the impact of outliers. Finally, experimental results on real data sets showed that both JGSC and RJGSC outperformed the state-of-the-art algorithms in terms of k -nearest neighbor classification performance.

Laser-based volumetric flow visualization by digital color imaging of a spectrally coded volume.

PubMed

McGregor, T J; Spence, D J; Coutts, D W

2008-01-01

We present the framework for volumetric laser-based flow visualization instrumentation using a spectrally coded volume to achieve three-component three-dimensional particle velocimetry. By delivering light from a frequency doubled Nd:YAG laser with an optical fiber, we exploit stimulated Raman scattering within the fiber to generate a continuum spanning the visible spectrum from 500 to 850 nm. We shape and disperse the continuum light to illuminate a measurement volume of 20 x 10 x 4 mm(3), in which light sheets of differing spectral properties overlap to form an unambiguous color variation along the depth direction. Using a digital color camera we obtain images of particle fields in this volume. We extract the full spatial distribution of particles with depth inferred from particle color. This paper provides a proof of principle of this instrument, examining the spatial distribution of a static field and a spray field of water droplets ejected by the nozzle of an airbrush.

Traleika Glacier X-Stack Extension Final Report

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

Fryman, Joshua

The XStack Extension Project continued along the direction of the XStack program in exploring the software tools and frameworks to support a task-based community runtime towards the goal of Exascale programming. The momentum built as part of the XStack project, with the development of the task-based Open Community Runtime (OCR) and related tools, was carried through during the XStack Extension with the focus areas of easing application development, improving performance and supporting more features. The infrastructure set up for a community-driven open-source development continued to be used towards these areas, with continued co-development of runtime and applications. A variety ofmore » OCR programming environments were studied, as described in Sections Revolutionary Programming Environments & Applications – to assist with application development on OCR, and we develop OCR Translator, a ROSE-based source-to-source compiler that parses high-level annotations in an MPI program to generate equivalent OCR code. Figure 2 compares the number of OCR objects needed to generate the 2D stencil workload using the translator, against manual approaches based on SPMD library or native coding. The rate of increase with the translator, with an increase in number of ranks, is consistent with other approaches. This is explored further in Section OCR Translator.« less

Compressible magma/mantle dynamics: 3-D, adaptive simulations in ASPECT

NASA Astrophysics Data System (ADS)

Dannberg, Juliane; Heister, Timo

2016-12-01

Melt generation and migration are an important link between surface processes and the thermal and chemical evolution of the Earth's interior. However, their vastly different timescales make it difficult to study mantle convection and melt migration in a unified framework, especially for 3-D global models. And although experiments suggest an increase in melt volume of up to 20 per cent from the depth of melt generation to the surface, previous computations have neglected the individual compressibilities of the solid and the fluid phase. Here, we describe our extension of the finite element mantle convection code ASPECT that adds melt generation and migration. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in areas where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high-resolution, 3-D, compressible, global mantle convection simulations coupled with melt migration. We evaluate the functionality and potential of this method using a series of benchmarks and model setups, compare results of the compressible and incompressible formulation, and show the effectiveness of adaptive mesh refinement when applied to melt migration. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modelling the generation of komatiites or other melts originating in greater depths. The implementation is available in the Open Source ASPECT repository.

High Order Modulation Protograph Codes

NASA Technical Reports Server (NTRS)

Nguyen, Thuy V. (Inventor); Nosratinia, Aria (Inventor); Divsalar, Dariush (Inventor)

2014-01-01

Digital communication coding methods for designing protograph-based bit-interleaved code modulation that is general and applies to any modulation. The general coding framework can support not only multiple rates but also adaptive modulation. The method is a two stage lifting approach. In the first stage, an original protograph is lifted to a slightly larger intermediate protograph. The intermediate protograph is then lifted via a circulant matrix to the expected codeword length to form a protograph-based low-density parity-check code.

Multi-channel EEG-based sleep stage classification with joint collaborative representation and multiple kernel learning.

PubMed

Shi, Jun; Liu, Xiao; Li, Yan; Zhang, Qi; Li, Yingjie; Ying, Shihui

2015-10-30

Electroencephalography (EEG) based sleep staging is commonly used in clinical routine. Feature extraction and representation plays a crucial role in EEG-based automatic classification of sleep stages. Sparse representation (SR) is a state-of-the-art unsupervised feature learning method suitable for EEG feature representation. Collaborative representation (CR) is an effective data coding method used as a classifier. Here we use CR as a data representation method to learn features from the EEG signal. A joint collaboration model is established to develop a multi-view learning algorithm, and generate joint CR (JCR) codes to fuse and represent multi-channel EEG signals. A two-stage multi-view learning-based sleep staging framework is then constructed, in which JCR and joint sparse representation (JSR) algorithms first fuse and learning the feature representation from multi-channel EEG signals, respectively. Multi-view JCR and JSR features are then integrated and sleep stages recognized by a multiple kernel extreme learning machine (MK-ELM) algorithm with grid search. The proposed two-stage multi-view learning algorithm achieves superior performance for sleep staging. With a K-means clustering based dictionary, the mean classification accuracy, sensitivity and specificity are 81.10 ± 0.15%, 71.42 ± 0.66% and 94.57 ± 0.07%, respectively; while with the dictionary learned using the submodular optimization method, they are 80.29 ± 0.22%, 71.26 ± 0.78% and 94.38 ± 0.10%, respectively. The two-stage multi-view learning based sleep staging framework outperforms all other classification methods compared in this work, while JCR is superior to JSR. The proposed multi-view learning framework has the potential for sleep staging based on multi-channel or multi-modality polysomnography signals. Copyright © 2015 Elsevier B.V. All rights reserved.

A Code of Ethics for All Adult Educators?

ERIC Educational Resources Information Center

Wood, George S., Jr.

1996-01-01

Offers a code of ethics for adult educators, outlining ethical responsibilities to society, to learners, to the sponsoring organization and other stakeholders, and to the profession. Stresses that this is more of a framework than a code, and adult educators can use it to reflect systematically upon the specifics of practice. (SK)

Smoothed Particle Hydrodynamic Simulator

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

2016-10-05

This code is a highly modular framework for developing smoothed particle hydrodynamic (SPH) simulations running on parallel platforms. The compartmentalization of the code allows for rapid development of new SPH applications and modifications of existing algorithms. The compartmentalization also allows changes in one part of the code used by many applications to instantly be made available to all applications.

Benchmark studies of the gyro-Landau-fluid code and gyro-kinetic codes on kinetic ballooning modes

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

Tang, T. F.; Lawrence Livermore National Laboratory, Livermore, California 94550; Xu, X. Q.

2016-03-15

A Gyro-Landau-Fluid (GLF) 3 + 1 model has been recently implemented in BOUT++ framework, which contains full Finite-Larmor-Radius effects, Landau damping, and toroidal resonance [Ma et al., Phys. Plasmas 22, 055903 (2015)]. A linear global beta scan has been conducted using the JET-like circular equilibria (cbm18 series), showing that the unstable modes are kinetic ballooning modes (KBMs). In this work, we use the GYRO code, which is a gyrokinetic continuum code widely used for simulation of the plasma microturbulence, to benchmark with GLF 3 + 1 code on KBMs. To verify our code on the KBM case, we first perform the beta scan basedmore » on “Cyclone base case parameter set.” We find that the growth rate is almost the same for two codes, and the KBM mode is further destabilized as beta increases. For JET-like global circular equilibria, as the modes localize in peak pressure gradient region, a linear local beta scan using the same set of equilibria has been performed at this position for comparison. With the drift kinetic electron module in the GYRO code by including small electron-electron collision to damp electron modes, GYRO generated mode structures and parity suggest that they are kinetic ballooning modes, and the growth rate is comparable to the GLF results. However, a radial scan of the pedestal for a particular set of cbm18 equilibria, using GYRO code, shows different trends for the low-n and high-n modes. The low-n modes show that the linear growth rate peaks at peak pressure gradient position as GLF results. However, for high-n modes, the growth rate of the most unstable mode shifts outward to the bottom of pedestal and the real frequency of what was originally the KBMs in ion diamagnetic drift direction steadily approaches and crosses over to the electron diamagnetic drift direction.« less

Decision-making in schizophrenia: A predictive-coding perspective.

PubMed

Sterzer, Philipp; Voss, Martin; Schlagenhauf, Florian; Heinz, Andreas

2018-05-31

Dysfunctional decision-making has been implicated in the positive and negative symptoms of schizophrenia. Decision-making can be conceptualized within the framework of hierarchical predictive coding as the result of a Bayesian inference process that uses prior beliefs to infer states of the world. According to this idea, prior beliefs encoded at higher levels in the brain are fed back as predictive signals to lower levels. Whenever these predictions are violated by the incoming sensory data, a prediction error is generated and fed forward to update beliefs encoded at higher levels. Well-documented impairments in cognitive decision-making support the view that these neural inference mechanisms are altered in schizophrenia. There is also extensive evidence relating the symptoms of schizophrenia to aberrant signaling of prediction errors, especially in the domain of reward and value-based decision-making. Moreover, the idea of altered predictive coding is supported by evidence for impaired low-level sensory mechanisms and motor processes. We review behavioral and neural findings from these research areas and provide an integrated view suggesting that schizophrenia may be related to a pervasive alteration in predictive coding at multiple hierarchical levels, including cognitive and value-based decision-making processes as well as sensory and motor systems. We relate these findings to decision-making processes and propose that varying degrees of impairment in the implicated brain areas contribute to the variety of psychotic experiences. Copyright © 2018 Elsevier Inc. All rights reserved.

Film grain noise modeling in advanced video coding

NASA Astrophysics Data System (ADS)

Oh, Byung Tae; Kuo, C.-C. Jay; Sun, Shijun; Lei, Shawmin

2007-01-01

A new technique for film grain noise extraction, modeling and synthesis is proposed and applied to the coding of high definition video in this work. The film grain noise is viewed as a part of artistic presentation by people in the movie industry. On one hand, since the film grain noise can boost the natural appearance of pictures in high definition video, it should be preserved in high-fidelity video processing systems. On the other hand, video coding with film grain noise is expensive. It is desirable to extract film grain noise from the input video as a pre-processing step at the encoder and re-synthesize the film grain noise and add it back to the decoded video as a post-processing step at the decoder. Under this framework, the coding gain of the denoised video is higher while the quality of the final reconstructed video can still be well preserved. Following this idea, we present a method to remove film grain noise from image/video without distorting its original content. Besides, we describe a parametric model containing a small set of parameters to represent the extracted film grain noise. The proposed model generates the film grain noise that is close to the real one in terms of power spectral density and cross-channel spectral correlation. Experimental results are shown to demonstrate the efficiency of the proposed scheme.

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

MELCOR computer code manuals: Primer and user`s guides, Version 1.8.3 September 1994. Volume 1

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

Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.

1995-03-01

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the US Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, andmore » combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users` Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.« less

Preliminary Results from the Application of Automated Adjoint Code Generation to CFL3D

NASA Technical Reports Server (NTRS)

Carle, Alan; Fagan, Mike; Green, Lawrence L.

1998-01-01

This report describes preliminary results obtained using an automated adjoint code generator for Fortran to augment a widely-used computational fluid dynamics flow solver to compute derivatives. These preliminary results with this augmented code suggest that, even in its infancy, the automated adjoint code generator can accurately and efficiently deliver derivatives for use in transonic Euler-based aerodynamic shape optimization problems with hundreds to thousands of independent design variables.

Formal Compiler Implementation in a Logical Framework

DTIC Science & Technology

2003-04-29

variable set [], we omit the brackets and use the simpler notation v. MetaPRL is a tactic-based prover that uses OCaml [20] as its meta-language. When a...rewrite is defined in MetaPRL, the framework creates an OCaml expression that can be used to apply the rewrite. Code to guide the application of...rewrites is written in OCaml , using a rich set of primitives provided by MetaPRL. MetaPRL automates the construction of most guidance code; we describe

Social responsibility of nursing: a global perspective.

PubMed

Tyer-Viola, Lynda; Nicholas, Patrice K; Corless, Inge B; Barry, Donna M; Hoyt, Pamela; Fitzpatrick, Joyce J; Davis, Sheila M

2009-05-01

This study addresses social responsibility in the discipline of nursing and implications for global health. The concept of social responsibility is explicated and its relevance for nursing is examined, grounded in the American Nurses Association Code of Ethics and the International Council of Nurses Code of Ethics. Social justice, human rights, nurse migration, and approaches to nursing education are discussed within the framework of nursing's social responsibility. Strategies for addressing nursing workforce issues and education within a framework of social responsibility are explored.

Statechart Analysis with Symbolic PathFinder

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.

2012-01-01

We report here on our on-going work that addresses the automated analysis and test case generation for software systems modeled using multiple Statechart formalisms. The work is motivated by large programs such as NASA Exploration, that involve multiple systems that interact via safety-critical protocols and are designed with different Statechart variants. To verify these safety-critical systems, we have developed Polyglot, a framework for modeling and analysis of model-based software written using different Statechart formalisms. Polyglot uses a common intermediate representation with customizable Statechart semantics and leverages the analysis and test generation capabilities of the Symbolic PathFinder tool. Polyglot is used as follows: First, the structure of the Statechart model (expressed in Matlab Stateflow or Rational Rhapsody) is translated into a common intermediate representation (IR). The IR is then translated into Java code that represents the structure of the model. The semantics are provided as "pluggable" modules.

The mismatch negativity: A review of underlying mechanisms

PubMed Central

Garrido, Marta I.; Kilner, James M.; Stephan, Klaas E.; Friston, Karl J.

2009-01-01

The mismatch negativity (MMN) is a brain response to violations of a rule, established by a sequence of sensory stimuli (typically in the auditory domain) [Näätänen R. Attention and brain function. Hillsdale, NJ: Lawrence Erlbaum; 1992]. The MMN reflects the brain’s ability to perform automatic comparisons between consecutive stimuli and provides an electrophysiological index of sensory learning and perceptual accuracy. Although the MMN has been studied extensively, the neurophysiological mechanisms underlying the MMN are not well understood. Several hypotheses have been put forward to explain the generation of the MMN; amongst these accounts, the “adaptation hypothesis” and the “model adjustment hypothesis” have received the most attention. This paper presents a review of studies that focus on neuronal mechanisms underlying the MMN generation, discusses the two major explanatory hypotheses, and proposes predictive coding as a general framework that attempts to unify both. PMID:19181570

A Compilation of MATLAB Scripts and Functions for MACGMC Analyses

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Bednarcyk, Brett A.; Mital, Subodh K.

2017-01-01

The primary aim of the current effort is to provide scripts that automate many of the repetitive pre- and post-processing tasks associated with composite materials analyses using the Micromechanics Analysis Code with the Generalized Method of Cells. This document consists of a compilation of hundreds of scripts that were developed in MATLAB (The Mathworks, Inc., Natick, MA) programming language and consolidated into 16 MATLAB functions. (MACGMC). MACGMC is a composite material and laminate analysis software code developed at NASA Glenn Research Center. The software package has been built around the generalized method of cells (GMC) family of micromechanics theories. The computer code is developed with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated to increase the user friendliness, as well as to make it more robust in terms of input preparation and code execution. Finally, classical lamination theory has been implemented within the software, wherein GMC is used to model the composite material response of each ply. Thus, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. The pre-processing tasks include generation of a multitude of different repeating unit cells (RUCs) for CMCs and PMCs, visualization of RUCs from MACGMC input and output files and generation of the RUC section of a MACGMC input file. The post-processing tasks include visualization of the predicted composite response, such as local stress and strain contours, damage initiation and progression, stress-strain behavior, and fatigue response. In addition to the above, several miscellaneous scripts have been developed that can be used to perform repeated Monte-Carlo simulations to enable probabilistic simulations with minimal manual intervention. This document is formatted to provide MATLAB source files and descriptions of how to utilize them. It is assumed that the user has a basic understanding of how MATLAB scripts work and some MATLAB programming experience.

Sfg

NASA Astrophysics Data System (ADS)

Fischer, R. X.; Baur, W. H.

This document is part of Subvolume E `Zeolite-Type Crystal Structures and their Chemistry. Framework Type Codes RON to STI' of Volume 14 `Microporous and other Framework Materials with Zeolite-Type Structures' of Landolt-Börnstein Group IV `Physical Chemistry'.

Vet

NASA Astrophysics Data System (ADS)

Fischer, R. X.; Baur, W. H.

This document is part of Subvolume F 'Zeolite-Type Crystal Structures and their Chemistry. Framework Type Codes STO to ZON' of Volume 14 'Microporous and other Framework Materials with Zeolite-Type Structures' of Landolt-Börnstein Group IV 'Physical Chemistry'.

Establishing the Common Community Physics Package by Transitioning the GFS Physics to a Collaborative Software Framework

NASA Astrophysics Data System (ADS)

Xue, L.; Firl, G.; Zhang, M.; Jimenez, P. A.; Gill, D.; Carson, L.; Bernardet, L.; Brown, T.; Dudhia, J.; Nance, L. B.; Stark, D. R.

2017-12-01

The Global Model Test Bed (GMTB) has been established to support the evolution of atmospheric physical parameterizations in NCEP global modeling applications. To accelerate the transition to the Next Generation Global Prediction System (NGGPS), a collaborative model development framework known as the Common Community Physics Package (CCPP) is created within the GMTB to facilitate engagement from the broad community on physics experimentation and development. A key component to this Research to Operation (R2O) software framework is the Interoperable Physics Driver (IPD) that hooks the physics parameterizations from one end to the dynamical cores on the other end with minimum implementation effort. To initiate the CCPP, scientists and engineers from the GMTB separated and refactored the GFS physics. This exercise demonstrated the process of creating IPD-compliant code and can serve as an example for other physics schemes to do the same and be considered for inclusion into the CCPP. Further benefits to this process include run-time physics suite configuration and considerably reduced effort for testing modifications to physics suites through GMTB's physics test harness. The implementation will be described and the preliminary results will be presented at the conference.

A new DWT/MC/DPCM video compression framework based on EBCOT

NASA Astrophysics Data System (ADS)

Mei, L. M.; Wu, H. R.; Tan, D. M.

2005-07-01

A novel Discrete Wavelet Transform (DWT)/Motion Compensation (MC)/Differential Pulse Code Modulation (DPCM) video compression framework is proposed in this paper. Although the Discrete Cosine Transform (DCT)/MC/DPCM is the mainstream framework for video coders in industry and international standards, the idea of DWT/MC/DPCM has existed for more than one decade in the literature and the investigation is still undergoing. The contribution of this work is twofold. Firstly, the Embedded Block Coding with Optimal Truncation (EBCOT) is used here as the compression engine for both intra- and inter-frame coding, which provides good compression ratio and embedded rate-distortion (R-D) optimization mechanism. This is an extension of the EBCOT application from still images to videos. Secondly, this framework offers a good interface for the Perceptual Distortion Measure (PDM) based on the Human Visual System (HVS) where the Mean Squared Error (MSE) can be easily replaced with the PDM in the R-D optimization. Some of the preliminary results are reported here. They are also compared with benchmarks such as MPEG-2 and MPEG-4 version 2. The results demonstrate that under specified condition the proposed coder outperforms the benchmarks in terms of rate vs. distortion.

InSAR Scientific Computing Environment

NASA Technical Reports Server (NTRS)

Rosen, Paul A.; Sacco, Gian Franco; Gurrola, Eric M.; Zabker, Howard A.

2011-01-01

This computing environment is the next generation of geodetic image processing technology for repeat-pass Interferometric Synthetic Aperture (InSAR) sensors, identified by the community as a needed capability to provide flexibility and extensibility in reducing measurements from radar satellites and aircraft to new geophysical products. This software allows users of interferometric radar data the flexibility to process from Level 0 to Level 4 products using a variety of algorithms and for a range of available sensors. There are many radar satellites in orbit today delivering to the science community data of unprecedented quantity and quality, making possible large-scale studies in climate research, natural hazards, and the Earth's ecosystem. The proposed DESDynI mission, now under consideration by NASA for launch later in this decade, would provide time series and multiimage measurements that permit 4D models of Earth surface processes so that, for example, climate-induced changes over time would become apparent and quantifiable. This advanced data processing technology, applied to a global data set such as from the proposed DESDynI mission, enables a new class of analyses at time and spatial scales unavailable using current approaches. This software implements an accurate, extensible, and modular processing system designed to realize the full potential of InSAR data from future missions such as the proposed DESDynI, existing radar satellite data, as well as data from the NASA UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar), and other airborne platforms. The processing approach has been re-thought in order to enable multi-scene analysis by adding new algorithms and data interfaces, to permit user-reconfigurable operation and extensibility, and to capitalize on codes already developed by NASA and the science community. The framework incorporates modern programming methods based on recent research, including object-oriented scripts controlling legacy and new codes, abstraction and generalization of the data model for efficient manipulation of objects among modules, and well-designed module interfaces suitable for command- line execution or GUI-programming. The framework is designed to allow users contributions to promote maximum utility and sophistication of the code, creating an open-source community that could extend the framework into the indefinite future.

Comparison of theoretical and flight-measured local flow aerodynamics for a low-aspect-ratio fin

NASA Technical Reports Server (NTRS)

Johnson, J. B.; Sandlin, D. R.

1984-01-01

Flight test and theoretical aerodynamic data were obtained for a flight test fixture mounted on the underside of an F-104G aircraft. The theoretical data were generated using two codes, a two dimensional transonic code called Code H, and a three dimensional subsonic and supersonic code call wing-body. Pressure distributions generated by the codes for the flight test fixture as well as boundary layer displacement thickness generated by the two dimensional code were compared to the flight test data. The two dimensional code pressure distributions compared well except at the minimum pressure point and trailing edge. Shock locations compared well except at high transonic speeds. The three dimensional code pressure distributions compared well except at the trailing edge of the flight test fixture. The two dimensional code does not predict displacement thickness of the flight test fixture well.

Using hidden Markov models and observed evolution to annotate viral genomes.

PubMed

McCauley, Stephen; Hein, Jotun

2006-06-01

ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

Parallel Index and Query for Large Scale Data Analysis

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

Chou, Jerry; Wu, Kesheng; Ruebel, Oliver

2011-07-18

Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies are critical for facilitating interactive exploration of large datasets, but numerous challenges remain in terms of designing a system for process- ing general scientific datasets. The system needs to be able to run on distributed multi-core platforms, efficiently utilize underlying I/O infrastructure, and scale to massive datasets. We present FastQuery, a novel software framework that address these challenges. FastQuery utilizes a state-of-the-art index and query technology (FastBit) and is designed to process mas- sive datasets on modern supercomputing platforms. We apply FastQuery to processing ofmore » a massive 50TB dataset generated by a large scale accelerator modeling code. We demonstrate the scalability of the tool to 11,520 cores. Motivated by the scientific need to search for inter- esting particles in this dataset, we use our framework to reduce search time from hours to tens of seconds.« less

The Space Weather Modeling Framework (SWMF): Models and Validation

NASA Astrophysics Data System (ADS)

Gombosi, Tamas; Toth, Gabor; Sokolov, Igor; de Zeeuw, Darren; van der Holst, Bart; Ridley, Aaron; Manchester, Ward, IV

In the last decade our group at the Center for Space Environment Modeling (CSEM) has developed the Space Weather Modeling Framework (SWMF) that efficiently couples together different models describing the interacting regions of the space environment. Many of these domain models (such as the global solar corona, the inner heliosphere or the global magneto-sphere) are based on MHD and are represented by our multiphysics code, BATS-R-US. SWMF is a powerful tool for coupling regional models describing the space environment from the solar photosphere to the bottom of the ionosphere. Presently, SWMF contains over a dozen components: the solar corona (SC), eruptive event generator (EE), inner heliosphere (IE), outer heliosphere (OH), solar energetic particles (SE), global magnetosphere (GM), inner magnetosphere (IM), radiation belts (RB), plasmasphere (PS), ionospheric electrodynamics (IE), polar wind (PW), upper atmosphere (UA) and lower atmosphere (LA). This talk will present an overview of SWMF, new results obtained with improved physics as well as some validation studies.

Scout: high-performance heterogeneous computing made simple

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

Jablin, James; Mc Cormick, Patrick; Herlihy, Maurice

2011-01-26

Researchers must often write their own simulation and analysis software. During this process they simultaneously confront both computational and scientific problems. Current strategies for aiding the generation of performance-oriented programs do not abstract the software development from the science. Furthermore, the problem is becoming increasingly complex and pressing with the continued development of many-core and heterogeneous (CPU-GPU) architectures. To acbieve high performance, scientists must expertly navigate both software and hardware. Co-design between computer scientists and research scientists can alleviate but not solve this problem. The science community requires better tools for developing, optimizing, and future-proofing codes, allowing scientists to focusmore » on their research while still achieving high computational performance. Scout is a parallel programming language and extensible compiler framework targeting heterogeneous architectures. It provides the abstraction required to buffer scientists from the constantly-shifting details of hardware while still realizing higb-performance by encapsulating software and hardware optimization within a compiler framework.« less

A multi-level simulation platform of natural gas internal reforming solid oxide fuel cell-gas turbine hybrid generation system - Part II. Balancing units model library and system simulation

NASA Astrophysics Data System (ADS)

Bao, Cheng; Cai, Ningsheng; Croiset, Eric

2011-10-01

Following our integrated hierarchical modeling framework of natural gas internal reforming solid oxide fuel cell (IRSOFC), this paper firstly introduces the model libraries of main balancing units, including some state-of-the-art achievements and our specific work. Based on gPROMS programming code, flexible configuration and modular design are fully realized by specifying graphically all unit models in each level. Via comparison with the steady-state experimental data of Siemens-Westinghouse demonstration system, the in-house multi-level SOFC-gas turbine (GT) simulation platform is validated to be more accurate than the advanced power system analysis tool (APSAT). Moreover, some units of the demonstration system are designed reversely for analysis of a typically part-load transient process. The framework of distributed and dynamic modeling in most of units is significant for the development of control strategies in the future.

Topologically Guided, Automated Construction of Metal–Organic Frameworks and Their Evaluation for Energy-Related Applications

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

Colón, Yamil J.; Gómez-Gualdrón, Diego A.; Snurr, Randall Q.

Metal-organic frameworks (MOFs) are promising materials for a range of energy and environmental applications. Here we describe in detail a computational algorithm and code to generate MOFs based on edge-transitive topological nets for subsequent evaluation via molecular simulation. This algorithm has been previously used by us to construct and evaluate 13 512 MOFs of 41 different topologies for cryo-adsorbed hydrogen storage. Grand canonical Monte Carlo simulations are used here to evaluate the 13 512 structures for the storage of gaseous fuels such as hydrogen and methane and nondistillative separation of xenon/krypton mixtures at various operating conditions. MOF performance for bothmore » gaseous fuel storage and xenon/krypton separation is influenced by topology. Simulation data suggest that gaseous fuel storage performance is topology-dependent due to MOF properties such as void fraction and surface area combining differently in different topologies, whereas xenon/krypton separation performance is topology-dependent due to how topology constrains the pore size distribution.« less

Coupling between a multi-physics workflow engine and an optimization framework

NASA Astrophysics Data System (ADS)

Di Gallo, L.; Reux, C.; Imbeaux, F.; Artaud, J.-F.; Owsiak, M.; Saoutic, B.; Aiello, G.; Bernardi, P.; Ciraolo, G.; Bucalossi, J.; Duchateau, J.-L.; Fausser, C.; Galassi, D.; Hertout, P.; Jaboulay, J.-C.; Li-Puma, A.; Zani, L.

2016-03-01

A generic coupling method between a multi-physics workflow engine and an optimization framework is presented in this paper. The coupling architecture has been developed in order to preserve the integrity of the two frameworks. The objective is to provide the possibility to replace a framework, a workflow or an optimizer by another one without changing the whole coupling procedure or modifying the main content in each framework. The coupling is achieved by using a socket-based communication library for exchanging data between the two frameworks. Among a number of algorithms provided by optimization frameworks, Genetic Algorithms (GAs) have demonstrated their efficiency on single and multiple criteria optimization. Additionally to their robustness, GAs can handle non-valid data which may appear during the optimization. Consequently GAs work on most general cases. A parallelized framework has been developed to reduce the time spent for optimizations and evaluation of large samples. A test has shown a good scaling efficiency of this parallelized framework. This coupling method has been applied to the case of SYCOMORE (SYstem COde for MOdeling tokamak REactor) which is a system code developed in form of a modular workflow for designing magnetic fusion reactors. The coupling of SYCOMORE with the optimization platform URANIE enables design optimization along various figures of merit and constraints.

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes

PubMed Central

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-01-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. PMID:29367403

Programming (Tips) for Physicists & Engineers

ScienceCinema

Ozcan, Erkcan

2018-02-19

Programming for today's physicists and engineers. Work environment: today's astroparticle, accelerator experiments and information industry rely on large collaborations. Need more than ever: code sharing/resuse, code building--framework integration, documentation and good visualization, working remotely, not reinventing the wheel.

Programming (Tips) for Physicists & Engineers

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

Ozcan, Erkcan

2010-07-13

Programming for today's physicists and engineers. Work environment: today's astroparticle, accelerator experiments and information industry rely on large collaborations. Need more than ever: code sharing/resuse, code building--framework integration, documentation and good visualization, working remotely, not reinventing the wheel.

Civil Behavior, Safe-School Planning, and Dress Codes

ERIC Educational Resources Information Center

Studak, Cathryn M.; Workman, Jane E.

2007-01-01

This research examined news reports in order to identify incidents that precipitated dress code revisions. News reports were examined within the framework of rules for civil behavior. Using key words "school dress codes" and "violence," LEXIS/NEXIS was used to access 104 articles from 44 U.S. newspapers from December 3, 2004 to December 2, 2005.…

Revisiting Principles of Ethical Practice Using a Case Study Framework

ERIC Educational Resources Information Center

Combes, Bertina H.; Peak, Pamela W.; Barrio, Brenda L.; Lindo, Endia J.; Hovey, Katrina A.; Lim, Okyoung; Peterson-Ahmad, Maria; Dorel, Theresa G.; Goran, Lisa

2016-01-01

A code of ethics serves as a compass, guiding professionals as they perform the roles associated with their profession. These codes are evidence to the public that professionals are concerned about the services they provide and the individuals to whom they are provided. Codes of ethics should be living documents, changing focus as the fields they…

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

A Hybrid Optimization Framework with POD-based Order Reduction and Design-Space Evolution Scheme

NASA Astrophysics Data System (ADS)

Ghoman, Satyajit S.

The main objective of this research is to develop an innovative multi-fidelity multi-disciplinary design, analysis and optimization suite that integrates certain solution generation codes and newly developed innovative tools to improve the overall optimization process. The research performed herein is divided into two parts: (1) the development of an MDAO framework by integration of variable fidelity physics-based computational codes, and (2) enhancements to such a framework by incorporating innovative features extending its robustness. The first part of this dissertation describes the development of a conceptual Multi-Fidelity Multi-Strategy and Multi-Disciplinary Design Optimization Environment (M3 DOE), in context of aircraft wing optimization. M 3 DOE provides the user a capability to optimize configurations with a choice of (i) the level of fidelity desired, (ii) the use of a single-step or multi-step optimization strategy, and (iii) combination of a series of structural and aerodynamic analyses. The modularity of M3 DOE allows it to be a part of other inclusive optimization frameworks. The M 3 DOE is demonstrated within the context of shape and sizing optimization of the wing of a Generic Business Jet aircraft. Two different optimization objectives, viz. dry weight minimization, and cruise range maximization are studied by conducting one low-fidelity and two high-fidelity optimization runs to demonstrate the application scope of M3 DOE. The second part of this dissertation describes the development of an innovative hybrid optimization framework that extends the robustness of M 3 DOE by employing a proper orthogonal decomposition-based design-space order reduction scheme combined with the evolutionary algorithm technique. The POD method of extracting dominant modes from an ensemble of candidate configurations is used for the design-space order reduction. The snapshot of candidate population is updated iteratively using evolutionary algorithm technique of fitness-driven retention. This strategy capitalizes on the advantages of evolutionary algorithm as well as POD-based reduced order modeling, while overcoming the shortcomings inherent with these techniques. When linked with M3 DOE, this strategy offers a computationally efficient methodology for problems with high level of complexity and a challenging design-space. This newly developed framework is demonstrated for its robustness on a nonconventional supersonic tailless air vehicle wing shape optimization problem.

Validation of Framework Code Approach to a Life Prediction System for Fiber Reinforced Composites

NASA Technical Reports Server (NTRS)

Gravett, Phillip

1997-01-01

The grant was conducted by the MMC Life Prediction Cooperative, an industry/government collaborative team, Ohio Aerospace Institute (OAI) acted as the prime contractor on behalf of the Cooperative for this grant effort. See Figure I for the organization and responsibilities of team members. The technical effort was conducted during the period August 7, 1995 to June 30, 1996 in cooperation with Erwin Zaretsky, the LERC Program Monitor. Phil Gravett of Pratt & Whitney was the principal technical investigator. Table I documents all meeting-related coordination memos during this period. The effort under this grant was closely coordinated with an existing USAF sponsored program focused on putting into practice a life prediction system for turbine engine components made of metal matrix composites (MMC). The overall architecture of the NMC life prediction system was defined in the USAF sponsored program (prior to this grant). The efforts of this grant were focussed on implementing and tailoring of the life prediction system, the framework code within it and the damage modules within it to meet the specific requirements of the Cooperative. T'he tailoring of the life prediction system provides the basis for pervasive and continued use of this capability by the industry/government cooperative. The outputs of this grant are: 1. Definition of the framework code to analysis modules interfaces, 2. Definition of the interface between the materials database and the finite element model, and 3. Definition of the integration of the framework code into an FEM design tool.

Research on Automatic Programming

DTIC Science & Technology

1975-12-31

Sequential processes, deadlocks, and semaphore primitives , Ph.D. Thesis, Harvard University, November 1974; Center for Research in Computing...verified. 13 Code generated to effect the synchronization makes use of the ECL control extension facility (Prenner’s CI, see [Prenner]). The... semaphore operations [Dijkstra] is being developed. Initial results for this code generator are very encouraging; in many cases generated code is

Application of the BINS superheated drop detector spectrometer to the 9Be(p,xn) neutron energy spectrum determination

NASA Astrophysics Data System (ADS)

Di Fulvio, A.; Ciolini, R.; Mirzajani, N.; Romei, C.; d'Errico, F.; Bedogni, R.; Esposito, J.; Zafiropoulos, D.; Colautti, P.

2013-07-01

In the framework of TRASCO-BNCT project, a Bubble Interactive Neutron Spectrometer (BINS) device was applied to the characterization of the angle-and energy-differential neutron spectra generated by the 9Be(p,xn)reaction. The BINS spectrometer uses two superheated emulsion detectors, sequentially operated at different temperatures and thus provides a series of six sharp threshold responses, covering the 0.1-10 MeV neutron energy range. Spectrum unfolding of the data was performed by means of MAXED code. The obtained angle, energy-differential spectra were compared with those measured with a Bonner sphere spectrometer, a silicon telescope spectrometer and literature data.

WannierTools: An open-source software package for novel topological materials

NASA Astrophysics Data System (ADS)

Wu, QuanSheng; Zhang, ShengNan; Song, Hai-Feng; Troyer, Matthias; Soluyanov, Alexey A.

2018-03-01

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ).

Spent Pot Lining Characterization Framework

NASA Astrophysics Data System (ADS)

Ospina, Gustavo; Hassan, Mohamed I.

2017-09-01

Spent pot lining (SPL) management represents a major concern for aluminum smelters. There are two key elements for spent pot lining management: recycling and safe storage. Spent pot lining waste can potentially have beneficial uses in co-firing in cement plants. Also, safe storage of SPL is of utmost importance. Gas generation of SPL reaction with water and ignition sensitivity must be studied. However, determining the feasibility of SPL co-firing and developing the required procedures for safe storage rely on determining experimentally all the necessary SPL properties along with the appropriate test methods, recognized by emissions standards and fire safety design codes. The applicable regulations and relevant SPL properties for this purpose are presented along with the corresponding test methods.

Benchmarking and performance analysis of the CM-2. [SIMD computer

NASA Technical Reports Server (NTRS)

Myers, David W.; Adams, George B., II

1988-01-01

A suite of benchmarking routines testing communication, basic arithmetic operations, and selected kernel algorithms written in LISP and PARIS was developed for the CM-2. Experiment runs are automated via a software framework that sequences individual tests, allowing for unattended overnight operation. Multiple measurements are made and treated statistically to generate well-characterized results from the noisy values given by cm:time. The results obtained provide a comparison with similar, but less extensive, testing done on a CM-1. Tests were chosen to aid the algorithmist in constructing fast, efficient, and correct code on the CM-2, as well as gain insight into what performance criteria are needed when evaluating parallel processing machines.

Modelling Conditions and Health Care Processes in Electronic Health Records: An Application to Severe Mental Illness with the Clinical Practice Research Datalink.

PubMed

Olier, Ivan; Springate, David A; Ashcroft, Darren M; Doran, Tim; Reeves, David; Planner, Claire; Reilly, Siobhan; Kontopantelis, Evangelos

2016-01-01

The use of Electronic Health Records databases for medical research has become mainstream. In the UK, increasing use of Primary Care Databases is largely driven by almost complete computerisation and uniform standards within the National Health Service. Electronic Health Records research often begins with the development of a list of clinical codes with which to identify cases with a specific condition. We present a methodology and accompanying Stata and R commands (pcdsearch/Rpcdsearch) to help researchers in this task. We present severe mental illness as an example. We used the Clinical Practice Research Datalink, a UK Primary Care Database in which clinical information is largely organised using Read codes, a hierarchical clinical coding system. Pcdsearch is used to identify potentially relevant clinical codes and/or product codes from word-stubs and code-stubs suggested by clinicians. The returned code-lists are reviewed and codes relevant to the condition of interest are selected. The final code-list is then used to identify patients. We identified 270 Read codes linked to SMI and used them to identify cases in the database. We observed that our approach identified cases that would have been missed with a simpler approach using SMI registers defined within the UK Quality and Outcomes Framework. We described a framework for researchers of Electronic Health Records databases, for identifying patients with a particular condition or matching certain clinical criteria. The method is invariant to coding system or database and can be used with SNOMED CT, ICD or other medical classification code-lists.

Considerations for use of dental photography and electronic media in dental education and clinical practice.

PubMed

Stieber, Jane C; Nelson, Travis; Huebner, Colleen E

2015-04-01

Photography and electronic media are indispensable tools for dental education and clinical practice. Although previous research has focused on privacy issues and general strategies to protect patient privacy when sharing clinical photographs for educational purposes, there are no published recommendations for developing a functional, privacy-compliant institutional framework for the capture, storage, transfer, and use of clinical photographs and other electronic media. The aims of this study were to research patient rights relating to electronic media and propose a framework for the use of patient media in education and clinical care. After a review of the relevant literature and consultation with the University of Washington's director of privacy and compliance and assistant attorney general, the researchers developed a privacy-compliant framework to ensure appropriate capture, storage, transfer, and use of clinical photography and electronic media. A four-part framework was created to guide the use of patient media that reflects considerations of patient autonomy and privacy, informed consent, capture and storage of media, and its transfer, use, and display. The best practices proposed for capture, storage, transfer, and use of clinical photographs and electronic media adhere to the health care code of ethics (based on patient autonomy, nonmaleficence, beneficence, justice, and veracity), which is most effectively upheld by a practical framework designed to protect patients and limit institutional liability. Educators have the opportunity and duty to convey these principles to students who will become the next generation of dentists, researchers, and educators.

Secure ADS-B authentication system and method

NASA Technical Reports Server (NTRS)

Viggiano, Marc J (Inventor); Valovage, Edward M (Inventor); Samuelson, Kenneth B (Inventor); Hall, Dana L (Inventor)

2010-01-01

A secure system for authenticating the identity of ADS-B systems, including: an authenticator, including a unique id generator and a transmitter transmitting the unique id to one or more ADS-B transmitters; one or more ADS-B transmitters, including a receiver receiving the unique id, one or more secure processing stages merging the unique id with the ADS-B transmitter's identification, data and secret key and generating a secure code identification and a transmitter transmitting a response containing the secure code and ADSB transmitter's data to the authenticator; the authenticator including means for independently determining each ADS-B transmitter's secret key, a receiver receiving each ADS-B transmitter's response, one or more secure processing stages merging the unique id, ADS-B transmitter's identification and data and generating a secure code, and comparison processing comparing the authenticator-generated secure code and the ADS-B transmitter-generated secure code and providing an authentication signal based on the comparison result.

Scheduling Operations for Massive Heterogeneous Clusters

NASA Technical Reports Server (NTRS)

Humphrey, John; Spagnoli, Kyle

2013-01-01

High-performance computing (HPC) programming has become increasingly difficult with the advent of hybrid supercomputers consisting of multicore CPUs and accelerator boards such as the GPU. Manual tuning of software to achieve high performance on this type of machine has been performed by programmers. This is needlessly difficult and prone to being invalidated by new hardware, new software, or changes in the underlying code. A system was developed for task-based representation of programs, which when coupled with a scheduler and runtime system, allows for many benefits, including higher performance and utilization of computational resources, easier programming and porting, and adaptations of code during runtime. The system consists of a method of representing computer algorithms as a series of data-dependent tasks. The series forms a graph, which can be scheduled for execution on many nodes of a supercomputer efficiently by a computer algorithm. The schedule is executed by a dispatch component, which is tailored to understand all of the hardware types that may be available within the system. The scheduler is informed by a cluster mapping tool, which generates a topology of available resources and their strengths and communication costs. Software is decoupled from its hardware, which aids in porting to future architectures. A computer algorithm schedules all operations, which for systems of high complexity (i.e., most NASA codes), cannot be performed optimally by a human. The system aids in reducing repetitive code, such as communication code, and aids in the reduction of redundant code across projects. It adds new features to code automatically, such as recovering from a lost node or the ability to modify the code while running. In this project, the innovators at the time of this reporting intend to develop two distinct technologies that build upon each other and both of which serve as building blocks for more efficient HPC usage. First is the scheduling and dynamic execution framework, and the second is scalable linear algebra libraries that are built directly on the former.

IEP goals for school-age children with speech sound disorders.

PubMed

Farquharson, Kelly; Tambyraja, Sherine R; Justice, Laura M; Redle, Erin E

2014-01-01

The purpose of the current study was to describe the current state of practice for writing Individualized Education Program (IEP) goals for children with speech sound disorders (SSDs). IEP goals for 146 children receiving services for SSDs within public school systems across two states were coded for their dominant theoretical framework and overall quality. A dichotomous scheme was used for theoretical framework coding: cognitive-linguistic or sensory-motor. Goal quality was determined by examining 7 specific indicators outlined by an empirically tested rating tool. In total, 147 long-term and 490 short-term goals were coded. The results revealed no dominant theoretical framework for long-term goals, whereas short-term goals largely reflected a sensory-motor framework. In terms of quality, the majority of speech production goals were functional and generalizable in nature, but were not able to be easily targeted during common daily tasks or by other members of the IEP team. Short-term goals were consistently rated higher in quality domains when compared to long-term goals. The current state of practice for writing IEP goals for children with SSDs indicates that theoretical framework may be eclectic in nature and likely written to support the individual needs of children with speech sound disorders. Further investigation is warranted to determine the relations between goal quality and child outcomes. (1) Identify two predominant theoretical frameworks and discuss how they apply to IEP goal writing. (2) Discuss quality indicators as they relate to IEP goals for children with speech sound disorders. (3) Discuss the relationship between long-term goals level of quality and related theoretical frameworks. (4) Identify the areas in which business-as-usual IEP goals exhibit strong quality.

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

Ling Zou; Hongbin Zhang; Jess Gehin

A coupled TH/Neutronics/CRUD framework, which is able to simulate the CRUD deposits impact on CIPS phenomenon, was described in this paper. This framework includes the coupling among three essential physics, thermal-hydraulics, CRUD and neutronics. The overall framework was implemented by using the CFD software STAR-CCM+, developing CRUD codes, and using the neutronics code DeCART. The coupling was implemented by exchanging data between softwares using intermediate exchange files. A typical 3 by 3 PWR fuel pin problem was solved under this framework. The problem was solved in a 12 months length period of time. Time-dependent solutions were provided, including CRUD depositsmore » inventory and their distributions on fuels, boron hideout amount inside CRUD deposits, as well as power shape changing over time. The results clearly showed the power shape suppression in regions where CRUD deposits exist, which is a strong indication of CIPS phenomenon.« less

A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Mortensen, Mikael; Langtangen, Hans Petter; Wells, Garth N.

2011-09-01

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model.

Surface Modeling and Grid Generation of Orbital Sciences X34 Vehicle. Phase 1

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

1997-01-01

The surface modeling and grid generation requirements, motivations, and methods used to develop Computational Fluid Dynamic volume grids for the X34-Phase 1 are presented. The requirements set forth by the Aerothermodynamics Branch at the NASA Langley Research Center serve as the basis for the final techniques used in the construction of all volume grids, including grids for parametric studies of the X34. The Integrated Computer Engineering and Manufacturing code for Computational Fluid Dynamics (ICEM/CFD), the Grid Generation code (GRIDGEN), the Three-Dimensional Multi-block Advanced Grid Generation System (3DMAGGS) code, and Volume Grid Manipulator (VGM) code are used to enable the necessary surface modeling, surface grid generation, volume grid generation, and grid alterations, respectively. All volume grids generated for the X34, as outlined in this paper, were used for CFD simulations within the Aerothermodynamics Branch.

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

Parcels v0.9: prototyping a Lagrangian ocean analysis framework for the petascale age

NASA Astrophysics Data System (ADS)

Lange, Michael; van Sebille, Erik

2017-11-01

As ocean general circulation models (OGCMs) move into the petascale age, where the output of single simulations exceeds petabytes of storage space, tools to analyse the output of these models will need to scale up too. Lagrangian ocean analysis, where virtual particles are tracked through hydrodynamic fields, is an increasingly popular way to analyse OGCM output, by mapping pathways and connectivity of biotic and abiotic particulates. However, the current software stack of Lagrangian ocean analysis codes is not dynamic enough to cope with the increasing complexity, scale and need for customization of use-cases. Furthermore, most community codes are developed for stand-alone use, making it a nontrivial task to integrate virtual particles at runtime of the OGCM. Here, we introduce the new Parcels code, which was designed from the ground up to be sufficiently scalable to cope with petascale computing. We highlight its API design that combines flexibility and customization with the ability to optimize for HPC workflows, following the paradigm of domain-specific languages. Parcels is primarily written in Python, utilizing the wide range of tools available in the scientific Python ecosystem, while generating low-level C code and using just-in-time compilation for performance-critical computation. We show a worked-out example of its API, and validate the accuracy of the code against seven idealized test cases. This version 0.9 of Parcels is focused on laying out the API, with future work concentrating on support for curvilinear grids, optimization, efficiency and at-runtime coupling with OGCMs.

SMARTbot: A Behavioral Analysis Framework Augmented with Machine Learning to Identify Mobile Botnet Applications

PubMed Central

Karim, Ahmad; Salleh, Rosli; Khan, Muhammad Khurram

2016-01-01

Botnet phenomenon in smartphones is evolving with the proliferation in mobile phone technologies after leaving imperative impact on personal computers. It refers to the network of computers, laptops, mobile devices or tablets which is remotely controlled by the cybercriminals to initiate various distributed coordinated attacks including spam emails, ad-click fraud, Bitcoin mining, Distributed Denial of Service (DDoS), disseminating other malwares and much more. Likewise traditional PC based botnet, Mobile botnets have the same operational impact except the target audience is particular to smartphone users. Therefore, it is import to uncover this security issue prior to its widespread adaptation. We propose SMARTbot, a novel dynamic analysis framework augmented with machine learning techniques to automatically detect botnet binaries from malicious corpus. SMARTbot is a component based off-device behavioral analysis framework which can generate mobile botnet learning model by inducing Artificial Neural Networks’ back-propagation method. Moreover, this framework can detect mobile botnet binaries with remarkable accuracy even in case of obfuscated program code. The results conclude that, a classifier model based on simple logistic regression outperform other machine learning classifier for botnet apps’ detection, i.e 99.49% accuracy is achieved. Further, from manual inspection of botnet dataset we have extracted interesting trends in those applications. As an outcome of this research, a mobile botnet dataset is devised which will become the benchmark for future studies. PMID:26978523

SMARTbot: A Behavioral Analysis Framework Augmented with Machine Learning to Identify Mobile Botnet Applications.

PubMed

Karim, Ahmad; Salleh, Rosli; Khan, Muhammad Khurram

2016-01-01

Botnet phenomenon in smartphones is evolving with the proliferation in mobile phone technologies after leaving imperative impact on personal computers. It refers to the network of computers, laptops, mobile devices or tablets which is remotely controlled by the cybercriminals to initiate various distributed coordinated attacks including spam emails, ad-click fraud, Bitcoin mining, Distributed Denial of Service (DDoS), disseminating other malwares and much more. Likewise traditional PC based botnet, Mobile botnets have the same operational impact except the target audience is particular to smartphone users. Therefore, it is import to uncover this security issue prior to its widespread adaptation. We propose SMARTbot, a novel dynamic analysis framework augmented with machine learning techniques to automatically detect botnet binaries from malicious corpus. SMARTbot is a component based off-device behavioral analysis framework which can generate mobile botnet learning model by inducing Artificial Neural Networks' back-propagation method. Moreover, this framework can detect mobile botnet binaries with remarkable accuracy even in case of obfuscated program code. The results conclude that, a classifier model based on simple logistic regression outperform other machine learning classifier for botnet apps' detection, i.e 99.49% accuracy is achieved. Further, from manual inspection of botnet dataset we have extracted interesting trends in those applications. As an outcome of this research, a mobile botnet dataset is devised which will become the benchmark for future studies.

High-Performance Computer Modeling of the Cosmos-Iridium Collision

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

Olivier, S; Cook, K; Fasenfest, B

2009-08-28

This paper describes the application of a new, integrated modeling and simulation framework, encompassing the space situational awareness (SSA) enterprise, to the recent Cosmos-Iridium collision. This framework is based on a flexible, scalable architecture to enable efficient simulation of the current SSA enterprise, and to accommodate future advancements in SSA systems. In particular, the code is designed to take advantage of massively parallel, high-performance computer systems available, for example, at Lawrence Livermore National Laboratory. We will describe the application of this framework to the recent collision of the Cosmos and Iridium satellites, including (1) detailed hydrodynamic modeling of the satellitemore » collision and resulting debris generation, (2) orbital propagation of the simulated debris and analysis of the increased risk to other satellites (3) calculation of the radar and optical signatures of the simulated debris and modeling of debris detection with space surveillance radar and optical systems (4) determination of simulated debris orbits from modeled space surveillance observations and analysis of the resulting orbital accuracy, (5) comparison of these modeling and simulation results with Space Surveillance Network observations. We will also discuss the use of this integrated modeling and simulation framework to analyze the risks and consequences of future satellite collisions and to assess strategies for mitigating or avoiding future incidents, including the addition of new sensor systems, used in conjunction with the Space Surveillance Network, for improving space situational awareness.« less

The Spatial Coding Strategies of One-Year-Old Infants in a Locomotor Search Task.

ERIC Educational Resources Information Center

Bushnell, Emily W.; And Others

1995-01-01

Examined the ability of 1-year olds to remember the location of nonvisible targets. Found that infants were able to associate a nonvisible target with a direct landmark and to code its distance and direction with respect to themselves or the larger framework. Difficulty of coding with indirect landmarks was associated with cognitive complexity and…

Codes of professional conduct for Australian Defence Force military physicians: evenomating the serpent?

PubMed

O'Connor, Mike

2010-09-01

The scandal of health professionals' involvement in recent human rights abuses in United States military detention centres has prompted concern that Australian military physicians should be well protected against similar pressures to participate in harsh interrogations. A framework of military health ethics has been proposed. Would a code of professional conduct be a partial solution? This article examines the utility of professional codes: can they transform unethical behaviour or are they only of value to those who already behave ethically? How should such codes be designed, what support mechanisms should be in place and how should complaints be managed? A key recommendation is that codes of professional conduct should be accompanied by publicly transparent procedures for the investigation of serious infractions and appropriate disciplinary action when proven. The training of military physicians should also aim to develop a sound understanding of both humanitarian and human rights law. At present, both civil and military education of physicians generally lacks any component of human rights law. The Australian Defence Force (ADF) seems well placed to add codes of professional conduct to its existing ethical framework because of strong support at the highest executive levels.

Porting plasma physics simulation codes to modern computing architectures using the libmrc framework

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Abbott, Stephen

2015-11-01

Available computing power has continued to grow exponentially even after single-core performance satured in the last decade. The increase has since been driven by more parallelism, both using more cores and having more parallelism in each core, e.g. in GPUs and Intel Xeon Phi. Adapting existing plasma physics codes is challenging, in particular as there is no single programming model that covers current and future architectures. We will introduce the open-source libmrc framework that has been used to modularize and port three plasma physics codes: The extended MHD code MRCv3 with implicit time integration and curvilinear grids; the OpenGGCM global magnetosphere model; and the particle-in-cell code PSC. libmrc consolidates basic functionality needed for simulations based on structured grids (I/O, load balancing, time integrators), and also introduces a parallel object model that makes it possible to maintain multiple implementations of computational kernels, on e.g. conventional processors and GPUs. It handles data layout conversions and enables us to port performance-critical parts of a code to a new architecture step-by-step, while the rest of the code can remain unchanged. We will show examples of the performance gains and some physics applications.

Adaptive EAGLE dynamic solution adaptation and grid quality enhancement

NASA Technical Reports Server (NTRS)

Luong, Phu Vinh; Thompson, J. F.; Gatlin, B.; Mastin, C. W.; Kim, H. J.

1992-01-01

In the effort described here, the elliptic grid generation procedure in the EAGLE grid code was separated from the main code into a subroutine, and a new subroutine which evaluates several grid quality measures at each grid point was added. The elliptic grid routine can now be called, either by a computational fluid dynamics (CFD) code to generate a new adaptive grid based on flow variables and quality measures through multiple adaptation, or by the EAGLE main code to generate a grid based on quality measure variables through static adaptation. Arrays of flow variables can be read into the EAGLE grid code for use in static adaptation as well. These major changes in the EAGLE adaptive grid system make it easier to convert any CFD code that operates on a block-structured grid (or single-block grid) into a multiple adaptive code.

Scalable geocomputation: evolving an environmental model building platform from single-core to supercomputers

NASA Astrophysics Data System (ADS)

Schmitz, Oliver; de Jong, Kor; Karssenberg, Derek

2017-04-01

There is an increasing demand to run environmental models on a big scale: simulations over large areas at high resolution. The heterogeneity of available computing hardware such as multi-core CPUs, GPUs or supercomputer potentially provides significant computing power to fulfil this demand. However, this requires detailed knowledge of the underlying hardware, parallel algorithm design and the implementation thereof in an efficient system programming language. Domain scientists such as hydrologists or ecologists often lack this specific software engineering knowledge, their emphasis is (and should be) on exploratory building and analysis of simulation models. As a result, models constructed by domain specialists mostly do not take full advantage of the available hardware. A promising solution is to separate the model building activity from software engineering by offering domain specialists a model building framework with pre-programmed building blocks that they combine to construct a model. The model building framework, consequently, needs to have built-in capabilities to make full usage of the available hardware. Developing such a framework providing understandable code for domain scientists and being runtime efficient at the same time poses several challenges on developers of such a framework. For example, optimisations can be performed on individual operations or the whole model, or tasks need to be generated for a well-balanced execution without explicitly knowing the complexity of the domain problem provided by the modeller. Ideally, a modelling framework supports the optimal use of available hardware whichsoever combination of model building blocks scientists use. We demonstrate our ongoing work on developing parallel algorithms for spatio-temporal modelling and demonstrate 1) PCRaster, an environmental software framework (http://www.pcraster.eu) providing spatio-temporal model building blocks and 2) parallelisation of about 50 of these building blocks using the new Fern library (https://github.com/geoneric/fern/), an independent generic raster processing library. Fern is a highly generic software library and its algorithms can be configured according to the configuration of a modelling framework. With manageable programming effort (e.g. matching data types between programming and domain language) we created a binding between Fern and PCRaster. The resulting PCRaster Python multicore module can be used to execute existing PCRaster models without having to make any changes to the model code. We show initial results on synthetic and geoscientific models indicating significant runtime improvements provided by parallel local and focal operations. We further outline challenges in improving remaining algorithms such as flow operations over digital elevation maps and further potential improvements like enhancing disk I/O.

TerraFERMA: Harnessing Advanced Computational Libraries in Earth Science

NASA Astrophysics Data System (ADS)

Wilson, C. R.; Spiegelman, M.; van Keken, P.

2012-12-01

Many important problems in Earth sciences can be described by non-linear coupled systems of partial differential equations. These "multi-physics" problems include thermo-chemical convection in Earth and planetary interiors, interactions of fluids and magmas with the Earth's mantle and crust and coupled flow of water and ice. These problems are of interest to a large community of researchers but are complicated to model and understand. Much of this complexity stems from the nature of multi-physics where small changes in the coupling between variables or constitutive relations can lead to radical changes in behavior, which in turn affect critical computational choices such as discretizations, solvers and preconditioners. To make progress in understanding such coupled systems requires a computational framework where multi-physics problems can be described at a high-level while maintaining the flexibility to easily modify the solution algorithm. Fortunately, recent advances in computational science provide a basis for implementing such a framework. Here we present the Transparent Finite Element Rapid Model Assembler (TerraFERMA), which leverages several advanced open-source libraries for core functionality. FEniCS (fenicsproject.org) provides a high level language for describing the weak forms of coupled systems of equations, and an automatic code generator that produces finite element assembly code. PETSc (www.mcs.anl.gov/petsc) provides a wide range of scalable linear and non-linear solvers that can be composed into effective multi-physics preconditioners. SPuD (amcg.ese.ic.ac.uk/Spud) is an application neutral options system that provides both human and machine-readable interfaces based on a single xml schema. Our software integrates these libraries and provides the user with a framework for exploring multi-physics problems. A single options file fully describes the problem, including all equations, coefficients and solver options. Custom compiled applications are generated from this file but share an infrastructure for services common to all models, e.g. diagnostics, checkpointing and global non-linear convergence monitoring. This maximizes code reusability, reliability and longevity ensuring that scientific results and the methods used to acquire them are transparent and reproducible. TerraFERMA has been tested against many published geodynamic benchmarks including 2D/3D thermal convection problems, the subduction zone benchmarks and benchmarks for magmatic solitary waves. It is currently being used in the investigation of reactive cracking phenomena with applications to carbon sequestration, but we will principally discuss its use in modeling the migration of fluids in subduction zones. Subduction zones require an understanding of the highly nonlinear interactions of fluids with solids and thus provide an excellent scientific driver for the development of multi-physics software.

Simultaneous Semi-Distributed Model Calibration Guided by ...

EPA Pesticide Factsheets

Modelling approaches to transfer hydrologically-relevant information from locations with streamflow measurements to locations without such measurements continues to be an active field of research for hydrologists. The Pacific Northwest Hydrologic Landscapes (PNW HL) provide a solid conceptual classification framework based on our understanding of dominant processes. A Hydrologic Landscape code (5 letter descriptor based on physical and climatic properties) describes each assessment unit area, and these units average area 60km2. The core function of these HL codes is to relate and transfer hydrologically meaningful information between watersheds without the need for streamflow time series. We present a novel approach based on the HL framework to answer the question “How can we calibrate models across separate watersheds simultaneously, guided by our understanding of dominant processes?“. We should be able to apply the same parameterizations to assessment units of common HL codes if 1) the Hydrologic Landscapes contain hydrologic information transferable between watersheds at a sub-watershed-scale and 2) we use a conceptual hydrologic model and parameters that reflect the hydrologic behavior of a watershed. In this study, This work specifically tests the ability or inability to use HL-codes to inform and share model parameters across watersheds in the Pacific Northwest. EPA’s Western Ecology Division has published and is refining a framework for defining la

Toward enhancing the distributed video coder under a multiview video codec framework

NASA Astrophysics Data System (ADS)

Lee, Shih-Chieh; Chen, Jiann-Jone; Tsai, Yao-Hong; Chen, Chin-Hua

2016-11-01

The advance of video coding technology enables multiview video (MVV) or three-dimensional television (3-D TV) display for users with or without glasses. For mobile devices or wireless applications, a distributed video coder (DVC) can be utilized to shift the encoder complexity to decoder under the MVV coding framework, denoted as multiview distributed video coding (MDVC). We proposed to exploit both inter- and intraview video correlations to enhance side information (SI) and improve the MDVC performance: (1) based on the multiview motion estimation (MVME) framework, a categorized block matching prediction with fidelity weights (COMPETE) was proposed to yield a high quality SI frame for better DVC reconstructed images. (2) The block transform coefficient properties, i.e., DCs and ACs, were exploited to design the priority rate control for the turbo code, such that the DVC decoding can be carried out with fewest parity bits. In comparison, the proposed COMPETE method demonstrated lower time complexity, while presenting better reconstructed video quality. Simulations show that the proposed COMPETE can reduce the time complexity of MVME to 1.29 to 2.56 times smaller, as compared to previous hybrid MVME methods, while the image peak signal to noise ratios (PSNRs) of a decoded video can be improved 0.2 to 3.5 dB, as compared to H.264/AVC intracoding.

Adding kinetics and hydrodynamics to the CHEETAH thermochemical code

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

Fried, L.E., Howard, W.M., Souers, P.C.

1997-01-15

In FY96 we released CHEETAH 1.40, which made extensive improvements on the stability and user friendliness of the code. CHEETAH now has over 175 users in government, academia, and industry. Efforts have also been focused on adding new advanced features to CHEETAH 2.0, which is scheduled for release in FY97. We have added a new chemical kinetics capability to CHEETAH. In the past, CHEETAH assumed complete thermodynamic equilibrium and independence of time. The addition of a chemical kinetic framework will allow for modeling of time-dependent phenomena, such as partial combustion and detonation in composite explosives with large reaction zones. Wemore » have implemented a Wood-Kirkwood detonation framework in CHEETAH, which allows for the treatment of nonideal detonations and explosive failure. A second major effort in the project this year has been linking CHEETAH to hydrodynamic codes to yield an improved HE product equation of state. We have linked CHEETAH to 1- and 2-D hydrodynamic codes, and have compared the code to experimental data. 15 refs., 13 figs., 1 tab.« less

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; O'Nualláin, Breanndán; Heggie, Douglas; Lombardi, James; Hut, Piet; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Fuji, Michiko; Gaburov, Evghenii; Glebbeek, Evert; Groen, Derek; Harfst, Stefan; Izzard, Rob; Jurić, Mario; Justham, Stephen; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

We present MUSE, a software framework for tying together existing computational tools for different astrophysical domains into a single multiphysics, multiscale workload. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for a generalized stellar systems workload. MUSE has now reached a "Noah's Ark" milestone, with two available numerical solvers for each domain. MUSE can treat small stellar associations, galaxies and everything in between, including planetary systems, dense stellar clusters and galactic nuclei. Here we demonstrate an examples calculated with MUSE: the merger of two galaxies. In addition we demonstrate the working of MUSE on a distributed computer. The current MUSE code base is publicly available as open source at http://muse.li.

A Secure Information Framework with APRQ Properties

NASA Astrophysics Data System (ADS)

Rupa, Ch.

2017-08-01

Internet of the things is the most trending topics in the digital world. Security issues are rampant. In the corporate or institutional setting, security risks are apparent from the outset. Market leaders are unable to use the cryptographic techniques due to their complexities. Hence many bits of private information, including ID, are readily available for third parties to see and to utilize. There is a need to decrease the complexity and increase the robustness of the cryptographic approaches. In view of this, a new cryptographic technique as good encryption pact with adjacency, random prime number and quantum code properties has been proposed. Here, encryption can be done by using quantum photons with gray code. This approach uses the concepts of physics and mathematics with no external key exchange to improve the security of the data. It also reduces the key attacks by generation of a key at the party side instead of sharing. This method makes the security more robust than with the existing approach. Important properties of gray code and quantum are adjacency property and different photons to a single bit (0 or 1). These can reduce the avalanche effect. Cryptanalysis of the proposed method shows that it is resistant to various attacks and stronger than the existing approaches.

Data Analysis Approaches for the Risk-Informed Safety Margins Characterization Toolkit

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

Mandelli, Diego; Alfonsi, Andrea; Maljovec, Daniel P.

2016-09-01

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, RELAP-7, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually calledmore » Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, “extracting information” means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework.« less

Mapping the polysaccharide degradation potential of Aspergillus niger

PubMed Central

2012-01-01

Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger. PMID:22799883

Mapping the polysaccharide degradation potential of Aspergillus niger.

PubMed

Andersen, Mikael R; Giese, Malene; de Vries, Ronald P; Nielsen, Jens

2012-07-16

The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.

Using Python to generate AHPS-based precipitation simulations over CONUS using Amazon distributed computing

NASA Astrophysics Data System (ADS)

Machalek, P.; Kim, S. M.; Berry, R. D.; Liang, A.; Small, T.; Brevdo, E.; Kuznetsova, A.

2012-12-01

We describe how the Climate Corporation uses Python and Clojure, a language impleneted on top of Java, to generate climatological forecasts for precipitation based on the Advanced Hydrologic Prediction Service (AHPS) radar based daily precipitation measurements. A 2-year-long forecasts is generated on each of the ~650,000 CONUS land based 4-km AHPS grids by constructing 10,000 ensembles sampled from a 30-year reconstructed AHPS history for each grid. The spatial and temporal correlations between neighboring AHPS grids and the sampling of the analogues are handled by Python. The parallelization for all the 650,000 CONUS stations is further achieved by utilizing the MAP-REDUCE framework (http://code.google.com/edu/parallel/mapreduce-tutorial.html). Each full scale computational run requires hundreds of nodes with up to 8 processors each on the Amazon Elastic MapReduce (http://aws.amazon.com/elasticmapreduce/) distributed computing service resulting in 3 terabyte datasets. We further describe how we have productionalized a monthly run of the simulations process at full scale of the 4km AHPS grids and how the resultant terabyte sized datasets are handled.

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

PubMed

Chiba, Hirokazu; Uchiyama, Ikuo

2017-02-08

Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data. SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

On the decoding process in ternary error-correcting output codes.

PubMed

Escalera, Sergio; Pujol, Oriol; Radeva, Petia

2010-01-01

A common way to model multiclass classification problems is to design a set of binary classifiers and to combine them. Error-Correcting Output Codes (ECOC) represent a successful framework to deal with these type of problems. Recent works in the ECOC framework showed significant performance improvements by means of new problem-dependent designs based on the ternary ECOC framework. The ternary framework contains a larger set of binary problems because of the use of a "do not care" symbol that allows us to ignore some classes by a given classifier. However, there are no proper studies that analyze the effect of the new symbol at the decoding step. In this paper, we present a taxonomy that embeds all binary and ternary ECOC decoding strategies into four groups. We show that the zero symbol introduces two kinds of biases that require redefinition of the decoding design. A new type of decoding measure is proposed, and two novel decoding strategies are defined. We evaluate the state-of-the-art coding and decoding strategies over a set of UCI Machine Learning Repository data sets and into a real traffic sign categorization problem. The experimental results show that, following the new decoding strategies, the performance of the ECOC design is significantly improved.

Analysis of steam generator loss-of-feedwater experiments with APROS and RELAP5/MOD3.1 computer codes

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

Virtanen, E.; Haapalehto, T.; Kouhia, J.

1995-09-01

Three experiments were conducted to study the behavior of the new horizontal steam generator construction of the PACTEL test facility. In the experiments the secondary side coolant level was reduced stepwise. The experiments were calculated with two computer codes RELAP5/MOD3.1 and APROS version 2.11. A similar nodalization scheme was used for both codes to that the results may be compared. Only the steam generator was modelled and the rest of the facility was given as a boundary condition. The results show that both codes calculate well the behaviour of the primary side of the steam generator. On the secondary sidemore » both codes calculate lower steam temperatures in the upper part of the heat exchange tube bundle than was measured in the experiments.« less

Modelling Conditions and Health Care Processes in Electronic Health Records: An Application to Severe Mental Illness with the Clinical Practice Research Datalink

PubMed Central

Olier, Ivan; Springate, David A.; Ashcroft, Darren M.; Doran, Tim; Reeves, David; Planner, Claire; Reilly, Siobhan; Kontopantelis, Evangelos

2016-01-01

Background The use of Electronic Health Records databases for medical research has become mainstream. In the UK, increasing use of Primary Care Databases is largely driven by almost complete computerisation and uniform standards within the National Health Service. Electronic Health Records research often begins with the development of a list of clinical codes with which to identify cases with a specific condition. We present a methodology and accompanying Stata and R commands (pcdsearch/Rpcdsearch) to help researchers in this task. We present severe mental illness as an example. Methods We used the Clinical Practice Research Datalink, a UK Primary Care Database in which clinical information is largely organised using Read codes, a hierarchical clinical coding system. Pcdsearch is used to identify potentially relevant clinical codes and/or product codes from word-stubs and code-stubs suggested by clinicians. The returned code-lists are reviewed and codes relevant to the condition of interest are selected. The final code-list is then used to identify patients. Results We identified 270 Read codes linked to SMI and used them to identify cases in the database. We observed that our approach identified cases that would have been missed with a simpler approach using SMI registers defined within the UK Quality and Outcomes Framework. Conclusion We described a framework for researchers of Electronic Health Records databases, for identifying patients with a particular condition or matching certain clinical criteria. The method is invariant to coding system or database and can be used with SNOMED CT, ICD or other medical classification code-lists. PMID:26918439

RIO: a new computational framework for accurate initial data of binary black holes

NASA Astrophysics Data System (ADS)

Barreto, W.; Clemente, P. C. M.; de Oliveira, H. P.; Rodriguez-Mueller, B.

2018-06-01

We present a computational framework ( Rio) in the ADM 3+1 approach for numerical relativity. This work enables us to carry out high resolution calculations for initial data of two arbitrary black holes. We use the transverse conformal treatment, the Bowen-York and the puncture methods. For the numerical solution of the Hamiltonian constraint we use the domain decomposition and the spectral decomposition of Galerkin-Collocation. The nonlinear numerical code solves the set of equations for the spectral modes using the standard Newton-Raphson method, LU decomposition and Gaussian quadratures. We show the convergence of the Rio code. This code allows for easy deployment of large calculations. We show how the spin of one of the black holes is manifest in the conformal factor.

Statistical Analysis of CFD Solutions from the Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Hemsch, Michael J.

2002-01-01

A simple, graphical framework is presented for robust statistical evaluation of results obtained from N-Version testing of a series of RANS CFD codes. The solutions were obtained by a variety of code developers and users for the June 2001 Drag Prediction Workshop sponsored by the AIAA Applied Aerodynamics Technical Committee. The aerodynamic configuration used for the computational tests is the DLR-F4 wing-body combination previously tested in several European wind tunnels and for which a previous N-Version test had been conducted. The statistical framework is used to evaluate code results for (1) a single cruise design point, (2) drag polars and (3) drag rise. The paper concludes with a discussion of the meaning of the results, especially with respect to predictability, Validation, and reporting of solutions.

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

IGB grid: User's manual (A turbomachinery grid generation code)

NASA Technical Reports Server (NTRS)

Beach, T. A.; Hoffman, G.

1992-01-01

A grid generation code called IGB is presented for use in computational investigations of turbomachinery flowfields. It contains a combination of algebraic and elliptic techniques coded for use on an interactive graphics workstation. The instructions for use and a test case are included.

TIGER: Turbomachinery interactive grid generation

NASA Technical Reports Server (NTRS)

Soni, Bharat K.; Shih, Ming-Hsin; Janus, J. Mark

1992-01-01

A three dimensional, interactive grid generation code, TIGER, is being developed for analysis of flows around ducted or unducted propellers. TIGER is a customized grid generator that combines new technology with methods from general grid generation codes. The code generates multiple block, structured grids around multiple blade rows with a hub and shroud for either C grid or H grid topologies. The code is intended for use with a Euler/Navier-Stokes solver also being developed, but is general enough for use with other flow solvers. TIGER features a silicon graphics interactive graphics environment that displays a pop-up window, graphics window, and text window. The geometry is read as a discrete set of points with options for several industrial standard formats and NASA standard formats. Various splines are available for defining the surface geometries. Grid generation is done either interactively or through a batch mode operation using history files from a previously generated grid. The batch mode operation can be done either with a graphical display of the interactive session or with no graphics so that the code can be run on another computer system. Run time can be significantly reduced by running on a Cray-YMP.

Why do you fear the bogeyman? An embodied predictive coding model of perceptual inference.

PubMed

Pezzulo, Giovanni

2014-09-01

Why are we scared by nonperceptual entities such as the bogeyman, and why does the bogeyman only visit us during the night? Why does hearing a window squeaking in the night suggest to us the unlikely idea of a thief or a killer? And why is this more likely to happen after watching a horror movie? To answer these and similar questions, we need to put mind and body together again and consider the embodied nature of perceptual and cognitive inference. Predictive coding provides a general framework for perceptual inference; I propose to extend it by including interoceptive and bodily information. The resulting embodied predictive coding inference permits one to compare alternative hypotheses (e.g., is the sound I hear generated by a thief or the wind?) using the same inferential scheme as in predictive coding, but using both sensory and interoceptive information as evidence, rather than just considering sensory events. If you hear a window squeaking in the night after watching a horror movie, you may consider plausible a very unlikely hypothesis (e.g., a thief, or even the bogeyman) because it explains both what you sense (e.g., the window squeaking in the night) and how you feel (e.g., your high heart rate). The good news is that the inference that I propose is fully rational and gives minds and bodies equal dignity. The bad news is that it also gives an embodiment to the bogeyman, and a reason to fear it.

Field-scale multi-phase LNAPL remediation: Validating a new computational framework against sequential field pilot trials.

PubMed

Sookhak Lari, Kaveh; Johnston, Colin D; Rayner, John L; Davis, Greg B

2018-03-05

Remediation of subsurface systems, including groundwater, soil and soil gas, contaminated with light non-aqueous phase liquids (LNAPLs) is challenging. Field-scale pilot trials of multi-phase remediation were undertaken at a site to determine the effectiveness of recovery options. Sequential LNAPL skimming and vacuum-enhanced skimming, with and without water table drawdown were trialled over 78days; in total extracting over 5m 3 of LNAPL. For the first time, a multi-component simulation framework (including the multi-phase multi-component code TMVOC-MP and processing codes) was developed and applied to simulate the broad range of multi-phase remediation and recovery methods used in the field trials. This framework was validated against the sequential pilot trials by comparing predicted and measured LNAPL mass removal rates and compositional changes. The framework was tested on both a Cray supercomputer and a cluster. Simulations mimicked trends in LNAPL recovery rates (from 0.14 to 3mL/s) across all remediation techniques each operating over periods of 4-14days over the 78day trial. The code also approximated order of magnitude compositional changes of hazardous chemical concentrations in extracted gas during vacuum-enhanced recovery. The verified framework enables longer term prediction of the effectiveness of remediation approaches allowing better determination of remediation endpoints and long-term risks. Copyright © 2017 Commonwealth Scientific and Industrial Research Organisation. Published by Elsevier B.V. All rights reserved.

Adapting an existing visualization application for browser-based deployment: A case study from the Tropical Rainfall Measuring Mission

NASA Astrophysics Data System (ADS)

Kelley, Owen A.

2013-02-01

THOR, the Tool for High-resolution Observation Review, is a data viewer for the Tropical Rainfall Measuring Mission (TRMM) and the upcoming Global Precipitation Measurement (GPM) mission. THOR began as a desktop application, but now it can be accessed with a web browser, making THOR one of the first online tools for visualizing TRMM satellite data (http://pps.gsfc.nasa.gov/thor). In this effort, the reuse of the existing visualization code was maximized and the complexity of new code was minimized by avoiding unnecessary functionality, frameworks, or libraries. The simplicity of this approach makes it potentially attractive to researchers wishing to adapt their visualization applications for online deployment. To enable THOR to run within a web browser, three new pieces of code are written. First, the graphical user interface (GUI) of the desktop application is translated into HTML, JavaScript, and CSS. Second, a simple communication mechanism is developed over HTTP. Third, a virtual GUI is created on the server that interfaces with the image-generating routines of the existing desktop application so that these routines do not need to be modified for online use. While the basic functionality of THOR is now available online, prototyping is ongoing for enhanced 3D imaging and other aspects of both THOR Desktop and THOR Online. Because TRMM data products are complex and periodically reprocessed with improved algorithms, having a tool such as THOR is important to analysts at the Precipitation Processing System where the algorithms are tested and the products generated, stored, and distributed. Researchers also have found THOR useful for taking a first look at individual files before writing their own software to perform specialized calculations and analyses.

Generalized Background Error covariance matrix model (GEN_BE v2.0)

NASA Astrophysics Data System (ADS)

Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.

2014-07-01

The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model to allow for a simpler, flexible, robust, and community-oriented framework that gathers methods used by meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks and showing some of the new features on data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to involve new control variables. While the generation of the background errors statistics code has been first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily extended to other domains of science and be chosen as a testbed for diagnostic and new modeling of B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

Generalized background error covariance matrix model (GEN_BE v2.0)

NASA Astrophysics Data System (ADS)

Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.; Barré, J.

2015-03-01

The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model. GEN_BE allows for a simpler, flexible, robust, and community-oriented framework that gathers methods used by some meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks of different modeling of B and showing some of the new features in data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to implement new control variables. While the generation of the background errors statistics code was first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily applied to other domains of science and chosen to diagnose and model B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

Space-time adaptive solution of inverse problems with the discrete adjoint method

NASA Astrophysics Data System (ADS)

Alexe, Mihai; Sandu, Adrian

2014-08-01

This paper develops a framework for the construction and analysis of discrete adjoint sensitivities in the context of time dependent, adaptive grid, adaptive step models. Discrete adjoints are attractive in practice since they can be generated with low effort using automatic differentiation. However, this approach brings several important challenges. The space-time adjoint of the forward numerical scheme may be inconsistent with the continuous adjoint equations. A reduction in accuracy of the discrete adjoint sensitivities may appear due to the inter-grid transfer operators. Moreover, the optimization algorithm may need to accommodate state and gradient vectors whose dimensions change between iterations. This work shows that several of these potential issues can be avoided through a multi-level optimization strategy using discontinuous Galerkin (DG) hp-adaptive discretizations paired with Runge-Kutta (RK) time integration. We extend the concept of dual (adjoint) consistency to space-time RK-DG discretizations, which are then shown to be well suited for the adaptive solution of time-dependent inverse problems. Furthermore, we prove that DG mesh transfer operators on general meshes are also dual consistent. This allows the simultaneous derivation of the discrete adjoint for both the numerical solver and the mesh transfer logic with an automatic code generation mechanism such as algorithmic differentiation (AD), potentially speeding up development of large-scale simulation codes. The theoretical analysis is supported by numerical results reported for a two-dimensional non-stationary inverse problem.

MTpy: A Python toolbox for magnetotellurics

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared R.

2014-11-01

We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

Contribution of large scale coherence to wind turbine power: A large eddy simulation study in periodic wind farms

NASA Astrophysics Data System (ADS)

Chatterjee, Tanmoy; Peet, Yulia T.

2018-03-01

Length scales of eddies involved in the power generation of infinite wind farms are studied by analyzing the spectra of the turbulent flux of mean kinetic energy (MKE) from large eddy simulations (LES). Large-scale structures with an order of magnitude bigger than the turbine rotor diameter (D ) are shown to have substantial contribution to wind power. Varying dynamics in the intermediate scales (D -10 D ) are also observed from a parametric study involving interturbine distances and hub height of the turbines. Further insight about the eddies responsible for the power generation have been provided from the scaling analysis of two-dimensional premultiplied spectra of MKE flux. The LES code is developed in a high Reynolds number near-wall modeling framework, using an open-source spectral element code Nek5000, and the wind turbines have been modelled using a state-of-the-art actuator line model. The LES of infinite wind farms have been validated against the statistical results from the previous literature. The study is expected to improve our understanding of the complex multiscale dynamics in the domain of large wind farms and identify the length scales that contribute to the power. This information can be useful for design of wind farm layout and turbine placement that take advantage of the large-scale structures contributing to wind turbine power.

An intergenerational study of perceptions of changes in active free play among families from rural areas of Western Canada.

PubMed

Holt, Nicholas L; Neely, Kacey C; Spence, John C; Carson, Valerie; Pynn, Shannon R; Boyd, Kassi A; Ingstrup, Meghan; Robinson, Zac

2016-08-19

Children's engagement in active free play has declined across recent generations. Therefore, the purpose of this study was to examine perceptions of intergenerational changes in active free play among families from rural areas. We addressed two research questions: (1) How has active free play changed across three generations? (2) What suggestions do participants have for reviving active free play? Data were collected via 49 individual interviews with members of 16 families (15 grandparents, 16 parents, and 18 children) residing in rural areas/small towns in the Province of Alberta (Canada). Interview recordings were transcribed verbatim and subjected to thematic analysis guided by an ecological framework of active free play. Factors that depicted the changing nature of active free play were coded in the themes of less imagination/more technology, safety concerns, surveillance, other children to play with, purposeful physical activity, play spaces/organized activities, and the good parenting ideal. Suggestions for reviving active free play were coded in the themes of enhance facilities to keep kids entertained, provide more opportunities for supervised play, create more community events, and decrease use of technology. These results reinforce the need to consider multiple levels of social ecology in the study of active free play, and highlight the importance of community-based initiatives to revive active free play in ways that are consistent with contemporary notions of good parenting.

Construction of optimal resources for concatenated quantum protocols

NASA Astrophysics Data System (ADS)

Pirker, A.; Wallnöfer, J.; Briegel, H. J.; Dür, W.

2017-06-01

We consider the explicit construction of resource states for measurement-based quantum information processing. We concentrate on special-purpose resource states that are capable to perform a certain operation or task, where we consider unitary Clifford circuits as well as non-trace-preserving completely positive maps, more specifically probabilistic operations including Clifford operations and Pauli measurements. We concentrate on 1 →m and m →1 operations, i.e., operations that map one input qubit to m output qubits or vice versa. Examples of such operations include encoding and decoding in quantum error correction, entanglement purification, or entanglement swapping. We provide a general framework to construct optimal resource states for complex tasks that are combinations of these elementary building blocks. All resource states only contain input and output qubits, and are hence of minimal size. We obtain a stabilizer description of the resulting resource states, which we also translate into a circuit pattern to experimentally generate these states. In particular, we derive recurrence relations at the level of stabilizers as key analytical tool to generate explicit (graph) descriptions of families of resource states. This allows us to explicitly construct resource states for encoding, decoding, and syndrome readout for concatenated quantum error correction codes, code switchers, multiple rounds of entanglement purification, quantum repeaters, and combinations thereof (such as resource states for entanglement purification of encoded states).

A concatenated coding scheme for error control

NASA Technical Reports Server (NTRS)

Lin, S.

1985-01-01

A concatenated coding scheme for error control in data communications is analyzed. The inner code is used for both error correction and detection, however the outer code is used only for error detection. A retransmission is requested if the outer code detects the presence of errors after the inner code decoding. The probability of undetected error of the above error control scheme is derived and upper bounded. Two specific exmaples are analyzed. In the first example, the inner code is a distance-4 shortened Hamming code with generator polynomial (X+1)(X(6)+X+1) = X(7)+X(6)+X(2)+1 and the outer code is a distance-4 shortened Hamming code with generator polynomial (X+1)X(15+X(14)+X(13)+X(12)+X(4)+X(3)+X(2)+X+1) = X(16)+X(12)+X(5)+1 which is the X.25 standard for packet-switched data network. This example is proposed for error control on NASA telecommand links. In the second example, the inner code is the same as that in the first example but the outer code is a shortened Reed-Solomon code with symbols from GF(2(8)) and generator polynomial (X+1)(X+alpha) where alpha is a primitive element in GF(z(8)).

Fractal-Based Image Compression

DTIC Science & Technology

1989-09-01

6. A Mercedes Benz symbol generated using an IFS code ................. 21 7. (a) U-A fern and (b) A-0 fern generated with RIFS codes...22 8. Construction of the Mercedes - Benz symbol using RIFS ................ 23 9. The regenerated perfect image of the Mercedes - Benz symbol using R IF...quite often, it cannot be done with a reasonable number of transforms. As an example, the Mercedes Benz symbol generated using an IFS code is illustrated

Model-Driven Engineering: Automatic Code Generation and Beyond

DTIC Science & Technology

2015-03-01

and Weblogic as well as cloud environments such as Mi- crosoft Azure and Amazon Web Services®. Finally, while the generated code has dependencies on...code generation in the context of the full system lifecycle from development to sustainment. Acquisition programs in govern- ment or large commercial...Acquirers are concerned with the full system lifecycle, and they need confidence that the development methods will enable the system to meet the functional

Performance and accuracy of criticality calculations performed using WARP – A framework for continuous energy Monte Carlo neutron transport in general 3D geometries on GPUs

DOE PAGES

Bergmann, Ryan M.; Rowland, Kelly L.; Radnović, Nikola; ...

2017-05-01

In this companion paper to "Algorithmic Choices in WARP - A Framework for Continuous Energy Monte Carlo Neutron Transport in General 3D Geometries on GPUs" (doi:10.1016/j.anucene.2014.10.039), the WARP Monte Carlo neutron transport framework for graphics processing units (GPUs) is benchmarked against production-level central processing unit (CPU) Monte Carlo neutron transport codes for both performance and accuracy. We compare neutron flux spectra, multiplication factors, runtimes, speedup factors, and costs of various GPU and CPU platforms running either WARP, Serpent 2.1.24, or MCNP 6.1. WARP compares well with the results of the production-level codes, and it is shown that on the newestmore » hardware considered, GPU platforms running WARP are between 0.8 to 7.6 times as fast as CPU platforms running production codes. Also, the GPU platforms running WARP were between 15% and 50% as expensive to purchase and between 80% to 90% as expensive to operate as equivalent CPU platforms performing at an equal simulation rate.« less

Performance and accuracy of criticality calculations performed using WARP – A framework for continuous energy Monte Carlo neutron transport in general 3D geometries on GPUs

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

Bergmann, Ryan M.; Rowland, Kelly L.; Radnović, Nikola

In this companion paper to "Algorithmic Choices in WARP - A Framework for Continuous Energy Monte Carlo Neutron Transport in General 3D Geometries on GPUs" (doi:10.1016/j.anucene.2014.10.039), the WARP Monte Carlo neutron transport framework for graphics processing units (GPUs) is benchmarked against production-level central processing unit (CPU) Monte Carlo neutron transport codes for both performance and accuracy. We compare neutron flux spectra, multiplication factors, runtimes, speedup factors, and costs of various GPU and CPU platforms running either WARP, Serpent 2.1.24, or MCNP 6.1. WARP compares well with the results of the production-level codes, and it is shown that on the newestmore » hardware considered, GPU platforms running WARP are between 0.8 to 7.6 times as fast as CPU platforms running production codes. Also, the GPU platforms running WARP were between 15% and 50% as expensive to purchase and between 80% to 90% as expensive to operate as equivalent CPU platforms performing at an equal simulation rate.« less

A Subband Coding Method for HDTV

NASA Technical Reports Server (NTRS)

Chung, Wilson; Kossentini, Faouzi; Smith, Mark J. T.

1995-01-01

This paper introduces a new HDTV coder based on motion compensation, subband coding, and high order conditional entropy coding. The proposed coder exploits the temporal and spatial statistical dependencies inherent in the HDTV signal by using intra- and inter-subband conditioning for coding both the motion coordinates and the residual signal. The new framework provides an easy way to control the system complexity and performance, and inherently supports multiresolution transmission. Experimental results show that the coder outperforms MPEG-2, while still maintaining relatively low complexity.

The Nuremberg Code: its history and implications.

PubMed

Kious, B M

2001-01-01

The Nuremberg Code is a foundational document in the ethics of medical research and human experimentation; the principle its authors espoused in 1946 have provided the framework for modern codes that address the same issues, and have received little challenge and only slight modification in decades since. By analyzing the Code's tragic genesis and its normative implications, it is possible to understand some of the essence of modern experimental ethics, as well as certain outstanding controversies that still plague medical science.

Alfvénic wave packets collision in a kinetic plasma

NASA Astrophysics Data System (ADS)

Pezzi, Oreste; Parashar, Tulasi N.; Servidio, Sergio; Valentini, Francesco; Malara, Francesco; Matthaeus, William H.; Veltri, Pierluigi

2016-04-01

The problem of two colliding and counter-propagating Alfvénic wave packets has been investigated in detail since the late Seventies. In particular Moffatt [1] and Parker [2] showed that, in the framework of the incompressible magnetohydrodynamics (MHD), nonlinear interactions can develop only during the overlapping of the two packets. Here we describe a similar problem in the framework of the kinetic physics. The collision of two quasi-Alfvénic packets has been analyzed by means of MHD, Hall-MHD and kinetic simulations performed with two different hybrid codes: a PIC code [3] and a Vlasov-Maxwell code [4]. Due to the huge computational cost, only a 2D-3V phase space is allowed (two dimensions in the physical space, three dimensions in the velocity space). Preliminary results suggest that, as well as in the MHD case, the most relevant nonlinear effects occur during the overlapping of the two packets. For both the PIC and Vlasov cases, strong temperature anisotropies are present during the evolution of the wave packets. Moreover, due to the absence of numerical noise, Vlasov simulations show that the collision of the counter-propagating solitary waves produces a significant beam in the velocity distribution functions [5], which, instead, cannot be appreciated in PIC simulations. We remark that, beyond the interest of studying a well-known MHD problem in the realm of the kinetic physics, our results allows also to compare different numerical codes. [1] H.K. Moffatt, Field generation in electrically conducting fluids (Cambridge University Press, 1978). [2] E.N. Parker, Cosmical magnetic fields: their origin and their activity (Oxford University Press, 1979). [3] T.N. Parashar, M.A. Shay, P.A. Cassak and W.H. Matthaeus, Physics of Plasmas 16, 032310 (2009). [4] F. Valentini, P. Trávníček, F. Califano, P. Hellinger & A. Mangeney, Journal of Computational Physics 225, 753-770 (2007). [5] J. He, C. Tu, E. Marsch, C.H. Chen, L. Wang, Z. Pei, L. Zhang, C.S. Salem and S.D. Bale, The Astrophysical Journal Letters 813, L30 (2015).

Introducing Python tools for magnetotellurics: MTpy

NASA Astrophysics Data System (ADS)

Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

2013-12-01

Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South Australia. Workflow of MT data processing. Within the structural diagram, the MTpy sub-packages are shown in red (time series data processing), green (handling of EDI files and impedance tensor data), yellow (connection to modelling/inversion algorithms), black (impedance tensor interpretation, e.g. by Phase Tensor calculations), and blue (generation of visual representations, e.g pseudo sections or resistivity models).

Collisions of two Alfvénic wave packets in a kinetic plasma

NASA Astrophysics Data System (ADS)

Pezzi, O.; Servidio, S.; Valentini, F.; Parashar, T.; Malara, F.; Matthaeus, W. H.; Veltri, P.

2016-12-01

The problem of two colliding and counter-propagating Alfvénic wave packets has been investigated in detail since the late Seventies. In particular Moffatt [1] and Parker [2] showed that, in the framework of the incompressible magnetohydrodynamics (MHD), nonlinear interactions can develop only during the overlapping of the two packets. Here we describe a similar problem in the framework of the kinetic physics. The collision of two quasi-Alfvénic packets has been analyzed by means of MHD, Hall-MHD and kinetic simulations performed with two different hybrid codes: a PIC code [3] and a Vlasov-Maxwell code [4]. Due to the huge computational cost, only a 2D-3V phase space is allowed (two dimensions in the physical space, three dimensions in the velocity space). Preliminary results suggest that, as well as in the MHD case, the most relevant nonlinear effects occur during the overlapping of the two packets. For both the PIC and Vlasov cases, strong temperature anisotropies are present during the evolution of the wave packets. Moreover, due to the absence of numerical noise, Vlasov simulations show that the collision of the counter-propagating solitary waves produces a significant beam in the velocity distribution functions [5], which, instead, cannot be appreciated in PIC simulations. We remark that, beyond the interest of studying a well-known MHD problem in the realm of the kinetic physics, our results allows also to compare different numerical codes. [1] H.K. Moffatt, Field generation in electrically conducting fluids (Cambridge University Press, 1978). [2] E.N. Parker, Cosmical magnetic fields: their origin and their activity (Oxford University Press, 1979). [3] T.N. Parashar, M.A. Shay, P.A. Cassak and W.H. Matthaeus, Physics of Plasmas 16, 032310 (2009). [4] F. Valentini, P. Trávníček, F. Califano, P. Hellinger & A. Mangeney, Journal of Computational Physics 225, 753-770 (2007). [5] J. He, C. Tu, E. Marsch, C.H. Chen, L. Wang, Z. Pei, L. Zhang, C.S. Salem and S.D. Bale, The Astrophysical Journal Letters 813, L30 (2015).

Deductive Glue Code Synthesis for Embedded Software Systems Based on Code Patterns

NASA Technical Reports Server (NTRS)

Liu, Jian; Fu, Jicheng; Zhang, Yansheng; Bastani, Farokh; Yen, I-Ling; Tai, Ann; Chau, Savio N.

2006-01-01

Automated code synthesis is a constructive process that can be used to generate programs from specifications. It can, thus, greatly reduce the software development cost and time. The use of formal code synthesis approach for software generation further increases the dependability of the system. Though code synthesis has many potential benefits, the synthesis techniques are still limited. Meanwhile, components are widely used in embedded system development. Applying code synthesis to component based software development (CBSD) process can greatly enhance the capability of code synthesis while reducing the component composition efforts. In this paper, we discuss the issues and techniques for applying deductive code synthesis techniques to CBSD. For deductive synthesis in CBSD, a rule base is the key for inferring appropriate component composition. We use the code patterns to guide the development of rules. Code patterns have been proposed to capture the typical usages of the components. Several general composition operations have been identified to facilitate systematic composition. We present the technique for rule development and automated generation of new patterns from existing code patterns. A case study of using this method in building a real-time control system is also presented.

A Flexible Online Metadata Editing and Management System

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

Aguilar, Raul; Pan, Jerry Yun; Gries, Corinna

2010-01-01

A metadata editing and management system is being developed employing state of the art XML technologies. A modular and distributed design was chosen for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool or schema walker used to generate code for the actual online editor, a native XML database, and an online user access management application. The design tool is a Java Swing application that reads an XML schema, provides the designer with options to combine input fields into online forms and give the fieldsmore » user friendly tags. Based on design decisions, the tool generates code for the online metadata editor. The code generated is an implementation of the XForms standard using the Orbeon Framework. The design tool fulfills two requirements: First, data entry forms based on one schema may be customized at design time and second data entry applications may be generated for any valid XML schema without relying on custom information in the schema. However, the customized information generated at design time is saved in a configuration file which may be re-used and changed again in the design tool. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services. Additional styling of the finished editor is accomplished via cascading style sheets which may be further customized and different look-and-feels may be accumulated through the community process. The customized editor produces XML files in compliance with the original schema, however, data from the current page is saved into a native XML database whenever the user moves to the next screen or pushes the save button independently of validity. Currently the system uses the open source XML database eXist for storage and management, which comes with third party online and desktop management tools. However, access to metadata files in the application introduced here is managed in a custom online module, using a MySQL backend accessed by a simple Java Server Faces front end. A flexible system with three grouping options, organization, group and single editing access is provided. Three levels were chosen to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.« less

Cracking the Neural Code for Sensory Perception by Combining Statistics, Intervention, and Behavior.

PubMed

Panzeri, Stefano; Harvey, Christopher D; Piasini, Eugenio; Latham, Peter E; Fellin, Tommaso

2017-02-08

The two basic processes underlying perceptual decisions-how neural responses encode stimuli, and how they inform behavioral choices-have mainly been studied separately. Thus, although many spatiotemporal features of neural population activity, or "neural codes," have been shown to carry sensory information, it is often unknown whether the brain uses these features for perception. To address this issue, we propose a new framework centered on redefining the neural code as the neural features that carry sensory information used by the animal to drive appropriate behavior; that is, the features that have an intersection between sensory and choice information. We show how this framework leads to a new statistical analysis of neural activity recorded during behavior that can identify such neural codes, and we discuss how to combine intersection-based analysis of neural recordings with intervention on neural activity to determine definitively whether specific neural activity features are involved in a task. Copyright © 2017 Elsevier Inc. All rights reserved.

An expanded framework to define and measure shared decision-making in dialogue: A 'top-down' and 'bottom-up' approach.

PubMed

Callon, Wynne; Beach, Mary Catherine; Links, Anne R; Wasserman, Carly; Boss, Emily F

2018-03-11

We aimed to develop a comprehensive, descriptive framework to measure shared decision making (SDM) in clinical encounters. We combined a top-down (theoretical) approach with a bottom-up approach based on audio-recorded dialogue to identify all communication processes related to decision making. We coded 55 pediatric otolaryngology visits using the framework and report interrater reliability. We identified 14 clinician behaviors and 5 patient behaviors that have not been previously described, and developed a new SDM framework that is descriptive (what does happen) rather than normative (what should happen). Through the bottom-up approach we identified three broad domains not present in other SDM frameworks: socioemotional support, understandability of clinician dialogue, and recommendation-giving. We also specify the ways in which decision-making roles are assumed implicitly rather than discussed explicitly. Interrater reliability was >75% for 92% of the coded behaviors. This SDM framework allows for a more expansive understanding and analysis of how decision making takes place in clinical encounters, including new domains and behaviors not present in existing measures. We hope that this new framework will bring attention to a broader conception of SDM and allow researchers to further explore the new domains and behaviors identified. Copyright © 2018. Published by Elsevier B.V.

SIGACE Code for Generating High-Temperature ACE Files; Validation and Benchmarking

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

Sharma, Amit R.; Ganesan, S.; Trkov, A.

2005-05-24

A code named SIGACE has been developed as a tool for MCNP users within the scope of a research contract awarded by the Nuclear Data Section of the International Atomic Energy Agency (IAEA) (Ref: 302-F4-IND-11566 B5-IND-29641). A new recipe has been evolved for generating high-temperature ACE files for use with the MCNP code. Under this scheme the low-temperature ACE file is first converted to an ENDF formatted file using the ACELST code and then Doppler broadened, essentially limited to the data in the resolved resonance region, to any desired higher temperature using SIGMA1. The SIGACE code then generates a high-temperaturemore » ACE file for use with the MCNP code. A thinning routine has also been introduced in the SIGACE code for reducing the size of the ACE files. The SIGACE code and the recipe for generating ACE files at higher temperatures has been applied to the SEFOR fast reactor benchmark problem (sodium-cooled fast reactor benchmark described in ENDF-202/BNL-19302, 1974 document). The calculated Doppler coefficient is in good agreement with the experimental value. A similar calculation using ACE files generated directly with the NJOY system also agrees with our SIGACE computed results. The SIGACE code and the recipe is further applied to study the numerical benchmark configuration of selected idealized PWR pin cell configurations with five different fuel enrichments as reported by Mosteller and Eisenhart. The SIGACE code that has been tested with several FENDL/MC files will be available, free of cost, upon request, from the Nuclear Data Section of the IAEA.« less

Creation and Delivery of New Superpixelized DIRBE Map Products

NASA Technical Reports Server (NTRS)

Weiland, J.

1998-01-01

Phase 1 called for the following tasks: (1) completion of code to generate intermediate files containing the individual DIRBE observations which would be used to make the superpixelized maps; (2) completion of code necessary to generate the maps themselves; and (3) quality control on test-case maps in the form of point-source extraction and photometry. Items 1 and 2 are well in hand and the tested code is nearly complete. A few test maps have been generated for the tests mentioned in item 3. Map generation is not in production mode yet.

Ant-Based Cyber Defense (also known as

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

Glenn Fink, PNNL

2015-09-29

ABCD is a four-level hierarchy with human supervisors at the top, a top-level agent called a Sergeant controlling each enclave, Sentinel agents located at each monitored host, and mobile Sensor agents that swarm through the enclaves to detect cyber malice and misconfigurations. The code comprises four parts: (1) the core agent framework, (2) the user interface and visualization, (3) test-range software to create a network of virtual machines including a simulated Internet and user and host activity emulation scripts, and (4) a test harness to allow the safe running of adversarial code within the framework of monitored virtual machines.

A video coding scheme based on joint spatiotemporal and adaptive prediction.

PubMed

Jiang, Wenfei; Latecki, Longin Jan; Liu, Wenyu; Liang, Hui; Gorman, Ken

2009-05-01

We propose a video coding scheme that departs from traditional Motion Estimation/DCT frameworks and instead uses Karhunen-Loeve Transform (KLT)/Joint Spatiotemporal Prediction framework. In particular, a novel approach that performs joint spatial and temporal prediction simultaneously is introduced. It bypasses the complex H.26x interframe techniques and it is less computationally intensive. Because of the advantage of the effective joint prediction and the image-dependent color space transformation (KLT), the proposed approach is demonstrated experimentally to consistently lead to improved video quality, and in many cases to better compression rates and improved computational speed.

A framework for capturing clinical data sets from computerized sources.

PubMed

McDonald, C J; Overhage, J M; Dexter, P; Takesue, B Y; Dwyer, D M

1997-10-15

The pressure to improve health care and provide better care at a lower cost has generated the need for efficient capture of clinical data. Many data sets are now being defined to analyze health care. Historically, review and research organizations have simply determined what data they wanted to collect, developed forms, and then gathered the information through chart review without regard to what is already available institutionally in computerized databases. Today, much electronic patient information is available in operational data systems (for example, laboratory systems, pharmacy systems, and surgical scheduling systems) and is accessible by agencies and organizations through standards for messages, codes, and encrypted electronic mail. Such agencies and organizations should define the elements of their data sets in terms of standardized operational data, and data producers should fully adopt these code and message standards. The Health Plan Employer Data and Information Set and the Council of State and Territorial Epidemiologists in collaboration with the Centers for Disease Control and Prevention and the Association of State and Territorial Public Health Laboratory Directors provide examples of how this can be done.

jFuzz: A Concolic Whitebox Fuzzer for Java

NASA Technical Reports Server (NTRS)

Jayaraman, Karthick; Harvison, David; Ganesh, Vijay; Kiezun, Adam

2009-01-01

We present jFuzz, a automatic testing tool for Java programs. jFuzz is a concolic whitebox fuzzer, built on the NASA Java PathFinder, an explicit-state Java model checker, and a framework for developing reliability and analysis tools for Java. Starting from a seed input, jFuzz automatically and systematically generates inputs that exercise new program paths. jFuzz uses a combination of concrete and symbolic execution, and constraint solving. Time spent on solving constraints can be significant. We implemented several well-known optimizations and name-independent caching, which aggressively normalizes the constraints to reduce the number of calls to the constraint solver. We present preliminary results due to the optimizations, and demonstrate the effectiveness of jFuzz in creating good test inputs. The source code of jFuzz is available as part of the NASA Java PathFinder. jFuzz is intended to be a research testbed for investigating new testing and analysis techniques based on concrete and symbolic execution. The source code of jFuzz is available as part of the NASA Java PathFinder.

MACARON: A python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data.

PubMed

Khan, Waqasuddin; Saripella, Ganapathi Varma-; Ludwig, Thomas; Cuppens, Tania; Thibord, Florian; Génin, Emmanuelle; Deleuze, Jean-Francois; Trégouët, David-Alexandre

2018-05-03

Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings. MACARON is written in python with codes available on the GENMED website (www.genmed.fr). david-alexandre.tregouet@inserm.fr. Supplementary data are available at Bioinformatics online.

Modeling of RF/MHD coupling using NIMROD and GENRAY

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Schnack, D. D.; Sovinec, C. R.; Hegna, C. C.; Callen, J. D.; Ebrahimi, F.; Kruger, S. E.; Carlsson, J.; Held, E. D.; Ji, J.-Y.; Harvey, R. W.; Smirnov, A. P.

2008-11-01

We summarize ongoing theoretical/numerical work relevant to the development of a self--consistent framework for the inclusion of RF effects in fluid simulations, specifically considering the stabilization of resistive tearing modes in tokamak (DIII--D--like) geometry by electron cyclotron current drive. Previous investigations [T. G. Jenkins et al., Bull. APS 52, 131 (2007)] have demonstrated that relatively simple (though non--self--consistent) models for the RF--induced currents can be incorporated into the fluid equations, and that these currents can markedly reduce the width of the nonlinearly saturated magnetic islands generated by tearing modes. We report our progress toward the self--consistent modeling of these RF--induced currents. The initial interfacing of the NIMROD* code with the GENRAY/CQL3D** codes (which calculate RF propagation and energy/momentum deposition) is explained, equilibration of RF--induced currents over the plasma flux surfaces is investigated, and initial studies exploring the efficient reduction of saturated island widths through time modulation of the ECCD are presented. Conducted as part of the SWIM*** project; funded by U. S. DoE. *www.nimrodteam.org **www.compxco.com ***www.cswim.org

A Combinatorial Geometry Computer Description of the MEP-021A Generator Set

DTIC Science & Technology

1979-02-01

Generator Computer Description Gasoline Generator GIFT MEP-021A 20. ABSTRACT fCbntteu* an rararaa eta* ft namamwaay anal Identify by block number) This... GIFT code is also stored on magnetic tape for future vulnerability analysis. 00,] 󈧚*7,1473 EDITION OF • NOV 65 IS OBSOLETE UNCLASSIFIED SECURITY...the Geometric Information for Targets ( GIFT ) computer code. The GIFT code traces shotlines through a COM-GEOM description from any specified attack

ATLAS offline software performance monitoring and optimization

NASA Astrophysics Data System (ADS)

Chauhan, N.; Kabra, G.; Kittelmann, T.; Langenberg, R.; Mandrysch, R.; Salzburger, A.; Seuster, R.; Ritsch, E.; Stewart, G.; van Eldik, N.; Vitillo, R.; Atlas Collaboration

2014-06-01

In a complex multi-developer, multi-package software environment, such as the ATLAS offline framework Athena, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide the optimization work. The first tool we used to instrument the code is PAPI, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles, instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event results in a good understanding of the algorithm level performance of ATLAS code. Further data can be obtained using Pin, a dynamic binary instrumentation tool. Pin tools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is also possible. Pin tools can additionally interrogate the arguments to functions, like those in linear algebra libraries, so that a detailed usage profile can be obtained. These tools have characterized the extensive use of vector and matrix operations in ATLAS tracking. Currently, CLHEP is used here, which is not an optimal choice. To help evaluate replacement libraries a testbed has been setup allowing comparison of the performance of different linear algebra libraries (including CLHEP, Eigen and SMatrix/SVector). Results are then presented via the ATLAS Performance Management Board framework, which runs daily with the current development branch of the code and monitors reconstruction and Monte-Carlo jobs. This framework analyses the CPU and memory performance of algorithms and an overview of results are presented on a web page. These tools have provided the insight necessary to plan and implement performance enhancements in ATLAS code by identifying the most common operations, with the call parameters well understood, and allowing improvements to be quantified in detail.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-10-31

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

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

NASA Astrophysics Data System (ADS)

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

2012-01-01

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

RELAP-7 Theory Manual

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

Berry, Ray Alden; Zou, Ling; Zhao, Haihua

This document summarizes the physical models and mathematical formulations used in the RELAP-7 code. In summary, the MOOSE based RELAP-7 code development is an ongoing effort. The MOOSE framework enables rapid development of the RELAP-7 code. The developmental efforts and results demonstrate that the RELAP-7 project is on a path to success. This theory manual documents the main features implemented into the RELAP-7 code. Because the code is an ongoing development effort, this RELAP-7 Theory Manual will evolve with periodic updates to keep it current with the state of the development, implementation, and model additions/revisions.

An object-oriented framework for medical image registration, fusion, and visualization.

PubMed

Zhu, Yang-Ming; Cochoff, Steven M

2006-06-01

An object-oriented framework for image registration, fusion, and visualization was developed based on the classic model-view-controller paradigm. The framework employs many design patterns to facilitate legacy code reuse, manage software complexity, and enhance the maintainability and portability of the framework. Three sample applications built a-top of this framework are illustrated to show the effectiveness of this framework: the first one is for volume image grouping and re-sampling, the second one is for 2D registration and fusion, and the last one is for visualization of single images as well as registered volume images.

Automatic Testcase Generation for Flight Software

NASA Technical Reports Server (NTRS)

Bushnell, David Henry; Pasareanu, Corina; Mackey, Ryan M.

2008-01-01

The TacSat3 project is applying Integrated Systems Health Management (ISHM) technologies to an Air Force spacecraft for operational evaluation in space. The experiment will demonstrate the effectiveness and cost of ISHM and vehicle systems management (VSM) technologies through onboard operation for extended periods. We present two approaches to automatic testcase generation for ISHM: 1) A blackbox approach that views the system as a blackbox, and uses a grammar-based specification of the system's inputs to automatically generate *all* inputs that satisfy the specifications (up to prespecified limits); these inputs are then used to exercise the system. 2) A whitebox approach that performs analysis and testcase generation directly on a representation of the internal behaviour of the system under test. The enabling technologies for both these approaches are model checking and symbolic execution, as implemented in the Ames' Java PathFinder (JPF) tool suite. Model checking is an automated technique for software verification. Unlike simulation and testing which check only some of the system executions and therefore may miss errors, model checking exhaustively explores all possible executions. Symbolic execution evaluates programs with symbolic rather than concrete values and represents variable values as symbolic expressions. We are applying the blackbox approach to generating input scripts for the Spacecraft Command Language (SCL) from Interface and Control Systems. SCL is an embedded interpreter for controlling spacecraft systems. TacSat3 will be using SCL as the controller for its ISHM systems. We translated the SCL grammar into a program that outputs scripts conforming to the grammars. Running JPF on this program generates all legal input scripts up to a prespecified size. Script generation can also be targeted to specific parts of the grammar of interest to the developers. These scripts are then fed to the SCL Executive. ICS's in-house coverage tools will be run to measure code coverage. Because the scripts exercise all parts of the grammar, we expect them to provide high code coverage. This blackbox approach is suitable for systems for which we do not have access to the source code. We are applying whitebox test generation to the Spacecraft Health INference Engine (SHINE) that is part of the ISHM system. In TacSat3, SHINE will execute an on-board knowledge base for fault detection and diagnosis. SHINE converts its knowledge base into optimized C code which runs onboard TacSat3. SHINE can translate its rules into an intermediate representation (Java) suitable for analysis with JPF. JPF will analyze SHINE's Java output using symbolic execution, producing testcases that can provide either complete or directed coverage of the code. Automatically generated test suites can provide full code coverage and be quickly regenerated when code changes. Because our tools analyze executable code, they fully cover the delivered code, not just models of the code. This approach also provides a way to generate tests that exercise specific sections of code under specific preconditions. This capability gives us more focused testing of specific sections of code.

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm.

PubMed

Wu, Wei-Sheng; Jhou, Meng-Jhun

2017-01-13

Missing value imputation is important for microarray data analyses because microarray data with missing values would significantly degrade the performance of the downstream analyses. Although many microarray missing value imputation algorithms have been developed, an objective and comprehensive performance comparison framework is still lacking. To solve this problem, we previously proposed a framework which can perform a comprehensive performance comparison of different existing algorithms. Also the performance of a new algorithm can be evaluated by our performance comparison framework. However, constructing our framework is not an easy task for the interested researchers. To save researchers' time and efforts, here we present an easy-to-use web tool named MVIAeval (Missing Value Imputation Algorithm evaluator) which implements our performance comparison framework. MVIAeval provides a user-friendly interface allowing users to upload the R code of their new algorithm and select (i) the test datasets among 20 benchmark microarray (time series and non-time series) datasets, (ii) the compared algorithms among 12 existing algorithms, (iii) the performance indices from three existing ones, (iv) the comprehensive performance scores from two possible choices, and (v) the number of simulation runs. The comprehensive performance comparison results are then generated and shown as both figures and tables. MVIAeval is a useful tool for researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be represented as a matrix form (e.g. NGS data or proteomics data). Thus, MVIAeval will greatly expedite the progress in the research of missing value imputation algorithms.

Defining a Communications Satellite Policy System for the 21st Century: A Model for a International Legal Framework and A New _Code of Conduct_

NASA Astrophysics Data System (ADS)

Pelton, Joseph N.

1996-02-01

This paper addresses the changing international communications environment and explores the key elements of a new policy framework for the 21st Century. It addresses the issues related to changing markets, trade considerations, standards, regulatory changes and international institutions and law. The most important aspects will related to new international policy and regulatory frameworks and in particular to a new international code of ethics and behavior in the field of satellite communications. A new communications satellite policy framework requires systematically addressing the following points: • Multi-lateral agreements at the nation state and the operating entity level • Systematic means to access both private and public capital • Meshing ITU regulations with regional and national policy guidelines including • landing rights" and national allocation procedures. • Systematic approach to local partnerships • Resolving the issue of the relative standing of various satellite systems (i.e. GEO, MEO, and LEO systems) • Resolving the rights, duties, and priorities of satellite facility providers versus types of service prviders. Beyond this policy framework and generalized legal infrastructure there is also another need. This is a need that arises from both increased globalism and competitive international markets. This is what might quite simply be called a "code of reasonable conduct:" To provide global and international communications services effectively and well in the 21st Century will require more than meeting minimum international legal requirements. A new "code of conduct" for global satellite communications will thus likely need to address: • Privacy and surveillance • Ethics of transborder data flow • Censorship and moral values • Cultural and linguistic sensitivity • Freedom of the press and respect for journalistic standards As expanding global information and telecommunications systems grow and impact every aspect of modern life, the need for new international policy and especially new suitable standards of conduct in the field of satellite communications become ever more apparent and necessary.

The use of Tcl and Tk to improve design and code reutilization

NASA Technical Reports Server (NTRS)

Rodriguez, Lisbet; Reinholtz, Kirk

1995-01-01

Tcl and Tk facilitate design and code reuse in the ZIPSIM series of high-performance, high-fidelity spacecraft simulators. Tcl and Tk provide a framework for the construction of the Graphical User Interfaces for the simulators. The interfaces are architected such that a large proportion of the design and code is used for several applications, which has reduced design time and life-cycle costs.

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

Lee, Seyong; Kim, Jungwon; Vetter, Jeffrey S

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, thismore » design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.« less

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

PubMed

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-04-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

ScaffoldSeq: Software for characterization of directed evolution populations.

PubMed

Woldring, Daniel R; Holec, Patrick V; Hackel, Benjamin J

2016-07-01

ScaffoldSeq is software designed for the numerous applications-including directed evolution analysis-in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population. A common scenario for enzyme maturation, antibody screening, and alternative scaffold engineering involves naïve and evolved populations that contain diversified regions, varying in both sequence and length, within a conserved framework. Analyzing the diversified regions of such populations is facilitated by high-throughput sequencing platforms; however, length variability within these regions (e.g., antibody CDRs) encumbers the alignment process. To overcome this challenge, the ScaffoldSeq algorithm takes advantage of conserved framework sequences to quickly identify diverse regions. Beyond this, unintended biases in sequence frequency are generated throughout the experimental workflow required to evolve and isolate clones of interest prior to DNA sequencing. ScaffoldSeq software uniquely handles this issue by providing tools to quantify and remove background sequences, cluster similar protein families, and dampen the impact of dominant clones. The software produces graphical and tabular summaries for each region of interest, allowing users to evaluate diversity in a site-specific manner as well as identify epistatic pairwise interactions. The code and detailed information are freely available at http://research.cems.umn.edu/hackel. Proteins 2016; 84:869-874. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A Community Framework for Integrative, Coupled Modeling of Human-Earth Systems

NASA Astrophysics Data System (ADS)

Barton, C. M.; Nelson, G. C.; Tucker, G. E.; Lee, A.; Porter, C.; Ullah, I.; Hutton, E.; Hoogenboom, G.; Rogers, K. G.; Pritchard, C.

2017-12-01

We live today in a humanized world, where critical zone dynamics are driven by coupled human and biophysical processes. First generation modeling platforms have been invaluable in providing insight into dynamics of biophysical systems and social systems. But to understand today's humanized planet scientifically and to manage it sustainably, we need integrative modeling of this coupled human-Earth system. To address both scientific and policy questions, we also need modeling that can represent variable combinations of human-Earth system processes at multiple scales. Simply adding more code needed to do this to large, legacy first generation models is impractical, expensive, and will make them even more difficult to evaluate or understand. We need an approach to modeling that mirrors and benefits from the architecture of the complexly coupled systems we hope to model. Building on a series of international workshops over the past two years, we present a community framework to enable and support an ecosystem of diverse models as components that can be interconnected as needed to facilitate understanding of a range of complex human-earth systems interactions. Models are containerized in Docker to make them platform independent. A Basic Modeling Interface and Standard Names ontology (developed by the Community Surface Dynamics Modeling System) is applied to make them interoperable. They are then transformed into RESTful micro-services to allow them to be connected and run in a browser environment. This enables a flexible, multi-scale modeling environment to help address diverse issues with combinations of smaller, focused, component models that are easier to understand and evaluate. We plan to develop, deploy, and maintain this framework for integrated, coupled modeling in an open-source collaborative development environment that can democratize access to advanced technology and benefit from diverse global participation in model development. We also present an initial proof-of-concept of this framework, coupling a widely used agricultural crop model (DSSAT) with a widely used hydrology model (TopoFlow).

Nowcasting Ground Magnetic Perturbations with the Space Weather Modeling Framework

NASA Astrophysics Data System (ADS)

Welling, D. T.; Toth, G.; Singer, H. J.; Millward, G. H.; Gombosi, T. I.

2015-12-01

Predicting ground-based magnetic perturbations is a critical step towards specifying and predicting geomagnetically induced currents (GICs) in high voltage transmission lines. Currently, the Space Weather Modeling Framework (SWMF), a flexible modeling framework for simulating the multi-scale space environment, is being transitioned from research to operational use (R2O) by NOAA's Space Weather Prediction Center. Upon completion of this transition, the SWMF will provide localized B/t predictions using real-time solar wind observations from L1 and the F10.7 proxy for EUV as model input. This presentation describes the operational SWMF setup and summarizes the changes made to the code to enable R2O progress. The framework's algorithm for calculating ground-based magnetometer observations will be reviewed. Metrics from data-model comparisons will be reviewed to illustrate predictive capabilities. Early data products, such as regional-K index and grids of virtual magnetometer stations, will be presented. Finally, early successes will be shared, including the code's ability to reproduce the recent March 2015 St. Patrick's Day Storm.

Predictive Coding: A Possible Explanation of Filling-In at the Blind Spot

PubMed Central

Raman, Rajani; Sarkar, Sandip

2016-01-01

Filling-in at the blind spot is a perceptual phenomenon in which the visual system fills the informational void, which arises due to the absence of retinal input corresponding to the optic disc, with surrounding visual attributes. It is known that during filling-in, nonlinear neural responses are observed in the early visual area that correlates with the perception, but the knowledge of underlying neural mechanism for filling-in at the blind spot is far from complete. In this work, we attempted to present a fresh perspective on the computational mechanism of filling-in process in the framework of hierarchical predictive coding, which provides a functional explanation for a range of neural responses in the cortex. We simulated a three-level hierarchical network and observe its response while stimulating the network with different bar stimulus across the blind spot. We find that the predictive-estimator neurons that represent blind spot in primary visual cortex exhibit elevated non-linear response when the bar stimulated both sides of the blind spot. Using generative model, we also show that these responses represent the filling-in completion. All these results are consistent with the finding of psychophysical and physiological studies. In this study, we also demonstrate that the tolerance in filling-in qualitatively matches with the experimental findings related to non-aligned bars. We discuss this phenomenon in the predictive coding paradigm and show that all our results could be explained by taking into account the efficient coding of natural images along with feedback and feed-forward connections that allow priors and predictions to co-evolve to arrive at the best prediction. These results suggest that the filling-in process could be a manifestation of the general computational principle of hierarchical predictive coding of natural images. PMID:26959812

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

DOE PAGES

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.; ...

2017-01-26

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

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

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

PubMed

Newe, Axel; Ganslandt, Thomas

2013-01-01

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D--it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

Peer assisted learning as a formal instructional tool.

PubMed

Naqi, Syed Asghar

2014-03-01

To explore the utility of peer assisted learning (PAL) in medical schools as a formal instructional tool. Grounded theory approach. King Edward Medical University, Lahore, from July 2011 to December 2011. A study was designed using semi-structured in-depth interviews to collect data from final year medical students (n=6), residents (n=4) and faculty members (n=3), selected on the basis of non-probability purposive sampling. The qualitative data thus generated was first translated in English and transcribed and organized into major categories by using a coding framework. Participants were interviewed two more times to further explore their perceptions and experiences related to emergent categories. An iterative process was employed using grounded theory analysis technique to eventually generate theory. PAL was perceived as rewarding in terms of fostering higher order thinking, effective teaching skills and in improving self efficacy among learners. PAL can offer learning opportunity to medical students, residents and faculty members. It can improve depth of their knowledge and skills.

GlycoRDF: an ontology to standardize glycomics data in RDF.

PubMed

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-03-15

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Experimental Stage Separation Tool Development in NASA Langley's Aerothermodynamics Laboratory

NASA Technical Reports Server (NTRS)

Murphy, Kelly J.; Scallion, William I.

2005-01-01

As part of the research effort at NASA in support of the stage separation and ascent aerothermodynamics research program, proximity testing of a generic bimese wing-body configuration was conducted in NASA Langley's Aerothermodynamics Laboratory in the 20-Inch Mach 6 Air Tunnel. The objective of this work is the development of experimental tools and testing methodologies to apply to hypersonic stage separation problems for future multi-stage launch vehicle systems. Aerodynamic force and moment proximity data were generated at a nominal Mach number of 6 over a small range of angles of attack. The generic bimese configuration was tested in a belly-to-belly and back-to-belly orientation at 86 relative proximity locations. Over 800 aerodynamic proximity data points were taken to serve as a database for code validation. Longitudinal aerodynamic data generated in this test program show very good agreement with viscous computational predictions. Thus a framework has been established to study separation problems in the hypersonic regime using coordinated experimental and computational tools.

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

Kaurov, Alexander A., E-mail: kaurov@uchicago.edu

The methods for studying the epoch of cosmic reionization vary from full radiative transfer simulations to purely analytical models. While numerical approaches are computationally expensive and are not suitable for generating many mock catalogs, analytical methods are based on assumptions and approximations. We explore the interconnection between both methods. First, we ask how the analytical framework of excursion set formalism can be used for statistical analysis of numerical simulations and visual representation of the morphology of ionization fronts. Second, we explore the methods of training the analytical model on a given numerical simulation. We present a new code which emergedmore » from this study. Its main application is to match the analytical model with a numerical simulation. Then, it allows one to generate mock reionization catalogs with volumes exceeding the original simulation quickly and computationally inexpensively, meanwhile reproducing large-scale statistical properties. These mock catalogs are particularly useful for cosmic microwave background polarization and 21 cm experiments, where large volumes are required to simulate the observed signal.« less

A tuned mesh-generation strategy for image representation based on data-dependent triangulation.

PubMed

Li, Ping; Adams, Michael D

2013-05-01

A mesh-generation framework for image representation based on data-dependent triangulation is proposed. The proposed framework is a modified version of the frameworks of Rippa and Garland and Heckbert that facilitates the development of more effective mesh-generation methods. As the proposed framework has several free parameters, the effects of different choices of these parameters on mesh quality are studied, leading to the recommendation of a particular set of choices for these parameters. A mesh-generation method is then introduced that employs the proposed framework with these best parameter choices. This method is demonstrated to produce meshes of higher quality (both in terms of squared error and subjectively) than those generated by several competing approaches, at a relatively modest computational and memory cost.

MARTe: A Multiplatform Real-Time Framework

NASA Astrophysics Data System (ADS)

Neto, André C.; Sartori, Filippo; Piccolo, Fabio; Vitelli, Riccardo; De Tommasi, Gianmaria; Zabeo, Luca; Barbalace, Antonio; Fernandes, Horacio; Valcarcel, Daniel F.; Batista, Antonio J. N.

2010-04-01

Development of real-time applications is usually associated with nonportable code targeted at specific real-time operating systems. The boundary between hardware drivers, system services, and user code is commonly not well defined, making the development in the target host significantly difficult. The Multithreaded Application Real-Time executor (MARTe) is a framework built over a multiplatform library that allows the execution of the same code in different operating systems. The framework provides the high-level interfaces with hardware, external configuration programs, and user interfaces, assuring at the same time hard real-time performances. End-users of the framework are required to define and implement algorithms inside a well-defined block of software, named Generic Application Module (GAM), that is executed by the real-time scheduler. Each GAM is reconfigurable with a set of predefined configuration meta-parameters and interchanges information using a set of data pipes that are provided as inputs and required as output. Using these connections, different GAMs can be chained either in series or parallel. GAMs can be developed and debugged in a non-real-time system and, only once the robustness of the code and correctness of the algorithm are verified, deployed to the real-time system. The software also supplies a large set of utilities that greatly ease the interaction and debugging of a running system. Among the most useful are a highly efficient real-time logger, HTTP introspection of real-time objects, and HTTP remote configuration. MARTe is currently being used to successfully drive the plasma vertical stabilization controller on the largest magnetic confinement fusion device in the world, with a control loop cycle of 50 ?s and a jitter under 1 ?s. In this particular project, MARTe is used with the Real-Time Application Interface (RTAI)/Linux operating system exploiting the new ?86 multicore processors technology.

Progressive Dictionary Learning with Hierarchical Predictive Structure for Scalable Video Coding.

PubMed

Dai, Wenrui; Shen, Yangmei; Xiong, Hongkai; Jiang, Xiaoqian; Zou, Junni; Taubman, David

2017-04-12

Dictionary learning has emerged as a promising alternative to the conventional hybrid coding framework. However, the rigid structure of sequential training and prediction degrades its performance in scalable video coding. This paper proposes a progressive dictionary learning framework with hierarchical predictive structure for scalable video coding, especially in low bitrate region. For pyramidal layers, sparse representation based on spatio-temporal dictionary is adopted to improve the coding efficiency of enhancement layers (ELs) with a guarantee of reconstruction performance. The overcomplete dictionary is trained to adaptively capture local structures along motion trajectories as well as exploit the correlations between neighboring layers of resolutions. Furthermore, progressive dictionary learning is developed to enable the scalability in temporal domain and restrict the error propagation in a close-loop predictor. Under the hierarchical predictive structure, online learning is leveraged to guarantee the training and prediction performance with an improved convergence rate. To accommodate with the stateof- the-art scalable extension of H.264/AVC and latest HEVC, standardized codec cores are utilized to encode the base and enhancement layers. Experimental results show that the proposed method outperforms the latest SHVC and HEVC simulcast over extensive test sequences with various resolutions.

Comparison of three coding strategies for a low cost structure light scanner

NASA Astrophysics Data System (ADS)

Xiong, Hanwei; Xu, Jun; Xu, Chenxi; Pan, Ming

2014-12-01

Coded structure light is widely used for 3D scanning, and different coding strategies are adopted to suit for different goals. In this paper, three coding strategies are compared, and one of them is selected to implement a low cost structure light scanner under the cost of €100. To reach this goal, the projector and the video camera must be the cheapest, which will lead to some problems related to light coding. For a cheapest projector, complex intensity pattern can't be generated; even if it can be generated, it can't be captured by a cheapest camera. Based on Gray code, three different strategies are implemented and compared, called phase-shift, line-shift, and bit-shift, respectively. The bit-shift Gray code is the contribution of this paper, in which a simple, stable light pattern is used to generate dense(mean points distance<0.4mm) and accurate(mean error<0.1mm) results. The whole algorithm details and some example are presented in the papers.

Imagery and Verbal Coding Approaches in Chinese Vocabulary Instruction

ERIC Educational Resources Information Center

Shen, Helen H.

2010-01-01

This study consists of two instructional experiments. Within the framework of dual coding theory, the study compares the learning effects of two instructional encoding methods used in Chinese vocabulary instruction among students learning beginning Chinese as a foreign language. One method uses verbal encoding only, and the other method uses…

A Coding Scheme to Analyse the Online Asynchronous Discussion Forums of University Students

ERIC Educational Resources Information Center

Biasutti, Michele

2017-01-01

The current study describes the development of a content analysis coding scheme to examine transcripts of online asynchronous discussion groups in higher education. The theoretical framework comprises the theories regarding knowledge construction in computer-supported collaborative learning (CSCL) based on a sociocultural perspective. The coding…

FY17 Status Report on NEAMS Neutronics Activities

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

Lee, C. H.; Jung, Y. S.; Smith, M. A.

2017-09-30

Under the U.S. DOE NEAMS program, the high-fidelity neutronics code system has been developed to support the multiphysics modeling and simulation capability named SHARP. The neutronics code system includes the high-fidelity neutronics code PROTEUS, the cross section library and preprocessing tools, the multigroup cross section generation code MC2-3, the in-house meshing generation tool, the perturbation and sensitivity analysis code PERSENT, and post-processing tools. The main objectives of the NEAMS neutronics activities in FY17 are to continue development of an advanced nodal solver in PROTEUS for use in nuclear reactor design and analysis projects, implement a simplified sub-channel based thermal-hydraulic (T/H)more » capability into PROTEUS to efficiently compute the thermal feedback, improve the performance of PROTEUS-MOCEX using numerical acceleration and code optimization, improve the cross section generation tools including MC2-3, and continue to perform verification and validation tests for PROTEUS.« less

Chaos-Based Simultaneous Compression and Encryption for Hadoop.

PubMed

Usama, Muhammad; Zakaria, Nordin

2017-01-01

Data compression and encryption are key components of commonly deployed platforms such as Hadoop. Numerous data compression and encryption tools are presently available on such platforms and the tools are characteristically applied in sequence, i.e., compression followed by encryption or encryption followed by compression. This paper focuses on the open-source Hadoop framework and proposes a data storage method that efficiently couples data compression with encryption. A simultaneous compression and encryption scheme is introduced that addresses an important implementation issue of source coding based on Tent Map and Piece-wise Linear Chaotic Map (PWLM), which is the infinite precision of real numbers that result from their long products. The approach proposed here solves the implementation issue by removing fractional components that are generated by the long products of real numbers. Moreover, it incorporates a stealth key that performs a cyclic shift in PWLM without compromising compression capabilities. In addition, the proposed approach implements a masking pseudorandom keystream that enhances encryption quality. The proposed algorithm demonstrated a congruent fit within the Hadoop framework, providing robust encryption security and compression.

Reconfigurable, Intelligently-Adaptive, Communication System, an SDR Platform

NASA Technical Reports Server (NTRS)

Roche, Rigoberto

2016-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework to abstract the application software from the radio platform hardware. STRS aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. The Glenn Research Center (GRC) team made a software-defined radio (SDR) platform STRS compliant by adding an STRS operating environment and a field programmable gate array (FPGA) wrapper, capable of implementing each of the platforms interfaces, as well as a test waveform to exercise those interfaces. This effort serves to provide a framework toward waveform development on an STRS compliant platform to support future space communication systems for advanced exploration missions. Validated STRS compliant applications provided tested code with extensive documentation to potentially reduce risk, cost and efforts in development of space-deployable SDRs. This paper discusses the advantages of STRS, the integration of STRS onto a Reconfigurable, Intelligently-Adaptive, Communication System (RIACS) SDR platform, the sample waveform, and wrapper development efforts. The paper emphasizes the infusion of the STRS Architecture onto the RIACS platform for potential use in next generation SDRs for advance exploration missions.

Supervised graph hashing for histopathology image retrieval and classification.

PubMed

Shi, Xiaoshuang; Xing, Fuyong; Xu, KaiDi; Xie, Yuanpu; Su, Hai; Yang, Lin

2017-12-01

In pathology image analysis, morphological characteristics of cells are critical to grade many diseases. With the development of cell detection and segmentation techniques, it is possible to extract cell-level information for further analysis in pathology images. However, it is challenging to conduct efficient analysis of cell-level information on a large-scale image dataset because each image usually contains hundreds or thousands of cells. In this paper, we propose a novel image retrieval based framework for large-scale pathology image analysis. For each image, we encode each cell into binary codes to generate image representation using a novel graph based hashing model and then conduct image retrieval by applying a group-to-group matching method to similarity measurement. In order to improve both computational efficiency and memory requirement, we further introduce matrix factorization into the hashing model for scalable image retrieval. The proposed framework is extensively validated with thousands of lung cancer images, and it achieves 97.98% classification accuracy and 97.50% retrieval precision with all cells of each query image used. Copyright © 2017 Elsevier B.V. All rights reserved.

Chaos-Based Simultaneous Compression and Encryption for Hadoop

PubMed Central

Zakaria, Nordin

2017-01-01

Data compression and encryption are key components of commonly deployed platforms such as Hadoop. Numerous data compression and encryption tools are presently available on such platforms and the tools are characteristically applied in sequence, i.e., compression followed by encryption or encryption followed by compression. This paper focuses on the open-source Hadoop framework and proposes a data storage method that efficiently couples data compression with encryption. A simultaneous compression and encryption scheme is introduced that addresses an important implementation issue of source coding based on Tent Map and Piece-wise Linear Chaotic Map (PWLM), which is the infinite precision of real numbers that result from their long products. The approach proposed here solves the implementation issue by removing fractional components that are generated by the long products of real numbers. Moreover, it incorporates a stealth key that performs a cyclic shift in PWLM without compromising compression capabilities. In addition, the proposed approach implements a masking pseudorandom keystream that enhances encryption quality. The proposed algorithm demonstrated a congruent fit within the Hadoop framework, providing robust encryption security and compression. PMID:28072850

A Procedural Content Generation-Based Framework for Educational Games: Toward a Tailored Data-Driven Game for Developing Early English Reading Skills

ERIC Educational Resources Information Center

Hooshyar, Danial; Yousefi, Moslem; Lim, Heuiseok

2018-01-01

Automated content generation for educational games has become an emerging research problem, as manual authoring is often time consuming and costly. In this article, we present a procedural content generation framework that intends to produce educational game content from the viewpoint of both designer and user. This framework generates content by…

Automatic generation of user material subroutines for biomechanical growth analysis.

PubMed

Young, Jonathan M; Yao, Jiang; Ramasubramanian, Ashok; Taber, Larry A; Perucchio, Renato

2010-10-01

The analysis of the biomechanics of growth and remodeling in soft tissues requires the formulation of specialized pseudoelastic constitutive relations. The nonlinear finite element analysis package ABAQUS allows the user to implement such specialized material responses through the coding of a user material subroutine called UMAT. However, hand coding UMAT subroutines is a challenge even for simple pseudoelastic materials and requires substantial time to debug and test the code. To resolve this issue, we develop an automatic UMAT code generation procedure for pseudoelastic materials using the symbolic mathematics package MATHEMATICA and extend the UMAT generator to include continuum growth. The performance of the automatically coded UMAT is tested by simulating the stress-stretch response of a material defined by a Fung-orthotropic strain energy function, subject to uniaxial stretching, equibiaxial stretching, and simple shear in ABAQUS. The MATHEMATICA UMAT generator is then extended to include continuum growth by adding a growth subroutine to the automatically generated UMAT. The MATHEMATICA UMAT generator correctly derives the variables required in the UMAT code, quickly providing a ready-to-use UMAT. In turn, the UMAT accurately simulates the pseudoelastic response. In order to test the growth UMAT, we simulate the growth-based bending of a bilayered bar with differing fiber directions in a nongrowing passive layer. The anisotropic passive layer, being topologically tied to the growing isotropic layer, causes the bending bar to twist laterally. The results of simulations demonstrate the validity of the automatically coded UMAT, used in both standardized tests of hyperelastic materials and for a biomechanical growth analysis.

HOMAR: A computer code for generating homotopic grids using algebraic relations: User's manual

NASA Technical Reports Server (NTRS)

Moitra, Anutosh

1989-01-01

A computer code for fast automatic generation of quasi-three-dimensional grid systems for aerospace configurations is described. The code employs a homotopic method to algebraically generate two-dimensional grids in cross-sectional planes, which are stacked to produce a three-dimensional grid system. Implementation of the algebraic equivalents of the homotopic relations for generating body geometries and grids are explained. Procedures for controlling grid orthogonality and distortion are described. Test cases with description and specification of inputs are presented in detail. The FORTRAN computer program and notes on implementation and use are included.

Introduction: A Sociological Code for the Description of World Society and Its Change.

ERIC Educational Resources Information Center

Heintz, Peter

1982-01-01

Examines the dimensions of an emerging awareness of a world society. A sociological framework for describing worldwide societal systems and how they interact is presented. Major traits of the image of a world society, as derived from the framework, are described. (AM)

Construction of self-dual codes in the Rosenbloom-Tsfasman metric

NASA Astrophysics Data System (ADS)

Krisnawati, Vira Hari; Nisa, Anzi Lina Ukhtin

2017-12-01

Linear code is a very basic code and very useful in coding theory. Generally, linear code is a code over finite field in Hamming metric. Among the most interesting families of codes, the family of self-dual code is a very important one, because it is the best known error-correcting code. The concept of Hamming metric is develop into Rosenbloom-Tsfasman metric (RT-metric). The inner product in RT-metric is different from Euclid inner product that is used to define duality in Hamming metric. Most of the codes which are self-dual in Hamming metric are not so in RT-metric. And, generator matrix is very important to construct a code because it contains basis of the code. Therefore in this paper, we give some theorems and methods to construct self-dual codes in RT-metric by considering properties of the inner product and generator matrix. Also, we illustrate some examples for every kind of the construction.

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions.

PubMed

Chang, Ivan; Baldi, Pierre

2013-05-15

Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation-reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to a single system or set of conditions. To address these limitations, we introduce a novel unifying modeling framework for kinetic descriptions of oxidoreductases. The framework is based on a set of seven elementary reactions that (i) form the basis for 69 pairs of enzyme state transitions for encoding various specific microscopic intra-enzyme reaction networks (micro-models), and (ii) lead to various specific macroscopic steady-state kinetic equations (macro-models) via thermodynamic assumptions. Thus, a synergistic bridge between the micro and macro kinetics can be achieved, enabling us to extract unitary rate constants, simulate reaction variance and validate the micro-models using steady-state empirical data. To help facilitate the application of this framework, we make available RedoxMech: a Mathematica™ software package that automates the generation and customization of micro-models. The Mathematica™ source code for RedoxMech, the documentation and the experimental datasets are all available from: http://www.igb.uci.edu/tools/sb/metabolic-modeling. pfbaldi@ics.uci.edu Supplementary data are available at Bioinformatics online.

Multi-Disciplinary Analysis and Optimization Frameworks

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2009-01-01

Since July 2008, the Multidisciplinary Analysis & Optimization Working Group (MDAO WG) of the Systems Analysis Design & Optimization (SAD&O) discipline in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project completed one major milestone, Define Architecture & Interfaces for Next Generation Open Source MDAO Framework Milestone (9/30/08), and is completing the Generation 1 Framework validation milestone, which is due December 2008. Included in the presentation are: details of progress on developing the Open MDAO framework, modeling and testing the Generation 1 Framework, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexander E; Gschwind, Michael K; Gunnels, John A

2013-10-29

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexandre E [Chappaqua, NY; Gschwind, Michael K [Chappaqua, NY; Gunnels, John A [Yorktown Heights, NY

2012-08-28

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Child Support Enforcement: A Framework for Evaluating Costs, Benefits, and Effects.

DTIC Science & Technology

1991-03-01

efforts to gain and enforce child support awards might yield additional collections on behalf of these children, they would surely entail additional...framework for evaluating the full costs and ne . effects of child support enforcement.I This framework could assist your office and others in planning...following results of our develop- S . ............. .. mental work: (1) models of the child support enforcement system activi- AvajiabilitY Codes. ties

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

NASA Technical Reports Server (NTRS)

Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

1989-01-01

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

Validation of the WIMSD4M cross-section generation code with benchmark results

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

Leal, L.C.; Deen, J.R.; Woodruff, W.L.

1995-02-01

The WIMSD4 code has been adopted for cross-section generation in support of the Reduced Enrichment for Research and Test (RERTR) program at Argonne National Laboratory (ANL). Subsequently, the code has undergone several updates, and significant improvements have been achieved. The capability of generating group-collapsed micro- or macroscopic cross sections from the ENDF/B-V library and the more recent evaluation, ENDF/B-VI, in the ISOTXS format makes the modified version of the WIMSD4 code, WIMSD4M, very attractive, not only for the RERTR program, but also for the reactor physics community. The intent of the present paper is to validate the procedure to generatemore » cross-section libraries for reactor analyses and calculations utilizing the WIMSD4M code. To do so, the results of calculations performed with group cross-section data generated with the WIMSD4M code will be compared against experimental results. These results correspond to calculations carried out with thermal reactor benchmarks of the Oak Ridge National Laboratory(ORNL) unreflected critical spheres, the TRX critical experiments, and calculations of a modified Los Alamos highly-enriched heavy-water moderated benchmark critical system. The benchmark calculations were performed with the discrete-ordinates transport code, TWODANT, using WIMSD4M cross-section data. Transport calculations using the XSDRNPM module of the SCALE code system are also included. In addition to transport calculations, diffusion calculations with the DIF3D code were also carried out, since the DIF3D code is used in the RERTR program for reactor analysis and design. For completeness, Monte Carlo results of calculations performed with the VIM and MCNP codes are also presented.« less

Assessing Quality of Critical Thought in Online Discussion

ERIC Educational Resources Information Center

Weltzer-Ward, Lisa; Baltes, Beate; Lynn, Laura Knight

2009-01-01

Purpose: The purpose of this paper is to describe a theoretically based coding framework for an integrated analysis and assessment of critical thinking in online discussion. Design/methodology/approach: The critical thinking assessment framework (TAF) is developed through review of theory and previous research, verified by comparing results to…

A CellML simulation compiler and code generator using ODE solving schemes

PubMed Central

2012-01-01

Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler. PMID:23083065

Adding EUNIS and VAULT rocket data to the VSO with Modern Perl frameworks

NASA Astrophysics Data System (ADS)

Mansky, Edmund

2017-08-01

A new Perl code is described, that uses the modern Object-oriented Moose framework, to add EUNIS and VAULT rocket data to the Virtual Solar Observatory website. The code permits the easy fixing of FITS header fields in the case where some FITS fields that are required are missing from the original data files. The code makes novel use of the Moose extensions “before” and “after” to build in dependencies so that database creation of tables occurs before the loading of data, and that the validation of file-dependent tables occurs after the loading is completed. Also described is the computation and loading of the deferred FITS field CHECKSUM into the database following the loading and validation of the file-dependent tables. The loading of the EUNIS 2006 and 2007 flight data, and the VAULT 2.0 flight data is described in detail as illustrative examples.

Fostering integrity in postgraduate research: an evidence-based policy and support framework.

PubMed

Mahmud, Saadia; Bretag, Tracey

2014-01-01

Postgraduate research students have a unique position in the debate on integrity in research as students and novice researchers. To assess how far policies for integrity in postgraduate research meet the needs of students as "research trainees," we reviewed online policies for integrity in postgraduate research at nine particular Australian universities against the Australian Code for Responsible Conduct of Research (the Code) and the five core elements of exemplary academic integrity policy identified by Bretag et al. (2011 ), i.e., access, approach, responsibility, detail, and support. We found inconsistency with the Code in the definition of research misconduct and a lack of adequate detail and support. Based on our analysis, previous research, and the literature, we propose a framework for policy and support for postgraduate research that encompasses a consistent and educative approach to integrity maintained across the university at all levels of scholarship and for all stakeholders.

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

Heuristic rules embedded genetic algorithm for in-core fuel management optimization

NASA Astrophysics Data System (ADS)

Alim, Fatih

The objective of this study was to develop a unique methodology and a practical tool for designing loading pattern (LP) and burnable poison (BP) pattern for a given Pressurized Water Reactor (PWR) core. Because of the large number of possible combinations for the fuel assembly (FA) loading in the core, the design of the core configuration is a complex optimization problem. It requires finding an optimal FA arrangement and BP placement in order to achieve maximum cycle length while satisfying the safety constraints. Genetic Algorithms (GA) have been already used to solve this problem for LP optimization for both PWR and Boiling Water Reactor (BWR). The GA, which is a stochastic method works with a group of solutions and uses random variables to make decisions. Based on the theories of evaluation, the GA involves natural selection and reproduction of the individuals in the population for the next generation. The GA works by creating an initial population, evaluating it, and then improving the population by using the evaluation operators. To solve this optimization problem, a LP optimization package, GARCO (Genetic Algorithm Reactor Code Optimization) code is developed in the framework of this thesis. This code is applicable for all types of PWR cores having different geometries and structures with an unlimited number of FA types in the inventory. To reach this goal, an innovative GA is developed by modifying the classical representation of the genotype. To obtain the best result in a shorter time, not only the representation is changed but also the algorithm is changed to use in-core fuel management heuristics rules. The improved GA code was tested to demonstrate and verify the advantages of the new enhancements. The developed methodology is explained in this thesis and preliminary results are shown for the VVER-1000 reactor hexagonal geometry core and the TMI-1 PWR. The improved GA code was tested to verify the advantages of new enhancements. The core physics code used for VVER in this research is Moby-Dick, which was developed to analyze the VVER by SKODA Inc. The SIMULATE-3 code, which is an advanced two-group nodal code, is used to analyze the TMI-1.

CTF (Subchannel) Calculations and Validation L3:VVI.H2L.P15.01

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

Gordon, Natalie

The goal of the Verification and Validation Implementation (VVI) High to Low (Hi2Lo) process is utilizing a validated model in a high resolution code to generate synthetic data for improvement of the same model in a lower resolution code. This process is useful in circumstances where experimental data does not exist or it is not sufficient in quantity or resolution. Data from the high-fidelity code is treated as calibration data (with appropriate uncertainties and error bounds) which can be used to train parameters that affect solution accuracy in the lower-fidelity code model, thereby reducing uncertainty. This milestone presents a demonstrationmore » of the Hi2Lo process derived in the VVI focus area. The majority of the work performed herein describes the steps of the low-fidelity code used in the process with references to the work detailed in the companion high-fidelity code milestone (Reference 1). The CASL low-fidelity code used to perform this work was Cobra Thermal Fluid (CTF) and the high-fidelity code was STAR-CCM+ (STAR). The master branch version of CTF (pulled May 5, 2017 – Reference 2) was utilized for all CTF analyses performed as part of this milestone. The statistical and VVUQ components of the Hi2Lo framework were performed using Dakota version 6.6 (release date May 15, 2017 – Reference 3). Experimental data from Westinghouse Electric Company (WEC – Reference 4) was used throughout the demonstrated process to compare with the high-fidelity STAR results. A CTF parameter called Beta was chosen as the calibration parameter for this work. By default, Beta is defined as a constant mixing coefficient in CTF and is essentially a tuning parameter for mixing between subchannels. Since CTF does not have turbulence models like STAR, Beta is the parameter that performs the most similar function to the turbulence models in STAR. The purpose of the work performed in this milestone is to tune Beta to an optimal value that brings the CTF results closer to those measured in the WEC experiments.« less

A Data Driven Framework for Integrating Regional Climate Models

NASA Astrophysics Data System (ADS)

Lansing, C.; Kleese van Dam, K.; Liu, Y.; Elsethagen, T.; Guillen, Z.; Stephan, E.; Critchlow, T.; Gorton, I.

2012-12-01

There are increasing needs for research addressing complex climate sensitive issues of concern to decision-makers and policy planners at a regional level. Decisions about allocating scarce water across competing municipal, agricultural, and ecosystem demands is just one of the challenges ahead, along with decisions regarding competing land use priorities such as biofuels, food, and species habitat. Being able to predict the extent of future climate change in the context of introducing alternative energy production strategies requires a new generation of modeling capabilities. We will also need more complete representations of human systems at regional scales, incorporating the influences of population centers, land use, agriculture and existing and planned electrical demand and generation infrastructure. At PNNL we are working towards creating a first-of-a-kind capability known as the Integrated Regional Earth System Model (iRESM). The fundamental goal of the iRESM initiative is the critical analyses of the tradeoffs and consequences of decision and policy making for integrated human and environmental systems. This necessarily combines different scientific processes, bridging different temporal and geographic scales and resolving the semantic differences between them. To achieve this goal, iRESM is developing a modeling framework and supporting infrastructure that enable the scientific team to evaluate different scenarios in light of specific stakeholder questions such as "How do regional changes in mean climate states and climate extremes affect water storage and energy consumption and how do such decisions influence possible mitigation and carbon management schemes?" The resulting capability will give analysts a toolset to gain insights into how regional economies can respond to climate change mitigation policies and accelerated deployment of alternative energy technologies. The iRESM framework consists of a collection of coupled models working with high resolution data that can represent the climate, geography, economy, energy supply, and demand of a region under study; an integrated data management framework that captures information about models, model couplings (workflows), observational and derived data sets, numerical experiments, and the provenance metadata connecting them; and a collaborative environment that enables scientific users to explore the datasets, register models and codes, launch workflows, retrieve provenance, and analyze results. In this presentation we address the challenges of coupling heterogeneous codes and handling large data sets. We describe our integration approach, which is based on a loosely coupled software architecture that supports experimentation and evolution of models on different datasets. We present our software prototype and show the scalability of our approach to handle a large number ( > 17,000) of model runs and a significant quantity of data in the order of terabytes. The resulting environment is now used by domain scientists and has proven useful to improve productivity in the evolving development of iRESM model coupling.

Etude des performances de solveurs deterministes sur un coeur rapide a caloporteur sodium

NASA Astrophysics Data System (ADS)

Bay, Charlotte

The reactors of next generation, in particular SFR model, represent a true challenge for current codes and solvers, used mainly for thermic cores. There is no guarantee that their competences could be straight adapted to fast neutron spectrum, or to major design differences. Thus it is necessary to assess the validity of solvers and their potential shortfall in the case of fast neutron reactors. As part of an internship with CEA (France), and at the instigation of EPM Nuclear Institute, this study concerns the following codes : DRAGON/DONJON, ERANOS, PARIS and APOLLO3. The precision assessment has been performed using Monte Carlo code TRIPOLI4. Only core calculation was of interest, namely numerical methods competences in precision and rapidity. Lattice code was not part of the study, that is to say nuclear data, self-shielding, or isotopic compositions. Nor was tackled burnup or time evolution effects. The study consists in two main steps : first evaluating the sensitivity of each solver to calculation parameters, and obtain its optimal calculation set ; then compare their competences in terms of precision and rapidity, by collecting usual quantities (effective multiplication factor, reaction rates map), but also more specific quantities which are crucial to the SFR design, namely control rod worth and sodium void effect. The calculation time is also a key factor. Whatever conclusion or recommendation that could be drawn from this study, they must first of all be applied within similar frameworks, that is to say small fast neutron cores with hexagonal geometry. Eventual adjustments for big cores will have to be demonstrated in developments of this study.

Ethics in Engineering: Student Perceptions and Their Professional Identity Development

ERIC Educational Resources Information Center

Stappenbelt, Brad

2013-01-01

Professional ethics instruction in engineering is commonly conducted by examining case studies in light of the code of conduct of a suitable professional body. Although graphical presentations of spectacular failures, sobering stories of the repercussions and the solid framework provided by the tenets of a code of ethics may leave a lasting…

English-Afrikaans Intrasentential Code Switching: Testing a Feature Checking Account

ERIC Educational Resources Information Center

van Dulm, Ondene

2009-01-01

The work presented here aims to account for the structure of intrasentential code switching between English and Afrikaans within the framework of feature checking theory, a theory associated with minimalist syntax. Six constructions in which verb position differs between English and Afrikaans were analysed in terms of differences in the strength…

QX MAN: Q and X file manipulation

NASA Technical Reports Server (NTRS)

Krein, Mark A.

1992-01-01

QX MAN is a grid and solution file manipulation program written primarily for the PARC code and the GRIDGEN family of grid generation codes. QX MAN combines many of the features frequently encountered in grid generation, grid refinement, the setting-up of initial conditions, and post processing. QX MAN allows the user to manipulate single block and multi-block grids (and their accompanying solution files) by splitting, concatenating, rotating, translating, re-scaling, and stripping or adding points. In addition, QX MAN can be used to generate an initial solution file for the PARC code. The code was written to provide several formats for input and output in order for it to be useful in a broad spectrum of applications.

Automatically generated code for relativistic inhomogeneous cosmologies

NASA Astrophysics Data System (ADS)

Bentivegna, Eloisa

2017-02-01

The applications of numerical relativity to cosmology are on the rise, contributing insight into such cosmological problems as structure formation, primordial phase transitions, gravitational-wave generation, and inflation. In this paper, I present the infrastructure for the computation of inhomogeneous dust cosmologies which was used recently to measure the effect of nonlinear inhomogeneity on the cosmic expansion rate. I illustrate the code's architecture, provide evidence for its correctness in a number of familiar cosmological settings, and evaluate its parallel performance for grids of up to several billion points. The code, which is available as free software, is based on the Einstein Toolkit infrastructure, and in particular leverages the automated code generation capabilities provided by its component Kranc.

Anticounterfeiting Quick Response Code with Emission Color of Invisible Metal-Organic Frameworks as Encoding Information.

PubMed

Wang, Yong-Mei; Tian, Xue-Tao; Zhang, Hui; Yang, Zhong-Rui; Yin, Xue-Bo

2018-06-21

Counterfeiting is a global epidemic that is compelling the development of new anticounterfeiting strategy. Herein, we report a novel multiple anticounterfeiting encoding strategy of invisible fluorescent quick response (QR) codes with emission color as information storage unit. The strategy requires red, green, and blue (RGB) light-emitting materials for different emission colors as encrypting information, single excitation for all of the emission for practicability, and ultraviolet (UV) excitation for invisibility under daylight. Therefore, RGB light-emitting nanoscale metal-organic frameworks (NMOFs) are designed as inks to construct the colorful light-emitting boxes for information encrypting, while three black vertex boxes were used for positioning. Full-color emissions are obtained by mixing the trichromatic NMOFs inks through inkjet printer. The encrypting information capacity is easily adjusted by the number of light-emitting boxes with the infinite emission colors. The information is decoded with specific excitation light at 275 nm, making the QR codes invisible under daylight. The composition of inks, invisibility, inkjet printing, and the abundant encrypting information all contribute to multiple anticounterfeiting. The proposed QR codes pattern holds great potential for advanced anticounterfeiting.

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning.

PubMed

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝ d , and the dictionary is learned from the training data using the vector space structure of ℝ d and its Euclidean L 2 -metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis.

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning

PubMed Central

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝd, and the dictionary is learned from the training data using the vector space structure of ℝd and its Euclidean L2-metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis. PMID:24129583

An FPGA design of generalized low-density parity-check codes for rate-adaptive optical transport networks

NASA Astrophysics Data System (ADS)

Zou, Ding; Djordjevic, Ivan B.

2016-02-01

Forward error correction (FEC) is as one of the key technologies enabling the next-generation high-speed fiber optical communications. In this paper, we propose a rate-adaptive scheme using a class of generalized low-density parity-check (GLDPC) codes with a Hamming code as local code. We show that with the proposed unified GLDPC decoder architecture, a variable net coding gains (NCGs) can be achieved with no error floor at BER down to 10-15, making it a viable solution in the next-generation high-speed fiber optical communications.

The Socioculturally Constructed Multivoiced Self as a Framework for Christian Education of Second-Generation Korean American Young Adults

ERIC Educational Resources Information Center

Kang, S. Steve

2002-01-01

This article proposes a new framework for theory and practice of Christian education for second-generation Korean American young adults using the literature of sociocultural constructionism and the multivoiced self. This framework can provide holistic nurture and future trajectories in which to encourage a reflexive, praxis-generating faith. The…

DARTAB: a program to combine airborne radionuclide environmental exposure data with dosimetric and health effects data to generate tabulations of predicted health impacts

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

Begovich, C.L.; Eckerman, K.F.; Schlatter, E.C.

1981-08-01

The DARTAB computer code combines radionuclide environmental exposure data with dosimetric and health effects data to generate tabulations of the predicted impact of radioactive airborne effluents. DARTAB is independent of the environmental transport code used to generate the environmental exposure data and the codes used to produce the dosimetric and health effects data. Therefore human dose and risk calculations need not be added to every environmental transport code. Options are included in DARTAB to permit the user to request tabulations by various topics (e.g., cancer site, exposure pathway, etc.) to facilitate characterization of the human health impacts of the effluents.more » The DARTAB code was written at ORNL for the US Environmental Protection Agency, Office of Radiation Programs.« less

Development of an Automatic Differentiation Version of the FPX Rotor Code

NASA Technical Reports Server (NTRS)

Hu, Hong

1996-01-01

The ADIFOR2.0 automatic differentiator is applied to the FPX rotor code along with the grid generator GRGN3. The FPX is an eXtended Full-Potential CFD code for rotor calculations. The automatic differentiation version of the code is obtained, which provides both non-geometry and geometry sensitivity derivatives. The sensitivity derivatives via automatic differentiation are presented and compared with divided difference generated derivatives. The study shows that automatic differentiation method gives accurate derivative values in an efficient manner.

Local Laplacian Coding From Theoretical Analysis of Local Coding Schemes for Locally Linear Classification.

PubMed

Pang, Junbiao; Qin, Lei; Zhang, Chunjie; Zhang, Weigang; Huang, Qingming; Yin, Baocai

2015-12-01

Local coordinate coding (LCC) is a framework to approximate a Lipschitz smooth function by combining linear functions into a nonlinear one. For locally linear classification, LCC requires a coding scheme that heavily determines the nonlinear approximation ability, posing two main challenges: 1) the locality making faraway anchors have smaller influences on current data and 2) the flexibility balancing well between the reconstruction of current data and the locality. In this paper, we address the problem from the theoretical analysis of the simplest local coding schemes, i.e., local Gaussian coding and local student coding, and propose local Laplacian coding (LPC) to achieve the locality and the flexibility. We apply LPC into locally linear classifiers to solve diverse classification tasks. The comparable or exceeded performances of state-of-the-art methods demonstrate the effectiveness of the proposed method.

Subspace-Aware Index Codes

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

Kailkhura, Bhavya; Theagarajan, Lakshmi Narasimhan; Varshney, Pramod K.

In this paper, we generalize the well-known index coding problem to exploit the structure in the source-data to improve system throughput. In many applications (e.g., multimedia), the data to be transmitted may lie (or can be well approximated) in a low-dimensional subspace. We exploit this low-dimensional structure of the data using an algebraic framework to solve the index coding problem (referred to as subspace-aware index coding) as opposed to the traditional index coding problem which is subspace-unaware. Also, we propose an efficient algorithm based on the alternating minimization approach to obtain near optimal index codes for both subspace-aware and -unawaremore » cases. In conclusion, our simulations indicate that under certain conditions, a significant throughput gain (about 90%) can be achieved by subspace-aware index codes over conventional subspace-unaware index codes.« less

Subspace-Aware Index Codes

DOE PAGES

Kailkhura, Bhavya; Theagarajan, Lakshmi Narasimhan; Varshney, Pramod K.

2017-04-12

In this paper, we generalize the well-known index coding problem to exploit the structure in the source-data to improve system throughput. In many applications (e.g., multimedia), the data to be transmitted may lie (or can be well approximated) in a low-dimensional subspace. We exploit this low-dimensional structure of the data using an algebraic framework to solve the index coding problem (referred to as subspace-aware index coding) as opposed to the traditional index coding problem which is subspace-unaware. Also, we propose an efficient algorithm based on the alternating minimization approach to obtain near optimal index codes for both subspace-aware and -unawaremore » cases. In conclusion, our simulations indicate that under certain conditions, a significant throughput gain (about 90%) can be achieved by subspace-aware index codes over conventional subspace-unaware index codes.« less

Visual Persons Behavior Diary Generation Model based on Trajectories and Pose Estimation

NASA Astrophysics Data System (ADS)

Gang, Chen; Bin, Chen; Yuming, Liu; Hui, Li

2018-03-01

The behavior pattern of persons was the important output of the surveillance analysis. This paper focus on the generation model of visual person behavior diary. The pipeline includes the person detection, tracking, and the person behavior classify. This paper adopts the deep convolutional neural model YOLO (You Only Look Once)V2 for person detection module. Multi person tracking was based on the detection framework. The Hungarian assignment algorithm was used to the matching. The person appearance model was integrated by HSV color model and Hash code model. The person object motion was estimated by the Kalman Filter. The multi objects were matching with exist tracklets through the appearance and motion location distance by the Hungarian assignment method. A long continuous trajectory for one person was get by the spatial-temporal continual linking algorithm. And the face recognition information was used to identify the trajectory. The trajectories with identification information can be used to generate the visual diary of person behavior based on the scene context information and person action estimation. The relevant modules are tested in public data sets and our own capture video sets. The test results show that the method can be used to generate the visual person behavior pattern diary with certain accuracy.