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.

Automating Traceability for Generated Software Artifacts

NASA Technical Reports Server (NTRS)

Richardson, Julian; Green, Jeffrey

2004-01-01

Program synthesis automatically derives programs from specifications of their behavior. One advantage of program synthesis, as opposed to manual coding, is that there is a direct link between the specification and the derived program. This link is, however, not very fine-grained: it can be best characterized as Program is-derived- from Specification. When the generated program needs to be understood or modified, more $ne-grained linking is useful. In this paper, we present a novel technique for automatically deriving traceability relations between parts of a specification and parts of the synthesized program. The technique is very lightweight and works -- with varying degrees of success - for any process in which one artifact is automatically derived from another. We illustrate the generality of the technique by applying it to two kinds of automatic generation: synthesis of Kalman Filter programs from speci3cations using the Aut- oFilter program synthesis system, and generation of assembly language programs from C source code using the GCC C compilel: We evaluate the effectiveness of the technique in the latter application.

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.

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.

Fully automatic adjoints: a robust and efficient mechanism for generating adjoint ocean models

NASA Astrophysics Data System (ADS)

Ham, D. A.; Farrell, P. E.; Funke, S. W.; Rognes, M. E.

2012-04-01

The problem of generating and maintaining adjoint models is sufficiently difficult that typically only the most advanced and well-resourced community ocean models achieve it. There are two current technologies which each suffer from their own limitations. Algorithmic differentiation, also called automatic differentiation, is employed by models such as the MITGCM [2] and the Alfred Wegener Institute model FESOM [3]. This technique is very difficult to apply to existing code, and requires a major initial investment to prepare the code for automatic adjoint generation. AD tools may also have difficulty with code employing modern software constructs such as derived data types. An alternative is to formulate the adjoint differential equation and to discretise this separately. This approach, known as the continuous adjoint and employed in ROMS [4], has the disadvantage that two different model code bases must be maintained and manually kept synchronised as the model develops. The discretisation of the continuous adjoint is not automatically consistent with that of the forward model, producing an additional source of error. The alternative presented here is to formulate the flow model in the high level language UFL (Unified Form Language) and to automatically generate the model using the software of the FEniCS project. In this approach it is the high level code specification which is differentiated, a task very similar to the formulation of the continuous adjoint [5]. However since the forward and adjoint models are generated automatically, the difficulty of maintaining them vanishes and the software engineering process is therefore robust. The scheduling and execution of the adjoint model, including the application of an appropriate checkpointing strategy is managed by libadjoint [1]. In contrast to the conventional algorithmic differentiation description of a model as a series of primitive mathematical operations, libadjoint employs a new abstraction of the simulation process as a sequence of discrete equations which are assembled and solved. It is the coupling of the respective abstractions employed by libadjoint and the FEniCS project which produces the adjoint model automatically, without further intervention from the model developer. This presentation will demonstrate this new technology through linear and non-linear shallow water test cases. The exceptionally simple model syntax will be highlighted and the correctness of the resulting adjoint simulations will be demonstrated using rigorous convergence tests.

Automated encoding of clinical documents based on natural language processing.

PubMed

Friedman, Carol; Shagina, Lyudmila; Lussier, Yves; Hripcsak, George

2004-01-01

The aim of this study was to develop a method based on natural language processing (NLP) that automatically maps an entire clinical document to codes with modifiers and to quantitatively evaluate the method. An existing NLP system, MedLEE, was adapted to automatically generate codes. The method involves matching of structured output generated by MedLEE consisting of findings and modifiers to obtain the most specific code. Recall and precision applied to Unified Medical Language System (UMLS) coding were evaluated in two separate studies. Recall was measured using a test set of 150 randomly selected sentences, which were processed using MedLEE. Results were compared with a reference standard determined manually by seven experts. Precision was measured using a second test set of 150 randomly selected sentences from which UMLS codes were automatically generated by the method and then validated by experts. Recall of the system for UMLS coding of all terms was .77 (95% CI.72-.81), and for coding terms that had corresponding UMLS codes recall was .83 (.79-.87). Recall of the system for extracting all terms was .84 (.81-.88). Recall of the experts ranged from .69 to .91 for extracting terms. The precision of the system was .89 (.87-.91), and precision of the experts ranged from .61 to .91. Extraction of relevant clinical information and UMLS coding were accomplished using a method based on NLP. The method appeared to be comparable to or better than six experts. The advantage of the method is that it maps text to codes along with other related information, rendering the coded output suitable for effective retrieval.

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.

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

Verification and Validation in a Rapid Software Development Process

NASA Technical Reports Server (NTRS)

Callahan, John R.; Easterbrook, Steve M.

1997-01-01

The high cost of software production is driving development organizations to adopt more automated design and analysis methods such as rapid prototyping, computer-aided software engineering (CASE) tools, and high-level code generators. Even developers of safety-critical software system have adopted many of these new methods while striving to achieve high levels Of quality and reliability. While these new methods may enhance productivity and quality in many cases, we examine some of the risks involved in the use of new methods in safety-critical contexts. We examine a case study involving the use of a CASE tool that automatically generates code from high-level system designs. We show that while high-level testing on the system structure is highly desirable, significant risks exist in the automatically generated code and in re-validating releases of the generated code after subsequent design changes. We identify these risks and suggest process improvements that retain the advantages of rapid, automated development methods within the quality and reliability contexts of safety-critical projects.

Automatic code generation in SPARK: Applications of computer algebra and compiler-compilers

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

Nataf, J.M.; Winkelmann, F.

We show how computer algebra and compiler-compilers are used for automatic code generation in the Simulation Problem Analysis and Research Kernel (SPARK), an object oriented environment for modeling complex physical systems that can be described by differential-algebraic equations. After a brief overview of SPARK, we describe the use of computer algebra in SPARK's symbolic interface, which generates solution code for equations that are entered in symbolic form. We also describe how the Lex/Yacc compiler-compiler is used to achieve important extensions to the SPARK simulation language, including parametrized macro objects and steady-state resetting of a dynamic simulation. The application of thesemore » methods to solving the partial differential equations for two-dimensional heat flow is illustrated.« less

Automatic code generation in SPARK: Applications of computer algebra and compiler-compilers

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

Nataf, J.M.; Winkelmann, F.

We show how computer algebra and compiler-compilers are used for automatic code generation in the Simulation Problem Analysis and Research Kernel (SPARK), an object oriented environment for modeling complex physical systems that can be described by differential-algebraic equations. After a brief overview of SPARK, we describe the use of computer algebra in SPARK`s symbolic interface, which generates solution code for equations that are entered in symbolic form. We also describe how the Lex/Yacc compiler-compiler is used to achieve important extensions to the SPARK simulation language, including parametrized macro objects and steady-state resetting of a dynamic simulation. The application of thesemore » methods to solving the partial differential equations for two-dimensional heat flow is illustrated.« less

Automatic mathematical modeling for space application

NASA Technical Reports Server (NTRS)

Wang, Caroline K.

1987-01-01

A methodology for automatic mathematical modeling is described. The major objective is to create a very friendly environment for engineers to design, maintain and verify their model and also automatically convert the mathematical model into FORTRAN code for conventional computation. A demonstration program was designed for modeling the Space Shuttle Main Engine simulation mathematical model called Propulsion System Automatic Modeling (PSAM). PSAM provides a very friendly and well organized environment for engineers to build a knowledge base for base equations and general information. PSAM contains an initial set of component process elements for the Space Shuttle Main Engine simulation and a questionnaire that allows the engineer to answer a set of questions to specify a particular model. PSAM is then able to automatically generate the model and the FORTRAN code. A future goal is to download the FORTRAN code to the VAX/VMS system for conventional computation.

A procedure for automating CFD simulations of an inlet-bleed problem

NASA Technical Reports Server (NTRS)

Chyu, Wei J.; Rimlinger, Mark J.; Shih, Tom I.-P.

1995-01-01

A procedure was developed to improve the turn-around time for computational fluid dynamics (CFD) simulations of an inlet-bleed problem involving oblique shock-wave/boundary-layer interactions on a flat plate with bleed into a plenum through one or more circular holes. This procedure is embodied in a preprocessor called AUTOMAT. With AUTOMAT, once data for the geometry and flow conditions have been specified (either interactively or via a namelist), it will automatically generate all input files needed to perform a three-dimensional Navier-Stokes simulation of the prescribed inlet-bleed problem by using the PEGASUS and OVERFLOW codes. The input files automatically generated by AUTOMAT include those for the grid system and those for the initial and boundary conditions. The grid systems automatically generated by AUTOMAT are multi-block structured grids of the overlapping type. Results obtained by using AUTOMAT are presented to illustrate its capability.

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

NASA Astrophysics Data System (ADS)

Wiebusch, Martin

2015-10-01

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools.

A comparison of different methods to implement higher order derivatives of density functionals

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

van Dam, Hubertus J.J.

Density functional theory is the dominant approach in electronic structure methods today. To calculate properties higher order derivatives of the density functionals are required. These derivatives might be implemented manually,by automatic differentiation, or by symbolic algebra programs. Different authors have cited different reasons for using the particular method of their choice. This paper presents work where all three approaches were used and the strengths and weaknesses of each approach are considered. It is found that all three methods produce code that is suffficiently performanted for practical applications, despite the fact that our symbolic algebra generated code and our automatic differentiationmore » code still have scope for significant optimization. The automatic differentiation approach is the best option for producing readable and maintainable code.« less

Multiblock grid generation with automatic zoning

NASA Technical Reports Server (NTRS)

Eiseman, Peter R.

1995-01-01

An overview will be given for multiblock grid generation with automatic zoning. We shall explore the many advantages and benefits of this exciting technology and will also see how to apply it to a number of interesting cases. The technology is available in the form of a commercial code, GridPro(registered trademark)/az3000. This code takes surface geometry definitions and patterns of points as its primary input and produces high quality grids as its output. Before we embark upon our exploration, we shall first give a brief background of the environment in which this technology fits.

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

Automated Translation of Safety Critical Application Software Specifications into PLC Ladder Logic

NASA Technical Reports Server (NTRS)

Leucht, Kurt W.; Semmel, Glenn S.

2008-01-01

The numerous benefits of automatic application code generation are widely accepted within the software engineering community. A few of these benefits include raising the abstraction level of application programming, shorter product development time, lower maintenance costs, and increased code quality and consistency. Surprisingly, code generation concepts have not yet found wide acceptance and use in the field of programmable logic controller (PLC) software development. Software engineers at the NASA Kennedy Space Center (KSC) recognized the need for PLC code generation while developing their new ground checkout and launch processing system. They developed a process and a prototype software tool that automatically translates a high-level representation or specification of safety critical application software into ladder logic that executes on a PLC. This process and tool are expected to increase the reliability of the PLC code over that which is written manually, and may even lower life-cycle costs and shorten the development schedule of the new control system at KSC. This paper examines the problem domain and discusses the process and software tool that were prototyped by the KSC software engineers.

Secure web-based invocation of large-scale plasma simulation codes

NASA Astrophysics Data System (ADS)

Dimitrov, D. A.; Busby, R.; Exby, J.; Bruhwiler, D. L.; Cary, J. R.

2004-12-01

We present our design and initial implementation of a web-based system for running, both in parallel and serial, Particle-In-Cell (PIC) codes for plasma simulations with automatic post processing and generation of visual diagnostics.

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.

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.

Automatic programming of simulation models

NASA Technical Reports Server (NTRS)

Schroer, Bernard J.; Tseng, Fan T.; Zhang, Shou X.; Dwan, Wen S.

1990-01-01

The concepts of software engineering were used to improve the simulation modeling environment. Emphasis was placed on the application of an element of rapid prototyping, or automatic programming, to assist the modeler define the problem specification. Then, once the problem specification has been defined, an automatic code generator is used to write the simulation code. The following two domains were selected for evaluating the concepts of software engineering for discrete event simulation: manufacturing domain and a spacecraft countdown network sequence. The specific tasks were to: (1) define the software requirements for a graphical user interface to the Automatic Manufacturing Programming System (AMPS) system; (2) develop a graphical user interface for AMPS; and (3) compare the AMPS graphical interface with the AMPS interactive user interface.

Some User's Insights Into ADIFOR 2.0D

NASA Technical Reports Server (NTRS)

Giesy, Daniel P.

2002-01-01

Some insights are given which were gained by one user through experience with the use of the ADIFOR 2.0D software for automatic differentiation of Fortran code. These insights are generally in the area of the user interface with the generated derivative code - particularly the actual form of the interface and the use of derivative objects, including "seed" matrices. Some remarks are given as to how to iterate application of ADIFOR in order to generate second derivative code.

Kinetic modelling of the oxidation of large aliphatic hydrocarbons using an automatic mechanism generation.

PubMed

Muharam, Yuswan; Warnatz, Jürgen

2007-08-21

A mechanism generator code to automatically generate mechanisms for the oxidation of large hydrocarbons has been successfully modified and considerably expanded in this work. The modification was through (1) improvement of the existing rules such as cyclic-ether reactions and aldehyde reactions, (2) inclusion of some additional rules to the code, such as ketone reactions, hydroperoxy cyclic-ether formations and additional reactions of alkenes, (3) inclusion of small oxygenates, produced by the code but not included in the handwritten C(1)-C(4) sub-mechanism yet, to the handwritten C(1)-C(4) sub-mechanism. In order to evaluate mechanisms generated by the code, simulations of observed results in different experimental environments have been carried out. Experimentally derived and numerically predicted ignition delays of n-heptane-air and n-decane-air mixtures in high-pressure shock tubes in a wide range of temperatures, pressures and equivalence ratios agree very well. Concentration profiles of the main products and intermediates of n-heptane and n-decane oxidation in jet-stirred reactors at a wide range of temperatures and equivalence ratios are generally well reproduced. In addition, the ignition delay times of different normal alkanes was numerically studied.

An Analysis of Elliptic Grid Generation Techniques Using an Implicit Euler Solver.

DTIC Science & Technology

1986-06-09

automatic determination of the control fu.nction, . elements of covariant metric tensor in the elliptic grid generation system , from the Cm = 1,2,3...computational fluid d’nan1-cs code. Tne code Inclues a tnree-dimensional current research is aimed primaril: at algebraic generation system based on transfinite...start the iterative solution of the f. ow, nea, transfer, and combustion proble:s. elliptic generation system . Tn13 feature also .:ven-.ts :.t be made

Automatic mathematical modeling for real time simulation system

NASA Technical Reports Server (NTRS)

Wang, Caroline; Purinton, Steve

1988-01-01

A methodology for automatic mathematical modeling and generating simulation models is described. The models will be verified by running in a test environment using standard profiles with the results compared against known results. The major objective is to create a user friendly environment for engineers to design, maintain, and verify their model and also automatically convert the mathematical model into conventional code for conventional computation. A demonstration program was designed for modeling the Space Shuttle Main Engine Simulation. It is written in LISP and MACSYMA and runs on a Symbolic 3670 Lisp Machine. The program provides a very friendly and well organized environment for engineers to build a knowledge base for base equations and general information. It contains an initial set of component process elements for the Space Shuttle Main Engine Simulation and a questionnaire that allows the engineer to answer a set of questions to specify a particular model. The system is then able to automatically generate the model and FORTRAN code. The future goal which is under construction is to download the FORTRAN code to VAX/VMS system for conventional computation. The SSME mathematical model will be verified in a test environment and the solution compared with the real data profile. The use of artificial intelligence techniques has shown that the process of the simulation modeling can be simplified.

The Use of a Code-generating System for the Derivation of the Equations for Wind Turbine Dynamics

NASA Astrophysics Data System (ADS)

Ganander, Hans

2003-10-01

For many reasons the size of wind turbines on the rapidly growing wind energy market is increasing. Relations between aeroelastic properties of these new large turbines change. Modifications of turbine designs and control concepts are also influenced by growing size. All these trends require development of computer codes for design and certification. Moreover, there is a strong desire for design optimization procedures, which require fast codes. General codes, e.g. finite element codes, normally allow such modifications and improvements of existing wind turbine models. This is done relatively easy. However, the calculation times of such codes are unfavourably long, certainly for optimization use. The use of an automatic code generating system is an alternative for relevance of the two key issues, the code and the design optimization. This technique can be used for rapid generation of codes of particular wind turbine simulation models. These ideas have been followed in the development of new versions of the wind turbine simulation code VIDYN. The equations of the simulation model were derived according to the Lagrange equation and using Mathematica®, which was directed to output the results in Fortran code format. In this way the simulation code is automatically adapted to an actual turbine model, in terms of subroutines containing the equations of motion, definitions of parameters and degrees of freedom. Since the start in 1997, these methods, constituting a systematic way of working, have been used to develop specific efficient calculation codes. The experience with this technique has been very encouraging, inspiring the continued development of new versions of the simulation code as the need has arisen, and the interest for design optimization is growing.

Design and implementation of online automatic judging system

NASA Astrophysics Data System (ADS)

Liang, Haohui; Chen, Chaojie; Zhong, Xiuyu; Chen, Yuefeng

2017-06-01

For lower efficiency and poorer reliability in programming training and competition by currently artificial judgment, design an Online Automatic Judging (referred to as OAJ) System. The OAJ system including the sandbox judging side and Web side, realizes functions of automatically compiling and running the tested codes, and generating evaluation scores and corresponding reports. To prevent malicious codes from damaging system, the OAJ system utilizes sandbox, ensuring the safety of the system. The OAJ system uses thread pools to achieve parallel test, and adopt database optimization mechanism, such as horizontal split table, to improve the system performance and resources utilization rate. The test results show that the system has high performance, high reliability, high stability and excellent extensibility.

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.

Binary translation using peephole translation rules

DOEpatents

Bansal, Sorav; Aiken, Alex

2010-05-04

An efficient binary translator uses peephole translation rules to directly translate executable code from one instruction set to another. In a preferred embodiment, the translation rules are generated using superoptimization techniques that enable the translator to automatically learn translation rules for translating code from the source to target instruction set architecture.

AMPS/PC - AUTOMATIC MANUFACTURING PROGRAMMING SYSTEM

NASA Technical Reports Server (NTRS)

Schroer, B. J.

1994-01-01

The AMPS/PC system is a simulation tool designed to aid the user in defining the specifications of a manufacturing environment and then automatically writing code for the target simulation language, GPSS/PC. The domain of problems that AMPS/PC can simulate are manufacturing assembly lines with subassembly lines and manufacturing cells. The user defines the problem domain by responding to the questions from the interface program. Based on the responses, the interface program creates an internal problem specification file. This file includes the manufacturing process network flow and the attributes for all stations, cells, and stock points. AMPS then uses the problem specification file as input for the automatic code generator program to produce a simulation program in the target language GPSS. The output of the generator program is the source code of the corresponding GPSS/PC simulation program. The system runs entirely on an IBM PC running PC DOS Version 2.0 or higher and is written in Turbo Pascal Version 4 requiring 640K memory and one 360K disk drive. To execute the GPSS program, the PC must have resident the GPSS/PC System Version 2.0 from Minuteman Software. The AMPS/PC program was developed in 1988.

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.

Computer-Aided Parallelizer and Optimizer

NASA Technical Reports Server (NTRS)

Jin, Haoqiang

2011-01-01

The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

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

SYMBOD - A computer program for the automatic generation of symbolic equations of motion for systems of hinge-connected rigid bodies

NASA Technical Reports Server (NTRS)

Macala, G. A.

1983-01-01

A computer program is described that can automatically generate symbolic equations of motion for systems of hinge-connected rigid bodies with tree topologies. The dynamical formulation underlying the program is outlined, and examples are given to show how a symbolic language is used to code the formulation. The program is applied to generate the equations of motion for a four-body model of the Galileo spacecraft. The resulting equations are shown to be a factor of three faster in execution time than conventional numerical subroutines.

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

Design of Provider-Provisioned Website Protection Scheme against Malware Distribution

NASA Astrophysics Data System (ADS)

Yagi, Takeshi; Tanimoto, Naoto; Hariu, Takeo; Itoh, Mitsutaka

Vulnerabilities in web applications expose computer networks to security threats, and many websites are used by attackers as hopping sites to attack other websites and user terminals. These incidents prevent service providers from constructing secure networking environments. To protect websites from attacks exploiting vulnerabilities in web applications, service providers use web application firewalls (WAFs). WAFs filter accesses from attackers by using signatures, which are generated based on the exploit codes of previous attacks. However, WAFs cannot filter unknown attacks because the signatures cannot reflect new types of attacks. In service provider environments, the number of exploit codes has recently increased rapidly because of the spread of vulnerable web applications that have been developed through cloud computing. Thus, generating signatures for all exploit codes is difficult. To solve these problems, our proposed scheme detects and filters malware downloads that are sent from websites which have already received exploit codes. In addition, to collect information for detecting malware downloads, web honeypots, which automatically extract the communication records of exploit codes, are used. According to the results of experiments using a prototype, our scheme can filter attacks automatically so that service providers can provide secure and cost-effective network environments.

Reading Aloud Is Not Automatic: Processing Capacity Is Required to Generate a Phonological Code from Print

ERIC Educational Resources Information Center

Reynolds, Michael; Besner, Derek

2006-01-01

The present experiments tested the claim that phonological recoding occurs "automatically" by assessing whether it uses central attention in the context of the psychological refractory period paradigm. Task 1 was a tone discrimination task and Task 2 was reading aloud. The joint effects of long-lag word repetition priming and stimulus onset…

Formal Safety Certification of Aerospace Software

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2005-01-01

In principle, formal methods offer many advantages for aerospace software development: they can help to achieve ultra-high reliability, and they can be used to provide evidence of the reliability claims which can then be subjected to external scrutiny. However, despite years of research and many advances in the underlying formalisms of specification, semantics, and logic, formal methods are not much used in practice. In our opinion this is related to three major shortcomings. First, the application of formal methods is still expensive because they are labor- and knowledge-intensive. Second, they are difficult to scale up to complex systems because they are based on deep mathematical insights about the behavior of the systems (t.e., they rely on the "heroic proof"). Third, the proofs can be difficult to interpret, and typically stand in isolation from the original code. In this paper, we describe a tool for formally demonstrating safety-relevant aspects of aerospace software, which largely circumvents these problems. We focus on safely properties because it has been observed that safety violations such as out-of-bounds memory accesses or use of uninitialized variables constitute the majority of the errors found in the aerospace domain. In our approach, safety means that the program will not violate a set of rules that can range for the simple memory access rules to high-level flight rules. These different safety properties are formalized as different safety policies in Hoare logic, which are then used by a verification condition generator along with the code and logical annotations in order to derive formal safety conditions; these are then proven using an automated theorem prover. Our certification system is currently integrated into a model-based code generation toolset that generates the annotations together with the code. However, this automated formal certification technology is not exclusively constrained to our code generator and could, in principle, also be integrated with other code generators such as RealTime Workshop or even applied to legacy code. Our approach circumvents the historical problems with formal methods by increasing the degree of automation on all levels. The restriction to safety policies (as opposed to arbitrary functional behavior) results in simpler proof problems that can generally be solved by fully automatic theorem proves. An automated linking mechanism between the safety conditions and the code provides some of the traceability mandated by process standards such as DO-178B. An automated explanation mechanism uses semantic markup added by the verification condition generator to produce natural-language explanations of the safety conditions and thus supports their interpretation in relation to the code. It shows an automatically generated certification browser that lets users inspect the (generated) code along with the safety conditions (including textual explanations), and uses hyperlinks to automate tracing between the two levels. Here, the explanations reflect the logical structure of the safety obligation but the mechanism can in principle be customized using different sets of domain concepts. The interface also provides some limited control over the certification process itself. Our long-term goal is a seamless integration of certification, code generation, and manual coding that results in a "certified pipeline" in which specifications are automatically transformed into executable code, together with the supporting artifacts necessary for achieving and demonstrating the high level of assurance needed in the aerospace domain.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

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.

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

Geometry modeling and multi-block grid generation for turbomachinery configurations

NASA Technical Reports Server (NTRS)

Shih, Ming H.; Soni, Bharat K.

1992-01-01

An interactive 3D grid generation code, Turbomachinery Interactive Grid genERation (TIGER), was developed for general turbomachinery configurations. TIGER features the automatic generation of multi-block structured grids around multiple blade rows for either internal, external, or internal-external turbomachinery flow fields. Utilization of the Bezier's curves achieves a smooth grid and better orthogonality. TIGER generates the algebraic grid automatically based on geometric information provided by its built-in pseudo-AI algorithm. However, due to the large variation of turbomachinery configurations, this initial grid may not always be as good as desired. TIGER therefore provides graphical user interactions during the process which allow the user to design, modify, as well as manipulate the grid, including the capability of elliptic surface grid generation.

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

DOE PAGES

O'keefe, Matthew; Parr, Terence; Edgar, B. Kevin; ...

1995-01-01

Massively parallel processors (MPPs) hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. Wemore » have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.« less

On the symbolic manipulation and code generation for elasto-plastic material matrices

NASA Technical Reports Server (NTRS)

Chang, T. Y.; Saleeb, A. F.; Wang, P. S.; Tan, H. Q.

1991-01-01

A computerized procedure for symbolic manipulations and FORTRAN code generation of an elasto-plastic material matrix for finite element applications is presented. Special emphasis is placed on expression simplifications during intermediate derivations, optimal code generation, and interface with the main program. A systematic procedure is outlined to avoid redundant algebraic manipulations. Symbolic expressions of the derived material stiffness matrix are automatically converted to RATFOR code which is then translated into FORTRAN statements through a preprocessor. To minimize the interface problem with the main program, a template file is prepared so that the translated FORTRAN statements can be merged into the file to form a subroutine (or a submodule). Three constitutive models; namely, von Mises plasticity, Drucker-Prager model, and a concrete plasticity model, are used as illustrative examples.

Automatic Generation of Cycle-Approximate TLMs with Timed RTOS Model Support

NASA Astrophysics Data System (ADS)

Hwang, Yonghyun; Schirner, Gunar; Abdi, Samar

This paper presents a technique for automatically generating cycle-approximate transaction level models (TLMs) for multi-process applications mapped to embedded platforms. It incorporates three key features: (a) basic block level timing annotation, (b) RTOS model integration, and (c) RTOS overhead delay modeling. The inputs to TLM generation are application C processes and their mapping to processors in the platform. A processor data model, including pipelined datapath, memory hierarchy and branch delay model is used to estimate basic block execution delays. The delays are annotated to the C code, which is then integrated with a generated SystemC RTOS model. Our abstract RTOS provides dynamic scheduling and inter-process communication (IPC) with processor- and RTOS-specific pre-characterized timing. Our experiments using a MP3 decoder and a JPEG encoder show that timed TLMs, with integrated RTOS models, can be automatically generated in less than a minute. Our generated TLMs simulated three times faster than real-time and showed less than 10% timing error compared to board measurements.

Automated real-time software development

NASA Technical Reports Server (NTRS)

Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

1993-01-01

A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

Automatic Generation of OpenMP Directives and Its Application to Computational Fluid Dynamics Codes

NASA Technical Reports Server (NTRS)

Yan, Jerry; Jin, Haoqiang; Frumkin, Michael; Yan, Jerry (Technical Monitor)

2000-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate OpenMP-based parallel programs with nominal user assistance. We outline techniques used in the implementation of the tool and discuss the application of this tool on the NAS Parallel Benchmarks and several computational fluid dynamics codes. This work demonstrates the great potential of using the tool to quickly port parallel programs and also achieve good performance that exceeds some of the commercial tools.

Optimizing a liquid propellant rocket engine with an automated combustor design code (AUTOCOM)

NASA Technical Reports Server (NTRS)

Hague, D. S.; Reichel, R. H.; Jones, R. T.; Glatt, C. R.

1972-01-01

A procedure for automatically designing a liquid propellant rocket engine combustion chamber in an optimal fashion is outlined. The procedure is contained in a digital computer code, AUTOCOM. The code is applied to an existing engine, and design modifications are generated which provide a substantial potential payload improvement over the existing design. Computer time requirements for this payload improvement were small, approximately four minutes in the CDC 6600 computer.

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

A Comparison of Automatic Parallelization Tools/Compilers on the SGI Origin 2000 Using the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash; Frumkin, Michael; Hribar, Michelle; Jin, Hao-Qiang; Waheed, Abdul; Yan, Jerry

1998-01-01

Porting applications to new high performance parallel and distributed computing platforms is a challenging task. Since writing parallel code by hand is extremely time consuming and costly, porting codes would ideally be automated by using some parallelization tools and compilers. In this paper, we compare the performance of the hand written NAB Parallel Benchmarks against three parallel versions generated with the help of tools and compilers: 1) CAPTools: an interactive computer aided parallelization too] that generates message passing code, 2) the Portland Group's HPF compiler and 3) using compiler directives with the native FORTAN77 compiler on the SGI Origin2000.

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

Kim, Hang Bae

A reliability testing was performed for the software of Shutdown(SDS) Computers for Wolsong Nuclear Power Plants Units 2, 3 and 4. profiles to the SDS Computers and compared the outputs with the predicted results generated by the oracle. Test softwares were written to execute the test automatically. Random test profiles were generated using analysis code. 11 refs., 1 fig.

Data-Driven Hint Generation in Vast Solution Spaces: A Self-Improving Python Programming Tutor

ERIC Educational Resources Information Center

Rivers, Kelly; Koedinger, Kenneth R.

2017-01-01

To provide personalized help to students who are working on code-writing problems, we introduce a data-driven tutoring system, ITAP (Intelligent Teaching Assistant for Programming). ITAP uses state abstraction, path construction, and state reification to automatically generate personalized hints for students, even when given states that have not…

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

Integrated circuit test-port architecture and method and apparatus of test-port generation

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

Teifel, John

A method and apparatus are provided for generating RTL code for a test-port interface of an integrated circuit. In an embodiment, a test-port table is provided as input data. A computer automatically parses the test-port table into data structures and analyzes it to determine input, output, local, and output-enable port names. The computer generates address-detect and test-enable logic constructed from combinational functions. The computer generates one-hot multiplexer logic for at least some of the output ports. The one-hot multiplexer logic for each port is generated so as to enable the port to toggle between data signals and test signals. Themore » computer then completes the generation of the RTL code.« less

Research in Parallel Algorithms and Software for Computational Aerosciences

DOT National Transportation Integrated Search

1996-04-01

Phase I is complete for the development of a Computational Fluid Dynamics : with automatic grid generation and adaptation for the Euler : analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian : grid code developed at Lockheed...

The use of automatic programming techniques for fault tolerant computing systems

NASA Technical Reports Server (NTRS)

Wild, C.

1985-01-01

It is conjectured that the production of software for ultra-reliable computing systems such as required by Space Station, aircraft, nuclear power plants and the like will require a high degree of automation as well as fault tolerance. In this paper, the relationship between automatic programming techniques and fault tolerant computing systems is explored. Initial efforts in the automatic synthesis of code from assertions to be used for error detection as well as the automatic generation of assertions and test cases from abstract data type specifications is outlined. Speculation on the ability to generate truly diverse designs capable of recovery from errors by exploring alternate paths in the program synthesis tree is discussed. Some initial thoughts on the use of knowledge based systems for the global detection of abnormal behavior using expectations and the goal-directed reconfiguration of resources to meet critical mission objectives are given. One of the sources of information for these systems would be the knowledge captured during the automatic programming process.

Container-code recognition system based on computer vision and deep neural networks

NASA Astrophysics Data System (ADS)

Liu, Yi; Li, Tianjian; Jiang, Li; Liang, Xiaoyao

2018-04-01

Automatic container-code recognition system becomes a crucial requirement for ship transportation industry in recent years. In this paper, an automatic container-code recognition system based on computer vision and deep neural networks is proposed. The system consists of two modules, detection module and recognition module. The detection module applies both algorithms based on computer vision and neural networks, and generates a better detection result through combination to avoid the drawbacks of the two methods. The combined detection results are also collected for online training of the neural networks. The recognition module exploits both character segmentation and end-to-end recognition, and outputs the recognition result which passes the verification. When the recognition module generates false recognition, the result will be corrected and collected for online training of the end-to-end recognition sub-module. By combining several algorithms, the system is able to deal with more situations, and the online training mechanism can improve the performance of the neural networks at runtime. The proposed system is able to achieve 93% of overall recognition accuracy.

Automatic structured grid generation using Gridgen (some restrictions apply)

NASA Technical Reports Server (NTRS)

Chawner, John R.; Steinbrenner, John P.

1995-01-01

The authors have noticed in the recent grid generation literature an emphasis on the automation of structured grid generation. The motivation behind such work is clear; grid generation is easily the most despised task in the grid-analyze-visualize triad of computational analysis (CA). However, because grid generation is closely coupled to both the design and analysis software and because quantitative measures of grid quality are lacking, 'push button' grid generation usually results in a compromise between speed, control, and quality. Overt emphasis on automation obscures the substantive issues of providing users with flexible tools for generating and modifying high quality grids in a design environment. In support of this paper's tongue-in-cheek title, many features of the Gridgen software are described. Gridgen is by no stretch of the imagination an automatic grid generator. Despite this fact, the code does utilize many automation techniques that permit interesting regenerative features.

GridMan: A grid manipulation system

NASA Technical Reports Server (NTRS)

Eiseman, Peter R.; Wang, Zhu

1992-01-01

GridMan is an interactive grid manipulation system. It operates on grids to produce new grids which conform to user demands. The input grids are not constrained to come from any particular source. They may be generated by algebraic methods, elliptic methods, hyperbolic methods, parabolic methods, or some combination of methods. The methods are included in the various available structured grid generation codes. These codes perform the basic assembly function for the various elements of the initial grid. For block structured grids, the assembly can be quite complex due to a large number of clock corners, edges, and faces for which various connections and orientations must be properly identified. The grid generation codes are distinguished among themselves by their balance between interactive and automatic actions and by their modest variations in control. The basic form of GridMan provides a much more substantial level of grid control and will take its input from any of the structured grid generation codes. The communication link to the outside codes is a data file which contains the grid or section of grid.

LogiKit - assisting complex logic specification and implementation for embedded control systems

NASA Astrophysics Data System (ADS)

Diglio, A.; Nicolodi, B.

2002-07-01

LogiKit provides an overall lifecycle solution. LogiKit is a powerful software engineering case toolkit for requirements specification, simulation and documentation. LogiKit also provides an automatic ADA software design, code and unit test generator.

Applications of automatic differentiation in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Carle, A.; Bischof, C.; Haigler, Kara J.; Newman, Perry A.

1994-01-01

Automatic differentiation (AD) is a powerful computational method that provides for computing exact sensitivity derivatives (SD) from existing computer programs for multidisciplinary design optimization (MDO) or in sensitivity analysis. A pre-compiler AD tool for FORTRAN programs called ADIFOR has been developed. The ADIFOR tool has been easily and quickly applied by NASA Langley researchers to assess the feasibility and computational impact of AD in MDO with several different FORTRAN programs. These include a state-of-the-art three dimensional multigrid Navier-Stokes flow solver for wings or aircraft configurations in transonic turbulent flow. With ADIFOR the user specifies sets of independent and dependent variables with an existing computer code. ADIFOR then traces the dependency path throughout the code, applies the chain rule to formulate derivative expressions, and generates new code to compute the required SD matrix. The resulting codes have been verified to compute exact non-geometric and geometric SD for a variety of cases. in less time than is required to compute the SD matrix using centered divided differences.

Automatic choroid cells segmentation and counting based on approximate convexity and concavity of chain code in fluorescence microscopic image

NASA Astrophysics Data System (ADS)

Lu, Weihua; Chen, Xinjian; Zhu, Weifang; Yang, Lei; Cao, Zhaoyuan; Chen, Haoyu

2015-03-01

In this paper, we proposed a method based on the Freeman chain code to segment and count rhesus choroid-retinal vascular endothelial cells (RF/6A) automatically for fluorescence microscopy images. The proposed method consists of four main steps. First, a threshold filter and morphological transform were applied to reduce the noise. Second, the boundary information was used to generate the Freeman chain codes. Third, the concave points were found based on the relationship between the difference of the chain code and the curvature. Finally, cells segmentation and counting were completed based on the characteristics of the number of the concave points, the area and shape of the cells. The proposed method was tested on 100 fluorescence microscopic cell images, and the average true positive rate (TPR) is 98.13% and the average false positive rate (FPR) is 4.47%, respectively. The preliminary results showed the feasibility and efficiency of the proposed method.

Automatic Generation of Algorithms for the Statistical Analysis of Planetary Nebulae Images

NASA Technical Reports Server (NTRS)

Fischer, Bernd

2004-01-01

Analyzing data sets collected in experiments or by observations is a Core scientific activity. Typically, experimentd and observational data are &aught with uncertainty, and the analysis is based on a statistical model of the conjectured underlying processes, The large data volumes collected by modern instruments make computer support indispensible for this. Consequently, scientists spend significant amounts of their time with the development and refinement of the data analysis programs. AutoBayes [GF+02, FS03] is a fully automatic synthesis system for generating statistical data analysis programs. Externally, it looks like a compiler: it takes an abstract problem specification and translates it into executable code. Its input is a concise description of a data analysis problem in the form of a statistical model as shown in Figure 1; its output is optimized and fully documented C/C++ code which can be linked dynamically into the Matlab and Octave environments. Internally, however, it is quite different: AutoBayes derives a customized algorithm implementing the given model using a schema-based process, and then further refines and optimizes the algorithm into code. A schema is a parameterized code template with associated semantic constraints which define and restrict the template s applicability. The schema parameters are instantiated in a problem-specific way during synthesis as AutoBayes checks the constraints against the original model or, recursively, against emerging sub-problems. AutoBayes schema library contains problem decomposition operators (which are justified by theorems in a formal logic in the domain of Bayesian networks) as well as machine learning algorithms (e.g., EM, k-Means) and nu- meric optimization methods (e.g., Nelder-Mead simplex, conjugate gradient). AutoBayes augments this schema-based approach by symbolic computation to derive closed-form solutions whenever possible. This is a major advantage over other statistical data analysis systems which use numerical approximations even in cases where closed-form solutions exist. AutoBayes is implemented in Prolog and comprises approximately 75.000 lines of code. In this paper, we take one typical scientific data analysis problem-analyzing planetary nebulae images taken by the Hubble Space Telescope-and show how AutoBayes can be used to automate the implementation of the necessary anal- ysis programs. We initially follow the analysis described by Knuth and Hajian [KHO2] and use AutoBayes to derive code for the published models. We show the details of the code derivation process, including the symbolic computations and automatic integration of library procedures, and compare the results of the automatically generated and manually implemented code. We then go beyond the original analysis and use AutoBayes to derive code for a simple image segmentation procedure based on a mixture model which can be used to automate a manual preproceesing step. Finally, we combine the original approach with the simple segmentation which yields a more detailed analysis. This also demonstrates that AutoBayes makes it easy to combine different aspects of data analysis.

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations

NASA Astrophysics Data System (ADS)

Laloo, Jalal Z. A.; Laloo, Nassirah; Rhyman, Lydia; Ramasami, Ponnadurai

2017-07-01

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations.

PubMed

Laloo, Jalal Z A; Laloo, Nassirah; Rhyman, Lydia; Ramasami, Ponnadurai

2017-07-01

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.

Original data preprocessor for Femap/Nastran

NASA Astrophysics Data System (ADS)

Oanta, Emil M.; Panait, Cornel; Raicu, Alexandra

2016-12-01

Automatic data processing and visualization in the finite elements analysis of the structural problems is a long run concern in mechanical engineering. The paper presents the `common database' concept according to which the same information may be accessed from an analytical model, as well as from a numerical one. In this way, input data expressed as comma-separated-value (CSV) files are loaded into the Femap/Nastran environment using original API codes, being automatically generated: the geometry of the model, the loads and the constraints. The original API computer codes are general, being possible to generate the input data of any model. In the next stages, the user may create the discretization of the model, set the boundary conditions and perform a given analysis. If additional accuracy is needed, the analyst may delete the previous discretizations and using the same information automatically loaded, other discretizations and analyses may be done. Moreover, if new more accurate information regarding the loads or constraints is acquired, they may be modelled and then implemented in the data generating program which creates the `common database'. This means that new more accurate models may be easily generated. Other facility consists of the opportunity to control the CSV input files, several loading scenarios being possible to be generated in Femap/Nastran. In this way, using original intelligent API instruments the analyst is focused to accurately model the phenomena and on creative aspects, the repetitive and time-consuming activities being performed by the original computer-based instruments. Using this data processing technique we apply to the best Asimov's principle `minimum change required / maximum desired response'.

Systems, methods and apparatus for generation and verification of policies in autonomic computing systems

NASA Technical Reports Server (NTRS)

Rouff, Christopher A. (Inventor); Sterritt, Roy (Inventor); Truszkowski, Walter F. (Inventor); Hinchey, Michael G. (Inventor); Gracanin, Denis (Inventor); Rash, James L. (Inventor)

2011-01-01

Described herein is a method that produces fully (mathematically) tractable development of policies for autonomic systems from requirements through to code generation. This method is illustrated through an example showing how user formulated policies can be translated into a formal mode which can then be converted to code. The requirements-based programming method described provides faster, higher quality development and maintenance of autonomic systems based on user formulation of policies.Further, the systems, methods and apparatus described herein provide a way of analyzing policies for autonomic systems and facilities the generation of provably correct implementations automatically, which in turn provides reduced development time, reduced testing requirements, guarantees of correctness of the implementation with respect to the policies specified at the outset, and provides a higher degree of confidence that the policies are both complete and reasonable. The ability to specify the policy for the management of a system and then automatically generate an equivalent implementation greatly improves the quality of software, the survivability of future missions, in particular when the system will operate untended in very remote environments, and greatly reduces development lead times and costs.

Automated Testcase Generation for Numerical Support Functions in Embedded Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Schnieder, Stefan-Alexander

2014-01-01

We present a tool for the automatic generation of test stimuli for small numerical support functions, e.g., code for trigonometric functions, quaternions, filters, or table lookup. Our tool is based on KLEE to produce a set of test stimuli for full path coverage. We use a method of iterative deepening over abstractions to deal with floating-point values. During actual testing the stimuli exercise the code against a reference implementation. We illustrate our approach with results of experiments with low-level trigonometric functions, interpolation routines, and mathematical support functions from an open source UAS autopilot.

GRASP/Ada (Graphical Representations of Algorithms, Structures, and Processes for Ada): The development of a program analysis environment for Ada. Reverse engineering tools for Ada, task 1, phase 2

NASA Technical Reports Server (NTRS)

Cross, James H., II

1990-01-01

The study, formulation, and generation of structures for Ada (GRASP/Ada) are discussed in this second phase report of a three phase effort. Various graphical representations that can be extracted or generated from source code are described and categorized with focus on reverse engineering. The overall goal is to provide the foundation for a CASE (computer-aided software design) environment in which reverse engineering and forward engineering (development) are tightly coupled. Emphasis is on a subset of architectural diagrams that can be generated automatically from source code with the control structure diagram (CSD) included for completeness.

The Development of the Ducted Fan Noise Propagation and Radiation Code CDUCT-LaRC

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Farassat, F.; Pope, D. Stuart; Vatsa, Veer

2003-01-01

The development of the ducted fan noise propagation and radiation code CDUCT-LaRC at NASA Langley Research Center is described. This code calculates the propagation and radiation of given acoustic modes ahead of the fan face or aft of the exhaust guide vanes in the inlet or exhaust ducts, respectively. This paper gives a description of the modules comprising CDUCT-LaRC. The grid generation module provides automatic creation of numerical grids for complex (non-axisymmetric) geometries that include single or multiple pylons. Files for performing automatic inviscid mean flow calculations are also generated within this module. The duct propagation is based on the parabolic approximation theory of R. P. Dougherty. This theory allows the handling of complex internal geometries and the ability to study the effect of non-uniform (i.e. circumferentially and axially segmented) liners. Finally, the duct radiation module is based on the Ffowcs Williams-Hawkings (FW-H) equation with a penetrable data surface. Refraction of sound through the shear layer between the external flow and bypass duct flow is included. Results for benchmark annular ducts, as well as other geometries with pylons, are presented and compared with available analytical data.

Optimization Issues with Complex Rotorcraft Comprehensive Analysis

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Young, Katherine C.; Tarzanin, Frank J.; Hirsh, Joel E.; Young, Darrell K.

1998-01-01

This paper investigates the use of the general purpose automatic differentiation (AD) tool called Automatic Differentiation of FORTRAN (ADIFOR) as a means of generating sensitivity derivatives for use in Boeing Helicopter's proprietary comprehensive rotor analysis code (VII). ADIFOR transforms an existing computer program into a new program that performs a sensitivity analysis in addition to the original analysis. In this study both the pros (exact derivatives, no step-size problems) and cons (more CPU, more memory) of ADIFOR are discussed. The size (based on the number of lines) of the VII code after ADIFOR processing increased by 70 percent and resulted in substantial computer memory requirements at execution. The ADIFOR derivatives took about 75 percent longer to compute than the finite-difference derivatives. However, the ADIFOR derivatives are exact and are not functions of step-size. The VII sensitivity derivatives generated by ADIFOR are compared with finite-difference derivatives. The ADIFOR and finite-difference derivatives are used in three optimization schemes to solve a low vibration rotor design problem.

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Development of Automated Procedures to Generate Reference Building Models for ASHRAE Standard 90.1 and India’s Building Energy Code and Implementation in OpenStudio

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

Parker, Andrew; Haves, Philip; Jegi, Subhash

This paper describes a software system for automatically generating a reference (baseline) building energy model from the proposed (as-designed) building energy model. This system is built using the OpenStudio Software Development Kit (SDK) and is designed to operate on building energy models in the OpenStudio file format.

Automatic Data Traffic Control on DSM Architecture

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Jin, Hao-Qiang; Yan, Jerry; Kwak, Dochan (Technical Monitor)

2000-01-01

We study data traffic on distributed shared memory machines and conclude that data placement and grouping improve performance of scientific codes. We present several methods which user can employ to improve data traffic in his code. We report on implementation of a tool which detects the code fragments causing data congestions and advises user on improvements of data routing in these fragments. The capabilities of the tool include deduction of data alignment and affinity from the source code; detection of the code constructs having abnormally high cache or TLB misses; generation of data placement constructs. We demonstrate the capabilities of the tool on experiments with NAS parallel benchmarks and with a simple computational fluid dynamics application ARC3D.

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

A Survey of Automatic Code Generating Software

DTIC Science & Technology

1988-09-01

11189 Cincinnati, OH 45211 513-662-2300 69 LIST OF REFERENCES 1. Boehm, Barry W., "Software and Its Impact: A Quantita- tive Assessment," Daamtin, Vol...Decision SuDvort Systems: An Organizational Perspective, pp. 11- 12, Addison-Wesley Publishing Company, Inc., 1978. 6. Pressman , Roger S., Software

UFO - The Universal FEYNRULES Output

NASA Astrophysics Data System (ADS)

Degrande, Céline; Duhr, Claude; Fuks, Benjamin; Grellscheid, David; Mattelaer, Olivier; Reiter, Thomas

2012-06-01

We present a new model format for automatized matrix-element generators, the so-called Universal FEYNRULES Output (UFO). The format is universal in the sense that it features compatibility with more than one single generator and is designed to be flexible, modular and agnostic of any assumption such as the number of particles or the color and Lorentz structures appearing in the interaction vertices. Unlike other model formats where text files need to be parsed, the information on the model is encoded into a PYTHON module that can easily be linked to other computer codes. We then describe an interface for the MATHEMATICA package FEYNRULES that allows for an automatic output of models in the UFO format.

Putting Priors in Mixture Density Mercer Kernels

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2004-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly infinite dimensional feature space. We describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using predefined kernels. These data adaptive kernels can en- code prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS). The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains template for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic- algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code. The results show that the Mixture Density Mercer-Kernel described here outperforms tree-based classification in distinguishing high-redshift galaxies from low- redshift galaxies by approximately 16% on test data, bagged trees by approximately 7%, and bagged trees built on a much larger sample of data by approximately 2%.

Virtual Engineering and Science Team - Reusable Autonomy for Spacecraft Subsystems

NASA Technical Reports Server (NTRS)

Bailin, Sidney C.; Johnson, Michael A.; Rilee, Michael L.; Truszkowski, Walt; Thompson, Bryan; Day, John H. (Technical Monitor)

2002-01-01

In this paper we address the design, development, and evaluation of the Virtual Engineering and Science Team (VEST) tool - a revolutionary way to achieve onboard subsystem/instrument autonomy. VEST directly addresses the technology needed for advanced autonomy enablers for spacecraft subsystems. It will significantly support the efficient and cost effective realization of on-board autonomy and contribute directly to realizing the concept of an intelligent autonomous spacecraft. VEST will support the evolution of a subsystem/instrument model that is probably correct and from that model the automatic generation of the code needed to support the autonomous operation of what was modeled. VEST will directly support the integration of the efforts of engineers, scientists, and software technologists. This integration of efforts will be a significant advancement over the way things are currently accomplished. The model, developed through the use of VEST, will be the basis for the physical construction of the subsystem/instrument and the generated code will support its autonomous operation once in space. The close coupling between the model and the code, in the same tool environment, will help ensure that correct and reliable operational control of the subsystem/instrument is achieved.VEST will provide a thoroughly modern interface that will allow users to easily and intuitively input subsystem/instrument requirements and visually get back the system's reaction to the correctness and compatibility of the inputs as the model evolves. User interface/interaction, logic, theorem proving, rule-based and model-based reasoning, and automatic code generation are some of the basic technologies that will be brought into play in realizing VEST.

Generating Safety-Critical PLC Code From a High-Level Application Software Specification

NASA Technical Reports Server (NTRS)

2008-01-01

The benefits of automatic-application code generation are widely accepted within the software engineering community. These benefits include raised abstraction level of application programming, shorter product development time, lower maintenance costs, and increased code quality and consistency. Surprisingly, code generation concepts have not yet found wide acceptance and use in the field of programmable logic controller (PLC) software development. Software engineers at Kennedy Space Center recognized the need for PLC code generation while developing the new ground checkout and launch processing system, called the Launch Control System (LCS). Engineers developed a process and a prototype software tool that automatically translates a high-level representation or specification of application software into ladder logic that executes on a PLC. All the computer hardware in the LCS is planned to be commercial off the shelf (COTS), including industrial controllers or PLCs that are connected to the sensors and end items out in the field. Most of the software in LCS is also planned to be COTS, with only small adapter software modules that must be developed in order to interface between the various COTS software products. A domain-specific language (DSL) is a programming language designed to perform tasks and to solve problems in a particular domain, such as ground processing of launch vehicles. The LCS engineers created a DSL for developing test sequences of ground checkout and launch operations of future launch vehicle and spacecraft elements, and they are developing a tabular specification format that uses the DSL keywords and functions familiar to the ground and flight system users. The tabular specification format, or tabular spec, allows most ground and flight system users to document how the application software is intended to function and requires little or no software programming knowledge or experience. A small sample from a prototype tabular spec application is shown.

Testing Strategies for Model-Based Development

NASA Technical Reports Server (NTRS)

Heimdahl, Mats P. E.; Whalen, Mike; Rajan, Ajitha; Miller, Steven P.

2006-01-01

This report presents an approach for testing artifacts generated in a model-based development process. This approach divides the traditional testing process into two parts: requirements-based testing (validation testing) which determines whether the model implements the high-level requirements and model-based testing (conformance testing) which determines whether the code generated from a model is behaviorally equivalent to the model. The goals of the two processes differ significantly and this report explores suitable testing metrics and automation strategies for each. To support requirements-based testing, we define novel objective requirements coverage metrics similar to existing specification and code coverage metrics. For model-based testing, we briefly describe automation strategies and examine the fault-finding capability of different structural coverage metrics using tests automatically generated from the model.

Analysis and Defense of Vulnerabilities in Binary Code

DTIC Science & Technology

2008-09-29

language . We demonstrate our techniques by automatically generating input filters from vulnerable binary programs. vi Acknowledgments I thank my wife, family...21 2.2 The Vine Intermediate Language . . . . . . . . . . . . . . . . . . . . . . 21 ix 2.2.1 Normalized Memory...The Traditional Weakest Precondition Semantics . . . . . . . . . . . . . 44 3.2.1 The Guarded Command Language . . . . . . . . . . . . . . . . . 44

Method for rapid high-frequency seismogram calculation

NASA Astrophysics Data System (ADS)

Stabile, Tony Alfredo; De Matteis, Raffaella; Zollo, Aldo

2009-02-01

We present a method for rapid, high-frequency seismogram calculation that makes use of an algorithm to automatically generate an exhaustive set of seismic phases with an appreciable amplitude on the seismogram. The method uses a hierarchical order of ray and seismic-phase generation, taking into account some existing constraints for ray paths and some physical constraints. To compute synthetic seismograms, the COMRAD code (from the Italian: "COdice Multifase per il RAy-tracing Dinamico") uses as core a dynamic ray-tracing code. To validate the code, we have computed in a layered medium synthetic seismograms using both COMRAD and a code that computes the complete wave field by the discrete wave number method. The seismograms are compared according to a time-frequency misfit criteria based on the continuous wavelet transform of the signals. Although the number of phases is considerably reduced by the selection criteria, the results show that the loss in amplitude on the whole seismogram is negligible. Moreover, the time for the computing of the synthetics using the COMRAD code (truncating the ray series at the 10th generation) is 3-4-fold less than that needed for the AXITRA code (up to a frequency of 25 Hz).

Automatic Coding of Short Text Responses via Clustering in Educational Assessment

ERIC Educational Resources Information Center

Zehner, Fabian; Sälzer, Christine; Goldhammer, Frank

2016-01-01

Automatic coding of short text responses opens new doors in assessment. We implemented and integrated baseline methods of natural language processing and statistical modelling by means of software components that are available under open licenses. The accuracy of automatic text coding is demonstrated by using data collected in the "Programme…

ONR Far East Scientific Bulletin, Volume 7, Number 2, April-June 1982,

DTIC Science & Technology

1982-01-01

contained source code . - PAL (Program Automation Language) PAL is a system design language that automatically generates an executable program from a...NTIS c3&1 DTIC TliB Unn ’l.- A ElJustitt for _ By - Distrib~tion Availability Codes Avail and/or Di st Speojal iii 0- CONTENTS~ P age r’A Gflmpse at...tools exist at ECL in prototype forms. Like most major computer manufacturers, they have also extended high level languages such as FORTRAN , COBOL

An Ensemble Approach to Building Mercer Kernels with Prior Information

NASA Technical Reports Server (NTRS)

Srivastava, Ashok N.; Schumann, Johann; Fischer, Bernd

2005-01-01

This paper presents a new methodology for automatic knowledge driven data mining based on the theory of Mercer Kernels, which are highly nonlinear symmetric positive definite mappings from the original image space to a very high, possibly dimensional feature space. we describe a new method called Mixture Density Mercer Kernels to learn kernel function directly from data, rather than using pre-defined kernels. These data adaptive kernels can encode prior knowledge in the kernel using a Bayesian formulation, thus allowing for physical information to be encoded in the model. Specifically, we demonstrate the use of the algorithm in situations with extremely small samples of data. We compare the results with existing algorithms on data from the Sloan Digital Sky Survey (SDSS) and demonstrate the method's superior performance against standard methods. The code for these experiments has been generated with the AUTOBAYES tool, which automatically generates efficient and documented C/C++ code from abstract statistical model specifications. The core of the system is a schema library which contains templates for learning and knowledge discovery algorithms like different versions of EM, or numeric optimization methods like conjugate gradient methods. The template instantiation is supported by symbolic-algebraic computations, which allows AUTOBAYES to find closed-form solutions and, where possible, to integrate them into the code.

Domain Specific Language Support for Exascale

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

Sadayappan, Ponnuswamy

Domain-Specific Languages (DSLs) offer an attractive path to Exascale software since they provide expressive power through appropriate abstractions and enable domain-specific optimizations. But the advantages of a DSL compete with the difficulties of implementing a DSL, even for a narrowly defined domain. The DTEC project addresses how a variety of DSLs can be easily implemented to leverage existing compiler analysis and transformation capabilities within the ROSE open source compiler as part of a research program focusing on Exascale challenges. The OSU contributions to the DTEC project are in the area of code generation from high-level DSL descriptions, as well asmore » verification of the automatically-generated code.« less

Automatic computer procedure for generating exact and analytical kinetic energy operators based on the polyspherical approach: General formulation and removal of singularities

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

Ndong, Mamadou; Lauvergnat, David; Nauts, André

2013-11-28

We present new techniques for an automatic computation of the kinetic energy operator in analytical form. These techniques are based on the use of the polyspherical approach and are extended to take into account Cartesian coordinates as well. An automatic procedure is developed where analytical expressions are obtained by symbolic calculations. This procedure is a full generalization of the one presented in Ndong et al., [J. Chem. Phys. 136, 034107 (2012)]. The correctness of the new implementation is analyzed by comparison with results obtained from the TNUM program. We give several illustrations that could be useful for users of themore » code. In particular, we discuss some cyclic compounds which are important in photochemistry. Among others, we show that choosing a well-adapted parameterization and decomposition into subsystems can allow one to avoid singularities in the kinetic energy operator. We also discuss a relation between polyspherical and Z-matrix coordinates: this comparison could be helpful for building an interface between the new code and a quantum chemistry package.« less

a New Approach for the Semi-Automatic Texture Generation of the Buildings Facades, from Terrestrial Laser Scanner Data

NASA Astrophysics Data System (ADS)

Oniga, E.

2012-07-01

The result of the terrestrial laser scanning is an impressive number of spatial points, each of them being characterized as position by the X, Y and Z co-ordinates, by the value of the laser reflectance and their real color, expressed as RGB (Red, Green, Blue) values. The color code for each LIDAR point is taken from the georeferenced digital images, taken with a high resolution panoramic camera incorporated in the scanner system. In this article I propose a new algorithm for the semiautomatic texture generation, using the color information, the RGB values of every point that has been taken by terrestrial laser scanning technology and the 3D surfaces defining the buildings facades, generated with the Leica Cyclone software. The first step is when the operator defines the limiting value, i.e. the minimum distance between a point and the closest surface. The second step consists in calculating the distances, or the perpendiculars drawn from each point to the closest surface. In the third step we associate the points whose 3D coordinates are known, to every surface, depending on the limiting value. The fourth step consists in computing the Voronoi diagram for the points that belong to a surface. The final step brings automatic association between the RGB value of the color code and the corresponding polygon of the Voronoi diagram. The advantage of using this algorithm is that we can obtain, in a semi-automatic manner, a photorealistic 3D model of the building.

User`s and reference guide to the INEL RML/analytical radiochemistry sample tracking database version 1.00

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

Femec, D.A.

This report discusses the sample tracking database in use at the Idaho National Engineering Laboratory (INEL) by the Radiation Measurements Laboratory (RML) and Analytical Radiochemistry. The database was designed in-house to meet the specific needs of the RML and Analytical Radiochemistry. The report consists of two parts, a user`s guide and a reference guide. The user`s guide presents some of the fundamentals needed by anyone who will be using the database via its user interface. The reference guide describes the design of both the database and the user interface. Briefly mentioned in the reference guide are the code-generating tools, CREATE-SCHEMAmore » and BUILD-SCREEN, written to automatically generate code for the database and its user interface. The appendices contain the input files used by the these tools to create code for the sample tracking database. The output files generated by these tools are also included in the appendices.« less

Rapid algorithm prototyping and implementation for power quality measurement

NASA Astrophysics Data System (ADS)

Kołek, Krzysztof; Piątek, Krzysztof

2015-12-01

This article presents a Model-Based Design (MBD) approach to rapidly implement power quality (PQ) metering algorithms. Power supply quality is a very important aspect of modern power systems and will become even more important in future smart grids. In this case, maintaining the PQ parameters at the desired level will require efficient implementation methods of the metering algorithms. Currently, the development of new, advanced PQ metering algorithms requires new hardware with adequate computational capability and time intensive, cost-ineffective manual implementations. An alternative, considered here, is an MBD approach. The MBD approach focuses on the modelling and validation of the model by simulation, which is well-supported by a Computer-Aided Engineering (CAE) packages. This paper presents two algorithms utilized in modern PQ meters: a phase-locked loop based on an Enhanced Phase Locked Loop (EPLL), and the flicker measurement according to the IEC 61000-4-15 standard. The algorithms were chosen because of their complexity and non-trivial development. They were first modelled in the MATLAB/Simulink package, then tested and validated in a simulation environment. The models, in the form of Simulink diagrams, were next used to automatically generate C code. The code was compiled and executed in real-time on the Zynq Xilinx platform that combines a reconfigurable Field Programmable Gate Array (FPGA) with a dual-core processor. The MBD development of PQ algorithms, automatic code generation, and compilation form a rapid algorithm prototyping and implementation path for PQ measurements. The main advantage of this approach is the ability to focus on the design, validation, and testing stages while skipping over implementation issues. The code generation process renders production-ready code that can be easily used on the target hardware. This is especially important when standards for PQ measurement are in constant development, and the PQ issues in emerging smart grids will require tools for rapid development and implementation of such algorithms.

A manual for PARTI runtime primitives

NASA Technical Reports Server (NTRS)

Berryman, Harry; Saltz, Joel

1990-01-01

Primitives are presented that are designed to help users efficiently program irregular problems (e.g., unstructured mesh sweeps, sparse matrix codes, adaptive mesh partial differential equations solvers) on distributed memory machines. These primitives are also designed for use in compilers for distributed memory multiprocessors. Communications patterns are captured at runtime, and the appropriate send and receive messages are automatically generated.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

Automated Simplification of Full Chemical Mechanisms

NASA Technical Reports Server (NTRS)

Norris, A. T.

1997-01-01

A code has been developed to automatically simplify full chemical mechanisms. The method employed is based on the Intrinsic Low Dimensional Manifold (ILDM) method of Maas and Pope. The ILDM method is a dynamical systems approach to the simplification of large chemical kinetic mechanisms. By identifying low-dimensional attracting manifolds, the method allows complex full mechanisms to be parameterized by just a few variables; in effect, generating reduced chemical mechanisms by an automatic procedure. These resulting mechanisms however, still retain all the species used in the full mechanism. Full and skeletal mechanisms for various fuels are simplified to a two dimensional manifold, and the resulting mechanisms are found to compare well with the full mechanisms, and show significant improvement over global one step mechanisms, such as those by Westbrook and Dryer. In addition, by using an ILDM reaction mechanism in a CID code, a considerable improvement in turn-around time can be achieved.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

Auto identification technology and its impact on patient safety in the Operating Room of the Future.

PubMed

Egan, Marie T; Sandberg, Warren S

2007-03-01

Automatic identification technologies, such as bar coding and radio frequency identification, are ubiquitous in everyday life but virtually nonexistent in the operating room. User expectations, based on everyday experience with automatic identification technologies, have generated much anticipation that these systems will improve readiness, workflow, and safety in the operating room, with minimal training requirements. We report, in narrative form, a multi-year experience with various automatic identification technologies in the Operating Room of the Future Project at Massachusetts General Hospital. In each case, the additional human labor required to make these ;labor-saving' technologies function in the medical environment has proved to be their undoing. We conclude that while automatic identification technologies show promise, significant barriers to realizing their potential still exist. Nevertheless, overcoming these obstacles is necessary if the vision of an operating room of the future in which all processes are monitored, controlled, and optimized is to be achieved.

Design of efficient and simple interface testing equipment for opto-electric tracking system

NASA Astrophysics Data System (ADS)

Liu, Qiong; Deng, Chao; Tian, Jing; Mao, Yao

2016-10-01

Interface testing for opto-electric tracking system is one important work to assure system running performance, aiming to verify the design result of every electronic interface matching the communication protocols or not, by different levels. Opto-electric tracking system nowadays is more complicated, composed of many functional units. Usually, interface testing is executed between units manufactured completely, highly depending on unit design and manufacture progress as well as relative people. As a result, it always takes days or weeks, inefficiently. To solve the problem, this paper promotes an efficient and simple interface testing equipment for opto-electric tracking system, consisting of optional interface circuit card, processor and test program. The hardware cards provide matched hardware interface(s), easily offered from hardware engineer. Automatic code generation technique is imported, providing adaption to new communication protocols. Automatic acquiring items, automatic constructing code architecture and automatic encoding are used to form a new program quickly with adaption. After simple steps, a standard customized new interface testing equipment with matching test program and interface(s) is ready for a waiting-test system in minutes. The efficient and simple interface testing equipment for opto-electric tracking system has worked for many opto-electric tracking system to test entire or part interfaces, reducing test time from days to hours, greatly improving test efficiency, with high software quality and stability, without manual coding. Used as a common tool, the efficient and simple interface testing equipment for opto-electric tracking system promoted by this paper has changed traditional interface testing method and created much higher efficiency.

Cloudy - simulating the non-equilibrium microphysics of gas and dust, and its observed spectrum

NASA Astrophysics Data System (ADS)

Ferland, Gary J.

2014-01-01

Cloudy is an open-source plasma/spectral simulation code, last described in the open-access journal Revista Mexicana (Ferland et al. 2013, 2013RMxAA..49..137F). The project goal is a complete simulation of the microphysics of gas and dust over the full range of density, temperature, and ionization that we encounter in astrophysics, together with a prediction of the observed spectrum. Cloudy is one of the more widely used theory codes in astrophysics with roughly 200 papers citing its documentation each year. It is developed by graduate students, postdocs, and an international network of collaborators. Cloudy is freely available on the web at trac.nublado.org, the user community can post questions on http://groups.yahoo.com/neo/groups/cloudy_simulations/info, and summer schools are organized to learn more about Cloudy and its use (http://cloud9.pa.uky.edu gary/cloudy/CloudySummerSchool/). The code’s widespread use is possible because of extensive automatic testing. It is exercised over its full range of applicability whenever the source is changed. Changes in predicted quantities are automatically detected along with any newly introduced problems. The code is designed to be autonomous and self-aware. It generates a report at the end of a calculation that summarizes any problems encountered along with suggestions of potentially incorrect boundary conditions. This self-monitoring is a core feature since the code is now often used to generate large MPI grids of simulations, making it impossible for a user to verify each calculation by hand. I will describe some challenges in developing a large physics code, with its many interconnected physical processes, many at the frontier of research in atomic or molecular physics, all in an open environment.

Requirements to Design to Code: Towards a Fully Formal Approach to Automatic Code Generation

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Rouff, Christopher A.

2004-01-01

A general-purpose method to mechanically transform system requirements into a provably equivalent model has yet to appear. Such a method represents a necessary step toward high-dependability system engineering for numerous possible application domains, including sensor networks and autonomous systems. Currently available tools and methods that start with a formal model of a system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The gap that current tools and methods leave unfilled is that their formal models cannot be proven to be equivalent to the system requirements as originated by the customer. For the classes of systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements (expressed in restricted natural language, or in other appropriate graphical notations) into a provably equivalent formal model that can be used as the basis for code generation and other transformations.

An Efficient Functional Test Generation Method For Processors Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Hudec, Ján; Gramatová, Elena

2015-07-01

The paper presents a new functional test generation method for processors testing based on genetic algorithms and evolutionary strategies. The tests are generated over an instruction set architecture and a processor description. Such functional tests belong to the software-oriented testing. Quality of the tests is evaluated by code coverage of the processor description using simulation. The presented test generation method uses VHDL models of processors and the professional simulator ModelSim. The rules, parameters and fitness functions were defined for various genetic algorithms used in automatic test generation. Functionality and effectiveness were evaluated using the RISC type processor DP32.

Advanced information processing system: Hosting of advanced guidance, navigation and control algorithms on AIPS using ASTER

NASA Technical Reports Server (NTRS)

Brenner, Richard; Lala, Jaynarayan H.; Nagle, Gail A.; Schor, Andrei; Turkovich, John

1994-01-01

This program demonstrated the integration of a number of technologies that can increase the availability and reliability of launch vehicles while lowering costs. Availability is increased with an advanced guidance algorithm that adapts trajectories in real-time. Reliability is increased with fault-tolerant computers and communication protocols. Costs are reduced by automatically generating code and documentation. This program was realized through the cooperative efforts of academia, industry, and government. The NASA-LaRC coordinated the effort, while Draper performed the integration. Georgia Institute of Technology supplied a weak Hamiltonian finite element method for optimal control problems. Martin Marietta used MATLAB to apply this method to a launch vehicle (FENOC). Draper supplied the fault-tolerant computing and software automation technology. The fault-tolerant technology includes sequential and parallel fault-tolerant processors (FTP & FTPP) and authentication protocols (AP) for communication. Fault-tolerant technology was incrementally incorporated. Development culminated with a heterogeneous network of workstations and fault-tolerant computers using AP. Draper's software automation system, ASTER, was used to specify a static guidance system based on FENOC, navigation, flight control (GN&C), models, and the interface to a user interface for mission control. ASTER generated Ada code for GN&C and C code for models. An algebraic transform engine (ATE) was developed to automatically translate MATLAB scripts into ASTER.

Automating FEA programming

NASA Technical Reports Server (NTRS)

Sharma, Naveen

1992-01-01

In this paper we briefly describe a combined symbolic and numeric approach for solving mathematical models on parallel computers. An experimental software system, PIER, is being developed in Common Lisp to synthesize computationally intensive and domain formulation dependent phases of finite element analysis (FEA) solution methods. Quantities for domain formulation like shape functions, element stiffness matrices, etc., are automatically derived using symbolic mathematical computations. The problem specific information and derived formulae are then used to generate (parallel) numerical code for FEA solution steps. A constructive approach to specify a numerical program design is taken. The code generator compiles application oriented input specifications into (parallel) FORTRAN77 routines with the help of built-in knowledge of the particular problem, numerical solution methods and the target computer.

3DGRAPE/AL User's Manual

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.; Alter, Stephen J.

1995-01-01

This document is a users' manual for a new three-dimensional structured multiple-block volume g generator called 3DGRAPE/AL. It is a significantly improved version of the previously-released a widely-distributed programs 3DGRAPE and 3DMAGGS. It generates volume grids by iteratively solving the Poisson Equations in three-dimensions. The right-hand-side terms are designed so that user-specific; grid cell heights and user-specified grid cell skewness near boundary surfaces result automatically, with little user intervention. The code is written in Fortran-77, and can be installed with or without a simple graphical user interface which allows the user to watch as the grid is generated. An introduction describing the improvements over the antecedent 3DGRAPE code is presented first. Then follows a chapter on the basic grid generator program itself, and comments on installing it. The input is then described in detail. After that is a description of the Graphical User Interface. Five example cases are shown next, with plots of the results. Following that is a chapter on two input filters which allow use of input data generated elsewhere. Last is a treatment of the theory embodied in 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.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Automatic scheduling of outages of nuclear power plants with time windows. Final report, January-December 1995

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

Gomes, C.

This report describes a successful project for transference of advanced AI technology into the domain of planning of outages of nuclear power plants as part of DOD`s dual-use program. ROMAN (Rome Lab Outage Manager) is the prototype system that was developed as a result of this project. ROMAN`s main innovation compared to the current state-of-the-art of outage management tools is its capability to automatically enforce safety constraints during the planning and scheduling phase. Another innovative aspect of ROMAN is the generation of more robust schedules that are feasible over time windows. In other words, ROMAN generates a family of schedulesmore » by assigning time intervals as start times to activities rather than single start times, without affecting the overall duration of the project. ROMAN uses a constraint satisfaction paradigm combining a global search tactic with constraint propagation. The derivation of very specialized representations for the constraints to perform efficient propagation is a key aspect for the generation of very fast schedules - constraints are compiled into the code, which is a novel aspect of our work using an automatic programming system, KIDS.« less

Accuracy of automatic syndromic classification of coded emergency department diagnoses in identifying mental health-related presentations for public health surveillance.

PubMed

Liljeqvist, Henning T G; Muscatello, David; Sara, Grant; Dinh, Michael; Lawrence, Glenda L

2014-09-23

Syndromic surveillance in emergency departments (EDs) may be used to deliver early warnings of increases in disease activity, to provide situational awareness during events of public health significance, to supplement other information on trends in acute disease and injury, and to support the development and monitoring of prevention or response strategies. Changes in mental health related ED presentations may be relevant to these goals, provided they can be identified accurately and efficiently. This study aimed to measure the accuracy of using diagnostic codes in electronic ED presentation records to identify mental health-related visits. We selected a random sample of 500 records from a total of 1,815,588 ED electronic presentation records from 59 NSW public hospitals during 2010. ED diagnoses were recorded using any of ICD-9, ICD-10 or SNOMED CT classifications. Three clinicians, blinded to the automatically generated syndromic grouping and each other's classification, reviewed the triage notes and classified each of the 500 visits as mental health-related or not. A "mental health problem presentation" for the purposes of this study was defined as any ED presentation where either a mental disorder or a mental health problem was the reason for the ED visit. The combined clinicians' assessment of the records was used as reference standard to measure the sensitivity, specificity, and positive and negative predictive values of the automatic classification of coded emergency department diagnoses. Agreement between the reference standard and the automated coded classification was estimated using the Kappa statistic. Agreement between clinician's classification and automated coded classification was substantial (Kappa = 0.73. 95% CI: 0.58 - 0.87). The automatic syndromic grouping of coded ED diagnoses for mental health-related visits was found to be moderately sensitive (68% 95% CI: 46%-84%) and highly specific at 99% (95% CI: 98%-99.7%) when compared with the reference standard in identifying mental health related ED visits. Positive predictive value was 81% (95% CI: 0.57 - 0.94) and negative predictive value was 98% (95% CI: 0.97-0.99). Mental health presentations identified using diagnoses coded with various classifications in electronic ED presentation records offers sufficient accuracy for application in near real-time syndromic surveillance.

Automatic Multilevel Parallelization Using OpenMP

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

2002-01-01

In this paper we describe the extension of the CAPO parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report first results for several benchmark codes and one full application that have been parallelized using our system.

The Classification and Evaluation of Computer-Aided Software Engineering Tools

DTIC Science & Technology

1990-09-01

International Business Machines Corporation Customizer is a Registered Trademark of Index Technology Corporation Data Analyst is a Registered Trademark of...years, a rapid series of new approaches have been adopted including: information engineering, entity- relationship modeling, automatic code generation...support true information sharing among tools and automated consistency checking. Moreover, the repository must record and manage the relationships and

A manual for PARTI runtime primitives, revision 1

NASA Technical Reports Server (NTRS)

Das, Raja; Saltz, Joel; Berryman, Harry

1991-01-01

Primitives are presented that are designed to help users efficiently program irregular problems (e.g., unstructured mesh sweeps, sparse matrix codes, adaptive mesh partial differential equations solvers) on distributed memory machines. These primitives are also designed for use in compilers for distributed memory multiprocessors. Communications patterns are captured at runtime, and the appropriate send and receive messages are automatically generated.

Evidence Arguments for Using Formal Methods in Software Certification

NASA Technical Reports Server (NTRS)

Denney, Ewen W.; Pai, Ganesh

2013-01-01

We describe a generic approach for automatically integrating the output generated from a formal method/tool into a software safety assurance case, as an evidence argument, by (a) encoding the underlying reasoning as a safety case pattern, and (b) instantiating it using the data produced from the method/tool. We believe this approach not only improves the trustworthiness of the evidence generated from a formal method/tool, by explicitly presenting the reasoning and mechanisms underlying its genesis, but also provides a way to gauge the suitability of the evidence in the context of the wider assurance case. We illustrate our work by application to a real example-an unmanned aircraft system- where we invoke a formal code analysis tool from its autopilot software safety case, automatically transform the verification output into an evidence argument, and then integrate it into the former.

A new user-assisted segmentation and tracking technique for an object-based video editing system

NASA Astrophysics Data System (ADS)

Yu, Hong Y.; Hong, Sung-Hoon; Lee, Mike M.; Choi, Jae-Gark

2004-03-01

This paper presents a semi-automatic segmentation method which can be used to generate video object plane (VOP) for object based coding scheme and multimedia authoring environment. Semi-automatic segmentation can be considered as a user-assisted segmentation technique. A user can initially mark objects of interest around the object boundaries and then the user-guided and selected objects are continuously separated from the unselected areas through time evolution in the image sequences. The proposed segmentation method consists of two processing steps: partially manual intra-frame segmentation and fully automatic inter-frame segmentation. The intra-frame segmentation incorporates user-assistance to define the meaningful complete visual object of interest to be segmentation and decides precise object boundary. The inter-frame segmentation involves boundary and region tracking to obtain temporal coherence of moving object based on the object boundary information of previous frame. The proposed method shows stable efficient results that could be suitable for many digital video applications such as multimedia contents authoring, content based coding and indexing. Based on these results, we have developed objects based video editing system with several convenient editing functions.

Explicit robust schemes for implementation of a class of principal value-based constitutive models: Symbolic and numeric implementation

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.; Tan, H. Q.; Zhang, Y.

1993-01-01

The issue of developing effective and robust schemes to implement a class of the Ogden-type hyperelastic constitutive models is addressed. To this end, special purpose functions (running under MACSYMA) are developed for the symbolic derivation, evaluation, and automatic FORTRAN code generation of explicit expressions for the corresponding stress function and material tangent stiffness tensors. These explicit forms are valid over the entire deformation range, since the singularities resulting from repeated principal-stretch values have been theoretically removed. The required computational algorithms are outlined, and the resulting FORTRAN computer code is presented.

Optimizing Tensor Contraction Expressions for Hybrid CPU-GPU Execution

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

Ma, Wenjing; Krishnamoorthy, Sriram; Villa, Oreste

2013-03-01

Tensor contractions are generalized multidimensional matrix multiplication operations that widely occur in quantum chemistry. Efficient execution of tensor contractions on Graphics Processing Units (GPUs) requires several challenges to be addressed, including index permutation and small dimension-sizes reducing thread block utilization. Moreover, to apply the same optimizations to various expressions, we need a code generation tool. In this paper, we present our approach to automatically generate CUDA code to execute tensor contractions on GPUs, including management of data movement between CPU and GPU. To evaluate our tool, GPU-enabled code is generated for the most expensive contractions in CCSD(T), a key coupledmore » cluster method, and incorporated into NWChem, a popular computational chemistry suite. For this method, we demonstrate speedup over a factor of 8.4 using one GPU (instead of one core per node) and over 2.6 when utilizing the entire system using hybrid CPU+GPU solution with 2 GPUs and 5 cores (instead of 7 cores per node). Finally, we analyze the implementation behavior on future GPU systems.« less

SOL - SIZING AND OPTIMIZATION LANGUAGE COMPILER

NASA Technical Reports Server (NTRS)

Scotti, S. J.

1994-01-01

SOL is a computer language which is geared to solving design problems. SOL includes the mathematical modeling and logical capabilities of a computer language like FORTRAN but also includes the additional power of non-linear mathematical programming methods (i.e. numerical optimization) at the language level (as opposed to the subroutine level). The language-level use of optimization has several advantages over the traditional, subroutine-calling method of using an optimizer: first, the optimization problem is described in a concise and clear manner which closely parallels the mathematical description of optimization; second, a seamless interface is automatically established between the optimizer subroutines and the mathematical model of the system being optimized; third, the results of an optimization (objective, design variables, constraints, termination criteria, and some or all of the optimization history) are output in a form directly related to the optimization description; and finally, automatic error checking and recovery from an ill-defined system model or optimization description is facilitated by the language-level specification of the optimization problem. Thus, SOL enables rapid generation of models and solutions for optimum design problems with greater confidence that the problem is posed correctly. The SOL compiler takes SOL-language statements and generates the equivalent FORTRAN code and system calls. Because of this approach, the modeling capabilities of SOL are extended by the ability to incorporate existing FORTRAN code into a SOL program. In addition, SOL has a powerful MACRO capability. The MACRO capability of the SOL compiler effectively gives the user the ability to extend the SOL language and can be used to develop easy-to-use shorthand methods of generating complex models and solution strategies. The SOL compiler provides syntactic and semantic error-checking, error recovery, and detailed reports containing cross-references to show where each variable was used. The listings summarize all optimizations, listing the objective functions, design variables, and constraints. The compiler offers error-checking specific to optimization problems, so that simple mistakes will not cost hours of debugging time. The optimization engine used by and included with the SOL compiler is a version of Vanderplatt's ADS system (Version 1.1) modified specifically to work with the SOL compiler. SOL allows the use of the over 100 ADS optimization choices such as Sequential Quadratic Programming, Modified Feasible Directions, interior and exterior penalty function and variable metric methods. Default choices of the many control parameters of ADS are made for the user, however, the user can override any of the ADS control parameters desired for each individual optimization. The SOL language and compiler were developed with an advanced compiler-generation system to ensure correctness and simplify program maintenance. Thus, SOL's syntax was defined precisely by a LALR(1) grammar and the SOL compiler's parser was generated automatically from the LALR(1) grammar with a parser-generator. Hence unlike ad hoc, manually coded interfaces, the SOL compiler's lexical analysis insures that the SOL compiler recognizes all legal SOL programs, can recover from and correct for many errors and report the location of errors to the user. This version of the SOL compiler has been implemented on VAX/VMS computer systems and requires 204 KB of virtual memory to execute. Since the SOL compiler produces FORTRAN code, it requires the VAX FORTRAN compiler to produce an executable program. The SOL compiler consists of 13,000 lines of Pascal code. It was developed in 1986 and last updated in 1988. The ADS and other utility subroutines amount to 14,000 lines of FORTRAN code and were also updated in 1988.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.

Automatic Coding of Dialogue Acts in Collaboration Protocols

ERIC Educational Resources Information Center

Erkens, Gijsbert; Janssen, Jeroen

2008-01-01

Although protocol analysis can be an important tool for researchers to investigate the process of collaboration and communication, the use of this method of analysis can be time consuming. Hence, an automatic coding procedure for coding dialogue acts was developed. This procedure helps to determine the communicative function of messages in online…

GPU-accelerated simulations of isolated black holes

NASA Astrophysics Data System (ADS)

Lewis, Adam G. M.; Pfeiffer, Harald P.

2018-05-01

We present a port of the numerical relativity code SpEC which is capable of running on NVIDIA GPUs. Since this code must be maintained in parallel with SpEC itself, a primary design consideration is to perform as few explicit code changes as possible. We therefore rely on a hierarchy of automated porting strategies. At the highest level we use TLoops, a C++ library of our design, to automatically emit CUDA code equivalent to tensorial expressions written into C++ source using a syntax similar to analytic calculation. Next, we trace out and cache explicit matrix representations of the numerous linear transformations in the SpEC code, which allows these to be performed on the GPU using pre-existing matrix-multiplication libraries. We port the few remaining important modules by hand. In this paper we detail the specifics of our port, and present benchmarks of it simulating isolated black hole spacetimes on several generations of NVIDIA GPU.

Cryptanalysis of the Sodark Family of Cipher Algorithms

DTIC Science & Technology

2017-09-01

software project for building three-bit LUT circuit representations of S- boxes is available as a GitHub repository [40]. It contains several improvements...DISTRIBUTION / AVAILABILITY STATEMENT Approved for public release. Distribution is unlimited. 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) The...second- and third-generation automatic link establishment (ALE) systems for high frequency radios. Radios utilizing ALE technology are in use by a

ASA24 enables multiple automatically coded self-administered 24-hour recalls and food records

Cancer.gov

A freely available web-based tool for epidemiologic, interventional, behavioral, or clinical research from NCI that enables multiple automatically coded self-administered 24-hour recalls and food records.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

A method for modeling co-occurrence propensity of clinical codes with application to ICD-10-PCS auto-coding.

PubMed

Subotin, Michael; Davis, Anthony R

2016-09-01

Natural language processing methods for medical auto-coding, or automatic generation of medical billing codes from electronic health records, generally assign each code independently of the others. They may thus assign codes for closely related procedures or diagnoses to the same document, even when they do not tend to occur together in practice, simply because the right choice can be difficult to infer from the clinical narrative. We propose a method that injects awareness of the propensities for code co-occurrence into this process. First, a model is trained to estimate the conditional probability that one code is assigned by a human coder, given than another code is known to have been assigned to the same document. Then, at runtime, an iterative algorithm is used to apply this model to the output of an existing statistical auto-coder to modify the confidence scores of the codes. We tested this method in combination with a primary auto-coder for International Statistical Classification of Diseases-10 procedure codes, achieving a 12% relative improvement in F-score over the primary auto-coder baseline. The proposed method can be used, with appropriate features, in combination with any auto-coder that generates codes with different levels of confidence. The promising results obtained for International Statistical Classification of Diseases-10 procedure codes suggest that the proposed method may have wider applications in auto-coding. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Crustal Fracturing Field and Presence of Fluid as Revealed by Seismic Anisotropy

NASA Astrophysics Data System (ADS)

Pastori, M.; Piccinini, D.; de Gori, P.; Margheriti, L.; Barchi, M. R.; di Bucci, D.

2010-12-01

In the last three years, we developed, tested and improved an automatic analysis code (Anisomat+) to calculate the shear wave splitting parameters, fast polarization direction (φ) and delay time (∂t). The code is a set of MatLab scripts able to retrieve crustal anisotropy parameters from three-component seismic recording of local earthquakes using horizontal component cross-correlation method. The analysis procedure consists in choosing an appropriate frequency range, that better highlights the signal containing the shear waves, and a length of time window on the seismogram centered on the S arrival (the temporal window contains at least one cycle of S wave). The code was compared to other two automatic analysis code (SPY and SHEBA) and tested on three Italian areas (Val d’Agri, Tiber Valley and L’Aquila surrounding) along the Apennine mountains. For each region we used the anisotropic parameters resulting from the automatic computation as a tool to determine the fracture field geometries connected with the active stress field. We compare the temporal variations of anisotropic parameters to the evolution of vp/vs ratio for the same seismicity. The anisotropic fast directions are used to define the active stress field (EDA model), finding a general consistence between fast direction and main stress indicators (focal mechanism and borehole break-out). The magnitude of delay time is used to define the fracture field intensity finding higher value in the volume where micro-seismicity occurs. Furthermore we studied temporal variations of anisotropic parameters and vp/vs ratio in order to explain if fluids play an important role in the earthquake generation process. The close association of anisotropic and vp/vs parameters variations and seismicity rate changes supports the hypothesis that the background seismicity is influenced by the fluctuation of pore fluid pressure in the rocks.

High-order space charge effects using automatic differentiation

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

Reusch, Michael F.; Bruhwiler, David L.; Computer Accelerator Physics Conference Williamsburg, Virginia 1996

1997-02-01

The Northrop Grumman Topkark code has been upgraded to Fortran 90, making use of operator overloading, so the same code can be used to either track an array of particles or construct a Taylor map representation of the accelerator lattice. We review beam optics and beam dynamics simulations conducted with TOPKARK in the past and we present a new method for modeling space charge forces to high-order with automatic differentiation. This method generates an accurate, high-order, 6-D Taylor map of the phase space variable trajectories for a bunched, high-current beam. The spatial distribution is modeled as the product of amore » Taylor Series times a Gaussian. The variables in the argument of the Gaussian are normalized to the respective second moments of the distribution. This form allows for accurate representation of a wide range of realistic distributions, including any asymmetries, and allows for rapid calculation of the space charge fields with free space boundary conditions. An example problem is presented to illustrate our approach.« less

Automated reduction of sub-millimetre single-dish heterodyne data from the James Clerk Maxwell Telescope using ORAC-DR

NASA Astrophysics Data System (ADS)

Jenness, Tim; Currie, Malcolm J.; Tilanus, Remo P. J.; Cavanagh, Brad; Berry, David S.; Leech, Jamie; Rizzi, Luca

2015-10-01

With the advent of modern multidetector heterodyne instruments that can result in observations generating thousands of spectra per minute it is no longer feasible to reduce these data as individual spectra. We describe the automated data reduction procedure used to generate baselined data cubes from heterodyne data obtained at the James Clerk Maxwell Telescope (JCMT). The system can automatically detect baseline regions in spectra and automatically determine regridding parameters, all without input from a user. Additionally, it can detect and remove spectra suffering from transient interference effects or anomalous baselines. The pipeline is written as a set of recipes using the ORAC-DR pipeline environment with the algorithmic code using Starlink software packages and infrastructure. The algorithms presented here can be applied to other heterodyne array instruments and have been applied to data from historical JCMT heterodyne instrumentation.

Requirements to Design to Code: Towards a Fully Formal Approach to Automatic Code Generation

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Rouff, Christopher A.

2005-01-01

A general-purpose method to mechanically transform system requirements into a provably equivalent model has yet to appear. Such a method represents a necessary step toward high-dependability system engineering for numerous possible application domains, including distributed software systems, sensor networks, robot operation, complex scripts for spacecraft integration and testing, and autonomous systems. Currently available tools and methods that start with a formal model of a system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The gap that current tools and methods leave unfilled is that their formal models cannot be proven to be equivalent to the system requirements as originated by the customer. For the classes of systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements (expressed in restricted natural language, or in other appropriate graphical notations) into a provably equivalent formal model that can be used as the basis for code generation and other transformations.

Requirements to Design to Code: Towards a Fully Formal Approach to Automatic Code Generation

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Rouff, Christopher A.

2005-01-01

A general-purpose method to mechanically transform system requirements into a provably equivalent model has yet to appear. Such a method represents a necessary step toward high-dependability system engineering for numerous possible application domains, including distributed software systems, sensor networks, robot operation, complex scripts for spacecraft integration and testing, and autonomous systems. Currently available tools and methods that start with a formal model of a: system and mechanically produce a provably equivalent implementation are valuable but not sufficient. The "gap" that current tools and methods leave unfilled is that their formal models cannot be proven to be equivalent to the system requirements as originated by the customer. For the ciasses of systems whose behavior can be described as a finite (but significant) set of scenarios, we offer a method for mechanically transforming requirements (expressed in restricted natural language, or in other appropriate graphical notations) into a provably equivalent formal model that can be used as the basis for code generation and other transformations.

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.

A review of automatic patient identification options for public health care centers with restricted budgets.

PubMed

García-Betances, Rebeca I; Huerta, Mónica K

2012-01-01

A comparative review is presented of available technologies suitable for automatic reading of patient identification bracelet tags. Existing technologies' backgrounds, characteristics, advantages and disadvantages, are described in relation to their possible use by public health care centers with budgetary limitations. A comparative assessment is presented of suitable automatic identification systems based on graphic codes, both one- (1D) and two-dimensional (2D), printed on labels, as well as those based on radio frequency identification (RFID) tags. The analysis looks at the tradeoffs of these technologies to provide guidance to hospital administrator looking to deploy patient identification technology. The results suggest that affordable automatic patient identification systems can be easily and inexpensively implemented using 2D code printed on low cost bracelet labels, which can then be read and automatically decoded by ordinary mobile smart phones. Because of mobile smart phones' present versatility and ubiquity, the implantation and operation of 2D code, and especially Quick Response® (QR) Code, technology emerges as a very attractive alternative to automate the patients' identification processes in low-budget situations.

A Review of Automatic Patient Identification Options for Public Health Care Centers with Restricted Budgets

PubMed Central

García-Betances, Rebeca I.; Huerta, Mónica K.

2012-01-01

A comparative review is presented of available technologies suitable for automatic reading of patient identification bracelet tags. Existing technologies’ backgrounds, characteristics, advantages and disadvantages, are described in relation to their possible use by public health care centers with budgetary limitations. A comparative assessment is presented of suitable automatic identification systems based on graphic codes, both one- (1D) and two-dimensional (2D), printed on labels, as well as those based on radio frequency identification (RFID) tags. The analysis looks at the tradeoffs of these technologies to provide guidance to hospital administrator looking to deploy patient identification technology. The results suggest that affordable automatic patient identification systems can be easily and inexpensively implemented using 2D code printed on low cost bracelet labels, which can then be read and automatically decoded by ordinary mobile smart phones. Because of mobile smart phones’ present versatility and ubiquity, the implantation and operation of 2D code, and especially Quick Response® (QR) Code, technology emerges as a very attractive alternative to automate the patients’ identification processes in low-budget situations. PMID:23569629

Automatic Multilevel Parallelization Using OpenMP

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

2002-01-01

In this paper we describe the extension of the CAPO (CAPtools (Computer Aided Parallelization Toolkit) OpenMP) parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report some results for several benchmark codes and one full application that have been parallelized using our system.

Detailed study of spontaneous rotation generation in diverted H-mode plasma using the full-f gyrokinetic code XGC1

NASA Astrophysics Data System (ADS)

Seo, Janghoon; Chang, C. S.; Ku, S.; Kwon, J. M.; Yoon, E. S.

2013-10-01

The Full-f gyrokinetic code XGC1 is used to study the details of toroidal momentum generation in H-mode plasma. Diverted DIII-D geometry is used, with Monte Carlo neutral particles that are recycled at the limiter wall. Nonlinear Coulomb collisions conserve particle, momentum, and energy. Gyrokinetic ions and adiabatic electrons are used in the present simulation to include the effects from ion gyrokinetic turbulence and neoclassical physics, under self-consistent radial electric field generation. Ion orbit loss physics is automatically included. Simulations show a strong co-Ip flow in the H-mode layer at outside midplane, similarly to the experimental observation from DIII-D and ASDEX-U. The co-Ip flow in the edge propagates inward into core. It is found that the strong co-Ip flow generation is mostly from neoclassical physics. On the other hand, the inward momentum transport is from turbulence physics, consistently with the theory of residual stress from symmetry breaking. Therefore, interaction between the neoclassical and turbulence physics is a key factor in the spontaneous momentum generation.

Data-driven backward chaining

NASA Technical Reports Server (NTRS)

Haley, Paul

1991-01-01

The C Language Integrated Production System (CLIPS) cannot effectively perform sound and complete logical inference in most real-world contexts. The problem facing CLIPS is its lack of goal generation. Without automatic goal generation and maintenance, forward chaining can only deduce all instances of a relationship. Backward chaining, which requires goal generation, allows deduction of only that subset of what is logically true which is also relevant to ongoing problem solving. Goal generation can be mimicked in simple cases using forward chaining. However, such mimicry requires manual coding of additional rules which can assert an inadequate goal representation for every condition in every rule that can have corresponding facts derived by backward chaining. In general, for N rules with an average of M conditions per rule the number of goal generation rules required is on the order of N*M. This is clearly intractable from a program maintenance perspective. We describe the support in Eclipse for backward chaining which it automatically asserts as it checks rule conditions. Important characteristics of this extension are that it does not assert goals which cannot match any rule conditions, that 2 equivalent goals are never asserted, and that goals persist as long as, but no longer than, they remain relevant.

A New Design Method of Automotive Electronic Real-time Control System

NASA Astrophysics Data System (ADS)

Zuo, Wenying; Li, Yinguo; Wang, Fengjuan; Hou, Xiaobo

Structure and functionality of automotive electronic control system is becoming more and more complex. The traditional manual programming development mode to realize automotive electronic control system can't satisfy development needs. So, in order to meet diversity and speedability of development of real-time control system, combining model-based design approach and auto code generation technology, this paper proposed a new design method of automotive electronic control system based on Simulink/RTW. Fristly, design algorithms and build a control system model in Matlab/Simulink. Then generate embedded code automatically by RTW and achieve automotive real-time control system development in OSEK/VDX operating system environment. The new development mode can significantly shorten the development cycle of automotive electronic control system, improve program's portability, reusability and scalability and had certain practical value for the development of real-time control system.

Palm: Easing the Burden of Analytical Performance Modeling

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

Tallent, Nathan R.; Hoisie, Adolfy

2014-06-01

Analytical (predictive) application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult because they must be both accurate and concise. To ease the burden of performance modeling, we developed Palm, a modeling tool that combines top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. To express insight, Palm defines a source code modeling annotation language. By coordinating models and source code, Palm's models are `first-class' and reproducible. Unlike prior work, Palm formally links models, functions, and measurements. As a result, Palm (a) uses functions to either abstract or express complexitymore » (b) generates hierarchical models (representing an application's static and dynamic structure); and (c) automatically incorporates measurements to focus attention, represent constant behavior, and validate models. We discuss generating models for three different applications.« less

Software engineering capability for Ada (GRASP/Ada Tool)

NASA Technical Reports Server (NTRS)

Cross, James H., II

1995-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada Source code. A new Motif compliant graphical user interface has been developed for the GRASP/Ada prototype.

High-fidelity simulations of blast loadings in urban environments using an overset meshing strategy

NASA Astrophysics Data System (ADS)

Wang, X.; Remotigue, M.; Arnoldus, Q.; Janus, M.; Luke, E.; Thompson, D.; Weed, R.; Bessette, G.

2017-05-01

Detailed blast propagation and evolution through multiple structures representing an urban environment were simulated using the code Loci/BLAST, which employs an overset meshing strategy. The use of overset meshes simplifies mesh generation by allowing meshes for individual component geometries to be generated independently. Detailed blast propagation and evolution through multiple structures, wave reflection and interaction between structures, and blast loadings on structures were simulated and analyzed. Predicted results showed good agreement with experimental data generated by the US Army Engineer Research and Development Center. Loci/BLAST results were also found to compare favorably to simulations obtained using the Second-Order Hydrodynamic Automatic Mesh Refinement Code (SHAMRC). The results obtained demonstrated that blast reflections in an urban setting significantly increased the blast loads on adjacent buildings. Correlations of computational results with experimental data yielded valuable insights into the physics of blast propagation, reflection, and interaction under an urban setting and verified the use of Loci/BLAST as a viable tool for urban blast analysis.

Parallel Calculation of Sensitivity Derivatives for Aircraft Design using Automatic Differentiation

NASA Technical Reports Server (NTRS)

Bischof, c. H.; Green, L. L.; Haigler, K. J.; Knauff, T. L., Jr.

1994-01-01

Sensitivity derivative (SD) calculation via automatic differentiation (AD) typical of that required for the aerodynamic design of a transport-type aircraft is considered. Two ways of computing SD via code generated by the ADIFOR automatic differentiation tool are compared for efficiency and applicability to problems involving large numbers of design variables. A vector implementation on a Cray Y-MP computer is compared with a coarse-grained parallel implementation on an IBM SP1 computer, employing a Fortran M wrapper. The SD are computed for a swept transport wing in turbulent, transonic flow; the number of geometric design variables varies from 1 to 60 with coupling between a wing grid generation program and a state-of-the-art, 3-D computational fluid dynamics program, both augmented for derivative computation via AD. For a small number of design variables, the Cray Y-MP implementation is much faster. As the number of design variables grows, however, the IBM SP1 becomes an attractive alternative in terms of compute speed, job turnaround time, and total memory available for solutions with large numbers of design variables. The coarse-grained parallel implementation also can be moved easily to a network of workstations.

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 System for Mailpiece ZIP Code Assignment through Contextual Analysis. Phase 2

DTIC Science & Technology

1991-03-01

Segmentation Address Block Interpretation Automatic Feature Generation Word Recognition Feature Detection Word Verification Optical Character Recognition Directory...in the Phase III effort. 1.1 Motivation The United States Postal Service (USPS) deploys large numbers of optical character recognition (OCR) machines...4):208-218, November 1986. [2] Gronmeyer, L. K., Ruffin, B. W., Lybanon, M. A., Neely, P. L., and Pierce, S. E. An Overview of Optical Character Recognition (OCR

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

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

NASA Technical Reports Server (NTRS)

Cooke, Daniel; Rushton, Nelson

2013-01-01

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less costly than development of comparable parallel code. Moreover, SequenceL not only automatically parallelizes the code, but since it is based on CSP-NT, it is provably race free, thus eliminating the largest quality challenge the parallelized software developer faces.

A preliminary architecture for building communication software from traffic captures

NASA Astrophysics Data System (ADS)

Acosta, Jaime C.; Estrada, Pedro

2017-05-01

Security analysts are tasked with identifying and mitigating network service vulnerabilities. A common problem associated with in-depth testing of network protocols is the availability of software that communicates across disparate protocols. Many times, the software required to communicate with these services is not publicly available. Developing this software is a time-consuming undertaking that requires expertise and understanding of the protocol specification. The work described in this paper aims at developing a software package that is capable of automatically creating communication clients by using packet capture (pcap) and TShark dissectors. Currently, our focus is on simple protocols with fixed fields. The methodologies developed as part of this work will extend to other complex protocols such as the Gateway Load Balancing Protocol (GLBP), Port Aggregation Protocol (PAgP), and Open Shortest Path First (OSPF). Thus far, we have architected a modular pipeline for an automatic traffic-based software generator. We start the transformation of captured network traffic by employing TShark to convert packets into a Packet Details Markup Language (PDML) file. The PDML file contains a parsed, textual, representation of the packet data. Then, we extract field data, types, along with inter and intra-packet dependencies. This information is then utilized to construct an XML file that encompasses the protocol state machine and field vocabulary. Finally, this XML is converted into executable code. Using our methodology, and as a starting point, we have succeeded in automatically generating software that communicates with other hosts using an automatically generated Internet Control Message Protocol (ICMP) client program.

Near-line Archive Data Mining at the Goddard Distributed Active Archive Center

NASA Astrophysics Data System (ADS)

Pham, L.; Mack, R.; Eng, E.; Lynnes, C.

2002-12-01

NASA's Earth Observing System (EOS) is generating immense volumes of data, in some cases too much to provide to users with data-intensive needs. As an alternative to moving the data to the user and his/her research algorithms, we are providing a means to move the algorithms to the data. The Near-line Archive Data Mining (NADM) system is the Goddard Earth Sciences Distributed Active Archive Center's (GES DAAC) web data mining portal to the EOS Data and Information System (EOSDIS) data pool, a 50-TB online disk cache. The NADM web portal enables registered users to submit and execute data mining algorithm codes on the data in the EOSDIS data pool. A web interface allows the user to access the NADM system. The users first develops personalized data mining code on their home platform and then uploads them to the NADM system. The C, FORTRAN and IDL languages are currently supported. The user developed code is automatically audited for any potential security problems before it is installed within the NADM system and made available to the user. Once the code has been installed the user is provided a test environment where he/she can test the execution of the software against data sets of the user's choosing. When the user is satisfied with the results, he/she can promote their code to the "operational" environment. From here the user can interactively run his/her code on the data available in the EOSDIS data pool. The user can also set up a processing subscription. The subscription will automatically process new data as it becomes available in the EOSDIS data pool. The generated mined data products are then made available for FTP pickup. The NADM system uses the GES DAAC-developed Simple Scalable Script-based Science Processor (S4P) to automate tasks and perform the actual data processing. Users will also have the option of selecting a DAAC-provided data mining algorithm and using it to process the data of their choice.

An automatic and efficient pipeline for disease gene identification through utilizing family-based sequencing data.

PubMed

Song, Dandan; Li, Ning; Liao, Lejian

2015-01-01

Due to the generation of enormous amounts of data at both lower costs as well as in shorter times, whole-exome sequencing technologies provide dramatic opportunities for identifying disease genes implicated in Mendelian disorders. Since upwards of thousands genomic variants can be sequenced in each exome, it is challenging to filter pathogenic variants in protein coding regions and reduce the number of missing true variants. Therefore, an automatic and efficient pipeline for finding disease variants in Mendelian disorders is designed by exploiting a combination of variants filtering steps to analyze the family-based exome sequencing approach. Recent studies on the Freeman-Sheldon disease are revisited and show that the proposed method outperforms other existing candidate gene identification methods.

Integration of QR codes into an anesthesia information management system for resident case log management.

PubMed

Avidan, Alexander; Weissman, Charles; Levin, Phillip D

2015-04-01

Quick response (QR) codes containing anesthesia syllabus data were introduced into an anesthesia information management system. The code was generated automatically at the conclusion of each case and available for resident case logging using a smartphone or tablet. The goal of this study was to evaluate the use and usability/user-friendliness of such system. Resident case logging practices were assessed prior to introducing the QR codes. QR code use and satisfactions amongst residents was reassessed at three and six months. Before QR code introduction only 12/23 (52.2%) residents maintained a case log. Most of the remaining residents (9/23, 39.1%) expected to receive a case list from the anesthesia information management system database at the end of their residency. At three months and six months 17/26 (65.4%) and 15/25 (60.0%) residents, respectively, were using the QR codes. Satisfaction was rated as very good or good. QR codes for residents' case logging with smartphones or tablets were successfully introduced in an anesthesia information management system and used by most residents. QR codes can be successfully implemented into medical practice to support data transfer. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

System and method for integrating and accessing multiple data sources within a data warehouse architecture

DOEpatents

Musick, Charles R [Castro Valley, CA; Critchlow, Terence [Livermore, CA; Ganesh, Madhaven [San Jose, CA; Slezak, Tom [Livermore, CA; Fidelis, Krzysztof [Brentwood, CA

2006-12-19

A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

BGen: A UML Behavior Network Generator Tool

NASA Technical Reports Server (NTRS)

Huntsberger, Terry; Reder, Leonard J.; Balian, Harry

2010-01-01

BGen software was designed for autogeneration of code based on a graphical representation of a behavior network used for controlling automatic vehicles. A common format used for describing a behavior network, such as that used in the JPL-developed behavior-based control system, CARACaS ["Control Architecture for Robotic Agent Command and Sensing" (NPO-43635), NASA Tech Briefs, Vol. 32, No. 10 (October 2008), page 40] includes a graph with sensory inputs flowing through the behaviors in order to generate the signals for the actuators that drive and steer the vehicle. A computer program to translate Unified Modeling Language (UML) Freeform Implementation Diagrams into a legacy C implementation of Behavior Network has been developed in order to simplify the development of C-code for behavior-based control systems. UML is a popular standard developed by the Object Management Group (OMG) to model software architectures graphically. The C implementation of a Behavior Network is functioning as a decision tree.

Applang - A DSL for specification of mobile applications for android platform based on textX

NASA Astrophysics Data System (ADS)

Kosanović, Milan; Dejanović, Igor; Milosavljević, Gordana

2016-06-01

Mobile platforms become a ubiquitous part of our daily lives thus making more pressure to software developers to develop more applications faster and with the support for different mobile operating systems. To foster the faster development of mobile services and applications and to support various mobile operating systems a new software development approaches must be undertaken. Domain-Specific Languages (DSL) are a viable approach that promise to solve a problem of target platform diversity as well as to facilitate rapid application development and shorter time-to-market. This paper presents Applang, a DSL for the specification of mobile applications for the Android platform, based on textX meta-language. The application is described using Applang DSL and the source code for a target platform is automatically generated by the provided code generator. The same application defined using single Applang source can be transformed to various targets with little or no manual modifications.

PODIO: An Event-Data-Model Toolkit for High Energy Physics Experiments

NASA Astrophysics Data System (ADS)

Gaede, F.; Hegner, B.; Mato, P.

2017-10-01

PODIO is a C++ library that supports the automatic creation of event data models (EDMs) and efficient I/O code for HEP experiments. It is developed as a new EDM Toolkit for future particle physics experiments in the context of the AIDA2020 EU programme. Experience from LHC and the linear collider community shows that existing solutions partly suffer from overly complex data models with deep object-hierarchies or unfavorable I/O performance. The PODIO project was created in order to address these problems. PODIO is based on the idea of employing plain-old-data (POD) data structures wherever possible, while avoiding deep object-hierarchies and virtual inheritance. At the same time it provides the necessary high-level interface towards the developer physicist, such as the support for inter-object relations and automatic memory-management, as well as a Python interface. To simplify the creation of efficient data models PODIO employs code generation from a simple yaml-based markup language. In addition, it was developed with concurrency in mind in order to support the use of modern CPU features, for example giving basic support for vectorization techniques.

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.

High-order space charge effects using automatic differentiation

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

Reusch, M.F.; Bruhwiler, D.L.

1997-02-01

The Northrop Grumman Topkark code has been upgraded to Fortran 90, making use of operator overloading, so the same code can be used to either track an array of particles or construct a Taylor map representation of the accelerator lattice. We review beam optics and beam dynamics simulations conducted with TOPKARK in the past and we present a new method for modeling space charge forces to high-order with automatic differentiation. This method generates an accurate, high-order, 6-D Taylor map of the phase space variable trajectories for a bunched, high-current beam. The spatial distribution is modeled as the product of amore » Taylor Series times a Gaussian. The variables in the argument of the Gaussian are normalized to the respective second moments of the distribution. This form allows for accurate representation of a wide range of realistic distributions, including any asymmetries, and allows for rapid calculation of the space charge fields with free space boundary conditions. An example problem is presented to illustrate our approach. {copyright} {ital 1997 American Institute of Physics.}« less

C-MOS array design techniques

NASA Technical Reports Server (NTRS)

Feller, A.

1978-01-01

The entire complement of standard cells and components, except for the set-reset flip-flop, was completed. Two levels of checking were performed on each device. Logic cells and topological layout are described. All the related computer programs were coded and one level of debugging was completed. The logic for the test chip was modified and updated. This test chip served as the first test vehicle to exercise the standard cell complementary MOS(C-MOS) automatic artwork generation capability.

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.

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

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

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Integrating Multibody Simulation and CFD: toward Complex Multidisciplinary Design Optimization

NASA Astrophysics Data System (ADS)

Pieri, Stefano; Poloni, Carlo; Mühlmeier, Martin

This paper describes the use of integrated multidisciplinary analysis and optimization of a race car model on a predefined circuit. The objective is the definition of the most efficient geometric configuration that can guarantee the lowest lap time. In order to carry out this study it has been necessary to interface the design optimization software modeFRONTIER with the following softwares: CATIA v5, a three dimensional CAD software, used for the definition of the parametric geometry; A.D.A.M.S./Motorsport, a multi-body dynamic simulation software; IcemCFD, a mesh generator, for the automatic generation of the CFD grid; CFX, a Navier-Stokes code, for the fluid-dynamic forces prediction. The process integration gives the possibility to compute, for each geometrical configuration, a set of aerodynamic coefficients that are then used in the multiboby simulation for the computation of the lap time. Finally an automatic optimization procedure is started and the lap-time minimized. The whole process is executed on a Linux cluster running CFD simulations in parallel.

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.

Occupational self-coding and automatic recording (OSCAR): a novel web-based tool to collect and code lifetime job histories in large population-based studies.

PubMed

De Matteis, Sara; Jarvis, Deborah; Young, Heather; Young, Alan; Allen, Naomi; Potts, James; Darnton, Andrew; Rushton, Lesley; Cullinan, Paul

2017-03-01

Objectives The standard approach to the assessment of occupational exposures is through the manual collection and coding of job histories. This method is time-consuming and costly and makes it potentially unfeasible to perform high quality analyses on occupational exposures in large population-based studies. Our aim was to develop a novel, efficient web-based tool to collect and code lifetime job histories in the UK Biobank, a population-based cohort of over 500 000 participants. Methods We developed OSCAR (occupations self-coding automatic recording) based on the hierarchical structure of the UK Standard Occupational Classification (SOC) 2000, which allows individuals to collect and automatically code their lifetime job histories via a simple decision-tree model. Participants were asked to find each of their jobs by selecting appropriate job categories until they identified their job title, which was linked to a hidden 4-digit SOC code. For each occupation a job title in free text was also collected to estimate Cohen's kappa (κ) inter-rater agreement between SOC codes assigned by OSCAR and an expert manual coder. Results OSCAR was administered to 324 653 UK Biobank participants with an existing email address between June and September 2015. Complete 4-digit SOC-coded lifetime job histories were collected for 108 784 participants (response rate: 34%). Agreement between the 4-digit SOC codes assigned by OSCAR and the manual coder for a random sample of 400 job titles was moderately good [κ=0.45, 95% confidence interval (95% CI) 0.42-0.49], and improved when broader job categories were considered (κ=0.64, 95% CI 0.61-0.69 at a 1-digit SOC-code level). Conclusions OSCAR is a novel, efficient, and reasonably reliable web-based tool for collecting and automatically coding lifetime job histories in large population-based studies. Further application in other research projects for external validation purposes is warranted.

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

Davis, R. S.

The following are specific topics of this paper: 1.There is much creativity in the manner in which Dimensional Generator can be applied to a specific programming task [2]. This paper tells how Dimensional Generator was applied to a reactor-physics task. 2. In this first practical use, Dimensional Generator itself proved not to need change, but a better user interface was found necessary, essentially because the relevance of Dimensional Generator to reactor physics was initially underestimated. It is briefly described. 3. The use of Dimensional Generator helps make reactor-physics source code somewhat simpler. That is explained here with brief examples frommore » BURFEL-PC and WIMSBURF. 4. Most importantly, with the help of Dimensional Generator, all erroneous physical expressions were automatically detected. The errors are detailed here (in spite of the author's embarrassment) because they show clearly, both in theory and in practice, how Dimensional Generator offers quality enhancement of reactor-physics programming. (authors)« less

Traceability Through Automatic Program Generation

NASA Technical Reports Server (NTRS)

Richardson, Julian; Green, Jeff

2003-01-01

Program synthesis is a technique for automatically deriving programs from specifications of their behavior. One of the arguments made in favour of program synthesis is that it allows one to trace from the specification to the program. One way in which traceability information can be derived is to augment the program synthesis system so that manipulations and calculations it carries out during the synthesis process are annotated with information on what the manipulations and calculations were and why they were made. This information is then accumulated throughout the synthesis process, at the end of which, every artifact produced by the synthesis is annotated with a complete history relating it to every other artifact (including the source specification) which influenced its construction. This approach requires modification of the entire synthesis system - which is labor-intensive and hard to do without influencing its behavior. In this paper, we introduce a novel, lightweight technique for deriving traceability from a program specification to the corresponding synthesized code. Once a program has been successfully synthesized from a specification, small changes are systematically made to the specification and the effects on the synthesized program observed. We have partially automated the technique and applied it in an experiment to one of our program synthesis systems, AUTOFILTER, and to the GNU C compiler, GCC. The results are promising: 1. Manual inspection of the results indicates that most of the connections derived from the source (a specification in the case of AUTOFILTER, C source code in the case of GCC) to its generated target (C source code in the case of AUTOFILTER, assembly language code in the case of GCC) are correct. 2. Around half of the lines in the target can be traced to at least one line of the source. 3. Small changes in the source often induce only small changes in the target.

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.

Shape design sensitivity analysis and optimization of three dimensional elastic solids using geometric modeling and automatic regridding. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Yao, Tse-Min; Choi, Kyung K.

1987-01-01

An automatic regridding method and a three dimensional shape design parameterization technique were constructed and integrated into a unified theory of shape design sensitivity analysis. An algorithm was developed for general shape design sensitivity analysis of three dimensional eleastic solids. Numerical implementation of this shape design sensitivity analysis method was carried out using the finite element code ANSYS. The unified theory of shape design sensitivity analysis uses the material derivative of continuum mechanics with a design velocity field that represents shape change effects over the structural design. Automatic regridding methods were developed by generating a domain velocity field with boundary displacement method. Shape design parameterization for three dimensional surface design problems was illustrated using a Bezier surface with boundary perturbations that depend linearly on the perturbation of design parameters. A linearization method of optimization, LINRM, was used to obtain optimum shapes. Three examples from different engineering disciplines were investigated to demonstrate the accuracy and versatility of this shape design sensitivity analysis method.

Diagnosis - Using automatic test equipment and artificial intelligence expert systems

NASA Astrophysics Data System (ADS)

Ramsey, J. E., Jr.

Three expert systems (ATEOPS, ATEFEXPERS, and ATEFATLAS), which were created to direct automatic test equipment (ATE), are reviewed. The purpose of the project was to develop an expert system to troubleshoot the converter-programmer power supply card for the F-15 aircraft and have that expert system direct the automatic test equipment. Each expert system uses a different knowledge base or inference engine, basing the testing on the circuit schematic, test requirements document, or ATLAS code. Implementing generalized modules allows the expert systems to be used for any different unit under test. Using converted ATLAS to LISP code allows the expert system to direct any ATE using ATLAS. The constraint propagated frame system allows for the expansion of control by creating the ATLAS code, checking the code for good software engineering techniques, directing the ATE, and changing the test sequence as needed (planning).

Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries.

PubMed

Lin, Ching-Heng; Wu, Nai-Yuan; Lai, Wei-Shao; Liou, Der-Ming

2015-01-01

Electronic medical records with encoded entries should enhance the semantic interoperability of document exchange. However, it remains a challenge to encode the narrative concept and to transform the coded concepts into a standard entry-level document. This study aimed to use a novel approach for the generation of entry-level interoperable clinical documents. Using HL7 clinical document architecture (CDA) as the example, we developed three pipelines to generate entry-level CDA documents. The first approach was a semi-automatic annotation pipeline (SAAP), the second was a natural language processing (NLP) pipeline, and the third merged the above two pipelines. We randomly selected 50 test documents from the i2b2 corpora to evaluate the performance of the three pipelines. The 50 randomly selected test documents contained 9365 words, including 588 Observation terms and 123 Procedure terms. For the Observation terms, the merged pipeline had a significantly higher F-measure than the NLP pipeline (0.89 vs 0.80, p<0.0001), but a similar F-measure to that of the SAAP (0.89 vs 0.87). For the Procedure terms, the F-measure was not significantly different among the three pipelines. The combination of a semi-automatic annotation approach and the NLP application seems to be a solution for generating entry-level interoperable clinical documents. © The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.comFor numbered affiliation see end of article.

Proceedings Papers of the AFSC (Air Force Systems Command) Avionics Standardization Conference (2nd) Held at Dayton, Ohio on 30 November-2 December 1982. Volume 2

DTIC Science & Technology

1982-11-01

groups. The Air Force is concerned with such issues such as resource allocation to foster and prcomotc standards, transitioning from current to future...perform automatic resource allocation , generate MATE Intermediate code, and provide formatted output listings. d. MATE Test Executive (MTE). The MTE...AFFECTED BY THESE STANDARDS TO KNOW JUST WHAT IS AVAILABLE TO SUPPORT THEM: THE HARDWARE; THE COMPLIANCE TESTING ; THE TOOLS NECESSARY TO FACILITATE DESIGN

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

Sharma, Vishal C.; Gopalakrishnan, Ganesh; Krishnamoorthy, Sriram

The systems resilience research community has developed methods to manually insert additional source-program level assertions to trap errors, and also devised tools to conduct fault injection studies for scalar program codes. In this work, we contribute the first vector oriented LLVM-level fault injector VULFI to help study the effects of faults in vector architectures that are of growing importance, especially for vectorizing loops. Using VULFI, we conduct a resiliency study of nine real-world vector benchmarks using Intel’s AVX and SSE extensions as the target vector instruction sets, and offer the first reported understanding of how faults affect vector instruction sets.more » We take this work further toward automating the insertion of resilience assertions during compilation. This is based on our observation that during intermediate (e.g., LLVM-level) code generation to handle full and partial vectorization, modern compilers exploit (and explicate in their code-documentation) critical invariants. These invariants are turned into error-checking code. We confirm the efficacy of these automatically inserted low-overhead error detectors for vectorized for-loops.« less

Web Service Model for Plasma Simulations with Automatic Post Processing and Generation of Visual Diagnostics*

NASA Astrophysics Data System (ADS)

Exby, J.; Busby, R.; Dimitrov, D. A.; Bruhwiler, D.; Cary, J. R.

2003-10-01

We present our design and initial implementation of a web service model for running particle-in-cell (PIC) codes remotely from a web browser interface. PIC codes have grown significantly in complexity and now often require parallel execution on multiprocessor computers, which in turn requires sophisticated post-processing and data analysis. A significant amount of time and effort is required for a physicist to develop all the necessary skills, at the expense of actually doing research. Moreover, parameter studies with a computationally intensive code justify the systematic management of results with an efficient way to communicate them among a group of remotely located collaborators. Our initial implementation uses the OOPIC Pro code [1], Linux, Apache, MySQL, Python, and PHP. The Interactive Data Language is used for visualization. [1] D.L. Bruhwiler et al., Phys. Rev. ST-AB 4, 101302 (2001). * This work is supported by DOE grant # DE-FG02-03ER83857 and by Tech-X Corp. ** Also University of Colorado.

COMPOSE-HPC: A Transformational Approach to Exascale

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

Bernholdt, David E; Allan, Benjamin A.; Armstrong, Robert C.

2012-04-01

The goal of the COMPOSE-HPC project is to 'democratize' tools for automatic transformation of program source code so that it becomes tractable for the developers of scientific applications to create and use their own transformations reliably and safely. This paper describes our approach to this challenge, the creation of the KNOT tool chain, which includes tools for the creation of annotation languages to control the transformations (PAUL), to perform the transformations (ROTE), and optimization and code generation (BRAID), which can be used individually and in combination. We also provide examples of current and future uses of the KNOT tools, whichmore » include transforming code to use different programming models and environments, providing tests that can be used to detect errors in software or its execution, as well as composition of software written in different programming languages, or with different threading patterns.« less

Development of the FHR advanced natural circulation analysis code and application to FHR safety analysis

DOE PAGES

Guo, Z.; Zweibaum, N.; Shao, M.; ...

2016-04-19

The University of California, Berkeley (UCB) is performing thermal hydraulics safety analysis to develop the technical basis for design and licensing of fluoride-salt-cooled, high-temperature reactors (FHRs). FHR designs investigated by UCB use natural circulation for emergency, passive decay heat removal when normal decay heat removal systems fail. The FHR advanced natural circulation analysis (FANCY) code has been developed for assessment of passive decay heat removal capability and safety analysis of these innovative system designs. The FANCY code uses a one-dimensional, semi-implicit scheme to solve for pressure-linked mass, momentum and energy conservation equations. Graph theory is used to automatically generate amore » staggered mesh for complicated pipe network systems. Heat structure models have been implemented for three types of boundary conditions (Dirichlet, Neumann and Robin boundary conditions). Heat structures can be composed of several layers of different materials, and are used for simulation of heat structure temperature distribution and heat transfer rate. Control models are used to simulate sequences of events or trips of safety systems. A proportional-integral controller is also used to automatically make thermal hydraulic systems reach desired steady state conditions. A point kinetics model is used to model reactor kinetics behavior with temperature reactivity feedback. The underlying large sparse linear systems in these models are efficiently solved by using direct and iterative solvers provided by the SuperLU code on high performance machines. Input interfaces are designed to increase the flexibility of simulation for complicated thermal hydraulic systems. In conclusion, this paper mainly focuses on the methodology used to develop the FANCY code, and safety analysis of the Mark 1 pebble-bed FHR under development at UCB is performed.« less

Automating the generation of finite element dynamical cores with Firedrake

NASA Astrophysics Data System (ADS)

Ham, David; Mitchell, Lawrence; Homolya, Miklós; Luporini, Fabio; Gibson, Thomas; Kelly, Paul; Cotter, Colin; Lange, Michael; Kramer, Stephan; Shipton, Jemma; Yamazaki, Hiroe; Paganini, Alberto; Kärnä, Tuomas

2017-04-01

The development of a dynamical core is an increasingly complex software engineering undertaking. As the equations become more complete, the discretisations more sophisticated and the hardware acquires ever more fine-grained parallelism and deeper memory hierarchies, the problem of building, testing and modifying dynamical cores becomes increasingly complex. Here we present Firedrake, a code generation system for the finite element method with specialist features designed to support the creation of geoscientific models. Using Firedrake, the dynamical core developer writes the partial differential equations in weak form in a high level mathematical notation. Appropriate function spaces are chosen and time stepping loops written at the same high level. When the programme is run, Firedrake generates high performance C code for the resulting numerics which are executed in parallel. Models in Firedrake typically take a tiny fraction of the lines of code required by traditional hand-coding techniques. They support more sophisticated numerics than are easily achieved by hand, and the resulting code is frequently higher performance. Critically, debugging, modifying and extending a model written in Firedrake is vastly easier than by traditional methods due to the small, highly mathematical code base. Firedrake supports a wide range of key features for dynamical core creation: A vast range of discretisations, including both continuous and discontinuous spaces and mimetic (C-grid-like) elements which optimally represent force balances in geophysical flows. High aspect ratio layered meshes suitable for ocean and atmosphere domains. Curved elements for high accuracy representations of the sphere. Support for non-finite element operators, such as parametrisations. Access to PETSc, a world-leading library of programmable linear and nonlinear solvers. High performance adjoint models generated automatically by symbolically reasoning about the forward model. This poster will present the key features of the Firedrake system, as well as those of Gusto, an atmospheric dynamical core, and Thetis, a coastal ocean model, both of which are written in Firedrake.

Formally specifying the logic of an automatic guidance controller

NASA Technical Reports Server (NTRS)

Guaspari, David

1990-01-01

The following topics are covered in viewgraph form: (1) the Penelope Project; (2) the logic of an experimental automatic guidance control system for a 737; (3) Larch/Ada specification; (4) some failures of informal description; (5) description of mode changes caused by switches; (6) intuitive description of window status (chosen vs. current); (7) design of the code; (8) and specifying the code.

Automatic-repeat-request error control schemes

NASA Technical Reports Server (NTRS)

Lin, S.; Costello, D. J., Jr.; Miller, M. J.

1983-01-01

Error detection incorporated with automatic-repeat-request (ARQ) is widely used for error control in data communication systems. This method of error control is simple and provides high system reliability. If a properly chosen code is used for error detection, virtually error-free data transmission can be attained. Various types of ARQ and hybrid ARQ schemes, and error detection using linear block codes are surveyed.

An Evolving Ecosystem for Natural Language Processing in Department of Veterans Affairs.

PubMed

Garvin, Jennifer H; Kalsy, Megha; Brandt, Cynthia; Luther, Stephen L; Divita, Guy; Coronado, Gregory; Redd, Doug; Christensen, Carrie; Hill, Brent; Kelly, Natalie; Treitler, Qing Zeng

2017-02-01

In an ideal clinical Natural Language Processing (NLP) ecosystem, researchers and developers would be able to collaborate with others, undertake validation of NLP systems, components, and related resources, and disseminate them. We captured requirements and formative evaluation data from the Veterans Affairs (VA) Clinical NLP Ecosystem stakeholders using semi-structured interviews and meeting discussions. We developed a coding rubric to code interviews. We assessed inter-coder reliability using percent agreement and the kappa statistic. We undertook 15 interviews and held two workshop discussions. The main areas of requirements related to; design and functionality, resources, and information. Stakeholders also confirmed the vision of the second generation of the Ecosystem and recommendations included; adding mechanisms to better understand terms, measuring collaboration to demonstrate value, and datasets/tools to navigate spelling errors with consumer language, among others. Stakeholders also recommended capability to: communicate with developers working on the next version of the VA electronic health record (VistA Evolution), provide a mechanism to automatically monitor download of tools and to automatically provide a summary of the downloads to Ecosystem contributors and funders. After three rounds of coding and discussion, we determined the percent agreement of two coders to be 97.2% and the kappa to be 0.7851. The vision of the VA Clinical NLP Ecosystem met stakeholder needs. Interviews and discussion provided key requirements that inform the design of the VA Clinical NLP Ecosystem.

Chain of evidence generation for contrast enhancement in digital image forensics

NASA Astrophysics Data System (ADS)

Battiato, Sebastiano; Messina, Giuseppe; Strano, Daniela

2010-01-01

The quality of the images obtained by digital cameras has improved a lot since digital cameras early days. Unfortunately, it is not unusual in image forensics to find wrongly exposed pictures. This is mainly due to obsolete techniques or old technologies, but also due to backlight conditions. To extrapolate some invisible details a stretching of the image contrast is obviously required. The forensics rules to produce evidences require a complete documentation of the processing steps, enabling the replication of the entire process. The automation of enhancement techniques is thus quite difficult and needs to be carefully documented. This work presents an automatic procedure to find contrast enhancement settings, allowing both image correction and automatic scripting generation. The technique is based on a preprocessing step which extracts the features of the image and selects correction parameters. The parameters are thus saved through a JavaScript code that is used in the second step of the approach to correct the image. The generated script is Adobe Photoshop compliant (which is largely used in image forensics analysis) thus permitting the replication of the enhancement steps. Experiments on a dataset of images are also reported showing the effectiveness of the proposed methodology.

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.

Bidirectional automatic release of reserve for low voltage network made with low capacity PLCs

NASA Astrophysics Data System (ADS)

Popa, I.; Popa, G. N.; Diniş, C. M.; Deaconu, S. I.

2018-01-01

The article presents the design of a bidirectional automatic release of reserve made on two types low capacity programmable logic controllers: PS-3 from Klöckner-Moeller and Zelio from Schneider. It analyses the electronic timing circuits that can be used for making the bidirectional automatic release of reserve: time-on delay circuit and time-off delay circuit (two types). In the paper are present the sequences code for timing performed on the PS-3 PLC, the logical functions for the bidirectional automatic release of reserve, the classical control electrical diagram (with contacts, relays, and time relays), the electronic control diagram (with logical gates and timing circuits), the code (in IL language) made for the PS-3 PLC, and the code (in FBD language) made for Zelio PLC. A comparative analysis will be carried out on the use of the two types of PLC and will be present the advantages of using PLCs.

Thread concept for automatic task parallelization in image analysis

NASA Astrophysics Data System (ADS)

Lueckenhaus, Maximilian; Eckstein, Wolfgang

1998-09-01

Parallel processing of image analysis tasks is an essential method to speed up image processing and helps to exploit the full capacity of distributed systems. However, writing parallel code is a difficult and time-consuming process and often leads to an architecture-dependent program that has to be re-implemented when changing the hardware. Therefore it is highly desirable to do the parallelization automatically. For this we have developed a special kind of thread concept for image analysis tasks. Threads derivated from one subtask may share objects and run in the same context but may process different threads of execution and work on different data in parallel. In this paper we describe the basics of our thread concept and show how it can be used as basis of an automatic task parallelization to speed up image processing. We further illustrate the design and implementation of an agent-based system that uses image analysis threads for generating and processing parallel programs by taking into account the available hardware. The tests made with our system prototype show that the thread concept combined with the agent paradigm is suitable to speed up image processing by an automatic parallelization of image analysis tasks.

TIGER: A user-friendly interactive grid generation system for complicated turbomachinery and axis-symmetric configurations

NASA Technical Reports Server (NTRS)

Shih, Ming H.; Soni, Bharat K.

1993-01-01

The issue of time efficiency in grid generation is addressed by developing a user friendly graphical interface for interactive/automatic construction of structured grids around complex turbomachinery/axis-symmetric configurations. The accuracy of geometry modeling and its fidelity is accomplished by adapting the nonuniform rational b-spline (NURBS) representation. A customized interactive grid generation code, TIGER, has been developed to facilitate the grid generation process for complicated internal, external, and internal-external turbomachinery fields simulations. The FORMS Library is utilized to build user-friendly graphical interface. The algorithm allows a user to redistribute grid points interactively on curves/surfaces using NURBS formulation with accurate geometric definition. TIGER's features include multiblock, multiduct/shroud, multiblade row, uneven blade count, and patched/overlapping block interfaces. It has been applied to generate grids for various complicated turbomachinery geometries, as well as rocket and missile configurations.

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

Development of Integrated Modular Avionics Application Based on Simulink and XtratuM

NASA Astrophysics Data System (ADS)

Fons-Albert, Borja; Usach-Molina, Hector; Vila-Carbo, Joan; Crespo-Lorente, Alfons

2013-08-01

This paper presents an integral approach for designing avionics applications that meets the requirements for software development and execution of this application domain. Software design follows the Model-Based design process and is performed in Simulink. This approach allows easy and quick testbench development and helps satisfying DO-178B requirements through the use of proper tools. The software execution platform is based on XtratuM, a minimal bare-metal hypervisor designed in our research group. XtratuM provides support for IMA-SP (Integrated Modular Avionics for Space) architectures. This approach allows the code generation of a Simulink model to be executed on top of Lithos as XtratuM partition. Lithos is a ARINC-653 compliant RTOS for XtratuM. The paper concentrates in how to smoothly port Simulink designs to XtratuM solving problems like application partitioning, automatic code generation, real-time tasking, interfacing, and others. This process is illustrated with an autopilot design test using a flight simulator.

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

Agile Multi-Scale Decompositions for Automatic Image Registration

NASA Technical Reports Server (NTRS)

Murphy, James M.; Leija, Omar Navarro; Le Moigne, Jacqueline

2016-01-01

In recent works, the first and third authors developed an automatic image registration algorithm based on a multiscale hybrid image decomposition with anisotropic shearlets and isotropic wavelets. This prototype showed strong performance, improving robustness over registration with wavelets alone. However, this method imposed a strict hierarchy on the order in which shearlet and wavelet features were used in the registration process, and also involved an unintegrated mixture of MATLAB and C code. In this paper, we introduce a more agile model for generating features, in which a flexible and user-guided mix of shearlet and wavelet features are computed. Compared to the previous prototype, this method introduces a flexibility to the order in which shearlet and wavelet features are used in the registration process. Moreover, the present algorithm is now fully coded in C, making it more efficient and portable than the MATLAB and C prototype. We demonstrate the versatility and computational efficiency of this approach by performing registration experiments with the fully-integrated C algorithm. In particular, meaningful timing studies can now be performed, to give a concrete analysis of the computational costs of the flexible feature extraction. Examples of synthetically warped and real multi-modal images are analyzed.

Retrofitting the AutoBayes Program Synthesis System with Concrete Syntax

NASA Technical Reports Server (NTRS)

Fischer, Bernd; Visser, Eelco

2004-01-01

AutoBayes is a fully automatic, schema-based program synthesis system for statistical data analysis applications. Its core component is a schema library. i.e., a collection of generic code templates with associated applicability constraints which are instantiated in a problem-specific way during synthesis. Currently, AutoBayes is implemented in Prolog; the schemas thus use abstract syntax (i.e., Prolog terms) to formulate the templates. However, the conceptual distance between this abstract representation and the concrete syntax of the generated programs makes the schemas hard to create and maintain. In this paper we describe how AutoBayes is retrofitted with concrete syntax. We show how it is integrated into Prolog and describe how the seamless interaction of concrete syntax fragments with AutoBayes's remaining legacy meta-programming kernel based on abstract syntax is achieved. We apply the approach to gradually mitigate individual schemas without forcing a disruptive migration of the entire system to a different First experiences show that a smooth migration can be achieved. Moreover, it can result in a considerable reduction of the code size and improved readability of the code. In particular, abstracting out fresh-variable generation and second-order term construction allows the formulation of larger continuous fragments.

"Rate My Therapist": Automated Detection of Empathy in Drug and Alcohol Counseling via Speech and Language Processing.

PubMed

Xiao, Bo; Imel, Zac E; Georgiou, Panayiotis G; Atkins, David C; Narayanan, Shrikanth S

2015-01-01

The technology for evaluating patient-provider interactions in psychotherapy-observational coding-has not changed in 70 years. It is labor-intensive, error prone, and expensive, limiting its use in evaluating psychotherapy in the real world. Engineering solutions from speech and language processing provide new methods for the automatic evaluation of provider ratings from session recordings. The primary data are 200 Motivational Interviewing (MI) sessions from a study on MI training methods with observer ratings of counselor empathy. Automatic Speech Recognition (ASR) was used to transcribe sessions, and the resulting words were used in a text-based predictive model of empathy. Two supporting datasets trained the speech processing tasks including ASR (1200 transcripts from heterogeneous psychotherapy sessions and 153 transcripts and session recordings from 5 MI clinical trials). The accuracy of computationally-derived empathy ratings were evaluated against human ratings for each provider. Computationally-derived empathy scores and classifications (high vs. low) were highly accurate against human-based codes and classifications, with a correlation of 0.65 and F-score (a weighted average of sensitivity and specificity) of 0.86, respectively. Empathy prediction using human transcription as input (as opposed to ASR) resulted in a slight increase in prediction accuracies, suggesting that the fully automatic system with ASR is relatively robust. Using speech and language processing methods, it is possible to generate accurate predictions of provider performance in psychotherapy from audio recordings alone. This technology can support large-scale evaluation of psychotherapy for dissemination and process studies.

The KATE shell: An implementation of model-based control, monitor and diagnosis

NASA Technical Reports Server (NTRS)

Cornell, Matthew

1987-01-01

The conventional control and monitor software currently used by the Space Center for Space Shuttle processing has many limitations such as high maintenance costs, limited diagnostic capabilities and simulation support. These limitations have caused the development of a knowledge based (or model based) shell to generically control and monitor electro-mechanical systems. The knowledge base describes the system's structure and function and is used by a software shell to do real time constraints checking, low level control of components, diagnosis of detected faults, sensor validation, automatic generation of schematic diagrams and automatic recovery from failures. This approach is more versatile and more powerful than the conventional hard coded approach and offers many advantages over it, although, for systems which require high speed reaction times or aren't well understood, knowledge based control and monitor systems may not be appropriate.

C2M: Configurable Chemical Middleware

PubMed Central

Roosendaal, Hans E.; Geurts, Peter A. T. M.

2001-01-01

One of the vexing problems that besets concurrent use of multiple, heterogeneous resources is format multiplicity. C2M aims to equip scientists with a wrapper generator on their desktop. The wrapper generator can build wrappers, or converters that can convert data from or into different formats, from a high-level description of the formats. The language in which such a high-level description is expressed is easy enough for scientists to be able to write format descriptions at minimal cost. In C2M, wrappers and documentation for human reading are automatically obtained from the same user-supplied specifications. Initial experiments demonstrate that the idea can, indeed, lead to the advent of usergoverned wrapper generators. Future research will consolidate the code and extend the approach to a realistic variety of formats. PMID:18628869

Finite-element 3D simulation tools for high-current relativistic electron beams

NASA Astrophysics Data System (ADS)

Humphries, Stanley; Ekdahl, Carl

2002-08-01

The DARHT second-axis injector is a challenge for computer simulations. Electrons are subject to strong beam-generated forces. The fields are fully three-dimensional and accurate calculations at surfaces are critical. We describe methods applied in OmniTrak, a 3D finite-element code suite that can address DARHT and the full range of charged-particle devices. The system handles mesh generation, electrostatics, magnetostatics and self-consistent particle orbits. The MetaMesh program generates meshes of conformal hexahedrons to fit any user geometry. The code has the unique ability to create structured conformal meshes with cubic logic. Organized meshes offer advantages in speed and memory utilization in the orbit and field solutions. OmniTrak is a versatile charged-particle code that handles 3D electric and magnetic field solutions on independent meshes. The program can update both 3D field solutions from the calculated beam space-charge and current-density. We shall describe numerical methods for orbit tracking on a hexahedron mesh. Topics include: 1) identification of elements along the particle trajectory, 2) fast searches and adaptive field calculations, 3) interpolation methods to terminate orbits on material surfaces, 4) automatic particle generation on multiple emission surfaces to model space-charge-limited emission and field emission, 5) flexible Child law algorithms, 6) implementation of the dual potential model for 3D magnetostatics, and 7) assignment of charge and current from model particle orbits for self-consistent fields.

Skel: Generative Software for Producing Skeletal I/O Applications

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

Logan, J.; Klasky, S.; Lofstead, J.

2011-01-01

Massively parallel computations consist of a mixture of computation, communication, and I/O. As part of the co-design for the inevitable progress towards exascale computing, we must apply lessons learned from past work to succeed in this new age of computing. Of the three components listed above, implementing an effective parallel I/O solution has often been overlooked by application scientists and was usually added to large scale simulations only when existing serial techniques had failed. As scientists teams scaled their codes to run on hundreds of processors, it was common to call on an I/O expert to implement a set ofmore » more scalable I/O routines. These routines were easily separated from the calculations and communication, and in many cases, an I/O kernel was derived from the application which could be used for testing I/O performance independent of the application. These I/O kernels developed a life of their own used as a broad measure for comparing different I/O techniques. Unfortunately, as years passed and computation and communication changes required changes to the I/O, the separate I/O kernel used for benchmarking remained static no longer providing an accurate indicator of the I/O performance of the simulation making I/O research less relevant for the application scientists. In this paper we describe a new approach to this problem where I/O kernels are replaced with skeletal I/O applications automatically generated from an abstract set of simulation I/O parameters. We realize this abstraction by leveraging the ADIOS middleware's XML I/O specification with additional runtime parameters. Skeletal applications offer all of the benefits of I/O kernels including allowing I/O optimizations to focus on useful I/O patterns. Moreover, since they are automatically generated, it is easy to produce an updated I/O skeleton whenever the simulation's I/O changes. In this paper we analyze the performance of automatically generated I/O skeletal applications for the S3D and GTS codes. We show that these skeletal applications achieve performance comparable to that of the production applications. We wrap up the paper with a discussion of future changes to make the skeletal application better approximate the actual I/O performed in the simulation.« less

Experiences with a Requirements-Based Programming Approach to the Development of a NASA Autonomous Ground Control System

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Rouff, Christopher A.; Gracanin, Denis; Erickson, John

2005-01-01

Requirements-to-Design-to-Code (R2D2C) is an approach to the engineering of computer-based systems that embodies the idea of requirements-based programming in system development. It goes further; however, in that the approach offers not only an underlying formalism, but full formal development from requirements capture through to the automatic generation of provably-correct code. As such, the approach has direct application to the development of systems requiring autonomic properties. We describe a prototype tool to support the method, and illustrate its applicability to the development of LOGOS, a NASA autonomous ground control system, which exhibits autonomic behavior. Finally, we briefly discuss other areas where the approach and prototype tool are being considered for application.

Modeling Guidelines for Code Generation in the Railway Signaling Context

NASA Technical Reports Server (NTRS)

Ferrari, Alessio; Bacherini, Stefano; Fantechi, Alessandro; Zingoni, Niccolo

2009-01-01

Modeling guidelines constitute one of the fundamental cornerstones for Model Based Development. Their relevance is essential when dealing with code generation in the safety-critical domain. This article presents the experience of a railway signaling systems manufacturer on this issue. Introduction of Model-Based Development (MBD) and code generation in the industrial safety-critical sector created a crucial paradigm shift in the development process of dependable systems. While traditional software development focuses on the code, with MBD practices the focus shifts to model abstractions. The change has fundamental implications for safety-critical systems, which still need to guarantee a high degree of confidence also at code level. Usage of the Simulink/Stateflow platform for modeling, which is a de facto standard in control software development, does not ensure by itself production of high-quality dependable code. This issue has been addressed by companies through the definition of modeling rules imposing restrictions on the usage of design tools components, in order to enable production of qualified code. The MAAB Control Algorithm Modeling Guidelines (MathWorks Automotive Advisory Board)[3] is a well established set of publicly available rules for modeling with Simulink/Stateflow. This set of recommendations has been developed by a group of OEMs and suppliers of the automotive sector with the objective of enforcing and easing the usage of the MathWorks tools within the automotive industry. The guidelines have been published in 2001 and afterwords revisited in 2007 in order to integrate some additional rules developed by the Japanese division of MAAB [5]. The scope of the current edition of the guidelines ranges from model maintainability and readability to code generation issues. The rules are conceived as a reference baseline and therefore they need to be tailored to comply with the characteristics of each industrial context. Customization of these recommendations has been performed for the automotive control systems domain in order to enforce code generation [7]. The MAAB guidelines have been found profitable also in the aerospace/avionics sector [1] and they have been adopted by the MathWorks Aerospace Leadership Council (MALC). General Electric Transportation Systems (GETS) is a well known railway signaling systems manufacturer leading in Automatic Train Protection (ATP) systems technology. Inside an effort of adopting formal methods within its own development process, GETS decided to introduce system modeling by means of the MathWorks tools [2], and in 2008 chose to move to code generation. This article reports the experience performed by GETS in developing its own modeling standard through customizing the MAAB rules for the railway signaling domain and shows the result of this experience with a successful product development story.

[Development of a Software for Automatically Generated Contours in Eclipse TPS].

PubMed

Xie, Zhao; Hu, Jinyou; Zou, Lian; Zhang, Weisha; Zou, Yuxin; Luo, Kelin; Liu, Xiangxiang; Yu, Luxin

2015-03-01

The automatic generation of planning targets and auxiliary contours have achieved in Eclipse TPS 11.0. The scripting language autohotkey was used to develop a software for automatically generated contours in Eclipse TPS. This software is named Contour Auto Margin (CAM), which is composed of operational functions of contours, script generated visualization and script file operations. RESULTS Ten cases in different cancers have separately selected, in Eclipse TPS 11.0 scripts generated by the software could not only automatically generate contours but also do contour post-processing. For different cancers, there was no difference between automatically generated contours and manually created contours. The CAM is a user-friendly and powerful software, and can automatically generated contours fast in Eclipse TPS 11.0. With the help of CAM, it greatly save plan preparation time and improve working efficiency of radiation therapy physicists.

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

For many space projects the software development is facing great pressure with respect to quality, costs and schedule. One way to cope with these challenges is the application of CASE tools for automatic generation of code and documentation. This paper describes two CASE tools: Rhapsody (I-Logix) featuring UML and ISG (BSSE) that provides modeling of finite state machines. Both tools have been used at Kayser-Threde in different space projects for the development of on-board software. The tools are discussed with regard to the full software development cycle.

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.

Explicit robust schemes for implementation of general principal value-based constitutive models

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.; Tan, H. Q.; Zhang, Y.

1993-01-01

The issue of developing effective and robust schemes to implement general hyperelastic constitutive models is addressed. To this end, special purpose functions are used to symbolically derive, evaluate, and automatically generate the associated FORTRAN code for the explicit forms of the corresponding stress function and material tangent stiffness tensors. These explicit forms are valid for the entire deformation range. The analytical form of these explicit expressions is given here for the case in which the strain-energy potential is taken as a nonseparable polynomial function of the principle stretches.

Language and Program for Documenting Software Design

NASA Technical Reports Server (NTRS)

Kleine, H.; Zepko, T. M.

1986-01-01

Software Design and Documentation Language (SDDL) provides effective communication medium to support design and documentation of complex software applications. SDDL supports communication among all members of software design team and provides for production of informative documentation on design effort. Use of SDDL-generated document to analyze design makes it possible to eliminate many errors not detected until coding and testing attempted. SDDL processor program translates designer's creative thinking into effective document for communication. Processor performs as many automatic functions as possible, freeing designer's energy for creative effort. SDDL processor program written in PASCAL.

Energy efficient rateless codes for high speed data transfer over free space optical channels

NASA Astrophysics Data System (ADS)

Prakash, Geetha; Kulkarni, Muralidhar; Acharya, U. S.

2015-03-01

Terrestrial Free Space Optical (FSO) links transmit information by using the atmosphere (free space) as a medium. In this paper, we have investigated the use of Luby Transform (LT) codes as a means to mitigate the effects of data corruption induced by imperfect channel which usually takes the form of lost or corrupted packets. LT codes, which are a class of Fountain codes, can be used independent of the channel rate and as many code words as required can be generated to recover all the message bits irrespective of the channel performance. Achieving error free high data rates with limited energy resources is possible with FSO systems if error correction codes with minimal overheads on the power can be used. We also employ a combination of Binary Phase Shift Keying (BPSK) with provision for modification of threshold and optimized LT codes with belief propagation for decoding. These techniques provide additional protection even under strong turbulence regimes. Automatic Repeat Request (ARQ) is another method of improving link reliability. Performance of ARQ is limited by the number of retransmissions and the corresponding time delay. We prove through theoretical computations and simulations that LT codes consume less energy per bit. We validate the feasibility of using energy efficient LT codes over ARQ for FSO links to be used in optical wireless sensor networks within the eye safety limits.

GRASP/Ada 95: Reverse Engineering Tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1996-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped an algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD), and a new visualization for a fine-grained complexity metric called the Complexity Profile Graph (CPG). By synchronizing the CSD and the CPG, the CSD view of control structure, nesting, and source code is directly linked to the corresponding visualization of statement level complexity in the CPG. GRASP has been integrated with GNAT, the GNU Ada 95 Translator to provide a comprehensive graphical user interface and development environment for Ada 95. The user may view, edit, print, and compile source code as a CSD with no discernible addition to storage or computational overhead. The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada 95 source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. The current update has focused on the design and implementation of a new Motif compliant user interface, and a new CSD generator consisting of a tagger and renderer. The Complexity Profile Graph (CPG) is based on a set of functions that describes the context, content, and the scaling for complexity on a statement by statement basis. When combined graphicafly, the result is a composite profile of complexity for the program unit. Ongoing research includes the development and refinement of the associated functions, and the development of the CPG generator prototype. The current Version 5.0 prototype provides the capability for the user to generate CSDs and CPGs from Ada 95 source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. This report provides an overview of the GRASP/Ada project with an emphasis on the current update.

46 CFR 112.05-5 - Emergency power source.

Code of Federal Regulations, 2011 CFR

2011-10-01

... generator must be either a diesel engine or a gas turbine. [CGD 74-125A, 47 FR 15267, Apr. 8, 1982, as... power source (automatically connected storage battery or an automatically started generator) 36 hours.1... power source (automatically connected storage battery or an automatically started generator) 8 hours or...

46 CFR 112.05-5 - Emergency power source.

Code of Federal Regulations, 2010 CFR

2010-10-01

... generator must be either a diesel engine or a gas turbine. [CGD 74-125A, 47 FR 15267, Apr. 8, 1982, as... power source (automatically connected storage battery or an automatically started generator) 36 hours.1... power source (automatically connected storage battery or an automatically started generator) 8 hours or...

A Generic Software Safety Document Generator

NASA Technical Reports Server (NTRS)

Denney, Ewen; Venkatesan, Ram Prasad

2004-01-01

Formal certification is based on the idea that a mathematical proof of some property of a piece of software can be regarded as a certificate of correctness which, in principle, can be subjected to external scrutiny. In practice, however, proofs themselves are unlikely to be of much interest to engineers. Nevertheless, it is possible to use the information obtained from a mathematical analysis of software to produce a detailed textual justification of correctness. In this paper, we describe an approach to generating textual explanations from automatically generated proofs of program safety, where the proofs are of compliance with an explicit safety policy that can be varied. Key to this is tracing proof obligations back to the program, and we describe a tool which implements this to certify code auto-generated by AutoBayes and AutoFilter, program synthesis systems under development at the NASA Ames Research Center. Our approach is a step towards combining formal certification with traditional certification methods.

Information quality measurement of medical encoding support based on usability.

PubMed

Puentes, John; Montagner, Julien; Lecornu, Laurent; Cauvin, Jean-Michel

2013-12-01

Medical encoding support systems for diagnoses and medical procedures are an emerging technology that begins to play a key role in billing, reimbursement, and health policies decisions. A significant problem to exploit these systems is how to measure the appropriateness of any automatically generated list of codes, in terms of fitness for use, i.e. their quality. Until now, only information retrieval performance measurements have been applied to estimate the accuracy of codes lists as quality indicator. Such measurements do not give the value of codes lists for practical medical encoding, and cannot be used to globally compare the quality of multiple codes lists. This paper defines and validates a new encoding information quality measure that addresses the problem of measuring medical codes lists quality. It is based on a usability study of how expert coders and physicians apply computer-assisted medical encoding. The proposed measure, named ADN, evaluates codes Accuracy, Dispersion and Noise, and is adapted to the variable length and content of generated codes lists, coping with limitations of previous measures. According to the ADN measure, the information quality of a codes list is fully represented by a single point, within a suitably constrained feature space. Using one scheme, our approach is reliable to measure and compare the information quality of hundreds of codes lists, showing their practical value for medical encoding. Its pertinence is demonstrated by simulation and application to real data corresponding to 502 inpatient stays in four clinic departments. Results are compared to the consensus of three expert coders who also coded this anonymized database of discharge summaries, and to five information retrieval measures. Information quality assessment applying the ADN measure showed the degree of encoding-support system variability from one clinic department to another, providing a global evaluation of quality measurement trends. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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.

Unstructured Mesh Methods for the Simulation of Hypersonic Flows

NASA Technical Reports Server (NTRS)

Peraire, Jaime; Bibb, K. L. (Technical Monitor)

2001-01-01

This report describes the research work undertaken at the Massachusetts Institute of Technology. The aim of this research is to identify effective algorithms and methodologies for the efficient and routine solution of hypersonic viscous flows about re-entry vehicles. For over ten years we have received support from NASA to develop unstructured mesh methods for Computational Fluid Dynamics. As a result of this effort a methodology based on the use, of unstructured adapted meshes of tetrahedra and finite volume flow solvers has been developed. A number of gridding algorithms flow solvers, and adaptive strategies have been proposed. The most successful algorithms developed from the basis of the unstructured mesh system FELISA. The FELISA system has been extensively for the analysis of transonic and hypersonic flows about complete vehicle configurations. The system is highly automatic and allows for the routine aerodynamic analysis of complex configurations starting from CAD data. The code has been parallelized and utilizes efficient solution algorithms. For hypersonic flows, a version of the, code which incorporates real gas effects, has been produced. One of the latest developments before the start of this grant was to extend the system to include viscous effects. This required the development of viscous generators, capable of generating the anisotropic grids required to represent boundary layers, and viscous flow solvers. In figures I and 2, we show some sample hypersonic viscous computations using the developed viscous generators and solvers. Although these initial results were encouraging, it became apparent that in order to develop a fully functional capability for viscous flows, several advances in gridding, solution accuracy, robustness and efficiency were required. As part of this research we have developed: 1) automatic meshing techniques and the corresponding computer codes have been delivered to NASA and implemented into the GridEx system, 2) a finite element algorithm for the solution of the viscous compressible flow equations which can solve flows all the way down to the incompressible limit and that can use higher order (quadratic) approximations leading to highly accurate answers, and 3) and iterative algebraic multigrid solution techniques.

AELAS: Automatic ELAStic property derivations via high-throughput first-principles computation

NASA Astrophysics Data System (ADS)

Zhang, S. H.; Zhang, R. F.

2017-11-01

The elastic properties are fundamental and important for crystalline materials as they relate to other mechanical properties, various thermodynamic qualities as well as some critical physical properties. However, a complete set of experimentally determined elastic properties is only available for a small subset of known materials, and an automatic scheme for the derivations of elastic properties that is adapted to high-throughput computation is much demanding. In this paper, we present the AELAS code, an automated program for calculating second-order elastic constants of both two-dimensional and three-dimensional single crystal materials with any symmetry, which is designed mainly for high-throughput first-principles computation. Other derivations of general elastic properties such as Young's, bulk and shear moduli as well as Poisson's ratio of polycrystal materials, Pugh ratio, Cauchy pressure, elastic anisotropy and elastic stability criterion, are also implemented in this code. The implementation of the code has been critically validated by a lot of evaluations and tests on a broad class of materials including two-dimensional and three-dimensional materials, providing its efficiency and capability for high-throughput screening of specific materials with targeted mechanical properties. Program Files doi:http://dx.doi.org/10.17632/f8fwg4j9tw.1 Licensing provisions: BSD 3-Clause Programming language: Fortran Nature of problem: To automate the calculations of second-order elastic constants and the derivations of other elastic properties for two-dimensional and three-dimensional materials with any symmetry via high-throughput first-principles computation. Solution method: The space-group number is firstly determined by the SPGLIB code [1] and the structure is then redefined to unit cell with IEEE-format [2]. Secondly, based on the determined space group number, a set of distortion modes is automatically specified and the distorted structure files are generated. Afterwards, the total energy for each distorted structure is calculated by the first-principles codes, e.g. VASP [3]. Finally, the second-order elastic constants are determined from the quadratic coefficients of the polynomial fitting of the energies vs strain relationships and other elastic properties are accordingly derived. References [1] http://atztogo.github.io/spglib/. [2] A. Meitzler, H.F. Tiersten, A.W. Warner, D. Berlincourt, G.A. Couqin, F.S. Welsh III, IEEE standard on piezoelectricity, Society, 1988. [3] G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169.

Modelling Metamorphism by Abstract Interpretation

NASA Astrophysics Data System (ADS)

Dalla Preda, Mila; Giacobazzi, Roberto; Debray, Saumya; Coogan, Kevin; Townsend, Gregg M.

Metamorphic malware apply semantics-preserving transformations to their own code in order to foil detection systems based on signature matching. In this paper we consider the problem of automatically extract metamorphic signatures from these malware. We introduce a semantics for self-modifying code, later called phase semantics, and prove its correctness by showing that it is an abstract interpretation of the standard trace semantics. Phase semantics precisely models the metamorphic code behavior by providing a set of traces of programs which correspond to the possible evolutions of the metamorphic code during execution. We show that metamorphic signatures can be automatically extracted by abstract interpretation of the phase semantics, and that regular metamorphism can be modelled as finite state automata abstraction of the phase semantics.

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.

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

Guo, Z.; Zweibaum, N.; Shao, M.

The University of California, Berkeley (UCB) is performing thermal hydraulics safety analysis to develop the technical basis for design and licensing of fluoride-salt-cooled, high-temperature reactors (FHRs). FHR designs investigated by UCB use natural circulation for emergency, passive decay heat removal when normal decay heat removal systems fail. The FHR advanced natural circulation analysis (FANCY) code has been developed for assessment of passive decay heat removal capability and safety analysis of these innovative system designs. The FANCY code uses a one-dimensional, semi-implicit scheme to solve for pressure-linked mass, momentum and energy conservation equations. Graph theory is used to automatically generate amore » staggered mesh for complicated pipe network systems. Heat structure models have been implemented for three types of boundary conditions (Dirichlet, Neumann and Robin boundary conditions). Heat structures can be composed of several layers of different materials, and are used for simulation of heat structure temperature distribution and heat transfer rate. Control models are used to simulate sequences of events or trips of safety systems. A proportional-integral controller is also used to automatically make thermal hydraulic systems reach desired steady state conditions. A point kinetics model is used to model reactor kinetics behavior with temperature reactivity feedback. The underlying large sparse linear systems in these models are efficiently solved by using direct and iterative solvers provided by the SuperLU code on high performance machines. Input interfaces are designed to increase the flexibility of simulation for complicated thermal hydraulic systems. In conclusion, this paper mainly focuses on the methodology used to develop the FANCY code, and safety analysis of the Mark 1 pebble-bed FHR under development at UCB is performed.« less

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.

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.

"Think aloud" and "Near live" usability testing of two complex clinical decision support tools.

PubMed

Richardson, Safiya; Mishuris, Rebecca; O'Connell, Alexander; Feldstein, David; Hess, Rachel; Smith, Paul; McCullagh, Lauren; McGinn, Thomas; Mann, Devin

2017-10-01

Low provider adoption continues to be a significant barrier to realizing the potential of clinical decision support. "Think Aloud" and "Near Live" usability testing were conducted on two clinical decision support tools. Each was composed of an alert, a clinical prediction rule which estimated risk of either group A Streptococcus pharyngitis or pneumonia and an automatic order set based on risk. The objective of this study was to further understanding of the facilitators of usability and to evaluate the types of additional information gained from proceeding to "Near Live" testing after completing "Think Aloud". This was a qualitative observational study conducted at a large academic health care system with 12 primary care providers. During "Think Aloud" testing, participants were provided with written clinical scenarios and asked to verbalize their thought process while interacting with the tool. During "Near Live" testing participants interacted with a mock patient. Morae usability software was used to record full screen capture and audio during every session. Participant comments were placed into coding categories and analyzed for generalizable themes. Themes were compared across usability methods. "Think Aloud" and "Near Live" usability testing generated similar themes under the coding categories visibility, workflow, content, understand-ability and navigation. However, they generated significantly different themes under the coding categories usability, practical usefulness and medical usefulness. During both types of testing participants found the tool easier to use when important text was distinct in its appearance, alerts were passive and appropriately timed, content was up to date, language was clear and simple, and each component of the tool included obvious indicators of next steps. Participant comments reflected higher expectations for usability and usefulness during "Near Live" testing. For example, visit aids, such as automatically generated order sets, were felt to be less useful during "Near-Live" testing because they would not be all inclusive for the visit. These complementary types of usability testing generated unique and generalizable insights. Feedback during "Think Aloud" testing primarily helped to improve the tools' ease of use. The additional feedback from "Near Live" testing, which mimics a real clinical encounter, was helpful for eliciting key barriers and facilitators to provider workflow and adoption. Copyright © 2017 Elsevier B.V. All rights reserved.

ACSYNT - A standards-based system for parametric, computer aided conceptual design of aircraft

NASA Technical Reports Server (NTRS)

Jayaram, S.; Myklebust, A.; Gelhausen, P.

1992-01-01

A group of eight US aerospace companies together with several NASA and NAVY centers, led by NASA Ames Systems Analysis Branch, and Virginia Tech's CAD Laboratory agreed, through the assistance of Americal Technology Initiative, in 1990 to form the ACSYNT (Aircraft Synthesis) Institute. The Institute is supported by a Joint Sponsored Research Agreement to continue the research and development in computer aided conceptual design of aircraft initiated by NASA Ames Research Center and Virginia Tech's CAD Laboratory. The result of this collaboration, a feature-based, parametric computer aided aircraft conceptual design code called ACSYNT, is described. The code is based on analysis routines begun at NASA Ames in the early 1970's. ACSYNT's CAD system is based entirely on the ISO standard Programmer's Hierarchical Interactive Graphics System and is graphics-device independent. The code includes a highly interactive graphical user interface, automatically generated Hermite and B-Spline surface models, and shaded image displays. Numerous features to enhance aircraft conceptual design are described.

Extending compile-time reverse mode and exploiting partial separability in ADIFOR

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

Bischof, C.H.; El-Khadiri, M.

1992-10-01

The numerical methods employed in the solution of many scientific computing problems require the computation of the gradient of a function f: R[sup n] [yields] R. ADIFOR is a source translator that, given a collection of subroutines to compute f, generates Fortran 77 code for computing the derivative of this function. Using the so-called torsion problem from the MINPACK-2 test collection as an example, this paper explores two issues in automatic differentiation: the efficient computation of derivatives for partial separable functions and the use of the compile-time reverse mode for the generation of derivatives. We show that orders of magnitudesmore » of improvement are possible when exploiting partial separability and maximizing use of the reverse mode.« less

PFMCal : Photonic force microscopy calibration extended for its application in high-frequency microrheology

NASA Astrophysics Data System (ADS)

Butykai, A.; Domínguez-García, P.; Mor, F. M.; Gaál, R.; Forró, L.; Jeney, S.

2017-11-01

The present document is an update of the previously published MatLab code for the calibration of optical tweezers in the high-resolution detection of the Brownian motion of non-spherical probes [1]. In this instance, an alternative version of the original code, based on the same physical theory [2], but focused on the automation of the calibration of measurements using spherical probes, is outlined. The new added code is useful for high-frequency microrheology studies, where the probe radius is known but the viscosity of the surrounding fluid maybe not. This extended calibration methodology is automatic, without the need of a user's interface. A code for calibration by means of thermal noise analysis [3] is also included; this is a method that can be applied when using viscoelastic fluids if the trap stiffness is previously estimated [4]. The new code can be executed in MatLab and using GNU Octave. Program Files doi:http://dx.doi.org/10.17632/s59f3gz729.1 Licensing provisions: GPLv3 Programming language: MatLab 2016a (MathWorks Inc.) and GNU Octave 4.0 Operating system: Linux and Windows. Supplementary material: A new document README.pdf includes basic running instructions for the new code. Journal reference of previous version: Computer Physics Communications, 196 (2015) 599 Does the new version supersede the previous version?: No. It adds alternative but compatible code while providing similar calibration factors. Nature of problem (approx. 50-250 words): The original code uses a MatLab-provided user's interface, which is not available in GNU Octave, and cannot be used outside of a proprietary software as MatLab. Besides, the process of calibration when using spherical probes needs an automatic method when calibrating big amounts of different data focused to microrheology. Solution method (approx. 50-250 words): The new code can be executed in the latest version of MatLab and using GNU Octave, a free and open-source alternative to MatLab. This code generates an automatic calibration process which requires only to write the input data in the main script. Additionally, we include a calibration method based on thermal noise statistics, which can be used with viscoelastic fluids if the trap stiffness is previously estimated. Reasons for the new version: This version extends the functionality of PFMCal for the particular case of spherical probes and unknown fluid viscosities. The extended code is automatic, works in different operating systems and it is compatible with GNU Octave. Summary of revisions: The original MatLab program in the previous version, which is executed by PFMCal.m, is not changed. Here, we have added two additional main archives named PFMCal_auto.m and PFMCal_histo.m, which implement automatic calculations of the calibration process and calibration through Boltzmann statistics, respectively. The process of calibration using this code for spherical beads is described in the README.pdf file provided in the new code submission. Here, we obtain different calibration factors, β (given in μm/V), according to [2], related to two statistical quantities: the mean-squared displacement (MSD), βMSD, and the velocity autocorrelation function (VAF), βVAF. Using that methodology, the trap stiffness, k, and the zero-shear viscosity of the fluid, η, can be calculated if the value of the particle's radius, a, is previously known. For comparison, we include in the extended code the method of calibration using the corner frequency of the power-spectral density (PSD) [5], providing a calibration factor βPSD. Besides, with the prior estimation of the trap stiffness, along with the known value of the particle's radius, we can use thermal noise statistics to obtain calibration factors, β, according to the quadratic form of the optical potential, βE, and related to the Gaussian distribution of the bead's positions, βσ2. This method has been demonstrated to be applicable to the calibration of optical tweezers when using non-Newtonian viscoelastic polymeric liquids [4]. An example of the results using this calibration process is summarized in Table 1. Using the data provided in the new code submission, for water and acetone fluids, we calculate all the calibration factors by using the original PFMCal.m and by the new non-GUI code PFMCal_auto.m and PFMCal_histo.m. Regarding the new code, PFMCal_auto.m returns η, k, βMSD, βVAF and βPSD, while PFMCal_histo.m provides βσ2 and βE. Table 1 shows how we obtain the expected viscosity of the two fluids at this temperature and how the different methods provide good agreement between trap stiffnesses and calibration factors. Additional comments including Restrictions and Unusual features (approx. 50-250 words): The original code, PFMCal.m, runs under MatLab using the Statistics Toolbox. The extended code, PFMCal_auto.m and PFMCal_histo.m, can be executed without modification using MatLab or GNU Octave. The code has been tested in Linux and Windows operating systems.

Automatically Generated Vegetation Density Maps with LiDAR Survey for Orienteering Purpose

NASA Astrophysics Data System (ADS)

Petrovič, Dušan

2018-05-01

The focus of our research was to automatically generate the most adequate vegetation density maps for orienteering purpose. Application Karttapullatuin was used for automated generation of vegetation density maps, which requires LiDAR data to process an automatically generated map. A part of the orienteering map in the area of Kazlje-Tomaj was used to compare the graphical display of vegetation density. With different settings of parameters in the Karttapullautin application we changed the way how vegetation density of automatically generated map was presented, and tried to match it as much as possible with the orienteering map of Kazlje-Tomaj. Comparing more created maps of vegetation density the most suitable parameter settings to automatically generate maps on other areas were proposed, too.

The Role of Item Models in Automatic Item Generation

ERIC Educational Resources Information Center

Gierl, Mark J.; Lai, Hollis

2012-01-01

Automatic item generation represents a relatively new but rapidly evolving research area where cognitive and psychometric theories are used to produce tests that include items generated using computer technology. Automatic item generation requires two steps. First, test development specialists create item models, which are comparable to templates…

The Contributions of Vocabulary and Letter Writing Automaticity to Word Reading and Spelling for Kindergartners

ERIC Educational Resources Information Center

Kim, Young-Suk; Al Otaiba, Stephanie; Puranik, Cynthia; Folsom, Jessica Sidler; Gruelich, Luana

2014-01-01

In the present study we examined the relation between alphabet knowledge fluency (letter names and sounds) and letter writing automaticity, and unique relations of letter writing automaticity and semantic knowledge (i.e., vocabulary) to word reading and spelling over and above code-related skills such as phonological awareness and alphabet…

Optimal boundary conditions for ORCA-2 model

NASA Astrophysics Data System (ADS)

Kazantsev, Eugene

2013-08-01

A 4D-Var data assimilation technique is applied to ORCA-2 configuration of the NEMO in order to identify the optimal parametrization of boundary conditions on the lateral boundaries as well as on the bottom and on the surface of the ocean. The influence of boundary conditions on the solution is analyzed both within and beyond the assimilation window. It is shown that the optimal bottom and surface boundary conditions allow us to better represent the jet streams, such as Gulf Stream and Kuroshio. Analyzing the reasons of the jets reinforcement, we notice that data assimilation has a major impact on parametrization of the bottom boundary conditions for u and v. Automatic generation of the tangent and adjoint codes is also discussed. Tapenade software is shown to be able to produce the adjoint code that can be used after a memory usage optimization.

The Automatic Parallelisation of Scientific Application Codes Using a Computer Aided Parallelisation Toolkit

NASA Technical Reports Server (NTRS)

Ierotheou, C.; Johnson, S.; Leggett, P.; Cross, M.; Evans, E.; Jin, Hao-Qiang; Frumkin, M.; Yan, J.; Biegel, Bryan (Technical Monitor)

2001-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. Historically, the lack of a programming standard for using directives and the rather limited performance due to scalability have affected the take-up of this programming model approach. Significant progress has been made in hardware and software technologies, as a result the performance of parallel programs with compiler directives has also made improvements. The introduction of an industrial standard for shared-memory programming with directives, OpenMP, has also addressed the issue of portability. In this study, we have extended the computer aided parallelization toolkit (developed at the University of Greenwich), to automatically generate OpenMP based parallel programs with nominal user assistance. We outline the way in which loop types are categorized and how efficient OpenMP directives can be defined and placed using the in-depth interprocedural analysis that is carried out by the toolkit. We also discuss the application of the toolkit on the NAS Parallel Benchmarks and a number of real-world application codes. This work not only demonstrates the great potential of using the toolkit to quickly parallelize serial programs but also the good performance achievable on up to 300 processors for hybrid message passing and directive-based parallelizations.

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52)

NASA Astrophysics Data System (ADS)

Alvanos, Michail; Christoudias, Theodoros

2017-10-01

This paper presents an application of GPU accelerators in Earth system modeling. We focus on atmospheric chemical kinetics, one of the most computationally intensive tasks in climate-chemistry model simulations. We developed a software package that automatically generates CUDA kernels to numerically integrate atmospheric chemical kinetics in the global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC), used to study climate change and air quality scenarios. A source-to-source compiler outputs a CUDA-compatible kernel by parsing the FORTRAN code generated by the Kinetic PreProcessor (KPP) general analysis tool. All Rosenbrock methods that are available in the KPP numerical library are supported.Performance evaluation, using Fermi and Pascal CUDA-enabled GPU accelerators, shows achieved speed-ups of 4. 5 × and 20. 4 × , respectively, of the kernel execution time. A node-to-node real-world production performance comparison shows a 1. 75 × speed-up over the non-accelerated application using the KPP three-stage Rosenbrock solver. We provide a detailed description of the code optimizations used to improve the performance including memory optimizations, control code simplification, and reduction of idle time. The accuracy and correctness of the accelerated implementation are evaluated by comparing to the CPU-only code of the application. The median relative difference is found to be less than 0.000000001 % when comparing the output of the accelerated kernel the CPU-only code.The approach followed, including the computational workload division, and the developed GPU solver code can potentially be used as the basis for hardware acceleration of numerous geoscientific models that rely on KPP for atmospheric chemical kinetics applications.

A system for classifying wood-using industries and recording statistics for automatic data processing.

Treesearch

E.W. Fobes; R.W. Rowe

1968-01-01

A system for classifying wood-using industries and recording pertinent statistics for automatic data processing is described. Forms and coding instructions for recording data of primary processing plants are included.

Automatic Text Structuring and Summarization.

ERIC Educational Resources Information Center

Salton, Gerard; And Others

1997-01-01

Discussion of the use of information retrieval techniques for automatic generation of semantic hypertext links focuses on automatic text summarization. Topics include World Wide Web links, text segmentation, and evaluation of text summarization by comparing automatically generated abstracts with manually prepared abstracts. (Author/LRW)

FAMA: An automatic code for stellar parameter and abundance determination

NASA Astrophysics Data System (ADS)

Magrini, Laura; Randich, Sofia; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

2013-10-01

Context. The large amount of spectra obtained during the epoch of extensive spectroscopic surveys of Galactic stars needs the development of automatic procedures to derive their atmospheric parameters and individual element abundances. Aims: Starting from the widely-used code MOOG by C. Sneden, we have developed a new procedure to determine atmospheric parameters and abundances in a fully automatic way. The code FAMA (Fast Automatic MOOG Analysis) is presented describing its approach to derive atmospheric stellar parameters and element abundances. The code, freely distributed, is written in Perl and can be used on different platforms. Methods: The aim of FAMA is to render the computation of the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths (EWs) as automatic and as independent of any subjective approach as possible. It is based on the simultaneous search for three equilibria: excitation equilibrium, ionization balance, and the relationship between log n(Fe i) and the reduced EWs. FAMA also evaluates the statistical errors on individual element abundances and errors due to the uncertainties in the stellar parameters. The convergence criteria are not fixed "a priori" but are based on the quality of the spectra. Results: In this paper we present tests performed on the solar spectrum EWs that assess the method's dependency on the initial parameters and we analyze a sample of stars observed in Galactic open and globular clusters. The current version of FAMA is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/558/A38

Approaches to the automatic generation and control of finite element meshes

NASA Technical Reports Server (NTRS)

Shephard, Mark S.

1987-01-01

The algorithmic approaches being taken to the development of finite element mesh generators capable of automatically discretizing general domains without the need for user intervention are discussed. It is demonstrated that because of the modeling demands placed on a automatic mesh generator, all the approaches taken to date produce unstructured meshes. Consideration is also given to both a priori and a posteriori mesh control devices for automatic mesh generators as well as their integration with geometric modeling and adaptive analysis procedures.

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

PubMed

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans; Swertz, Morris A

2016-07-15

While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect : m.a.swertz@rug.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks

PubMed Central

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K. Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans

2016-01-01

Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect. Contact: m.a.swertz@rug.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153686

Real-time Shakemap implementation in Austria

NASA Astrophysics Data System (ADS)

Weginger, Stefan; Jia, Yan; Papi Isaba, Maria; Horn, Nikolaus

2017-04-01

ShakeMaps provide near-real-time maps of ground motion and shaking intensity following significant earthquakes. They are automatically generated within a few minutes after occurrence of an earthquake. We tested and included the USGS ShakeMap 4.0 (experimental code) based on python in the Antelope real-time system with local modified GMPE and Site Effects based on the conditions in Austria. The ShakeMaps are provided in terms of Intensity, PGA, PGV and PSA. Future presentation of ShakeMap contour lines and Ground Motion Parameter with interactive maps and data exchange over Web-Services are shown.

A Program Certification Assistant Based on Fully Automated Theorem Provers

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2005-01-01

We describe a certification assistant to support formal safety proofs for programs. It is based on a graphical user interface that hides the low-level details of first-order automated theorem provers while supporting limited interactivity: it allows users to customize and control the proof process on a high level, manages the auxiliary artifacts produced during this process, and provides traceability between the proof obligations and the relevant parts of the program. The certification assistant is part of a larger program synthesis system and is intended to support the deployment of automatically generated code in safety-critical applications.

Single Event Effects mitigation with TMRG tool

NASA Astrophysics Data System (ADS)

Kulis, S.

2017-01-01

Single Event Effects (SEE) are a major concern for integrated circuits exposed to radiation. There have been several techniques proposed to protect circuits against radiation-induced upsets. Among the others, the Triple Modular Redundancy (TMR) technique is one of the most popular. The purpose of the Triple Modular Redundancy Generator (TMRG) tool is to automatize the process of triplicating digital circuits freeing the designer from introducing the TMR code manually at the implementation stage. It helps to ensure that triplicated logic is maintained through the design process. Finally, the tool streamlines the process of introducing SEE in gate level simulations for final verification.

Methods for Ensuring High Quality of Coding of Cause of Death. The Mortality Register to Follow Southern Urals Populations Exposed to Radiation.

PubMed

Startsev, N; Dimov, P; Grosche, B; Tretyakov, F; Schüz, J; Akleyev, A

2015-01-01

To follow up populations exposed to several radiation accidents in the Southern Urals, a cause-of-death registry was established at the Urals Center capturing deaths in the Chelyabinsk, Kurgan and Sverdlovsk region since 1950. When registering deaths over such a long time period, quality measures need to be in place to maintain quality and reduce the impact of individual coders as well as quality changes in death certificates. To ensure the uniformity of coding, a method for semi-automatic coding was developed, which is described here. Briefly, the method is based on a dynamic thesaurus, database-supported coding and parallel coding by two different individuals. A comparison of the proposed method for organizing the coding process with the common procedure of coding showed good agreement, with, at the end of the coding process, 70  - 90% agreement for the three-digit ICD -9 rubrics. The semi-automatic method ensures a sufficiently high quality of coding by at the same time providing an opportunity to reduce the labor intensity inherent in the creation of large-volume cause-of-death registries.

Social priming of hemispatial neglect affects spatial coding: Evidence from the Simon task.

PubMed

Arend, Isabel; Aisenberg, Daniela; Henik, Avishai

2016-10-01

In the Simon effect (SE), choice reactions are fast if the location of the stimulus and the response correspond when stimulus location is task-irrelevant; therefore, the SE reflects the automatic processing of space. Priming of social concepts was found to affect automatic processing in the Stroop effect. We investigated whether spatial coding measured by the SE can be affected by the observer's mental state. We used two social priming manipulations of impairments: one involving spatial processing - hemispatial neglect (HN) and another involving color perception - achromatopsia (ACHM). In two experiments the SE was reduced in the "neglected" visual field (VF) under the HN, but not under the ACHM manipulation. Our results show that spatial coding is sensitive to spatial representations that are not derived from task-relevant parameters, but from the observer's cognitive state. These findings dispute stimulus-response interference models grounded on the idea of the automaticity of spatial processing. Copyright © 2016. Published by Elsevier Inc.

The development of a program analysis environment for Ada: Reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1991-01-01

The Graphical Representations of Algorithms, Structures, and Processes for Ada (GRASP/Ada) has successfully created and prototyped a new algorithm level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and thus improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under the Virtual Memory System (VMS) on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. In Phase 3 of the project, the prototype was prepared for limited distribution (GRASP/Ada Version 3.0) to facilitate evaluation. The user interface was extensively reworked. The current prototype provides the capability for the user to generate CSD from Ada source code in a reverse engineering mode with a level of flexibility suitable for practical application.

First- and Second-Order Sensitivity Analysis of a P-Version Finite Element Equation Via Automatic Differentiation

NASA Technical Reports Server (NTRS)

Hou, Gene

1998-01-01

Sensitivity analysis is a technique for determining derivatives of system responses with respect to design parameters. Among many methods available for sensitivity analysis, automatic differentiation has been proven through many applications in fluid dynamics and structural mechanics to be an accurate and easy method for obtaining derivatives. Nevertheless, the method can be computational expensive and can require a high memory space. This project will apply an automatic differentiation tool, ADIFOR, to a p-version finite element code to obtain first- and second- order then-nal derivatives, respectively. The focus of the study is on the implementation process and the performance of the ADIFOR-enhanced codes for sensitivity analysis in terms of memory requirement, computational efficiency, and accuracy.

Automatically Detecting Failures in Natural Language Processing Tools for Online Community Text.

PubMed

Park, Albert; Hartzler, Andrea L; Huh, Jina; McDonald, David W; Pratt, Wanda

2015-08-31

The prevalence and value of patient-generated health text are increasing, but processing such text remains problematic. Although existing biomedical natural language processing (NLP) tools are appealing, most were developed to process clinician- or researcher-generated text, such as clinical notes or journal articles. In addition to being constructed for different types of text, other challenges of using existing NLP include constantly changing technologies, source vocabularies, and characteristics of text. These continuously evolving challenges warrant the need for applying low-cost systematic assessment. However, the primarily accepted evaluation method in NLP, manual annotation, requires tremendous effort and time. The primary objective of this study is to explore an alternative approach-using low-cost, automated methods to detect failures (eg, incorrect boundaries, missed terms, mismapped concepts) when processing patient-generated text with existing biomedical NLP tools. We first characterize common failures that NLP tools can make in processing online community text. We then demonstrate the feasibility of our automated approach in detecting these common failures using one of the most popular biomedical NLP tools, MetaMap. Using 9657 posts from an online cancer community, we explored our automated failure detection approach in two steps: (1) to characterize the failure types, we first manually reviewed MetaMap's commonly occurring failures, grouped the inaccurate mappings into failure types, and then identified causes of the failures through iterative rounds of manual review using open coding, and (2) to automatically detect these failure types, we then explored combinations of existing NLP techniques and dictionary-based matching for each failure cause. Finally, we manually evaluated the automatically detected failures. From our manual review, we characterized three types of failure: (1) boundary failures, (2) missed term failures, and (3) word ambiguity failures. Within these three failure types, we discovered 12 causes of inaccurate mappings of concepts. We used automated methods to detect almost half of 383,572 MetaMap's mappings as problematic. Word sense ambiguity failure was the most widely occurring, comprising 82.22% of failures. Boundary failure was the second most frequent, amounting to 15.90% of failures, while missed term failures were the least common, making up 1.88% of failures. The automated failure detection achieved precision, recall, accuracy, and F1 score of 83.00%, 92.57%, 88.17%, and 87.52%, respectively. We illustrate the challenges of processing patient-generated online health community text and characterize failures of NLP tools on this patient-generated health text, demonstrating the feasibility of our low-cost approach to automatically detect those failures. Our approach shows the potential for scalable and effective solutions to automatically assess the constantly evolving NLP tools and source vocabularies to process patient-generated text.

Automatic 3d Building Model Generations with Airborne LiDAR Data

NASA Astrophysics Data System (ADS)

Yastikli, N.; Cetin, Z.

2017-11-01

LiDAR systems become more and more popular because of the potential use for obtaining the point clouds of vegetation and man-made objects on the earth surface in an accurate and quick way. Nowadays, these airborne systems have been frequently used in wide range of applications such as DEM/DSM generation, topographic mapping, object extraction, vegetation mapping, 3 dimensional (3D) modelling and simulation, change detection, engineering works, revision of maps, coastal management and bathymetry. The 3D building model generation is the one of the most prominent applications of LiDAR system, which has the major importance for urban planning, illegal construction monitoring, 3D city modelling, environmental simulation, tourism, security, telecommunication and mobile navigation etc. The manual or semi-automatic 3D building model generation is costly and very time-consuming process for these applications. Thus, an approach for automatic 3D building model generation is needed in a simple and quick way for many studies which includes building modelling. In this study, automatic 3D building models generation is aimed with airborne LiDAR data. An approach is proposed for automatic 3D building models generation including the automatic point based classification of raw LiDAR point cloud. The proposed point based classification includes the hierarchical rules, for the automatic production of 3D building models. The detailed analyses for the parameters which used in hierarchical rules have been performed to improve classification results using different test areas identified in the study area. The proposed approach have been tested in the study area which has partly open areas, forest areas and many types of the buildings, in Zekeriyakoy, Istanbul using the TerraScan module of TerraSolid. The 3D building model was generated automatically using the results of the automatic point based classification. The obtained results of this research on study area verified that automatic 3D building models can be generated successfully using raw LiDAR point cloud data.

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

Extending compile-time reverse mode and exploiting partial separability in ADIFOR. ADIFOR Working Note No. 7

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

Bischof, C.H.; El-Khadiri, M.

1992-10-01

The numerical methods employed in the solution of many scientific computing problems require the computation of the gradient of a function f: R{sup n} {yields} R. ADIFOR is a source translator that, given a collection of subroutines to compute f, generates Fortran 77 code for computing the derivative of this function. Using the so-called torsion problem from the MINPACK-2 test collection as an example, this paper explores two issues in automatic differentiation: the efficient computation of derivatives for partial separable functions and the use of the compile-time reverse mode for the generation of derivatives. We show that orders of magnitudesmore » of improvement are possible when exploiting partial separability and maximizing use of the reverse mode.« less

Applying Hierarchical Model Calibration to Automatically Generated Items.

ERIC Educational Resources Information Center

Williamson, David M.; Johnson, Matthew S.; Sinharay, Sandip; Bejar, Isaac I.

This study explored the application of hierarchical model calibration as a means of reducing, if not eliminating, the need for pretesting of automatically generated items from a common item model prior to operational use. Ultimately the successful development of automatic item generation (AIG) systems capable of producing items with highly similar…

Automatic Item Generation of Probability Word Problems

ERIC Educational Resources Information Center

Holling, Heinz; Bertling, Jonas P.; Zeuch, Nina

2009-01-01

Mathematical word problems represent a common item format for assessing student competencies. Automatic item generation (AIG) is an effective way of constructing many items with predictable difficulties, based on a set of predefined task parameters. The current study presents a framework for the automatic generation of probability word problems…

46 CFR 112.05-5 - Emergency power source.

Code of Federal Regulations, 2013 CFR

2013-10-01

... with § 112.05-1(c). Table 112.05-5(a) Size of vessel and service Type of emergency power source or... power source (automatically connected storage battery or an automatically started generator) 36 hours.1... power source (automatically connected storage battery or an automatically started generator) 8 hours or...

46 CFR 112.05-5 - Emergency power source.

Code of Federal Regulations, 2012 CFR

2012-10-01

... with § 112.05-1(c). Table 112.05-5(a) Size of vessel and service Type of emergency power source or... power source (automatically connected storage battery or an automatically started generator) 36 hours.1... power source (automatically connected storage battery or an automatically started generator) 8 hours or...

46 CFR 112.05-5 - Emergency power source.

Code of Federal Regulations, 2014 CFR

2014-10-01

... with § 112.05-1(c). Table 112.05-5(a) Size of vessel and service Type of emergency power source or... power source (automatically connected storage battery or an automatically started generator) 36 hours.1... power source (automatically connected storage battery or an automatically started generator) 8 hours or...

Use Them ... or Lose Them? The Case for and against Using QR Codes

ERIC Educational Resources Information Center

Cunningham, Chuck; Dull, Cassie

2011-01-01

A quick-response (QR) code is a two-dimensional, black-and-white square barcode and links directly to a URL of one's choice. When the code is scanned with a smartphone, it will automatically redirect the user to the designated URL. QR codes are popping up everywhere--billboards, magazines, posters, shop windows, TVs, computer screens, and more.…

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

Jones, J.P.; Bangs, A.L.; Butler, P.L.

Hetero Helix is a programming environment which simulates shared memory on a heterogeneous network of distributed-memory computers. The machines in the network may vary with respect to their native operating systems and internal representation of numbers. Hetero Helix presents a simple programming model to developers, and also considers the needs of designers, system integrators, and maintainers. The key software technology underlying Hetero Helix is the use of a compiler'' which analyzes the data structures in shared memory and automatically generates code which translates data representations from the format native to each machine into a common format, and vice versa. Themore » design of Hetero Helix was motivated in particular by the requirements of robotics applications. Hetero Helix has been used successfully in an integration effort involving 27 CPUs in a heterogeneous network and a body of software totaling roughly 100,00 lines of code. 25 refs., 6 figs.« less

A predictive coding account of MMN reduction in schizophrenia.

PubMed

Wacongne, Catherine

2016-04-01

The mismatch negativity (MMN) is thought to be an index of the automatic activation of a specialized network for active prediction and deviance detection in the auditory cortex. It is consistently reduced in schizophrenic patients and has received a lot of interest as a clinical and translational tool. The main neuronal hypothesis regarding the mechanisms leading to a reduced MMN in schizophrenic patients is a dysfunction of NMDA receptors (NMDA-R). However, this hypothesis has never been implemented in a neuronal model. In this paper, we examine the consequences of NMDA-R dysfunction in a neuronal model of MMN based on predictive coding principle. I also investigate how predictive processes may interact with synaptic adaptation in MMN generations and examine the consequences of this interaction for the use of MMN paradigms in schizophrenia research. Copyright © 2015 Elsevier B.V. All rights reserved.

Automatically Preparing Safe SQL Queries

NASA Astrophysics Data System (ADS)

Bisht, Prithvi; Sistla, A. Prasad; Venkatakrishnan, V. N.

We present the first sound program source transformation approach for automatically transforming the code of a legacy web application to employ PREPARE statements in place of unsafe SQL queries. Our approach therefore opens the way for eradicating the SQL injection threat vector from legacy web applications.

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations

PubMed Central

Langenkämper, Daniel; Jakobi, Tobias; Feld, Dustin; Jelonek, Lukas; Goesmann, Alexander; Nattkemper, Tim W.

2016-01-01

Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g., modern genomics. This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore, we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand. We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC). Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs) performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead. We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually no additional manual adjustment is required. In contrast, some automatic parallelizers targeting GPUs still lack maturity and are limited to simple statements and structures. PMID:26904094

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

PubMed

Langenkämper, Daniel; Jakobi, Tobias; Feld, Dustin; Jelonek, Lukas; Goesmann, Alexander; Nattkemper, Tim W

2016-01-01

Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g., modern genomics. This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore, we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand. We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC). Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs) performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead. We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually no additional manual adjustment is required. In contrast, some automatic parallelizers targeting GPUs still lack maturity and are limited to simple statements and structures.

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.

Unstructured Grids for Sonic Boom Analysis and Design

NASA Technical Reports Server (NTRS)

Campbell, Richard L.; Nayani, Sudheer N.

2015-01-01

An evaluation of two methods for improving the process for generating unstructured CFD grids for sonic boom analysis and design has been conducted. The process involves two steps: the generation of an inner core grid using a conventional unstructured grid generator such as VGRID, followed by the extrusion of a sheared and stretched collar grid through the outer boundary of the core grid. The first method evaluated, known as COB, automatically creates a cylindrical outer boundary definition for use in VGRID that makes the extrusion process more robust. The second method, BG, generates the collar grid by extrusion in a very efficient manner. Parametric studies have been carried out and new options evaluated for each of these codes with the goal of establishing guidelines for best practices for maintaining boom signature accuracy with as small a grid as possible. In addition, a preliminary investigation examining the use of the CDISC design method for reducing sonic boom utilizing these grids was conducted, with initial results confirming the feasibility of a new remote design approach.

Source Term Model for Vortex Generator Vanes in a Navier-Stokes Computer Code

NASA Technical Reports Server (NTRS)

Waithe, Kenrick A.

2004-01-01

A source term model for an array of vortex generators was implemented into a non-proprietary Navier-Stokes computer code, OVERFLOW. The source term models the side force created by a vortex generator vane. The model is obtained by introducing a side force to the momentum and energy equations that can adjust its strength automatically based on the local flow. The model was tested and calibrated by comparing data from numerical simulations and experiments of a single low profile vortex generator vane on a flat plate. In addition, the model was compared to experimental data of an S-duct with 22 co-rotating, low profile vortex generators. The source term model allowed a grid reduction of about seventy percent when compared with the numerical simulations performed on a fully gridded vortex generator on a flat plate without adversely affecting the development and capture of the vortex created. The source term model was able to predict the shape and size of the stream-wise vorticity and velocity contours very well when compared with both numerical simulations and experimental data. The peak vorticity and its location were also predicted very well when compared to numerical simulations and experimental data. The circulation predicted by the source term model matches the prediction of the numerical simulation. The source term model predicted the engine fan face distortion and total pressure recovery of the S-duct with 22 co-rotating vortex generators very well. The source term model allows a researcher to quickly investigate different locations of individual or a row of vortex generators. The researcher is able to conduct a preliminary investigation with minimal grid generation and computational time.

Experience in connecting the power generating units of thermal power plants to automatic secondary frequency regulation within the united power system of Russia

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

Zhukov, A. V.; Komarov, A. N.; Safronov, A. N.

The principles of central control of the power generating units of thermal power plants by automatic secondary frequency and active power overcurrent regulation systems, and the algorithms for interactions between automatic power control systems for the power production units in thermal power plants and centralized systems for automatic frequency and power regulation, are discussed. The order of switching the power generating units of thermal power plants over to control by a centralized system for automatic frequency and power regulation and by the Central Coordinating System for automatic frequency and power regulation is presented. The results of full-scale system tests ofmore » the control of power generating units of the Kirishskaya, Stavropol, and Perm GRES (State Regional Electric Power Plants) by the Central Coordinating System for automatic frequency and power regulation at the United Power System of Russia on September 23-25, 2008, are reported.« less

Introduction of the ASGARD code (Automated Selection and Grouping of events in AIA Regional Data)

NASA Astrophysics Data System (ADS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv K.; Fayock, Brian

2017-08-01

We have developed the ASGARD code to automatically detect and group brightenings ("events") in AIA data. The event selection and grouping can be optimized to the respective dataset with a multitude of control parameters. The code was initially written for IRIS data, but has since been optimized for AIA. However, the underlying algorithm is not limited to either and could be used for other data as well.Results from datasets in various AIA channels show that brightenings are reliably detected and that coherent coronal structures can be isolated by using the obtained information about the start, peak, and end times of events. We are presently working on a follow-up algorithm to automatically determine the heating and cooling timescales of coronal structures. This will be done by correlating the information from different AIA channels with different temperature responses. We will present the code and preliminary results.

Automatic vehicle location system

NASA Technical Reports Server (NTRS)

Hansen, G. R., Jr. (Inventor)

1973-01-01

An automatic vehicle detection system is disclosed, in which each vehicle whose location is to be detected carries active means which interact with passive elements at each location to be identified. The passive elements comprise a plurality of passive loops arranged in a sequence along the travel direction. Each of the loops is tuned to a chosen frequency so that the sequence of the frequencies defines the location code. As the vehicle traverses the sequence of the loops as it passes over each loop, signals only at the frequency of the loop being passed over are coupled from a vehicle transmitter to a vehicle receiver. The frequencies of the received signals in the receiver produce outputs which together represent a code of the traversed location. The code location is defined by a painted pattern which reflects light to a vehicle carried detector whose output is used to derive the code defined by the pattern.

Spectral-element Seismic Wave Propagation on CUDA/OpenCL Hardware Accelerators

NASA Astrophysics Data System (ADS)

Peter, D. B.; Videau, B.; Pouget, K.; Komatitsch, D.

2015-12-01

Seismic wave propagation codes are essential tools to investigate a variety of wave phenomena in the Earth. Furthermore, they can now be used for seismic full-waveform inversions in regional- and global-scale adjoint tomography. Although these seismic wave propagation solvers are crucial ingredients to improve the resolution of tomographic images to answer important questions about the nature of Earth's internal processes and subsurface structure, their practical application is often limited due to high computational costs. They thus need high-performance computing (HPC) facilities to improving the current state of knowledge. At present, numerous large HPC systems embed many-core architectures such as graphics processing units (GPUs) to enhance numerical performance. Such hardware accelerators can be programmed using either the CUDA programming environment or the OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted by additional hardware accelerators, like e.g. AMD graphic cards, ARM-based processors as well as Intel Xeon Phi coprocessors. For seismic wave propagation simulations using the open-source spectral-element code package SPECFEM3D_GLOBE, we incorporated an automatic source-to-source code generation tool (BOAST) which allows us to use meta-programming of all computational kernels for forward and adjoint runs. Using our BOAST kernels, we generate optimized source code for both CUDA and OpenCL languages within the source code package. Thus, seismic wave simulations are able now to fully utilize CUDA and OpenCL hardware accelerators. We show benchmarks of forward seismic wave propagation simulations using SPECFEM3D_GLOBE on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase I is complete for the development of a Computational Fluid Dynamics parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Floating-to-Fixed-Point Conversion for Digital Signal Processors

NASA Astrophysics Data System (ADS)

Menard, Daniel; Chillet, Daniel; Sentieys, Olivier

2006-12-01

Digital signal processing applications are specified with floating-point data types but they are usually implemented in embedded systems with fixed-point arithmetic to minimise cost and power consumption. Thus, methodologies which establish automatically the fixed-point specification are required to reduce the application time-to-market. In this paper, a new methodology for the floating-to-fixed point conversion is proposed for software implementations. The aim of our approach is to determine the fixed-point specification which minimises the code execution time for a given accuracy constraint. Compared to previous methodologies, our approach takes into account the DSP architecture to optimise the fixed-point formats and the floating-to-fixed-point conversion process is coupled with the code generation process. The fixed-point data types and the position of the scaling operations are optimised to reduce the code execution time. To evaluate the fixed-point computation accuracy, an analytical approach is used to reduce the optimisation time compared to the existing methods based on simulation. The methodology stages are described and several experiment results are presented to underline the efficiency of this approach.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Color categories affect pre-attentive color perception.

PubMed

Clifford, Alexandra; Holmes, Amanda; Davies, Ian R L; Franklin, Anna

2010-10-01

Categorical perception (CP) of color is the faster and/or more accurate discrimination of colors from different categories than equivalently spaced colors from the same category. Here, we investigate whether color CP at early stages of chromatic processing is independent of top-down modulation from attention. A visual oddball task was employed where frequent and infrequent colored stimuli were either same- or different-category, with chromatic differences equated across conditions. Stimuli were presented peripheral to a central distractor task to elicit an event-related potential (ERP) known as the visual mismatch negativity (vMMN). The vMMN is an index of automatic and pre-attentive visual change detection arising from generating loci in visual cortices. The results revealed a greater vMMN for different-category than same-category change detection when stimuli appeared in the lower visual field, and an absence of attention-related ERP components. The findings provide the first clear evidence for an automatic and pre-attentive categorical code for color. Copyright © 2010 Elsevier B.V. All rights reserved.

Development of Semi-Automatic Lathe by using Intelligent Soft Computing Technique

NASA Astrophysics Data System (ADS)

Sakthi, S.; Niresh, J.; Vignesh, K.; Anand Raj, G.

2018-03-01

This paper discusses the enhancement of conventional lathe machine to semi-automated lathe machine by implementing a soft computing method. In the present scenario, lathe machine plays a vital role in the engineering division of manufacturing industry. While the manual lathe machines are economical, the accuracy and efficiency are not up to the mark. On the other hand, CNC machine provide the desired accuracy and efficiency, but requires a huge capital. In order to over come this situation, a semi-automated approach towards the conventional lathe machine is developed by employing stepper motors to the horizontal and vertical drive, that can be controlled by Arduino UNO -microcontroller. Based on the input parameters of the lathe operation the arduino coding is been generated and transferred to the UNO board. Thus upgrading from manual to semi-automatic lathe machines can significantly increase the accuracy and efficiency while, at the same time, keeping a check on investment cost and consequently provide a much needed escalation to the manufacturing industry.

LexValueSets: An Approach for Context-Driven Value Sets Extraction

PubMed Central

Pathak, Jyotishman; Jiang, Guoqian; Dwarkanath, Sridhar O.; Buntrock, James D.; Chute, Christopher G.

2008-01-01

The ability to model, share and re-use value sets across multiple medical information systems is an important requirement. However, generating value sets semi-automatically from a terminology service is still an unresolved issue, in part due to the lack of linkage to clinical context patterns that provide the constraints in defining a concept domain and invocation of value sets extraction. Towards this goal, we develop and evaluate an approach for context-driven automatic value sets extraction based on a formal terminology model. The crux of the technique is to identify and define the context patterns from various domains of discourse and leverage them for value set extraction using two complementary ideas based on (i) local terms provided by the Subject Matter Experts (extensional) and (ii) semantic definition of the concepts in coding schemes (intensional). A prototype was implemented based on SNOMED CT rendered in the LexGrid terminology model and a preliminary evaluation is presented. PMID:18998955

An Application of Reverse Engineering to Automatic Item Generation: A Proof of Concept Using Automatically Generated Figures

ERIC Educational Resources Information Center

Lorié, William A.

2013-01-01

A reverse engineering approach to automatic item generation (AIG) was applied to a figure-based publicly released test item from the Organisation for Economic Cooperation and Development (OECD) Programme for International Student Assessment (PISA) mathematical literacy cognitive instrument as part of a proof of concept. The author created an item…

A Parameter Tuning Scheme of Sea-ice Model Based on Automatic Differentiation Technique

NASA Astrophysics Data System (ADS)

Kim, J. G.; Hovland, P. D.

2001-05-01

Automatic diferentiation (AD) technique was used to illustrate a new approach for parameter tuning scheme of an uncoupled sea-ice model. Atmospheric forcing field of 1992 obtained from NCEP data was used as enforcing variables in the study. The simulation results were compared with the observed ice movement provided by the International Arctic Buoy Programme (IABP). All of the numerical experiments were based on a widely used dynamic and thermodynamic model for simulating the seasonal sea-ice chnage of the main Arctic ocean. We selected five dynamic and thermodynamic parameters for the tuning process in which the cost function defined by the norm of the difference between observed and simulated ice drift locations was minimized. The selected parameters are the air and ocean drag coefficients, the ice strength constant, the turning angle at ice-air/ocean interface, and the bulk sensible heat transfer coefficient. The drag coefficients were the major parameters to control sea-ice movement and extent. The result of the study shows that more realistic simulations of ice thickness distribution was produced by tuning the simulated ice drift trajectories. In the tuning process, the L-BFCGS-B minimization algorithm of a quasi-Newton method was used. The derivative information required in the minimization iterations was provided by the AD processed Fortran code. Compared with a conventional approach, AD generated derivative code provided fast and robust computations of derivative information.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

PubMed Central

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun; Ibrahim, Yehia M.; Wilkins, Christopher S.; Renslow, Ryan S.; Thomas, Dennis G.; Payne, Samuel H.; Monroe, Matthew E.; Smith, Richard D.; Teeguarden, Justin G.; Baker, Erin S.; Metz, Thomas O.

2017-01-01

Abstract Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation: PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Contact: erin.baker@pnnl.gov or thomas.metz@pnnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28505286

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

PubMed

Ma, Jian; Casey, Cameron P; Zheng, Xueyun; Ibrahim, Yehia M; Wilkins, Christopher S; Renslow, Ryan S; Thomas, Dennis G; Payne, Samuel H; Monroe, Matthew E; Smith, Richard D; Teeguarden, Justin G; Baker, Erin S; Metz, Thomas O

2017-09-01

Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library . erin.baker@pnnl.gov or thomas.metz@pnnl.gov. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Interactive specification acquisition via scenarios: A proposal

NASA Technical Reports Server (NTRS)

Hall, Robert J.

1992-01-01

Some reactive systems are most naturally specified by giving large collections of behavior scenarios. These collections not only specify the behavior of the system, but also provide good test suites for validating the implemented system. Due to the complexity of the systems and the number of scenarios, however, it appears that automated assistance is necessary to make this software development process workable. Interactive Specification Acquisition Tool (ISAT) is a proposed interactive system for supporting the acquisition and maintenance of a formal system specification from scenarios, as well as automatic synthesis of control code and automated test generation. This paper discusses the background, motivation, proposed functions, and implementation status of ISAT.

A Software Engineering Approach based on WebML and BPMN to the Mediation Scenario of the SWS Challenge

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Ceri, Stefano; Valle, Emanuele Della; Facca, Federico M.; Tziviskou, Christina

Although Semantic Web Services are expected to produce a revolution in the development of Web-based systems, very few enterprise-wide design experiences are available; one of the main reasons is the lack of sound Software Engineering methods and tools for the deployment of Semantic Web applications. In this chapter, we present an approach to software development for the Semantic Web based on classical Software Engineering methods (i.e., formal business process development, computer-aided and component-based software design, and automatic code generation) and on semantic methods and tools (i.e., ontology engineering, semantic service annotation and discovery).

Distributed databases for materials study of thermo-kinetic properties

NASA Astrophysics Data System (ADS)

Toher, Cormac

2015-03-01

High-throughput computational materials science provides researchers with the opportunity to rapidly generate large databases of materials properties. To rapidly add thermal properties to the AFLOWLIB consortium and Materials Project repositories, we have implemented an automated quasi-harmonic Debye model, the Automatic GIBBS Library (AGL). This enables us to screen thousands of materials for thermal conductivity, bulk modulus, thermal expansion and related properties. The search and sort functions of the online database can then be used to identify suitable materials for more in-depth study using more precise computational or experimental techniques. AFLOW-AGL source code is public domain and will soon be released within the GNU-GPL license.

A strategy for automatically generating programs in the lucid programming language

NASA Technical Reports Server (NTRS)

Johnson, Sally C.

1987-01-01

A strategy for automatically generating and verifying simple computer programs is described. The programs are specified by a precondition and a postcondition in predicate calculus. The programs generated are in the Lucid programming language, a high-level, data-flow language known for its attractive mathematical properties and ease of program verification. The Lucid programming is described, and the automatic program generation strategy is described and applied to several example problems.

[Development of a Compared Software for Automatically Generated DVH in Eclipse TPS].

PubMed

Xie, Zhao; Luo, Kelin; Zou, Lian; Hu, Jinyou

2016-03-01

This study is to automatically calculate the dose volume histogram(DVH) for the treatment plan, then to compare it with requirements of doctor's prescriptions. The scripting language Autohotkey and programming language C# were used to develop a compared software for automatically generated DVH in Eclipse TPS. This software is named Show Dose Volume Histogram (ShowDVH), which is composed of prescription documents generation, operation functions of DVH, software visualization and DVH compared report generation. Ten cases in different cancers have been separately selected, in Eclipse TPS 11.0 ShowDVH could not only automatically generate DVH reports but also accurately determine whether treatment plans meet the requirements of doctor’s prescriptions, then reports gave direction for setting optimization parameters of intensity modulated radiated therapy. The ShowDVH is an user-friendly and powerful software, and can automatically generated compared DVH reports fast in Eclipse TPS 11.0. With the help of ShowDVH, it greatly saves plan designing time and improves working efficiency of radiation therapy physicists.

Social Risk and Depression: Evidence from Manual and Automatic Facial Expression Analysis

PubMed Central

Girard, Jeffrey M.; Cohn, Jeffrey F.; Mahoor, Mohammad H.; Mavadati, Seyedmohammad; Rosenwald, Dean P.

2014-01-01

Investigated the relationship between change over time in severity of depression symptoms and facial expression. Depressed participants were followed over the course of treatment and video recorded during a series of clinical interviews. Facial expressions were analyzed from the video using both manual and automatic systems. Automatic and manual coding were highly consistent for FACS action units, and showed similar effects for change over time in depression severity. For both systems, when symptom severity was high, participants made more facial expressions associated with contempt, smiled less, and those smiles that occurred were more likely to be accompanied by facial actions associated with contempt. These results are consistent with the “social risk hypothesis” of depression. According to this hypothesis, when symptoms are severe, depressed participants withdraw from other people in order to protect themselves from anticipated rejection, scorn, and social exclusion. As their symptoms fade, participants send more signals indicating a willingness to affiliate. The finding that automatic facial expression analysis was both consistent with manual coding and produced the same pattern of depression effects suggests that automatic facial expression analysis may be ready for use in behavioral and clinical science. PMID:24598859

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the technical aspects of debugging computer code that has been automatically converted for use in a parallel computing system. Shared memory parallelization and distributed memory parallelization entail separate and distinct challenges for a debugging program. A prototype system has been developed which integrates various tools for the debugging of automatically parallelized programs including the CAPTools Database which provides variable definition information across subroutines as well as array distribution information.

The numerical solution of ordinary differential equations by the Taylor series method

NASA Technical Reports Server (NTRS)

Silver, A. H.; Sullivan, E.

1973-01-01

A programming implementation of the Taylor series method is presented for solving ordinary differential equations. The compiler is written in PL/1, and the target language is FORTRAN IV. The reduction of a differential system to rational form is described along with the procedures required for automatic numerical integration. The Taylor method is compared with two other methods for a number of differential equations. Algorithms using the Taylor method to find the zeroes of a given differential equation and to evaluate partial derivatives are presented. An annotated listing of the PL/1 program which performs the reduction and code generation is given. Listings of the FORTRAN routines used by the Taylor series method are included along with a compilation of all the recurrence formulas used to generate the Taylor coefficients for non-rational functions.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

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.

ScaMo: Realisation of an OO-functional DSL for cross platform mobile applications development

NASA Astrophysics Data System (ADS)

Macos, Dragan; Solymosi, Andreas

2013-10-01

The software market is dynamically changing: the Internet is going mobile, the software applications are shifting from the desktop hardware onto the mobile devices. The largest markets are the mobile applications for iOS, Android and Windows Phone and for the purpose the typical programming languages include Objective-C, Java and C ♯. The realization of the native applications implies the integration of the developed software into the environments of mentioned mobile operating systems to enable the access to different hardware components of the devices: GPS module, display, GSM module, etc. This paper deals with the definition and possible implementation of an environment for the automatic application generation for multiple mobile platforms. It is based on a DSL for mobile application development, which includes the programming language Scala and a DSL defined in Scala. As part of a multi-stage cross-compiling algorithm, this language is translated into the language of the affected mobile platform. The advantage of our method lies in the expressiveness of the defined language and the transparent source code translation between different languages, which implies, for example, the advantages of debugging and development of the generated code.

Posteriori error determination and grid adaptation for AMR and ALE computational fluid dynamics

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

Lapenta, G. M.

2002-01-01

We discuss grid adaptation for application to AMR and ALE codes. Two new contributions are presented. First, a new method to locate the regions where the truncation error is being created due to an insufficient accuracy: the operator recovery error origin (OREO) detector. The OREO detector is automatic, reliable, easy to implement and extremely inexpensive. Second, a new grid motion technique is presented for application to ALE codes. The method is based on the Brackbill-Saltzman approach but it is directly linked to the OREO detector and moves the grid automatically to minimize the error.

An Expert System for the Development of Efficient Parallel Code

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Chun, Robert; Jin, Hao-Qiang; Labarta, Jesus; Gimenez, Judit

2004-01-01

We have built the prototype of an expert system to assist the user in the development of efficient parallel code. The system was integrated into the parallel programming environment that is currently being developed at NASA Ames. The expert system interfaces to tools for automatic parallelization and performance analysis. It uses static program structure information and performance data in order to automatically determine causes of poor performance and to make suggestions for improvements. In this paper we give an overview of our programming environment, describe the prototype implementation of our expert system, and demonstrate its usefulness with several case studies.

Introduction of the ASGARD Code

NASA Technical Reports Server (NTRS)

Bethge, Christian; Winebarger, Amy; Tiwari, Sanjiv; Fayock, Brian

2017-01-01

ASGARD stands for 'Automated Selection and Grouping of events in AIA Regional Data'. The code is a refinement of the event detection method in Ugarte-Urra & Warren (2014). It is intended to automatically detect and group brightenings ('events') in the AIA EUV channels, to record event parameters, and to find related events over multiple channels. Ultimately, the goal is to automatically determine heating and cooling timescales in the corona and to significantly increase statistics in this respect. The code is written in IDL and requires the SolarSoft library. It is parallelized and can run with multiple CPUs. Input files are regions of interest (ROIs) in time series of AIA images from the JSOC cutout service (http://jsoc.stanford.edu/ajax/exportdata.html). The ROIs need to be tracked, co-registered, and limited in time (typically 12 hours).

Vaccine Hesitancy in Discussion Forums: Computer-Assisted Argument Mining with Topic Models.

PubMed

Skeppstedt, Maria; Kerren, Andreas; Stede, Manfred

2018-01-01

Arguments used when vaccination is debated on Internet discussion forums might give us valuable insights into reasons behind vaccine hesitancy. In this study, we applied automatic topic modelling on a collection of 943 discussion posts in which vaccine was debated, and six distinct discussion topics were detected by the algorithm. When manually coding the posts ranked as most typical for these six topics, a set of semantically coherent arguments were identified for each extracted topic. This indicates that topic modelling is a useful method for automatically identifying vaccine-related discussion topics and for identifying debate posts where these topics are discussed. This functionality could facilitate manual coding of salient arguments, and thereby form an important component in a system for computer-assisted coding of vaccine-related discussions.

Automatic rule generation for high-level vision

NASA Technical Reports Server (NTRS)

Rhee, Frank Chung-Hoon; Krishnapuram, Raghu

1992-01-01

A new fuzzy set based technique that was developed for decision making is discussed. It is a method to generate fuzzy decision rules automatically for image analysis. This paper proposes a method to generate rule-based approaches to solve problems such as autonomous navigation and image understanding automatically from training data. The proposed method is also capable of filtering out irrelevant features and criteria from the rules.

SU-D-BRD-03: A Gateway for GPU Computing in Cancer Radiotherapy Research

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

Jia, X; Folkerts, M; Shi, F

Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers, and for developers to objectively benchmark their codes. Moreover, it is quite often to see repeated efforts spent on developing low-quality GPU codes. The goal of this project is to establish an infrastructure for testing GPU codes, cross comparing them, and facilitating code distributions in radiotherapy community. Methods: We developed a system called Gateway for GPU Computing in Cancer Radiotherapy Research (GCR2). A number of GPU codes developed by our group andmore » other developers can be accessed via a web interface. To use the services, researchers first upload their test data or use the standard data provided by our system. Then they can select the GPU device on which the code will be executed. Our system offers all mainstream GPU hardware for code benchmarking purpose. After the code running is complete, the system automatically summarizes and displays the computing results. We also released a SDK to allow the developers to build their own algorithm implementation and submit their binary codes to the system. The submitted code is then systematically benchmarked using a variety of GPU hardware and representative data provided by our system. The developers can also compare their codes with others and generate benchmarking reports. Results: It is found that the developed system is fully functioning. Through a user-friendly web interface, researchers are able to test various GPU codes. Developers also benefit from this platform by comprehensively benchmarking their codes on various GPU platforms and representative clinical data sets. Conclusion: We have developed an open platform allowing the clinical researchers and developers to access the GPUs and GPU codes. This development will facilitate the utilization of GPU in radiation therapy field.« less

Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.

PubMed

Aires-de-Sousa, João; Aires-de-Sousa, Luisa

2003-01-01

We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques. To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment. Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002

CHEETAH: A next generation thermochemical code

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

Fried, L.; Souers, P.

1994-11-01

CHEETAH is an effort to bring the TIGER thermochemical code into the 1990s. A wide variety of improvements have been made in Version 1.0. We have improved the robustness and ease of use of TIGER. All of TIGER`s solvers have been replaced by new algorithms. We find that CHEETAH solves a wider variety of problems with no user intervention (e.g. no guesses for the C-J state) than TIGER did. CHEETAH has been made simpler to use than TIGER; typical use of the code occurs with the new standard run command. CHEETAH will make the use of thermochemical codes more attractivemore » to practical explosive formulators. We have also made an extensive effort to improve over the results of TIGER. CHEETAH`s version of the BKW equation of state (BKWC) is able to accurately reproduce energies from cylinder tests; something that other BKW parameter sets have been unable to do. Calculations performed with BKWC execute very quickly; typical run times are under 10 seconds on a workstation. In the future we plan to improve the underlying science in CHEETAH. More accurate equations of state will be used in the gas and the condensed phase. A kinetics capability will be added to the code that will predict reaction zone thickness. Further ease of use features will eventually be added; an automatic formulator that adjusts concentrations to match desired properties is planned.« less

Leap Frog and Time Step Sub-Cycle Scheme for Coupled Neutronics and Thermal-Hydraulic Codes

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

Lu, S.

2002-07-01

As the result of the advancing TCP/IP based inter-process communication technology, more and more legacy thermal-hydraulic codes have been coupled with neutronics codes to provide best-estimate capabilities for reactivity related reactor transient analysis. Most of the coupling schemes are based on closely coupled serial or parallel approaches. Therefore, the execution of the coupled codes usually requires significant CPU time, when a complicated system is analyzed. Leap Frog scheme has been used to reduce the run time. The extent of the decoupling is usually determined based on a trial and error process for a specific analysis. It is the intent ofmore » this paper to develop a set of general criteria, which can be used to invoke the automatic Leap Frog algorithm. The algorithm will not only provide the run time reduction but also preserve the accuracy. The criteria will also serve as the base of an automatic time step sub-cycle scheme when a sudden reactivity change is introduced and the thermal-hydraulic code is marching with a relatively large time step. (authors)« less

Motion-adaptive model-assisted compatible coding with spatiotemporal scalability

NASA Astrophysics Data System (ADS)

Lee, JaeBeom; Eleftheriadis, Alexandros

1997-01-01

We introduce the concept of motion adaptive spatio-temporal model-assisted compatible (MA-STMAC) coding, a technique to selectively encode areas of different importance to the human eye in terms of space and time in moving images with the consideration of object motion. PRevious STMAC was proposed base don the fact that human 'eye contact' and 'lip synchronization' are very important in person-to-person communication. Several areas including the eyes and lips need different types of quality, since different areas have different perceptual significance to human observers. The approach provides a better rate-distortion tradeoff than conventional image coding techniques base don MPEG-1, MPEG- 2, H.261, as well as H.263. STMAC coding is applied on top of an encoder, taking full advantage of its core design. Model motion tracking in our previous STMAC approach was not automatic. The proposed MA-STMAC coding considers the motion of the human face within the STMAC concept using automatic area detection. Experimental results are given using ITU-T H.263, addressing very low bit-rate compression.

77 FR 66601 - Electronic Tariff Filings; Notice of Change to eTariff Type of Filing Codes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-06

... Tariff Filings; Notice of Change to eTariff Type of Filing Codes Take notice that, effective November 18, 2012, the list of available eTariff Type of Filing Codes (TOFC) will be modified to include a new TOFC... Energy's regulations. Tariff records included in such filings will be automatically accepted to be...

Using Psychometric Technology in Educational Assessment: The Case of a Schema-Based Isomorphic Approach to the Automatic Generation of Quantitative Reasoning Items

ERIC Educational Resources Information Center

Arendasy, Martin; Sommer, Markus

2007-01-01

This article deals with the investigation of the psychometric quality and constructs validity of algebra word problems generated by means of a schema-based version of the automatic min-max approach. Based on review of the research literature in algebra word problem solving and automatic item generation this new approach is introduced as a…

Building Automatic Grading Tools for Basic of Programming Lab in an Academic Institution

NASA Astrophysics Data System (ADS)

Harimurti, Rina; Iwan Nurhidayat, Andi; Asmunin

2018-04-01

The skills of computer programming is a core competency that must be mastered by students majoring in computer sciences. The best way to improve this skill is through the practice of writing many programs to solve various problems from simple to complex. It takes hard work and a long time to check and evaluate the results of student labs one by one, especially if the number of students a lot. Based on these constrain, web proposes Automatic Grading Tools (AGT), the application that can evaluate and deeply check the source code in C, C++. The application architecture consists of students, web-based applications, compilers, and operating systems. Automatic Grading Tools (AGT) is implemented MVC Architecture and using open source software, such as laravel framework version 5.4, PostgreSQL 9.6, Bootstrap 3.3.7, and jquery library. Automatic Grading Tools has also been tested for real problems by submitting source code in C/C++ language and then compiling. The test results show that the AGT application has been running well.

A Unified Overset Grid Generation Graphical Interface and New Concepts on Automatic Gridding Around Surface Discontinuities

NASA Technical Reports Server (NTRS)

Chan, William M.; Akien, Edwin (Technical Monitor)

2002-01-01

For many years, generation of overset grids for complex configurations has required the use of a number of different independently developed software utilities. Results created by each step were then visualized using a separate visualization tool before moving on to the next. A new software tool called OVERGRID was developed which allows the user to perform all the grid generation steps and visualization under one environment. OVERGRID provides grid diagnostic functions such as surface tangent and normal checks as well as grid manipulation functions such as extraction, extrapolation, concatenation, redistribution, smoothing, and projection. Moreover, it also contains hyperbolic surface and volume grid generation modules that are specifically suited for overset grid generation. It is the first time that such a unified interface existed for the creation of overset grids for complex geometries. New concepts on automatic overset surface grid generation around surface discontinuities will also be briefly presented. Special control curves on the surface such as intersection curves, sharp edges, open boundaries, are called seam curves. The seam curves are first automatically extracted from a multiple panel network description of the surface. Points where three or more seam curves meet are automatically identified and are called seam corners. Seam corner surface grids are automatically generated using a singular axis topology. Hyperbolic surface grids are then grown from the seam curves that are automatically trimmed away from the seam corners.

Automatic Thesaurus Generation for an Electronic Community System.

ERIC Educational Resources Information Center

Chen, Hsinchun; And Others

1995-01-01

This research reports an algorithmic approach to the automatic generation of thesauri for electronic community systems. The techniques used include term filtering, automatic indexing, and cluster analysis. The Worm Community System, used by molecular biologists studying the nematode worm C. elegans, was used as the testbed for this research.…

Automatic Semantic Generation and Arabic Translation of Mathematical Expressions on the Web

ERIC Educational Resources Information Center

Doush, Iyad Abu; Al-Bdarneh, Sondos

2013-01-01

Automatic processing of mathematical information on the web imposes some difficulties. This paper presents a novel technique for automatic generation of mathematical equations semantic and Arabic translation on the web. The proposed system facilitates unambiguous representation of mathematical equations by correlating equations to their known…

Flexible Automatic Discretization for Finite Differences: Eliminating the Human Factor

NASA Astrophysics Data System (ADS)

Pranger, Casper

2017-04-01

In the geophysical numerical modelling community, finite differences are (in part due to their small footprint) a popular spatial discretization method for PDEs in the regular-shaped continuum that is the earth. However, they rapidly become prone to programming mistakes when physics increase in complexity. To eliminate opportunities for human error, we have designed an automatic discretization algorithm using Wolfram Mathematica, in which the user supplies symbolic PDEs, the number of spatial dimensions, and a choice of symbolic boundary conditions, and the script transforms this information into matrix- and right-hand-side rules ready for use in a C++ code that will accept them. The symbolic PDEs are further used to automatically develop and perform manufactured solution benchmarks, ensuring at all stages physical fidelity while providing pragmatic targets for numerical accuracy. We find that this procedure greatly accelerates code development and provides a great deal of flexibility in ones choice of physics.

AutoBayes Program Synthesis System Users Manual

NASA Technical Reports Server (NTRS)

Schumann, Johann; Jafari, Hamed; Pressburger, Tom; Denney, Ewen; Buntine, Wray; Fischer, Bernd

2008-01-01

Program synthesis is the systematic, automatic construction of efficient executable code from high-level declarative specifications. AutoBayes is a fully automatic program synthesis system for the statistical data analysis domain; in particular, it solves parameter estimation problems. It has seen many successful applications at NASA and is currently being used, for example, to analyze simulation results for Orion. The input to AutoBayes is a concise description of a data analysis problem composed of a parameterized statistical model and a goal that is a probability term involving parameters and input data. The output is optimized and fully documented C/C++ code computing the values for those parameters that maximize the probability term. AutoBayes can solve many subproblems symbolically rather than having to rely on numeric approximation algorithms, thus yielding effective, efficient, and compact code. Statistical analysis is faster and more reliable, because effort can be focused on model development and validation rather than manual development of solution algorithms and code.

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.

Automatic building information model query generation

DOE PAGES

Jiang, Yufei; Yu, Nan; Ming, Jiang; ...

2015-12-01

Energy efficient building design and construction calls for extensive collaboration between different subfields of the Architecture, Engineering and Construction (AEC) community. Performing building design and construction engineering raises challenges on data integration and software interoperability. Using Building Information Modeling (BIM) data hub to host and integrate building models is a promising solution to address those challenges, which can ease building design information management. However, the partial model query mechanism of current BIM data hub collaboration model has several limitations, which prevents designers and engineers to take advantage of BIM. To address this problem, we propose a general and effective approachmore » to generate query code based on a Model View Definition (MVD). This approach is demonstrated through a software prototype called QueryGenerator. In conclusion, by demonstrating a case study using multi-zone air flow analysis, we show how our approach and tool can help domain experts to use BIM to drive building design with less labour and lower overhead cost.« less

Automatic building information model query generation

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

Jiang, Yufei; Yu, Nan; Ming, Jiang

Energy efficient building design and construction calls for extensive collaboration between different subfields of the Architecture, Engineering and Construction (AEC) community. Performing building design and construction engineering raises challenges on data integration and software interoperability. Using Building Information Modeling (BIM) data hub to host and integrate building models is a promising solution to address those challenges, which can ease building design information management. However, the partial model query mechanism of current BIM data hub collaboration model has several limitations, which prevents designers and engineers to take advantage of BIM. To address this problem, we propose a general and effective approachmore » to generate query code based on a Model View Definition (MVD). This approach is demonstrated through a software prototype called QueryGenerator. In conclusion, by demonstrating a case study using multi-zone air flow analysis, we show how our approach and tool can help domain experts to use BIM to drive building design with less labour and lower overhead cost.« less

A versatile calibration procedure for portable coded aperture gamma cameras and RGB-D sensors

NASA Astrophysics Data System (ADS)

Paradiso, V.; Crivellaro, A.; Amgarou, K.; de Lanaute, N. Blanc; Fua, P.; Liénard, E.

2018-04-01

The present paper proposes a versatile procedure for the geometrical calibration of coded aperture gamma cameras and RGB-D depth sensors, using only one radioactive point source and a simple experimental set-up. Calibration data is then used for accurately aligning radiation images retrieved by means of the γ-camera with the respective depth images computed with the RGB-D sensor. The system resulting from such a combination is thus able to retrieve, automatically, the distance of radioactive hotspots by means of pixel-wise mapping between gamma and depth images. This procedure is of great interest for a wide number of applications, ranging from precise automatic estimation of the shape and distance of radioactive objects to Augmented Reality systems. Incidentally, the corresponding results validated the choice of a perspective design model for a coded aperture γ-camera.

Combining Recurrence Analysis and Automatic Movement Extraction from Video Recordings to Study Behavioral Coupling in Face-to-Face Parent-Child Interactions.

PubMed

López Pérez, David; Leonardi, Giuseppe; Niedźwiecka, Alicja; Radkowska, Alicja; Rączaszek-Leonardi, Joanna; Tomalski, Przemysław

2017-01-01

The analysis of parent-child interactions is crucial for the understanding of early human development. Manual coding of interactions is a time-consuming task, which is a limitation in many projects. This becomes especially demanding if a frame-by-frame categorization of movement needs to be achieved. To overcome this, we present a computational approach for studying movement coupling in natural settings, which is a combination of a state-of-the-art automatic tracker, Tracking-Learning-Detection (TLD), and nonlinear time-series analysis, Cross-Recurrence Quantification Analysis (CRQA). We investigated the use of TLD to extract and automatically classify movement of each partner from 21 video recordings of interactions, where 5.5-month-old infants and mothers engaged in free play in laboratory settings. As a proof of concept, we focused on those face-to-face episodes, where the mother animated an object in front of the infant, in order to measure the coordination between the infants' head movement and the mothers' hand movement. We also tested the feasibility of using such movement data to study behavioral coupling between partners with CRQA. We demonstrate that movement can be extracted automatically from standard definition video recordings and used in subsequent CRQA to quantify the coupling between movement of the parent and the infant. Finally, we assess the quality of this coupling using an extension of CRQA called anisotropic CRQA and show asymmetric dynamics between the movement of the parent and the infant. When combined these methods allow automatic coding and classification of behaviors, which results in a more efficient manner of analyzing movements than manual coding.

Combining Recurrence Analysis and Automatic Movement Extraction from Video Recordings to Study Behavioral Coupling in Face-to-Face Parent-Child Interactions

PubMed Central

López Pérez, David; Leonardi, Giuseppe; Niedźwiecka, Alicja; Radkowska, Alicja; Rączaszek-Leonardi, Joanna; Tomalski, Przemysław

2017-01-01

The analysis of parent-child interactions is crucial for the understanding of early human development. Manual coding of interactions is a time-consuming task, which is a limitation in many projects. This becomes especially demanding if a frame-by-frame categorization of movement needs to be achieved. To overcome this, we present a computational approach for studying movement coupling in natural settings, which is a combination of a state-of-the-art automatic tracker, Tracking-Learning-Detection (TLD), and nonlinear time-series analysis, Cross-Recurrence Quantification Analysis (CRQA). We investigated the use of TLD to extract and automatically classify movement of each partner from 21 video recordings of interactions, where 5.5-month-old infants and mothers engaged in free play in laboratory settings. As a proof of concept, we focused on those face-to-face episodes, where the mother animated an object in front of the infant, in order to measure the coordination between the infants' head movement and the mothers' hand movement. We also tested the feasibility of using such movement data to study behavioral coupling between partners with CRQA. We demonstrate that movement can be extracted automatically from standard definition video recordings and used in subsequent CRQA to quantify the coupling between movement of the parent and the infant. Finally, we assess the quality of this coupling using an extension of CRQA called anisotropic CRQA and show asymmetric dynamics between the movement of the parent and the infant. When combined these methods allow automatic coding and classification of behaviors, which results in a more efficient manner of analyzing movements than manual coding. PMID:29312075

Update of GRASP/Ada reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1993-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional pretty printed Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype CSD generator (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3,e two update phases were completed. Update'92 focused on the initial analysis of evaluation data collected from software engineering students at Auburn University and the addition of significant enhancements to the user interface. Update'93 (the current update) focused on the statistical analysis of the data collected in the previous update and preparation of Version 3.4 of the prototype for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. An overview of the GRASP/Ada project with an emphasis on the current update is provided.

The efficiency of geophysical adjoint codes generated by automatic differentiation tools

NASA Astrophysics Data System (ADS)

Vlasenko, A. V.; Köhl, A.; Stammer, D.

2016-02-01

The accuracy of numerical models that describe complex physical or chemical processes depends on the choice of model parameters. Estimating an optimal set of parameters by optimization algorithms requires knowledge of the sensitivity of the process of interest to model parameters. Typically the sensitivity computation involves differentiation of the model, which can be performed by applying algorithmic differentiation (AD) tools to the underlying numerical code. However, existing AD tools differ substantially in design, legibility and computational efficiency. In this study we show that, for geophysical data assimilation problems of varying complexity, the performance of adjoint codes generated by the existing AD tools (i) Open_AD, (ii) Tapenade, (iii) NAGWare and (iv) Transformation of Algorithms in Fortran (TAF) can be vastly different. Based on simple test problems, we evaluate the efficiency of each AD tool with respect to computational speed, accuracy of the adjoint, the efficiency of memory usage, and the capability of each AD tool to handle modern FORTRAN 90-95 elements such as structures and pointers, which are new elements that either combine groups of variables or provide aliases to memory addresses, respectively. We show that, while operator overloading tools are the only ones suitable for modern codes written in object-oriented programming languages, their computational efficiency lags behind source transformation by orders of magnitude, rendering the application of these modern tools to practical assimilation problems prohibitive. In contrast, the application of source transformation tools appears to be the most efficient choice, allowing handling even large geophysical data assimilation problems. However, they can only be applied to numerical models written in earlier generations of programming languages. Our study indicates that applying existing AD tools to realistic geophysical problems faces limitations that urgently need to be solved to allow the continuous use of AD tools for solving geophysical problems on modern computer architectures.

The Role of Ontologies in Schema-based Program Synthesis

NASA Technical Reports Server (NTRS)

Bures, Tomas; Denney, Ewen; Fischer, Bernd; Nistor, Eugen C.

2004-01-01

Program synthesis is the process of automatically deriving executable code from (non-executable) high-level specifications. It is more flexible and powerful than conventional code generation techniques that simply translate algorithmic specifications into lower-level code or only create code skeletons from structural specifications (such as UML class diagrams). Key to building a successful synthesis system is specializing to an appropriate application domain. The AUTOBAYES and AUTOFILTER systems, under development at NASA Ames, operate in the two domains of data analysis and state estimation, respectively. The central concept of both systems is the schema, a representation of reusable computational knowledge. This can take various forms, including high-level algorithm templates, code optimizations, datatype refinements, or architectural information. A schema also contains applicability conditions that are used to determine when it can be applied safely. These conditions can refer to the initial specification, to intermediate results, or to elements of the partially-instantiated code. Schema-based synthesis uses AI technology to recursively apply schemas to gradually refine a specification into executable code. This process proceeds in two main phases. A front-end gradually transforms the problem specification into a program represented in an abstract intermediate code. A backend then compiles this further down into a concrete target programming language of choice. A core engine applies schemas on the initial problem specification, then uses the output of those schemas as the input for other schemas, until the full implementation is generated. Since there might be different schemas that implement different solutions to the same problem this process can generate an entire solution tree. AUTOBAYES and AUTOFILTER have reached the level of maturity where they enable users to solve interesting application problems, e.g., the analysis of Hubble Space Telescope images. They are large (in total around 100kLoC Prolog), knowledge intensive systems that employ complex symbolic reasoning to generate a wide range of non-trivial programs for complex application do- mains. Their schemas can have complex interactions, which make it hard to change them in isolation or even understand what an existing schema actually does. Adding more capabilities by increasing the number of schemas will only worsen this situation, ultimately leading to the entropy death of the synthesis system. The root came of this problem is that the domain knowledge is scattered throughout the entire system and only represented implicitly in the schema implementations. In our current work, we are addressing this problem by making explicit the knowledge from Merent parts of the synthesis system. Here; we discuss how Gruber's definition of an ontology as an explicit specification of a conceptualization matches our efforts in identifying and explicating the domain-specific concepts. We outline the dual role ontologies play in schema-based synthesis and argue that they address different audiences and serve different purposes. Their first role is descriptive: they serve as explicit documentation, and help to understand the internal structure of the system. Their second role is prescriptive: they provide the formal basis against which the other parts of the system (e.g., schemas) can be checked. Their final role is referential: ontologies also provide semantically meaningful "hooks" which allow schemas and tools to access the internal state of the program derivation process (e.g., fragments of the generated code) in domain-specific rather than language-specific terms, and thus to modify it in a controlled fashion. For discussion purposes we use AUTOLINEAR, a small synthesis system we are currently experimenting with, which can generate code for solving a system of linear equations, Az = b.

GOAL - A test engineer oriented language. [Ground Operations Aerospace Language for coding automatic test

NASA Technical Reports Server (NTRS)

Mitchell, T. R.

1974-01-01

The development of a test engineer oriented language has been under way at the Kennedy Space Center for several years. The result of this effort is the Ground Operations Aerospace Language, GOAL, a self-documenting, high-order language suitable for coding automatic test, checkout and launch procedures. GOAL is a highly readable, writable, retainable language that is easily learned by nonprogramming oriented engineers. It is sufficiently powerful for use at all levels of Space Shuttle ground processing, from line replaceable unit checkout to integrated launch day operations. This paper will relate the language development, and describe GOAL and its applications.

Management of natural resources through automatic cartographic inventory

NASA Technical Reports Server (NTRS)

Rey, P.; Gourinard, Y.; Cambou, F. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Significant results of the ARNICA program from August 1972 - January 1973 have been: (1) establishment of image to object correspondence codes for all types of soil use and forestry in northern Spain; (2) establishment of a transfer procedure between qualitative (remote identification and remote interpretation) and quantitative (numerization, storage, automatic statistical cartography) use of images; (3) organization of microdensitometric data processing and automatic cartography software; and (4) development of a system for measuring reflectance simultaneous with imagery.

Small passenger car transmission test: Mercury Lynx ATX transmission

NASA Technical Reports Server (NTRS)

Bujold, M. P.

1981-01-01

The testing of a Mercury Lynx automatic transmission is reported. The transmission was tested in accordance with a passenger car automatic transmission test code (SAE J65lb) which required drive performance, coast performance, and no load test conditions. Under these conditions, the transmission attained maximum efficiencies in the mid-ninety percent range both for drive performance test and coast performance tests. The torque, speed, and efficiency curves are presented, which provide the complete performance characteristics for the Mercury Lynx automatic transmission.

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).

Priority coding for control room alarms

DOEpatents

Scarola, Kenneth; Jamison, David S.; Manazir, Richard M.; Rescorl, Robert L.; Harmon, Daryl L.

1994-01-01

Indicating the priority of a spatially fixed, activated alarm tile on an alarm tile array by a shape coding at the tile, and preferably using the same shape coding wherever the same alarm condition is indicated elsewhere in the control room. The status of an alarm tile can change automatically or by operator acknowledgement, but tones and/or flashing cues continue to provide status information to the operator.

Motor automaticity in Parkinson’s disease

PubMed Central

Wu, Tao; Hallett, Mark; Chan, Piu

2017-01-01

Bradykinesia is the most important feature contributing to motor difficulties in Parkinson’s disease (PD). However, the pathophysiology underlying bradykinesia is not fully understood. One important aspect is that PD patients have difficulty in performing learned motor skills automatically, but this problem has been generally overlooked. Here we review motor automaticity associated motor deficits in PD, such as reduced arm swing, decreased stride length, freezing of gait, micrographia and reduced facial expression. Recent neuroimaging studies have revealed some neural mechanisms underlying impaired motor automaticity in PD, including less efficient neural coding of movement, failure to shift automated motor skills to the sensorimotor striatum, instability of the automatic mode within the striatum, and use of attentional control and/or compensatory efforts to execute movements usually performed automatically in healthy people. PD patients lose previously acquired automatic skills due to their impaired sensorimotor striatum, and have difficulty in acquiring new automatic skills or restoring lost motor skills. More investigations on the pathophysiology of motor automaticity, the effect of L-dopa or surgical treatments on automaticity, and the potential role of using measures of automaticity in early diagnosis of PD would be valuable. PMID:26102020

48 CFR 25.401 - Exceptions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Disabled; and (5) Other acquisitions not using full and open competition, if authorized by Subpart 6.2 or 6... table: The service(Federal Service Codes from the Federal Procurement Data System Product/Service Code... military services overseas. X X X X (2) (i) Automatic data processing (ADP) telecommunications and...

78 FR 13213 - Regional Reliability Standard PRC-006-NPCC-1- Automatic Underfrequency Load Shedding

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

...; Order No. 775] Regional Reliability Standard PRC-006-NPCC-1--Automatic Underfrequency Load Shedding... transferred to the system upon loss of the facility.'' \\27\\ Compensatory load shedding is automatic shedding of load adequate to compensate for the loss of a generator due to the generator tripping early (i.e...

System for Automatic Generation of Examination Papers in Discrete Mathematics

ERIC Educational Resources Information Center

Fridenfalk, Mikael

2013-01-01

A system was developed for automatic generation of problems and solutions for examinations in a university distance course in discrete mathematics and tested in a pilot experiment involving 200 students. Considering the success of such systems in the past, particularly including automatic assessment, it should not take long before such systems are…

Grid generation and surface modeling for CFD

NASA Technical Reports Server (NTRS)

Connell, Stuart D.; Sober, Janet S.; Lamson, Scott H.

1995-01-01

When computing the flow around complex three dimensional configurations, the generation of the mesh is the most time consuming part of any calculation. With some meshing technologies this can take of the order of a man month or more. The requirement for a number of design iterations coupled with ever decreasing time allocated for design leads to the need for a significant acceleration of this process. Of the two competing approaches, block-structured and unstructured, only the unstructured approach will allow fully automatic mesh generation directly from a CAD model. Using this approach coupled with the techniques described in this paper, it is possible to reduce the mesh generation time from man months to a few hours on a workstation. The desire to closely couple a CFD code with a design or optimization algorithm requires that the changes to the geometry be performed quickly and in a smooth manner. This need for smoothness necessitates the use of Bezier polynomials in place of the more usual NURBS or cubic splines. A two dimensional Bezier polynomial based design system is described.

GENIE(++): A Multi-Block Structured Grid System

NASA Technical Reports Server (NTRS)

Williams, Tonya; Nadenthiran, Naren; Thornburg, Hugh; Soni, Bharat K.

1996-01-01

The computer code GENIE++ is a continuously evolving grid system containing a multitude of proven geometry/grid techniques. The generation process in GENIE++ is based on an earlier version. The process uses several techniques either separately or in combination to quickly and economically generate sculptured geometry descriptions and grids for arbitrary geometries. The computational mesh is formed by using an appropriate algebraic method. Grid clustering is accomplished with either exponential or hyperbolic tangent routines which allow the user to specify a desired point distribution. Grid smoothing can be accomplished by using an elliptic solver with proper forcing functions. B-spline and Non-Uniform Rational B-splines (NURBS) algorithms are used for surface definition and redistribution. The built in sculptured geometry definition with desired distribution of points, automatic Bezier curve/surface generation for interior boundaries/surfaces, and surface redistribution is based on NURBS. Weighted Lagrance/Hermite transfinite interpolation methods, interactive geometry/grid manipulation modules, and on-line graphical visualization of the generation process are salient features of this system which result in a significant time savings for a given geometry/grid application.

Execution time supports for adaptive scientific algorithms on distributed memory machines

NASA Technical Reports Server (NTRS)

Berryman, Harry; Saltz, Joel; Scroggs, Jeffrey

1990-01-01

Optimizations are considered that are required for efficient execution of code segments that consists of loops over distributed data structures. The PARTI (Parallel Automated Runtime Toolkit at ICASE) execution time primitives are designed to carry out these optimizations and can be used to implement a wide range of scientific algorithms on distributed memory machines. These primitives allow the user to control array mappings in a way that gives an appearance of shared memory. Computations can be based on a global index set. Primitives are used to carry out gather and scatter operations on distributed arrays. Communications patterns are derived at runtime, and the appropriate send and receive messages are automatically generated.

Semantic Annotation of Complex Text Structures in Problem Reports

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Throop, David R.; Fleming, Land D.

2011-01-01

Text analysis is important for effective information retrieval from databases where the critical information is embedded in text fields. Aerospace safety depends on effective retrieval of relevant and related problem reports for the purpose of trend analysis. The complex text syntax in problem descriptions has limited statistical text mining of problem reports. The presentation describes an intelligent tagging approach that applies syntactic and then semantic analysis to overcome this problem. The tags identify types of problems and equipment that are embedded in the text descriptions. The power of these tags is illustrated in a faceted searching and browsing interface for problem report trending that combines automatically generated tags with database code fields and temporal information.

Execution time support for scientific programs on distributed memory machines

NASA Technical Reports Server (NTRS)

Berryman, Harry; Saltz, Joel; Scroggs, Jeffrey

1990-01-01

Optimizations are considered that are required for efficient execution of code segments that consists of loops over distributed data structures. The PARTI (Parallel Automated Runtime Toolkit at ICASE) execution time primitives are designed to carry out these optimizations and can be used to implement a wide range of scientific algorithms on distributed memory machines. These primitives allow the user to control array mappings in a way that gives an appearance of shared memory. Computations can be based on a global index set. Primitives are used to carry out gather and scatter operations on distributed arrays. Communications patterns are derived at runtime, and the appropriate send and receive messages are automatically generated.

Low-complexity piecewise-affine virtual sensors: theory and design

NASA Astrophysics Data System (ADS)

Rubagotti, Matteo; Poggi, Tomaso; Oliveri, Alberto; Pascucci, Carlo Alberto; Bemporad, Alberto; Storace, Marco

2014-03-01

This paper is focused on the theoretical development and the hardware implementation of low-complexity piecewise-affine direct virtual sensors for the estimation of unmeasured variables of interest of nonlinear systems. The direct virtual sensor is designed directly from measured inputs and outputs of the system and does not require a dynamical model. The proposed approach allows one to design estimators which mitigate the effect of the so-called 'curse of dimensionality' of simplicial piecewise-affine functions, and can be therefore applied to relatively high-order systems, enjoying convergence and optimality properties. An automatic toolchain is also presented to generate the VHDL code describing the digital circuit implementing the virtual sensor, starting from the set of measured input and output data. The proposed methodology is applied to generate an FPGA implementation of the virtual sensor for the estimation of vehicle lateral velocity, using a hardware-in-the-loop setting.

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

SimITK: rapid ITK prototyping using the Simulink visual programming environment

NASA Astrophysics Data System (ADS)

Dickinson, A. W. L.; Mousavi, P.; Gobbi, D. G.; Abolmaesumi, P.

2011-03-01

The Insight Segmentation and Registration Toolkit (ITK) is a long-established, software package used for image analysis, visualization, and image-guided surgery applications. This package is a collection of C++ libraries, that can pose usability problems for users without C++ programming experience. To bridge the gap between the programming complexities and the required learning curve of ITK, we present a higher-level visual programming environment that represents ITK methods and classes by wrapping them into "blocks" within MATLAB's visual programming environment, Simulink. These blocks can be connected to form workflows: visual schematics that closely represent the structure of a C++ program. Due to the heavily C++ templated nature of ITK, direct interaction between Simulink and ITK requires an intermediary to convert their respective datatypes and allow intercommunication. We have developed a "Virtual Block" that serves as an intermediate wrapper around the ITK class and is responsible for resolving the templated datatypes used by ITK to native types used by Simulink. Presently, the wrapping procedure for SimITK is semi-automatic in that it requires XML descriptions of the ITK classes as a starting point, as this data is used to create all other necessary integration files. The generation of all source code and object code from the XML is done automatically by a CMake build script that yields Simulink blocks as the final result. An example 3D segmentation workflow using cranial-CT data as well as a 3D MR-to-CT registration workflow are presented as a proof-of-concept.

ROOT.NET: Using ROOT from .NET languages like C# and F#

NASA Astrophysics Data System (ADS)

Watts, G.

2012-12-01

ROOT.NET provides an interface between Microsoft's Common Language Runtime (CLR) and .NET technology and the ubiquitous particle physics analysis tool, ROOT. ROOT.NET automatically generates a series of efficient wrappers around the ROOT API. Unlike pyROOT, these wrappers are statically typed and so are highly efficient as compared to the Python wrappers. The connection to .NET means that one gains access to the full series of languages developed for the CLR including functional languages like F# (based on OCaml). Many features that make ROOT objects work well in the .NET world are added (properties, IEnumerable interface, LINQ compatibility, etc.). Dynamic languages based on the CLR can be used as well, of course (Python, for example). Additionally it is now possible to access ROOT objects that are unknown to the translation tool. This poster will describe the techniques used to effect this translation, along with performance comparisons, and examples. All described source code is posted on the open source site CodePlex.

Finite Macro-Element Mesh Deformation in a Structured Multi-Block Navier-Stokes Code

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2005-01-01

A mesh deformation scheme is developed for a structured multi-block Navier-Stokes code consisting of two steps. The first step is a finite element solution of either user defined or automatically generated macro-elements. Macro-elements are hexagonal finite elements created from a subset of points from the full mesh. When assembled, the finite element system spans the complete flow domain. Macro-element moduli vary according to the distance to the nearest surface, resulting in extremely stiff elements near a moving surface and very pliable elements away from boundaries. Solution of the finite element system for the imposed boundary deflections generally produces smoothly varying nodal deflections. The manner in which distance to the nearest surface has been found to critically influence the quality of the element deformation. The second step is a transfinite interpolation which distributes the macro-element nodal deflections to the remaining fluid mesh points. The scheme is demonstrated for several two-dimensional applications.

Pythran: enabling static optimization of scientific Python programs

NASA Astrophysics Data System (ADS)

Guelton, Serge; Brunet, Pierrick; Amini, Mehdi; Merlini, Adrien; Corbillon, Xavier; Raynaud, Alan

2015-01-01

Pythran is an open source static compiler that turns modules written in a subset of Python language into native ones. Assuming that scientific modules do not rely much on the dynamic features of the language, it trades them for powerful, possibly inter-procedural, optimizations. These optimizations include detection of pure functions, temporary allocation removal, constant folding, Numpy ufunc fusion and parallelization, explicit thread-level parallelism through OpenMP annotations, false variable polymorphism pruning, and automatic vector instruction generation such as AVX or SSE. In addition to these compilation steps, Pythran provides a C++ runtime library that leverages the C++ STL to provide generic containers, and the Numeric Template Toolbox for Numpy support. It takes advantage of modern C++11 features such as variadic templates, type inference, move semantics and perfect forwarding, as well as classical idioms such as expression templates. Unlike the Cython approach, Pythran input code remains compatible with the Python interpreter. Output code is generally as efficient as the annotated Cython equivalent, if not more, but without the backward compatibility loss.

Software design and implementation of ship heave motion monitoring system based on MBD method

NASA Astrophysics Data System (ADS)

Yu, Yan; Li, Yuhan; Zhang, Chunwei; Kang, Won-Hee; Ou, Jinping

2015-03-01

Marine transportation plays a significant role in the modern transport sector due to its advantage of low cost, large capacity. It is being attached enormous importance to all over the world. Nowadays the related areas of product development have become an existing hot spot. DSP signal processors feature micro volume, low cost, high precision, fast processing speed, which has been widely used in all kinds of monitoring systems. But traditional DSP code development process is time-consuming, inefficiency, costly and difficult. MathWorks company proposed Model-based Design (MBD) to overcome these defects. By calling the target board modules in simulink library to compile and generate the corresponding code for the target processor. And then automatically call DSP integrated development environment CCS for algorithm validation on the target processor. This paper uses the MDB to design the algorithm for the ship heave motion monitoring system. It proves the effectiveness of the MBD run successfully on the processor.

Design Graphics

NASA Technical Reports Server (NTRS)

1990-01-01

A mathematician, David R. Hedgley, Jr. developed a computer program that considers whether a line in a graphic model of a three-dimensional object should or should not be visible. Known as the Hidden Line Computer Code, the program automatically removes superfluous lines and displays an object from a specific viewpoint, just as the human eye would see it. An example of how one company uses the program is the experience of Birdair which specializes in production of fabric skylights and stadium covers. The fabric called SHEERFILL is a Teflon coated fiberglass material developed in cooperation with DuPont Company. SHEERFILL glazed structures are either tension structures or air-supported tension structures. Both are formed by patterned fabric sheets supported by a steel or aluminum frame or cable network. Birdair uses the Hidden Line Computer Code, to illustrate a prospective structure to an architect or owner. The program generates a three- dimensional perspective with the hidden lines removed. This program is still used by Birdair and continues to be commercially available to the public.

Tools for Rapid Understanding of Malware Code

DTIC Science & Technology

2015-05-07

cloaking techniques. We used three malware detectors, covering a wide spectrum of detection technologies, for our experiments: VirusTotal, an online ...Analysis and Manipulation ( SCAM ), 2014. [9] Babak Yadegari, Brian Johannesmeyer, Benjamin Whitely, and Saumya Debray. A generic approach to automatic...and Manipulation ( SCAM ), 2014. [9] Babak Yadegari, Brian Johannesmeyer, Benjamin Whitely, and Saumya Debray. A generic approach to automatic

Update of GRASP/Ada reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1992-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation of Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAS 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3, the prototype was evaluated by software engineering students at Auburn University and then updated with significant enhancements to the user interface including editing capabilities. Version 3.2 of the prototype was prepared for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application.

Helium: lifting high-performance stencil kernels from stripped x86 binaries to halide DSL code

DOE PAGES

Mendis, Charith; Bosboom, Jeffrey; Wu, Kevin; ...

2015-06-03

Highly optimized programs are prone to bit rot, where performance quickly becomes suboptimal in the face of new hardware and compiler techniques. In this paper we show how to automatically lift performance-critical stencil kernels from a stripped x86 binary and generate the corresponding code in the high-level domain-specific language Halide. Using Halide's state-of-the-art optimizations targeting current hardware, we show that new optimized versions of these kernels can replace the originals to rejuvenate the application for newer hardware. The original optimized code for kernels in stripped binaries is nearly impossible to analyze statically. Instead, we rely on dynamic traces to regeneratemore » the kernels. We perform buffer structure reconstruction to identify input, intermediate and output buffer shapes. Here, we abstract from a forest of concrete dependency trees which contain absolute memory addresses to symbolic trees suitable for high-level code generation. This is done by canonicalizing trees, clustering them based on structure, inferring higher-dimensional buffer accesses and finally by solving a set of linear equations based on buffer accesses to lift them up to simple, high-level expressions. Helium can handle highly optimized, complex stencil kernels with input-dependent conditionals. We lift seven kernels from Adobe Photoshop giving a 75 % performance improvement, four kernels from Irfan View, leading to 4.97 x performance, and one stencil from the mini GMG multigrid benchmark netting a 4.25 x improvement in performance. We manually rejuvenated Photoshop by replacing eleven of Photoshop's filters with our lifted implementations, giving 1.12 x speedup without affecting the user experience.« less

A Semi-Automatic Image-Based Close Range 3D Modeling Pipeline Using a Multi-Camera Configuration

PubMed Central

Rau, Jiann-Yeou; Yeh, Po-Chia

2012-01-01

The generation of photo-realistic 3D models is an important task for digital recording of cultural heritage objects. This study proposes an image-based 3D modeling pipeline which takes advantage of a multi-camera configuration and multi-image matching technique that does not require any markers on or around the object. Multiple digital single lens reflex (DSLR) cameras are adopted and fixed with invariant relative orientations. Instead of photo-triangulation after image acquisition, calibration is performed to estimate the exterior orientation parameters of the multi-camera configuration which can be processed fully automatically using coded targets. The calibrated orientation parameters of all cameras are applied to images taken using the same camera configuration. This means that when performing multi-image matching for surface point cloud generation, the orientation parameters will remain the same as the calibrated results, even when the target has changed. Base on this invariant character, the whole 3D modeling pipeline can be performed completely automatically, once the whole system has been calibrated and the software was seamlessly integrated. Several experiments were conducted to prove the feasibility of the proposed system. Images observed include that of a human being, eight Buddhist statues, and a stone sculpture. The results for the stone sculpture, obtained with several multi-camera configurations were compared with a reference model acquired by an ATOS-I 2M active scanner. The best result has an absolute accuracy of 0.26 mm and a relative accuracy of 1:17,333. It demonstrates the feasibility of the proposed low-cost image-based 3D modeling pipeline and its applicability to a large quantity of antiques stored in a museum. PMID:23112656

A semi-automatic image-based close range 3D modeling pipeline using a multi-camera configuration.

PubMed

Rau, Jiann-Yeou; Yeh, Po-Chia

2012-01-01

The generation of photo-realistic 3D models is an important task for digital recording of cultural heritage objects. This study proposes an image-based 3D modeling pipeline which takes advantage of a multi-camera configuration and multi-image matching technique that does not require any markers on or around the object. Multiple digital single lens reflex (DSLR) cameras are adopted and fixed with invariant relative orientations. Instead of photo-triangulation after image acquisition, calibration is performed to estimate the exterior orientation parameters of the multi-camera configuration which can be processed fully automatically using coded targets. The calibrated orientation parameters of all cameras are applied to images taken using the same camera configuration. This means that when performing multi-image matching for surface point cloud generation, the orientation parameters will remain the same as the calibrated results, even when the target has changed. Base on this invariant character, the whole 3D modeling pipeline can be performed completely automatically, once the whole system has been calibrated and the software was seamlessly integrated. Several experiments were conducted to prove the feasibility of the proposed system. Images observed include that of a human being, eight Buddhist statues, and a stone sculpture. The results for the stone sculpture, obtained with several multi-camera configurations were compared with a reference model acquired by an ATOS-I 2M active scanner. The best result has an absolute accuracy of 0.26 mm and a relative accuracy of 1:17,333. It demonstrates the feasibility of the proposed low-cost image-based 3D modeling pipeline and its applicability to a large quantity of antiques stored in a museum.

Electrode channel selection based on backtracking search optimization in motor imagery brain-computer interfaces.

PubMed

Dai, Shengfa; Wei, Qingguo

2017-01-01

Common spatial pattern algorithm is widely used to estimate spatial filters in motor imagery based brain-computer interfaces. However, use of a large number of channels will make common spatial pattern tend to over-fitting and the classification of electroencephalographic signals time-consuming. To overcome these problems, it is necessary to choose an optimal subset of the whole channels to save computational time and improve the classification accuracy. In this paper, a novel method named backtracking search optimization algorithm is proposed to automatically select the optimal channel set for common spatial pattern. Each individual in the population is a N-dimensional vector, with each component representing one channel. A population of binary codes generate randomly in the beginning, and then channels are selected according to the evolution of these codes. The number and positions of 1's in the code denote the number and positions of chosen channels. The objective function of backtracking search optimization algorithm is defined as the combination of classification error rate and relative number of channels. Experimental results suggest that higher classification accuracy can be achieved with much fewer channels compared to standard common spatial pattern with whole channels.

Real-time range acquisition by adaptive structured light.

PubMed

Koninckx, Thomas P; Van Gool, Luc

2006-03-01

The goal of this paper is to provide a "self-adaptive" system for real-time range acquisition. Reconstructions are based on a single frame structured light illumination. Instead of using generic, static coding that is supposed to work under all circumstances, system adaptation is proposed. This occurs on-the-fly and renders the system more robust against instant scene variability and creates suitable patterns at startup. A continuous trade-off between speed and quality is made. A weighted combination of different coding cues--based upon pattern color, geometry, and tracking--yields a robust way to solve the correspondence problem. The individual coding cues are automatically adapted within a considered family of patterns. The weights to combine them are based on the average consistency with the result within a small time-window. The integration itself is done by reformulating the problem as a graph cut. Also, the camera-projector configuration is taken into account for generating the projection patterns. The correctness of the range maps is not guaranteed, but an estimation of the uncertainty is provided for each part of the reconstruction. Our prototype is implemented using unmodified consumer hardware only and, therefore, is cheap. Frame rates vary between 10 and 25 fps, dependent on scene complexity.

PEGASUS 5: An Automated Pre-Processor for Overset-Grid CFD

NASA Technical Reports Server (NTRS)

Suhs, Norman E.; Rogers, Stuart E.; Dietz, William E.; Kwak, Dochan (Technical Monitor)

2002-01-01

An all new, automated version of the PEGASUS software has been developed and tested. PEGASUS provides the hole-cutting and connectivity information between overlapping grids, and is used as the final part of the grid generation process for overset-grid computational fluid dynamics approaches. The new PEGASUS code (Version 5) has many new features: automated hole cutting; a projection scheme for fixing gaps in overset surfaces; more efficient interpolation search methods using an alternating digital tree; hole-size optimization based on adding additional layers of fringe points; and an automatic restart capability. The new code has also been parallelized using the Message Passing Interface standard. The parallelization performance provides efficient speed-up of the execution time by an order of magnitude, and up to a factor of 30 for very large problems. The results of three example cases are presented: a three-element high-lift airfoil, a generic business jet configuration, and a complete Boeing 777-200 aircraft in a high-lift landing configuration. Comparisons of the computed flow fields for the airfoil and 777 test cases between the old and new versions of the PEGASUS codes show excellent agreement with each other and with experimental results.

75 FR 80677 - The Low-Income Definition

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-23

... original regulatory text so it is consistent with the geo-coding software the agency uses to make the low... Union Act (Act) authorizes the NCUA Board (Board) to define ``low-income members'' so that credit unions... process of implementing geo- coding software to make the calculation automatically for credit unions...

Automatic Item Generation via Frame Semantics: Natural Language Generation of Math Word Problems.

ERIC Educational Resources Information Center

Deane, Paul; Sheehan, Kathleen

This paper is an exploration of the conceptual issues that have arisen in the course of building a natural language generation (NLG) system for automatic test item generation. While natural language processing techniques are applicable to general verbal items, mathematics word problems are particularly tractable targets for natural language…

Mechanisms of Habitual Approach

PubMed Central

Anderson, Brian A.; Folk, Charles L.; Garrison, Rebecca; Rogers, Leeland

2016-01-01

Reward learning has a powerful influence on the attention system, causing previously reward-associated stimuli to automatically capture attention. Difficulty ignoring stimuli associated with drug reward has been linked to addiction relapse, and the attention system of drug-dependent patients seems especially influenced by reward history. This and other evidence suggests that value-driven attention has consequences for behavior and decision-making, facilitating a bias to approach and consume the previously reward-associated stimulus even when doing so runs counter to current goals and priorities. Yet, a mechanism linking value-driven attention to behavioral responding and a general approach bias is lacking. Here we show that previously reward-associated stimuli escape inhibitory processing in a go/no-go task. Control experiments confirmed that this value-dependent failure of goal-directed inhibition could not be explained by search history or residual motivation, but depended specifically on the learned association between particular stimuli and reward outcome. When a previously high-value stimulus is encountered, the response codes generated by that stimulus are automatically afforded high priority, bypassing goal-directed cognitive processes involved in suppressing task-irrelevant behavior. PMID:27054684

Automatic differentiation evaluated as a tool for rotorcraft design and optimization

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Young, Katherine C.

1995-01-01

This paper investigates the use of automatic differentiation (AD) as a means for generating sensitivity analyses in rotorcraft design and optimization. This technique transforms an existing computer program into a new program that performs sensitivity analysis in addition to the original analysis. The original FORTRAN program calculates a set of dependent (output) variables from a set of independent (input) variables, the new FORTRAN program calculates the partial derivatives of the dependent variables with respect to the independent variables. The AD technique is a systematic implementation of the chain rule of differentiation, this method produces derivatives to machine accuracy at a cost that is comparable with that of finite-differencing methods. For this study, an analysis code that consists of the Langley-developed hover analysis HOVT, the comprehensive rotor analysis CAMRAD/JA, and associated preprocessors is processed through the AD preprocessor ADIFOR 2.0. The resulting derivatives are compared with derivatives obtained from finite-differencing techniques. The derivatives obtained with ADIFOR 2.0 are exact within machine accuracy and do not depend on the selection of step-size, as are the derivatives obtained with finite-differencing techniques.

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.

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

Downar, Thomas

This report summarizes the current status of VERA-CS Verification and Validation for PWR Core Follow operation and proposes a multi-phase plan for continuing VERA-CS V&V in FY17 and FY18. The proposed plan recognizes the hierarchical nature of a multi-physics code system such as VERA-CS and the importance of first achieving an acceptable level of V&V on each of the single physics codes before focusing on the V&V of the coupled physics solution. The report summarizes the V&V of each of the single physics codes systems currently used for core follow analysis (ie MPACT, CTF, Multigroup Cross Section Generation, and BISONmore » / Fuel Temperature Tables) and proposes specific actions to achieve a uniformly acceptable level of V&V in FY17. The report also recognizes the ongoing development of other codes important for PWR Core Follow (e.g. TIAMAT, MAMBA3D) and proposes Phase II (FY18) VERA-CS V&V activities in which those codes will also reach an acceptable level of V&V. The report then summarizes the current status of VERA-CS multi-physics V&V for PWR Core Follow and the ongoing PWR Core Follow V&V activities for FY17. An automated procedure and output data format is proposed for standardizing the output for core follow calculations and automatically generating tables and figures for the VERA-CS Latex file. A set of acceptance metrics is also proposed for the evaluation and assessment of core follow results that would be used within the script to automatically flag any results which require further analysis or more detailed explanation prior to being added to the VERA-CS validation base. After the Automation Scripts have been completed and tested using BEAVRS, the VERA-CS plan proposes the Watts Bar cycle depletion cases should be performed with the new cross section library and be included in the first draft of the new VERA-CS manual for release at the end of PoR15. Also, within the constraints imposed by the proprietary nature of plant data, as many as possible of the FY17 AMA Plant Core Follow cases should also be included in the VERA-CS manual at the end of PoR15. After completion of the ongoing development of TIAMAT for fully coupled, full core calculations with VERA-CS / BISON 1.5D, and after the completion of the refactoring of MAMBA3D for CIPS analysis in FY17, selected cases from the VERA-CS validation based should be performed, beginning with the legacy cases of Watts Bar and BEAVRS in PoR16. Finally, as potential Phase III future work some additional considerations are identified for extending the VERA-CS V&V to other reactor types such as the BWR.« less

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

PubMed Central

Melckenbeeck, Ine; Audenaert, Pieter; Michoel, Tom; Colle, Didier; Pickavet, Mario

2016-01-01

Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually finding all graphlets in a large graph can be time-consuming, however. As the graphlets grow in size, more different graphlets emerge and the time needed to find each graphlet also scales up. If it is not needed to find each instance of each graphlet, but knowing the number of graphlets touching each node of the graph suffices, the problem is less hard. Previous research shows a way to simplify counting the graphlets: instead of looking for the graphlets needed, smaller graphlets are searched, as well as the number of common neighbors of vertices. Solving a system of equations then gives the number of times a vertex is part of each graphlet of the desired size. However, until now, equations only exist to count graphlets with 4 or 5 nodes. In this paper, two new techniques are presented. The first allows to generate the equations needed in an automatic way. This eliminates the tedious work needed to do so manually each time an extra node is added to the graphlets. The technique is independent on the number of nodes in the graphlets and can thus be used to count larger graphlets than previously possible. The second technique gives all graphlets a unique ordering which is easily extended to name graphlets of any size. Both techniques were used to generate equations to count graphlets with 4, 5 and 6 vertices, which extends all previous results. Code can be found at https://github.com/IneMelckenbeeck/equation-generator and https://github.com/IneMelckenbeeck/graphlet-naming. PMID:26797021

Unsupervised Extraction of Diagnosis Codes from EMRs Using Knowledge-Based and Extractive Text Summarization Techniques

PubMed Central

Kavuluru, Ramakanth; Han, Sifei; Harris, Daniel

2017-01-01

Diagnosis codes are extracted from medical records for billing and reimbursement and for secondary uses such as quality control and cohort identification. In the US, these codes come from the standard terminology ICD-9-CM derived from the international classification of diseases (ICD). ICD-9 codes are generally extracted by trained human coders by reading all artifacts available in a patient’s medical record following specific coding guidelines. To assist coders in this manual process, this paper proposes an unsupervised ensemble approach to automatically extract ICD-9 diagnosis codes from textual narratives included in electronic medical records (EMRs). Earlier attempts on automatic extraction focused on individual documents such as radiology reports and discharge summaries. Here we use a more realistic dataset and extract ICD-9 codes from EMRs of 1000 inpatient visits at the University of Kentucky Medical Center. Using named entity recognition (NER), graph-based concept-mapping of medical concepts, and extractive text summarization techniques, we achieve an example based average recall of 0.42 with average precision 0.47; compared with a baseline of using only NER, we notice a 12% improvement in recall with the graph-based approach and a 7% improvement in precision using the extractive text summarization approach. Although diagnosis codes are complex concepts often expressed in text with significant long range non-local dependencies, our present work shows the potential of unsupervised methods in extracting a portion of codes. As such, our findings are especially relevant for code extraction tasks where obtaining large amounts of training data is difficult. PMID:28748227

Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit

PubMed Central

Bharioke, Arjun; Chklovskii, Dmitri B.

2015-01-01

Neurons must faithfully encode signals that can vary over many orders of magnitude despite having only limited dynamic ranges. For a correlated signal, this dynamic range constraint can be relieved by subtracting away components of the signal that can be predicted from the past, a strategy known as predictive coding, that relies on learning the input statistics. However, the statistics of input natural signals can also vary over very short time scales e.g., following saccades across a visual scene. To maintain a reduced transmission cost to signals with rapidly varying statistics, neuronal circuits implementing predictive coding must also rapidly adapt their properties. Experimentally, in different sensory modalities, sensory neurons have shown such adaptations within 100 ms of an input change. Here, we show first that linear neurons connected in a feedback inhibitory circuit can implement predictive coding. We then show that adding a rectification nonlinearity to such a feedback inhibitory circuit allows it to automatically adapt and approximate the performance of an optimal linear predictive coding network, over a wide range of inputs, while keeping its underlying temporal and synaptic properties unchanged. We demonstrate that the resulting changes to the linearized temporal filters of this nonlinear network match the fast adaptations observed experimentally in different sensory modalities, in different vertebrate species. Therefore, the nonlinear feedback inhibitory network can provide automatic adaptation to fast varying signals, maintaining the dynamic range necessary for accurate neuronal transmission of natural inputs. PMID:26247884

flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.

PubMed

Monaco, Gianni; Chen, Hao; Poidinger, Michael; Chen, Jinmiao; de Magalhães, João Pedro; Larbi, Anis

2016-08-15

Flow cytometry (FCM) is widely used in both clinical and basic research to characterize cell phenotypes and functions. The latest FCM instruments analyze up to 20 markers of individual cells, producing high-dimensional data. This requires the use of the latest clustering and dimensionality reduction techniques to automatically segregate cell sub-populations in an unbiased manner. However, automated analyses may lead to false discoveries due to inter-sample differences in quality and properties. We present an R package, flowAI, containing two methods to clean FCM files from unwanted events: (i) an automatic method that adopts algorithms for the detection of anomalies and (ii) an interactive method with a graphical user interface implemented into an R shiny application. The general approach behind the two methods consists of three key steps to check and remove suspected anomalies that derive from (i) abrupt changes in the flow rate, (ii) instability of signal acquisition and (iii) outliers in the lower limit and margin events in the upper limit of the dynamic range. For each file analyzed our software generates a summary of the quality assessment from the aforementioned steps. The software presented is an intuitive solution seeking to improve the results not only of manual but also and in particular of automatic analysis on FCM data. R source code available through Bioconductor: http://bioconductor.org/packages/flowAI/ CONTACTS: mongianni1@gmail.com or Anis_Larbi@immunol.a-star.edu.sg Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automated Construction of Node Software Using Attributes in a Ubiquitous Sensor Network Environment

PubMed Central

Lee, Woojin; Kim, Juil; Kang, JangMook

2010-01-01

In sensor networks, nodes must often operate in a demanding environment facing restrictions such as restricted computing resources, unreliable wireless communication and power shortages. Such factors make the development of ubiquitous sensor network (USN) applications challenging. To help developers construct a large amount of node software for sensor network applications easily and rapidly, this paper proposes an approach to the automated construction of node software for USN applications using attributes. In the proposed technique, application construction proceeds by first developing a model for the sensor network and then designing node software by setting the values of the predefined attributes. After that, the sensor network model and the design of node software are verified. The final source codes of the node software are automatically generated from the sensor network model. We illustrate the efficiency of the proposed technique by using a gas/light monitoring application through a case study of a Gas and Light Monitoring System based on the Nano-Qplus operating system. We evaluate the technique using a quantitative metric—the memory size of execution code for node software. Using the proposed approach, developers are able to easily construct sensor network applications and rapidly generate a large number of node softwares at a time in a ubiquitous sensor network environment. PMID:22163678

Automated construction of node software using attributes in a ubiquitous sensor network environment.

PubMed

Lee, Woojin; Kim, Juil; Kang, JangMook

2010-01-01

In sensor networks, nodes must often operate in a demanding environment facing restrictions such as restricted computing resources, unreliable wireless communication and power shortages. Such factors make the development of ubiquitous sensor network (USN) applications challenging. To help developers construct a large amount of node software for sensor network applications easily and rapidly, this paper proposes an approach to the automated construction of node software for USN applications using attributes. In the proposed technique, application construction proceeds by first developing a model for the sensor network and then designing node software by setting the values of the predefined attributes. After that, the sensor network model and the design of node software are verified. The final source codes of the node software are automatically generated from the sensor network model. We illustrate the efficiency of the proposed technique by using a gas/light monitoring application through a case study of a Gas and Light Monitoring System based on the Nano-Qplus operating system. We evaluate the technique using a quantitative metric-the memory size of execution code for node software. Using the proposed approach, developers are able to easily construct sensor network applications and rapidly generate a large number of node softwares at a time in a ubiquitous sensor network environment.

Automatic Activation of Phonological Code during Visual Word Recognition in Children: A Masked Priming Study in Grades 3 and 5

ERIC Educational Resources Information Center

Sauval, Karinne; Perre, Laetitia; Casalis, Séverine

2017-01-01

The present study aimed to investigate the development of automatic phonological processes involved in visual word recognition during reading acquisition in French. A visual masked priming lexical decision experiment was carried out with third, fifth graders and adult skilled readers. Three different types of partial overlap between the prime and…

Flexible Energy Scheduling Tool for Integrating Variable Generation | Grid

Science.gov Websites

, security-constrained economic dispatch, and automatic generation control programs. DOWNLOAD PAPER Electric commitment, security-constrained economic dispatch, and automatic generation control sub-models. Each sub resolutions and operating strategies can be explored. FESTIV produces not only economic metrics but also

Regional vertical total electron content (VTEC) modeling together with satellite and receiver differential code biases (DCBs) using semi-parametric multivariate adaptive regression B-splines (SP-BMARS)

NASA Astrophysics Data System (ADS)

Durmaz, Murat; Karslioglu, Mahmut Onur

2015-04-01

There are various global and regional methods that have been proposed for the modeling of ionospheric vertical total electron content (VTEC). Global distribution of VTEC is usually modeled by spherical harmonic expansions, while tensor products of compactly supported univariate B-splines can be used for regional modeling. In these empirical parametric models, the coefficients of the basis functions as well as differential code biases (DCBs) of satellites and receivers can be treated as unknown parameters which can be estimated from geometry-free linear combinations of global positioning system observables. In this work we propose a new semi-parametric multivariate adaptive regression B-splines (SP-BMARS) method for the regional modeling of VTEC together with satellite and receiver DCBs, where the parametric part of the model is related to the DCBs as fixed parameters and the non-parametric part adaptively models the spatio-temporal distribution of VTEC. The latter is based on multivariate adaptive regression B-splines which is a non-parametric modeling technique making use of compactly supported B-spline basis functions that are generated from the observations automatically. This algorithm takes advantage of an adaptive scale-by-scale model building strategy that searches for best-fitting B-splines to the data at each scale. The VTEC maps generated from the proposed method are compared numerically and visually with the global ionosphere maps (GIMs) which are provided by the Center for Orbit Determination in Europe (CODE). The VTEC values from SP-BMARS and CODE GIMs are also compared with VTEC values obtained through calibration using local ionospheric model. The estimated satellite and receiver DCBs from the SP-BMARS model are compared with the CODE distributed DCBs. The results show that the SP-BMARS algorithm can be used to estimate satellite and receiver DCBs while adaptively and flexibly modeling the daily regional VTEC.

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

FAMA: Fast Automatic MOOG Analysis

NASA Astrophysics Data System (ADS)

Magrini, Laura; Randich, Sofia; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

2014-02-01

FAMA (Fast Automatic MOOG Analysis), written in Perl, computes the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths (EWs) automatically and independently of any subjective approach. Based on the widely-used MOOG code, it simultaneously searches for three equilibria, excitation equilibrium, ionization balance, and the relationship between logn(FeI) and the reduced EWs. FAMA also evaluates the statistical errors on individual element abundances and errors due to the uncertainties in the stellar parameters. Convergence criteria are not fixed "a priori" but instead are based on the quality of the spectra.

[Coding Causes of Death with IRIS Software. Impact in Navarre Mortality Statistic].

PubMed

Floristán Floristán, Yugo; Delfrade Osinaga, Josu; Carrillo Prieto, Jesus; Aguirre Perez, Jesus; Moreno-Iribas, Conchi

2016-08-02

There are few studies that analyze changes in mortality statistics derived from the use of IRIS software, an automatic system for coding multiple causes of death and for the selection of the underlying cause of death, compared to manual coding. This study evaluated the impact of the use of IRIS in the Navarre mortality statistic. We proceeded to double coding 5,060 death certificates corresponding to residents in Navarra in 2014. We calculated coincidence between the two encodings for ICD10 chapters and for the list of causes of the Spanish National Statistics Institute (INE-102) and we estimated the change on mortality rates. IRIS automatically coded 90% of death certificates. The coincidence to 4 characters and in the same chapter of the CIE10 was 79.1% and 92.0%, respectively. Furthermore, coincidence with the short INE-102 list was 88.3%. Higher matches were found in death certificate of people under 65 years. In comparison with manual coding there was an increase in deaths from endocrine diseases (31%), mental disorders (19%) and disease of nervous system (9%), while a decrease of genitourinary system diseases was observed (21%). The coincidence at level of ICD10 chapters coding by IRIS in comparison to manual coding was 9 out of 10 deaths, similar to what is observed in other studies. The implementation of IRIS has led to increased of endocrine diseases, especially diabetes and hyperlipidaemia, and mental disorders, especially dementias.

Progress in The Semantic Analysis of Scientific Code

NASA Technical Reports Server (NTRS)

Stewart, Mark

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Automatic Rock Detection and Mapping from HiRISE Imagery

NASA Technical Reports Server (NTRS)

Huertas, Andres; Adams, Douglas S.; Cheng, Yang

2008-01-01

This system includes a C-code software program and a set of MATLAB software tools for statistical analysis and rock distribution mapping. The major functions include rock detection and rock detection validation. The rock detection code has been evolved into a production tool that can be used by engineers and geologists with minor training.

14 CFR 91.215 - ATC transponder and altitude reporting equipment and use.

Code of Federal Regulations, 2013 CFR

2013-01-01

... interrogations with the code specified by ATC, or a Mode S capability, replying to Mode 3/A interrogations with the code specified by ATC and intermode and Mode S interrogations in accordance with the applicable... equipment having a Mode C capability that automatically replies to Mode C interrogations by transmitting...

14 CFR 91.215 - ATC transponder and altitude reporting equipment and use.

Code of Federal Regulations, 2010 CFR

2010-01-01

... interrogations with the code specified by ATC, or a Mode S capability, replying to Mode 3/A interrogations with the code specified by ATC and intermode and Mode S interrogations in accordance with the applicable... equipment having a Mode C capability that automatically replies to Mode C interrogations by transmitting...

14 CFR 91.215 - ATC transponder and altitude reporting equipment and use.

Code of Federal Regulations, 2011 CFR

2011-01-01

... interrogations with the code specified by ATC, or a Mode S capability, replying to Mode 3/A interrogations with the code specified by ATC and intermode and Mode S interrogations in accordance with the applicable... equipment having a Mode C capability that automatically replies to Mode C interrogations by transmitting...

14 CFR 91.215 - ATC transponder and altitude reporting equipment and use.

Code of Federal Regulations, 2012 CFR

2012-01-01

... interrogations with the code specified by ATC, or a Mode S capability, replying to Mode 3/A interrogations with the code specified by ATC and intermode and Mode S interrogations in accordance with the applicable... equipment having a Mode C capability that automatically replies to Mode C interrogations by transmitting...

14 CFR 91.215 - ATC transponder and altitude reporting equipment and use.

Code of Federal Regulations, 2014 CFR

2014-01-01

... interrogations with the code specified by ATC, or a Mode S capability, replying to Mode 3/A interrogations with the code specified by ATC and intermode and Mode S interrogations in accordance with the applicable... equipment having a Mode C capability that automatically replies to Mode C interrogations by transmitting...

Automatic contact in DYNA3D for vehicle crashworthiness

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

Whirley, R.G.; Engelmann, B.E.

1993-07-15

This paper presents a new formulation for the automatic definition and treatment of mechanical contact in explicit nonlinear finite element analysis. Automatic contact offers the benefits of significantly reduced model construction time and fewer opportunities for user error, but faces significant challenges in reliability and computational costs. This paper discusses in detail a new four-step automatic contact algorithm. Key aspects of the proposed method include automatic identification of adjacent and opposite surfaces in the global search phase, and the use of a smoothly varying surface normal which allows a consistent treatment of shell intersection and corner contact conditions without ad-hocmore » rules. The paper concludes with three examples which illustrate the performance of the newly proposed algorithm in the public DYNA3D code.« less

Automatic energy calibration algorithm for an RBS setup

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

Silva, Tiago F.; Moro, Marcos V.; Added, Nemitala

2013-05-06

This work describes a computer algorithm for automatic extraction of the energy calibration parameters from a Rutherford Back-Scattering Spectroscopy (RBS) spectrum. Parameters like the electronic gain, electronic offset and detection resolution (FWHM) of a RBS setup are usually determined using a standard sample. In our case, the standard sample comprises of a multi-elemental thin film made of a mixture of Ti-Al-Ta that is analyzed at the beginning of each run at defined beam energy. A computer program has been developed to extract automatically the calibration parameters from the spectrum of the standard sample. The code evaluates the first derivative ofmore » the energy spectrum, locates the trailing edges of the Al, Ti and Ta peaks and fits a first order polynomial for the energy-channel relation. The detection resolution is determined fitting the convolution of a pre-calculated theoretical spectrum. To test the code, data of two years have been analyzed and the results compared with the manual calculations done previously, obtaining good agreement.« less

Integration of the Remote Agent for the NASA Deep Space One Autonomy Experiment

NASA Technical Reports Server (NTRS)

Dorais, Gregory A.; Bernard, Douglas E.; Gamble, Edward B., Jr.; Kanefsky, Bob; Kurien, James; Muscettola, Nicola; Nayak, P. Pandurang; Rajan, Kanna; Lau, Sonie (Technical Monitor)

1998-01-01

This paper describes the integration of the Remote Agent (RA), a spacecraft autonomy system which is scheduled to control the Deep Space 1 spacecraft during a flight experiment in 1999. The RA is a reusable, model-based autonomy system that is quite different from software typically used to control an aerospace system. We describe the integration challenges we faced, how we addressed them, and the lessons learned. We focus on those aspects of integrating the RA that were either easier or more difficult than integrating a more traditional large software application because the RA is a model-based autonomous system. A number of characteristics of the RA made integration process easier. One example is the model-based nature of RA. Since the RA is model-based, most of its behavior is not hard coded into procedural program code. Instead, engineers specify high level models of the spacecraft's components from which the Remote Agent automatically derives correct system-wide behavior on the fly. This high level, modular, and declarative software description allowed some interfaces between RA components and between RA and the flight software to be automatically generated and tested for completeness against the Remote Agent's models. In addition, the Remote Agent's model-based diagnosis system automatically diagnoses when the RA models are not consistent with the behavior of the spacecraft. In flight, this feature is used to diagnose failures in the spacecraft hardware. During integration, it proved valuable in finding problems in the spacecraft simulator or flight software. In addition, when modifications are made to the spacecraft hardware or flight software, the RA models are easily changed because they only capture a description of the spacecraft. one does not have to maintain procedural code that implements the correct behavior for every expected situation. On the other hand, several features of the RA made it more difficult to integrate than typical flight software. For example, the definition of correct behavior is more difficult to specify for a system that is expected to reason about and flexibly react to its environment than for a traditional flight software system. Consequently, whenever a change is made to the RA it is more time consuming to determine if the resulting behavior is correct. We conclude the paper with a discussion of future work on the Remote Agent as well as recommendations to ease integration of similar autonomy projects.

46 CFR 63.01-3 - Scope and applicability.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING AUTOMATIC AUXILIARY... automatic auxiliary boilers, automatic heating boilers, automatic waste heat boilers, donkey boilers... control systems) used for the generation of steam and/or oxidation of ordinary waste materials and garbage...

46 CFR 63.01-3 - Scope and applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING AUTOMATIC AUXILIARY... automatic auxiliary boilers, automatic heating boilers, automatic waste heat boilers, donkey boilers... control systems) used for the generation of steam and/or oxidation of ordinary waste materials and garbage...

Sonic Boom Prediction and Minimization of the Douglas Reference OPT5 Configuration

NASA Technical Reports Server (NTRS)

Siclari, Michael J.

1999-01-01

Conventional CFD methods and grids do not yield adequate resolution of the complex shock flow pattern generated by a real aircraft geometry. As a result, a unique grid topology and supersonic flow solver was developed at Northrop Grumman based on the characteristic behavior of supersonic wave patterns emanating from the aircraft. Using this approach, it was possible to compute flow fields with adequate resolution several body lengths below the aircraft. In this region, three-dimensional effects are diminished and conventional two-dimensional modified linear theory (MLT) can be applied to estimate ground pressure signatures or sonic booms. To accommodate real aircraft geometries and alleviate the burdensome grid generation task, an implicit marching multi-block, multi-grid finite-volume Euler code was developed as the basis for the sonic boom prediction methodology. The Thomas two-dimensional extrapolation method is built into the Euler code so that ground signatures can be obtained quickly and efficiently with minimum computational effort suitable to the aircraft design environment. The loudness levels of these signatures can then be determined using a NASA generated noise code. Since the Euler code is a three-dimensional flow field solver, the complete circumferential region below the aircraft is computed. The extrapolation of all this field data from a cylinder of constant radius leads to the definition of the entire boom corridor occurring directly below and off to the side of the aircraft's flight path yielding an estimate for the entire noise "annoyance" corridor in miles as well as its magnitude. An automated multidisciplinary sonic boom design optimization software system was developed during the latter part of HSR Phase 1. Using this system, it was found that sonic boom signatures could be reduced through optimization of a variety of geometric aircraft parameters. This system uses a gradient based nonlinear optimizer as the driver in conjunction with a computationally efficient Euler CFD solver (NIIM3DSB) for computing the three-dimensional near-field characteristics of the aircraft. The intent of the design system is to identify and optimize geometric design variables that have a beneficial impact on the ground sonic boom. The system uses a simple wave drag data format to specify the aircraft geometry. The geometry is internally enhanced and analytic methods are used to generate marching grids suitable for the multi-block Euler solver. The Thomas extrapolation method is integrated into this system, and hence, the aircraft's centerline ground sonic boom signature is also automatically computed for a specified cruise altitude and yields the parameters necessary to evaluate the design function. The entire design system has been automated since the gradient based optimization software requires many flow analyses in order to obtain the required sensitivity derivatives for each design variable in order to converge on an optimal solution. Hence, once the problem is defined which includes defining the objective function and geometric and aerodynamic constraints, the system will automatically regenerate the perturbed geometry, the necessary grids, the Euler solution, and finally the ground sonic boom signature at the request of the optimizer.

A Model-Based Method for Content Validation of Automatically Generated Test Items

ERIC Educational Resources Information Center

Zhang, Xinxin; Gierl, Mark

2016-01-01

The purpose of this study is to describe a methodology to recover the item model used to generate multiple-choice test items with a novel graph theory approach. Beginning with the generated test items and working backward to recover the original item model provides a model-based method for validating the content used to automatically generate test…

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

PubMed

Shapiro, Bruce E; Mjolsness, Eric

2016-02-15

We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales-Menten-Henri (MMH) and Gene-Regulation (GRN) to Monod-Wyman-Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface. Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases. Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Development of an Automatic Grid Generator for Multi-Element High-Lift Wings

NASA Technical Reports Server (NTRS)

Eberhardt, Scott; Wibowo, Pratomo; Tu, Eugene

1996-01-01

The procedure to generate the grid around a complex wing configuration is presented in this report. The automatic grid generation utilizes the Modified Advancing Front Method as a predictor and an elliptic scheme as a corrector. The scheme will advance the surface grid one cell outward and the newly obtained grid is corrected using the Laplace equation. The predictor-corrector step ensures that the grid produced will be smooth for every configuration. The predictor-corrector scheme is extended for a complex wing configuration. A new technique is developed to deal with the grid generation in the wing-gaps and on the flaps. It will create the grids that fill the gap on the wing surface and the gap created by the flaps. The scheme recognizes these configurations automatically so that minimal user input is required. By utilizing an appropriate sequence in advancing the grid points on a wing surface, the automatic grid generation for complex wing configurations is achieved.

How Does Reading Performance Modulate the Impact of Orthographic Knowledge on Speech Processing? A Comparison of Normal Readers and Dyslexic Adults

ERIC Educational Resources Information Center

Pattamadilok, Chotiga; Nelis, Aubéline; Kolinsky, Régine

2014-01-01

Studies on proficient readers showed that speech processing is affected by knowledge of the orthographic code. Yet, the automaticity of the orthographic influence depends on task demand. Here, we addressed this automaticity issue in normal and dyslexic adult readers by comparing the orthographic effects obtained in two speech processing tasks that…

DoD Is Not Properly Monitoring the Initiation of Maintenance for Facilities at Kandahar Airfield, Afghanistan (REDACTED)

DTIC Science & Technology

2013-09-30

fire sprinkler system during the initial construction of the RSOI facilities. The construction contract to build the RSOI...International Building Code. Compliant manual and automatic fire alarm and notification systems , portable fire extinguishers, fire sprinkler systems ...automatic fire sprinkler system that was not operational, a fire department connection that was obstructed, and a fire detection system

Curiosity Finds Hydrogen-Rich Area of Mars Subsurface

NASA Image and Video Library

2015-08-19

Curiosity's Russian-made instrument for checking hydration levels in the ground beneath the rover detected an unusually high amount at a site near "Marias Pass," prompting repeated passes over the area to map the hydrogen amounts. The instrument is named Dynamic Albedo of Neutrons, or DAN. It detects hydrogen by the effect of hydrogen atoms on neutrons entering the ground either from cosmic rays and Curiosity's power source (DAN's passive mode) or from the instrument's neutron pulse generator (DAN's active mode). DAN recognizes which neutrons have bounced off hydrogen from their rerduced energy level. This map, covering an area about 130 feet (40 meters) across, shows results from DAN's multiple traverses over the area, with color coding for levels of hydrogen detected. The red coding indicates amounts of hydrogen three to four times as high as the amounts detected anywhere previously along Curiosity's traverse of about 6.9 miles (11.1 kilometers) since landing in August 2012. The inset map at lower right shows the full traverse through Sol 1051 (July 21, 2015), with names assigned to rectangles within Gale Crater for geological mapping purposes. The vertical bar at left indicates the color coding according to counts per second in DAN's passive mode. The hydrogen detected by DAN is interpreted as water molecules or hydroxyl ions bound within minerals or water absorbed onto minerals in the rocks and soil, to a depth of about 3 feet (1 meter) beneath the rover. The amount of hydrogen is often expressed as "water equivalent hydrogen" based on two hydrogen atoms per molecule of water. In the same area where DAN detected an unusually high amount of hydration, Curiosity's Chemistry and Camera (ChemCam) instrument detected an unusually high amount of silica in several rock targets. The DAN and ChemCam findings led to the rover's science team choosing a rock target called "Buckskin" for collection of a drilled sample to be analyzed by the rover's internal laboratory instruments. Russia's Space Research Institute developed DAN in close cooperation with the N.L. Dukhov All-Russia Research Institute of Automatics, Moscow, and the Joint Institute for Nuclear Research, Dubna. The neutron generator development was supervised by the late technical designer German A. Smirnov of the All-Russia Institute of Automatics. Moscow. http://photojournal.jpl.nasa.gov/catalog/PIA19809

Automated software configuration in the MONSOON system

NASA Astrophysics Data System (ADS)

Daly, Philip N.; Buchholz, Nick C.; Moore, Peter C.

2004-09-01

MONSOON is the next generation OUV-IR controller project being developed at NOAO. The design is flexible, emphasizing code re-use, maintainability and scalability as key factors. The software needs to support widely divergent detector systems ranging from multi-chip mosaics (for LSST, QUOTA, ODI and NEWFIRM) down to large single or multi-detector laboratory development systems. In order for this flexibility to be effective and safe, the software must be able to configure itself to the requirements of the attached detector system at startup. The basic building block of all MONSOON systems is the PAN-DHE pair which make up a single data acquisition node. In this paper we discuss the software solutions used in the automatic PAN configuration system.

Computer-Aided Software Engineering - An approach to real-time software development

NASA Technical Reports Server (NTRS)

Walker, Carrie K.; Turkovich, John J.

1989-01-01

A new software engineering discipline is Computer-Aided Software Engineering (CASE), a technology aimed at automating the software development process. This paper explores the development of CASE technology, particularly in the area of real-time/scientific/engineering software, and a history of CASE is given. The proposed software development environment for the Advanced Launch System (ALS CASE) is described as an example of an advanced software development system for real-time/scientific/engineering (RT/SE) software. The Automated Programming Subsystem of ALS CASE automatically generates executable code and corresponding documentation from a suitably formatted specification of the software requirements. Software requirements are interactively specified in the form of engineering block diagrams. Several demonstrations of the Automated Programming Subsystem are discussed.

Towards Time Automata and Multi-Agent Systems

NASA Technical Reports Server (NTRS)

Hutzler, G.; Klaudel, H.; Wang, D. Y.

2004-01-01

The design of reactive systems must comply with logical correctness (the system does what it is supposed to do) and timeliness (the system has to satisfy a set of temporal constraints) criteria. In this paper, we propose a global approach for the design of adaptive reactive systems, i.e., systems that dynamically adapt their architecture depending on the context. We use the timed automata formalism for the design of the agents' behavior. This allows evaluating beforehand the properties of the system (regarding logical correctness and timeliness), thanks to model-checking and simulation techniques. This model is enhanced with tools that we developed for the automatic generation of code, allowing to produce very quickly a running multi-agent prototype satisfying the properties of the model.

Tenth-order QED contribution to the electron g-2 and an improved value of the fine structure constant.

PubMed

Aoyama, Tatsumi; Hayakawa, Masashi; Kinoshita, Toichiro; Nio, Makiko

2012-09-14

This letter presents the complete QED contribution to the electron g-2 up to the tenth order. With the help of the automatic code generator, we evaluate all 12,672 diagrams of the tenth-order diagrams and obtain 9.16 (58)(α/π)(5). We also improve the eighth-order contribution obtaining -1.9097 (20)(α/π)(4), which includes the mass-dependent contributions. These results lead to a(e)(theory)=1,159,652,181.78(77)×10(-12). The improved value of the fine-structure constant α(-1)=137.035999173 (35) [0.25 ppb] is also derived from the theory and measurement of a(e).

Automatic removal of cosmic ray signatures in Deep Impact images

NASA Astrophysics Data System (ADS)

Ipatov, S. I.; A'Hearn, M. F.; Klaasen, K. P.

The results of recognition of cosmic ray (CR) signatures on single images made during the Deep Impact mission were analyzed for several codes written by several authors. For automatic removal of CR signatures on many images, we suggest using the code imgclean ( http://pdssbn.astro.umd.edu/volume/didoc_0001/document/calibration_software/dical_v5/) written by E. Deutsch as other codes considered do not work properly automatically with a large number of images and do not run to completion for some images; however, other codes can be better for analysis of certain specific images. Sometimes imgclean detects false CR signatures near the edge of a comet nucleus, and it often does not recognize all pixels of long CR signatures. Our code rmcr is the only code among those considered that allows one to work with raw images. For most visual images made during low solar activity at exposure time t > 4 s, the number of clusters of bright pixels on an image per second per sq. cm of CCD was about 2-4, both for dark and normal sky images. At high solar activity, it sometimes exceeded 10. The ratio of the number of CR signatures consisting of n pixels obtained at high solar activity to that at low solar activity was greater for greater n. The number of clusters detected as CR signatures on a single infrared image is by at least a factor of several greater than the actual number of CR signatures; the number of clusters based on analysis of two successive dark infrared frames is in agreement with an expected number of CR signatures. Some glitches of false CR signatures include bright pixels repeatedly present on different infrared images. Our interactive code imr allows a user to choose the regions on a considered image where glitches detected by imgclean as CR signatures are ignored. In other regions chosen by the user, the brightness of some pixels is replaced by the local median brightness if the brightness of these pixels is greater by some factor than the median brightness. The interactive code allows one to delete long CR signatures and prevents removal of false CR signatures near the edge of the nucleus of the comet. The interactive code can be applied to editing any digital images. Results obtained can be used for other missions to comets.

Knowledge Base for Automatic Generation of Online IMS LD Compliant Course Structures

ERIC Educational Resources Information Center

Pacurar, Ecaterina Giacomini; Trigano, Philippe; Alupoaie, Sorin

2006-01-01

Our article presents a pedagogical scenarios-based web application that allows the automatic generation and development of pedagogical websites. These pedagogical scenarios are represented in the IMS Learning Design standard. Our application is a web portal helping teachers to dynamically generate web course structures, to edit pedagogical content…

26 CFR 26.6081-1 - Automatic extension of time for filing generation-skipping transfer tax returns.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 14 2011-04-01 2010-04-01 true Automatic extension of time for filing generation-skipping transfer tax returns. 26.6081-1 Section 26.6081-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX...

26 CFR 26.6081-1 - Automatic extension of time for filing generation-skipping transfer tax returns.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Automatic extension of time for filing generation-skipping transfer tax returns. 26.6081-1 Section 26.6081-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX...

26 CFR 26.6081-1 - Automatic extension of time for filing generation-skipping transfer tax returns.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 14 2013-04-01 2013-04-01 false Automatic extension of time for filing generation-skipping transfer tax returns. 26.6081-1 Section 26.6081-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX...

26 CFR 26.6081-1 - Automatic extension of time for filing generation-skipping transfer tax returns.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 14 2014-04-01 2013-04-01 true Automatic extension of time for filing generation-skipping transfer tax returns. 26.6081-1 Section 26.6081-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX...

26 CFR 26.6081-1 - Automatic extension of time for filing generation-skipping transfer tax returns.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 14 2012-04-01 2012-04-01 false Automatic extension of time for filing generation-skipping transfer tax returns. 26.6081-1 Section 26.6081-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) ESTATE AND GIFT TAXES GENERATION-SKIPPING TRANSFER TAX...

Coding hazardous tree failures for a data management system

Treesearch

Lee A. Paine

1978-01-01

Codes for automatic data processing (ADP) are provided for hazardous tree failure data submitted on Report of Tree Failure forms. Definitions of data items and suggestions for interpreting ambiguously worded reports are also included. The manual is intended to insure the production of accurate and consistent punched ADP cards which are used in transfer of the data to...

Frequency-Accommodating Manchester Decoder

NASA Technical Reports Server (NTRS)

Vasquez, Mario J.

1988-01-01

No adjustment necessary to cover a 10:1 frequency range. Decoding circuit converts biphase-level pulse-code modulation to nonreturn-to-zero (NRZ)-level pulse-code modulation plus clock signal. Circuit accommodates input data rate of 50 to 500 kb/s. Tracks gradual changes in rate automatically, eliminating need for extra circuits and manual switching to adjust to different rates.

Automatic detection of white-light flare kernels in SDO/HMI intensitygrams

NASA Astrophysics Data System (ADS)

Mravcová, Lucia; Švanda, Michal

2017-11-01

Solar flares with a broadband emission in the white-light range of the electromagnetic spectrum belong to most enigmatic phenomena on the Sun. The origin of the white-light emission is not entirely understood. We aim to systematically study the visible-light emission connected to solar flares in SDO/HMI observations. We developed a code for automatic detection of kernels of flares with HMI intensity brightenings and study properties of detected candidates. The code was tuned and tested and with a little effort, it could be applied to any suitable data set. By studying a few flare examples, we found indication that HMI intensity brightening might be an artefact of the simplified procedure used to compute HMI observables.

Automatic query formulations in information retrieval.

PubMed

Salton, G; Buckley, C; Fox, E A

1983-07-01

Modern information retrieval systems are designed to supply relevant information in response to requests received from the user population. In most retrieval environments the search requests consist of keywords, or index terms, interrelated by appropriate Boolean operators. Since it is difficult for untrained users to generate effective Boolean search requests, trained search intermediaries are normally used to translate original statements of user need into useful Boolean search formulations. Methods are introduced in this study which reduce the role of the search intermediaries by making it possible to generate Boolean search formulations completely automatically from natural language statements provided by the system patrons. Frequency considerations are used automatically to generate appropriate term combinations as well as Boolean connectives relating the terms. Methods are covered to produce automatic query formulations both in a standard Boolean logic system, as well as in an extended Boolean system in which the strict interpretation of the connectives is relaxed. Experimental results are supplied to evaluate the effectiveness of the automatic query formulation process, and methods are described for applying the automatic query formulation process in practice.

Posttest analysis of MIST Test 3109AA using TRAC-PF1/MOD1

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

Steiner, J.L.; Siebe, D.A.; Boyack, B.E.

This document discusses a posttest calculation and analysis of Multi-loop Integral System Test (MIST) 3109AA as the nominal test for the MIST program. It is a test of a small-break loss-of-coolant accident (SBLOCA) with a scaled 10-cm{sup 2} break in the B1 cold leg. The test exhibited the major post-SBLOCA phenomena, as expected, including depressurization to saturation, intermittent and interrupted loop flow, boiler-condenser mode cooling, refill, and postrefill cooldown. Full high-pressure injection and auxiliary feedwater were available, reactor coolant pumps were not available, and reactor-vessel vent valves and guard heaters were automatically controlled. Constant level control in the steam-generator secondariesmore » was used after steam-generator secondary refill and symmetric steam-generator pressure control was used. We performed the calculation using TRAC-PF1/MODI. Agreement between test data and the calculation was generally reasonable. All major trends and phenomena were correctly predicted. It is believed that the correct conclusions about trends and phenomena will be reached if the code is used in similar applications.« less

Posttest analysis of MIST Test 3109AA using TRAC-PF1/MOD1

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

Steiner, J.L.; Siebe, D.A.; Boyack, B.E.

This document discusses a posttest calculation and analysis of Multi-loop Integral System Test (MIST) 3109AA as the nominal test for the MIST program. It is a test of a small-break loss-of-coolant accident (SBLOCA) with a scaled 10-cm[sup 2] break in the B1 cold leg. The test exhibited the major post-SBLOCA phenomena, as expected, including depressurization to saturation, intermittent and interrupted loop flow, boiler-condenser mode cooling, refill, and postrefill cooldown. Full high-pressure injection and auxiliary feedwater were available, reactor coolant pumps were not available, and reactor-vessel vent valves and guard heaters were automatically controlled. Constant level control in the steam-generator secondariesmore » was used after steam-generator secondary refill and symmetric steam-generator pressure control was used. We performed the calculation using TRAC-PF1/MODI. Agreement between test data and the calculation was generally reasonable. All major trends and phenomena were correctly predicted. It is believed that the correct conclusions about trends and phenomena will be reached if the code is used in similar applications.« less

Advanced Unstructured Grid Generation for Complex Aerodynamic Applications

NASA Technical Reports Server (NTRS)

Pirzadeh, Shahyar Z.

2008-01-01

A new approach for distribution of grid points on the surface and in the volume has been developed and implemented in the NASA unstructured grid generation code VGRID. In addition to the point and line sources of prior work, the new approach utilizes surface and volume sources for automatic curvature-based grid sizing and convenient point distribution in the volume. A new exponential growth function produces smoother and more efficient grids and provides superior control over distribution of grid points in the field. All types of sources support anisotropic grid stretching which not only improves the grid economy but also provides more accurate solutions for certain aerodynamic applications. The new approach does not require a three-dimensional background grid as in the previous methods. Instead, it makes use of an efficient bounding-box auxiliary medium for storing grid parameters defined by surface sources. The new approach is less memory-intensive and more efficient computationally. The grids generated with the new method either eliminate the need for adaptive grid refinement for certain class of problems or provide high quality initial grids that would enhance the performance of many adaptation methods.

Automatic programming of simulation models

NASA Technical Reports Server (NTRS)

Schroer, Bernard J.; Tseng, Fan T.; Zhang, Shou X.; Dwan, Wen S.

1988-01-01

The objective of automatic programming is to improve the overall environment for describing the program. This improved environment is realized by a reduction in the amount of detail that the programmer needs to know and is exposed to. Furthermore, this improved environment is achieved by a specification language that is more natural to the user's problem domain and to the user's way of thinking and looking at the problem. The goal of this research is to apply the concepts of automatic programming (AP) to modeling discrete event simulation system. Specific emphasis is on the design and development of simulation tools to assist the modeler define or construct a model of the system and to then automatically write the corresponding simulation code in the target simulation language, GPSS/PC. A related goal is to evaluate the feasibility of various languages for constructing automatic programming simulation tools.

A computer based approach for Material, Manpower and Equipment managementin the Construction Projects

NASA Astrophysics Data System (ADS)

Sasidhar, Jaladanki; Muthu, D.; Venkatasubramanian, C.; Ramakrishnan, K.

2017-07-01

The success of any construction project will depend on efficient management of resources in a perfect manner to complete the project with a reasonable budget and time and the quality cannot be compromised. The efficient and timely procurement of material, deployment of adequate labor at correct time and mobilization of machinery lacking in time, all of them causes delay, lack of quality and finally affect the project cost. It is known factor that Project cost can be controlled by taking corrective actions on mobilization of resources at a right time. This research focuses on integration of management systems with the computer to generate the model which uses OOM data structure which decides to include automatic commodity code generation, automatic takeoff execution, intelligent purchase order generation, and components of design and schedule integration to overcome the problems of stock out. To overcome the problem in equipment management system inventory management module is suggested and the data set of equipment registration number, equipment number, description, date of purchase, manufacturer, equipment price, market value, life of equipment, production data of the equipment which includes equipment number, date, name of the job, hourly rate, insurance, depreciation cost of the equipment, taxes, storage cost, interest, oil, grease, and fuel consumption, etc. is analyzed and the decision support systems to overcome the problem arising out improper management is generated. The problem on labor is managed using scheduling, Strategic management of human resources. From the generated support systems tool, the resources are mobilized at a right time and help the project manager to finish project in time and thereby save the abnormal project cost and also provides the percentage that can be improved and also research focuses on determining the percentage of delays that are caused by lack of management of materials, manpower and machinery in different types of projects and how the percentage various from project to project.

An Experiment in Scientific Code Semantic Analysis

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1998-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, distributed expert parsers. These semantic parser are designed to recognize formulae in different disciplines including physical and mathematical formulae and geometrical position in a numerical scheme. The parsers will automatically recognize and document some static, semantic concepts and locate some program semantic errors. Results are shown for a subroutine test case and a collection of combustion code routines. This ability to locate some semantic errors and document semantic concepts in scientific and engineering code should reduce the time, risk, and effort of developing and using these codes.

ACPYPE - AnteChamber PYthon Parser interfacE.

PubMed

Sousa da Silva, Alan W; Vranken, Wim F

2012-07-23

ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein-ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

Automatic Commercial Permit Sets

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

Grana, Paul

Final report for Folsom Labs’ Solar Permit Generator project, which has successfully completed, resulting in the development and commercialization of a software toolkit within the cloud-based HelioScope software environment that enables solar engineers to automatically generate and manage draft documents for permit submission.

Automatic translation of MPI source into a latency-tolerant, data-driven form

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

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. We reformulate MPI source into a task dependency graph representation, which partially orders the tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotation for a variety ofmore » applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo’s performance meets or exceeds that of labor-intensive hand coding. As a result, the translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a well-known library.« less

Automatic translation of MPI source into a latency-tolerant, data-driven form

DOE PAGES

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric; ...

2017-03-06

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. We reformulate MPI source into a task dependency graph representation, which partially orders the tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotation for a variety ofmore » applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo’s performance meets or exceeds that of labor-intensive hand coding. As a result, the translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a well-known library.« less

Effect of normal aging and of Alzheimer's disease on, episodic memory.

PubMed

Le Moal, S; Reymann, J M; Thomas, V; Cattenoz, C; Lieury, A; Allain, H

1997-01-01

Performances of 12 patients with Alzheimer's disease (AD), 15 healthy elderly subjects and 20 young healthy volunteers were compared on two episodic memory tests. The first, a learning test of semantically related words, enabled an assessment of the effect of semantic relationships on word learning by controlling the encoding and retrieval processes. The second, a dual coding test, is about the assessment of automatic processes operating during drawings encoding. The results obtained demonstrated quantitative and qualitative differences between the population. Manifestations of episodic memory deficit in AD patients were shown not only by lower performance scores than in elderly controls, but also by the lack of any effect of semantic cues and the production of a large number of extra-list intrusions. Automatic processes underlying dual coding appear to be spared in AD, although more time is needed to process information than in young or elderly subjects. These findings confirm former data and emphasize the preservation of certain memory processes (dual coding) in AD which could be used in future therapeutic approaches.

Automatic translation of MPI source into a latency-tolerant, data-driven form

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

Nguyen, Tan; Cicotti, Pietro; Bylaska, Eric

Hiding communication behind useful computation is an important performance programming technique but remains an inscrutable programming exercise even for the expert. We present Bamboo, a code transformation framework that can realize communication overlap in applications written in MPI without the need to intrusively modify the source code. Bamboo reformulates MPI source into the form of a task dependency graph that expresses a partial ordering among tasks, enabling the program to execute in a data-driven fashion under the control of an external runtime system. Experimental results demonstrate that Bamboo significantly reduces communication delays while requiring only modest amounts of programmer annotationmore » for a variety of applications and platforms, including those employing co-processors and accelerators. Moreover, Bamboo's performance meets or exceeds that of labor-intensive hand coding. The translator is more than a means of hiding communication costs automatically; it demonstrates the utility of semantic level optimization against a wellknown library.« less

Analysis of automatic repeat request methods for deep-space downlinks

NASA Technical Reports Server (NTRS)

Pollara, F.; Ekroot, L.

1995-01-01

Automatic repeat request (ARQ) methods cannot increase the capacity of a memoryless channel. However, they can be used to decrease the complexity of the channel-coding system to achieve essentially error-free transmission and to reduce link margins when the channel characteristics are poorly predictable. This article considers ARQ methods on a power-limited channel (e.g., the deep-space channel), where it is important to minimize the total power needed to transmit the data, as opposed to a bandwidth-limited channel (e.g., terrestrial data links), where the spectral efficiency or the total required transmission time is the most relevant performance measure. In the analysis, we compare the performance of three reference concatenated coded systems used in actual deep-space missions to that obtainable by ARQ methods using the same codes, in terms of required power, time to transmit with a given number of retransmissions, and achievable probability of word error. The ultimate limits of ARQ with an arbitrary number of retransmissions are also derived.

Management of natural resources through automatic cartographic inventory

NASA Technical Reports Server (NTRS)

Rey, P. A.; Gourinard, Y.; Cambou, F. (Principal Investigator)

1974-01-01

The author has identified the following significant results. Significant correspondence codes relating ERTS imagery to ground truth from vegetation and geology maps have been established. The use of color equidensity and color composite methods for selecting zones of equal densitometric value on ERTS imagery was perfected. Primary interest of temporal color composite is stressed. A chain of transfer operations from ERTS imagery to the automatic mapping of natural resources was developed.

New Developments in Modeling MHD Systems on High Performance Computing Architectures

NASA Astrophysics Data System (ADS)

Germaschewski, K.; Raeder, J.; Larson, D. J.; Bhattacharjee, A.

2009-04-01

Modeling the wide range of time and length scales present even in fluid models of plasmas like MHD and X-MHD (Extended MHD including two fluid effects like Hall term, electron inertia, electron pressure gradient) is challenging even on state-of-the-art supercomputers. In the last years, HPC capacity has continued to grow exponentially, but at the expense of making the computer systems more and more difficult to program in order to get maximum performance. In this paper, we will present a new approach to managing the complexity caused by the need to write efficient codes: Separating the numerical description of the problem, in our case a discretized right hand side (r.h.s.), from the actual implementation of efficiently evaluating it. An automatic code generator is used to describe the r.h.s. in a quasi-symbolic form while leaving the translation into efficient and parallelized code to a computer program itself. We implemented this approach for OpenGGCM (Open General Geospace Circulation Model), a model of the Earth's magnetosphere, which was accelerated by a factor of three on regular x86 architecture and a factor of 25 on the Cell BE architecture (commonly known for its deployment in Sony's PlayStation 3).

Retargeting of existing FORTRAN program and development of parallel compilers

NASA Technical Reports Server (NTRS)

Agrawal, Dharma P.

1988-01-01

The software models used in implementing the parallelizing compiler for the B-HIVE multiprocessor system are described. The various models and strategies used in the compiler development are: flexible granularity model, which allows a compromise between two extreme granularity models; communication model, which is capable of precisely describing the interprocessor communication timings and patterns; loop type detection strategy, which identifies different types of loops; critical path with coloring scheme, which is a versatile scheduling strategy for any multicomputer with some associated communication costs; and loop allocation strategy, which realizes optimum overlapped operations between computation and communication of the system. Using these models, several sample routines of the AIR3D package are examined and tested. It may be noted that automatically generated codes are highly parallelized to provide the maximized degree of parallelism, obtaining the speedup up to a 28 to 32-processor system. A comparison of parallel codes for both the existing and proposed communication model, is performed and the corresponding expected speedup factors are obtained. The experimentation shows that the B-HIVE compiler produces more efficient codes than existing techniques. Work is progressing well in completing the final phase of the compiler. Numerous enhancements are needed to improve the capabilities of the parallelizing compiler.

UIVerify: A Web-Based Tool for Verification and Automatic Generation of User Interfaces

NASA Technical Reports Server (NTRS)

Shiffman, Smadar; Degani, Asaf; Heymann, Michael

2004-01-01

In this poster, we describe a web-based tool for verification and automatic generation of user interfaces. The verification component of the tool accepts as input a model of a machine and a model of its interface, and checks that the interface is adequate (correct). The generation component of the tool accepts a model of a given machine and the user's task, and then generates a correct and succinct interface. This write-up will demonstrate the usefulness of the tool by verifying the correctness of a user interface to a flight-control system. The poster will include two more examples of using the tool: verification of the interface to an espresso machine, and automatic generation of a succinct interface to a large hypothetical machine.

Methodology for sensitivity analysis, approximate analysis, and design optimization in CFD for multidisciplinary applications

NASA Technical Reports Server (NTRS)

Taylor, Arthur C., III; Hou, Gene W.

1994-01-01

The straightforward automatic-differentiation and the hand-differentiated incremental iterative methods are interwoven to produce a hybrid scheme that captures some of the strengths of each strategy. With this compromise, discrete aerodynamic sensitivity derivatives are calculated with the efficient incremental iterative solution algorithm of the original flow code. Moreover, the principal advantage of automatic differentiation is retained (i.e., all complicated source code for the derivative calculations is constructed quickly with accuracy). The basic equations for second-order sensitivity derivatives are presented; four methods are compared. Each scheme requires that large systems are solved first for the first-order derivatives and, in all but one method, for the first-order adjoint variables. Of these latter three schemes, two require no solutions of large systems thereafter. For the other two for which additional systems are solved, the equations and solution procedures are analogous to those for the first order derivatives. From a practical viewpoint, implementation of the second-order methods is feasible only with software tools such as automatic differentiation, because of the extreme complexity and large number of terms. First- and second-order sensitivities are calculated accurately for two airfoil problems, including a turbulent flow example; both geometric-shape and flow-condition design variables are considered. Several methods are tested; results are compared on the basis of accuracy, computational time, and computer memory. For first-order derivatives, the hybrid incremental iterative scheme obtained with automatic differentiation is competitive with the best hand-differentiated method; for six independent variables, it is at least two to four times faster than central finite differences and requires only 60 percent more memory than the original code; the performance is expected to improve further in the future.

Preparing a collection of radiology examinations for distribution and retrieval.

PubMed

Demner-Fushman, Dina; Kohli, Marc D; Rosenman, Marc B; Shooshan, Sonya E; Rodriguez, Laritza; Antani, Sameer; Thoma, George R; McDonald, Clement J

2016-03-01

Clinical documents made available for secondary use play an increasingly important role in discovery of clinical knowledge, development of research methods, and education. An important step in facilitating secondary use of clinical document collections is easy access to descriptions and samples that represent the content of the collections. This paper presents an approach to developing a collection of radiology examinations, including both the images and radiologist narrative reports, and making them publicly available in a searchable database. The authors collected 3996 radiology reports from the Indiana Network for Patient Care and 8121 associated images from the hospitals' picture archiving systems. The images and reports were de-identified automatically and then the automatic de-identification was manually verified. The authors coded the key findings of the reports and empirically assessed the benefits of manual coding on retrieval. The automatic de-identification of the narrative was aggressive and achieved 100% precision at the cost of rendering a few findings uninterpretable. Automatic de-identification of images was not quite as perfect. Images for two of 3996 patients (0.05%) showed protected health information. Manual encoding of findings improved retrieval precision. Stringent de-identification methods can remove all identifiers from text radiology reports. DICOM de-identification of images does not remove all identifying information and needs special attention to images scanned from film. Adding manual coding to the radiologist narrative reports significantly improved relevancy of the retrieved clinical documents. The de-identified Indiana chest X-ray collection is available for searching and downloading from the National Library of Medicine (http://openi.nlm.nih.gov/). Published by Oxford University Press on behalf of the American Medical Informatics Association 2015. This work is written by US Government employees and is in the public domain in the US.

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.

Proceedings of the U.S. Army Symposium on Gun Dynamics (5th) Held in Rensselaerville, New York on 23-25 September 1987

DTIC Science & Technology

1987-09-01

have shown that gun barrel heating, and hence thermal expansion , is both axially and circumferentially asymmetric. Circumferential, or cross-barrel...element code, which ended in the selection of ABAQUS . The code will perform static, dynamic, and thermal anal- ysis on a broad range of structures...analysis may be performed by a user supplied FORTRAN subroutine which is automatically linked to the code and supplements the stand- ard ABAQUS

MAPA: an interactive accelerator design code with GUI

NASA Astrophysics Data System (ADS)

Bruhwiler, David L.; Cary, John R.; Shasharina, Svetlana G.

1999-06-01

The MAPA code is an interactive accelerator modeling and design tool with an X/Motif GUI. MAPA has been developed in C++ and makes full use of object-oriented features. We present an overview of its features and describe how users can independently extend the capabilities of the entire application, including the GUI. For example, a user can define a new model for a focusing or accelerating element. If the appropriate form is followed, and the new element is "registered" with a single line in the specified file, then the GUI will fully support this user-defined element type after it has been compiled and then linked to the existing application. In particular, the GUI will bring up windows for modifying any relevant parameters of the new element type. At present, one can use the GUI for phase space tracking, finding fixed points and generating line plots for the Twiss parameters, the dispersion and the accelerator geometry. The user can define new types of simulations which the GUI will automatically support by providing a menu option to execute the simulation and subsequently rendering line plots of the resulting data.

Computation of Steady and Unsteady Laminar Flames: Theory

NASA Technical Reports Server (NTRS)

Hagstrom, Thomas; Radhakrishnan, Krishnan; Zhou, Ruhai

1999-01-01

In this paper we describe the numerical analysis underlying our efforts to develop an accurate and reliable code for simulating flame propagation using complex physical and chemical models. We discuss our spatial and temporal discretization schemes, which in our current implementations range in order from two to six. In space we use staggered meshes to define discrete divergence and gradient operators, allowing us to approximate complex diffusion operators while maintaining ellipticity. Our temporal discretization is based on the use of preconditioning to produce a highly efficient linearly implicit method with good stability properties. High order for time accurate simulations is obtained through the use of extrapolation or deferred correction procedures. We also discuss our techniques for computing stationary flames. The primary issue here is the automatic generation of initial approximations for the application of Newton's method. We use a novel time-stepping procedure, which allows the dynamic updating of the flame speed and forces the flame front towards a specified location. Numerical experiments are presented, primarily for the stationary flame problem. These illustrate the reliability of our techniques, and the dependence of the results on various code parameters.

Assume-Guarantee Verification of Source Code with Design-Level Assumptions

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Pasareanu, Corina S.; Cobleigh, Jamieson M.

2004-01-01

Model checking is an automated technique that can be used to determine whether a system satisfies certain required properties. To address the 'state explosion' problem associated with this technique, we propose to integrate assume-guarantee verification at different phases of system development. During design, developers build abstract behavioral models of the system components and use them to establish key properties of the system. To increase the scalability of model checking at this level, we have developed techniques that automatically decompose the verification task by generating component assumptions for the properties to hold. The design-level artifacts are subsequently used to guide the implementation of the system, but also to enable more efficient reasoning at the source code-level. In particular we propose to use design-level assumptions to similarly decompose the verification of the actual system implementation. We demonstrate our approach on a significant NASA application, where design-level models were used to identify; and correct a safety property violation, and design-level assumptions allowed us to check successfully that the property was presented by the implementation.

Northwest range-plant symbols adapted to automatic data processing.

Treesearch

George A. Garrison; Jon M. Skovlin

1960-01-01

Many range technicians, agronomists, foresters, biologists, and botanists of various educational institutions and government agencies in the Northwest have been using a four-letter symbol list or code compiled 12 years ago from records of plants collected by the U.S. Forest Service in Oregon and Washington, This code has served well as a means of entering plant names...

Strategies for automatic processing of large aftershock sequences

NASA Astrophysics Data System (ADS)

Kvaerna, T.; Gibbons, S. J.

2017-12-01

Aftershock sequences following major earthquakes present great challenges to seismic bulletin generation. The analyst resources needed to locate events increase with increased event numbers as the quality of underlying, fully automatic, event lists deteriorates. While current pipelines, designed a generation ago, are usually limited to single passes over the raw data, modern systems also allow multiple passes. Processing the raw data from each station currently generates parametric data streams that are later subject to phase-association algorithms which form event hypotheses. We consider a major earthquake scenario and propose to define a region of likely aftershock activity in which we will detect and accurately locate events using a separate, specially targeted, semi-automatic process. This effort may use either pattern detectors or more general algorithms that cover wider source regions without requiring waveform similarity. An iterative procedure to generate automatic bulletins would incorporate all the aftershock event hypotheses generated by the auxiliary process, and filter all phases from these events from the original detection lists prior to a new iteration of the global phase-association algorithm.

Research-oriented image registry for multimodal image integration.

PubMed

Tanaka, M; Sadato, N; Ishimori, Y; Yonekura, Y; Yamashita, Y; Komuro, H; Hayahsi, N; Ishii, Y

1998-01-01

To provide multimodal biomedical images automatically, we constructed the research-oriented image registry, Data Delivery System (DDS). DDS was constructed on the campus local area network. Machines which generate images (imagers: DSA, ultrasound, PET, MRI, SPECT and CT) were connected to the campus LAN. Once a patient is registered, all his images are automatically picked up by DDS as they are generated, transferred through the gateway server to the intermediate server, and copied into the directory of the user who registered the patient. DDS informs the user through e-mail that new data have been generated and transferred. Data format is automatically converted into one which is chosen by the user. Data inactive for a certain period in the intermediate server are automatically achieved into the final and permanent data server based on compact disk. As a soft link is automatically generated through this step, a user has access to all (old or new) image data of the patient of his interest. As DDS runs with minimal maintenance, cost and time for data transfer are significantly saved. By making the complex process of data transfer and conversion invisible, DDS has made it easy for naive-to-computer researchers to concentrate on their biomedical interest.

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

PubMed

Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

2010-10-26

AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine.

An Anisotropic A posteriori Error Estimator for CFD

NASA Astrophysics Data System (ADS)

Feijóo, Raúl A.; Padra, Claudio; Quintana, Fernando

In this article, a robust anisotropic adaptive algorithm is presented, to solve compressible-flow equations using a stabilized CFD solver and automatic mesh generators. The association includes a mesh generator, a flow solver, and an a posteriori error-estimator code. The estimator was selected among several choices available (Almeida et al. (2000). Comput. Methods Appl. Mech. Engng, 182, 379-400; Borges et al. (1998). "Computational mechanics: new trends and applications". Proceedings of the 4th World Congress on Computational Mechanics, Bs.As., Argentina) giving a powerful computational tool. The main aim is to capture solution discontinuities, in this case, shocks, using the least amount of computational resources, i.e. elements, compatible with a solution of good quality. This leads to high aspect-ratio elements (stretching). To achieve this, a directional error estimator was specifically selected. The numerical results show good behavior of the error estimator, resulting in strongly-adapted meshes in few steps, typically three or four iterations, enough to capture shocks using a moderate and well-distributed amount of elements.

Automatic Item Generation: A More Efficient Process for Developing Mathematics Achievement Items?

ERIC Educational Resources Information Center

Embretson, Susan E.; Kingston, Neal M.

2018-01-01

The continual supply of new items is crucial to maintaining quality for many tests. Automatic item generation (AIG) has the potential to rapidly increase the number of items that are available. However, the efficiency of AIG will be mitigated if the generated items must be submitted to traditional, time-consuming review processes. In two studies,…

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

Neuroadaptive technology enables implicit cursor control based on medial prefrontal cortex activity.

PubMed

Zander, Thorsten O; Krol, Laurens R; Birbaumer, Niels P; Gramann, Klaus

2016-12-27

The effectiveness of today's human-machine interaction is limited by a communication bottleneck as operators are required to translate high-level concepts into a machine-mandated sequence of instructions. In contrast, we demonstrate effective, goal-oriented control of a computer system without any form of explicit communication from the human operator. Instead, the system generated the necessary input itself, based on real-time analysis of brain activity. Specific brain responses were evoked by violating the operators' expectations to varying degrees. The evoked brain activity demonstrated detectable differences reflecting congruency with or deviations from the operators' expectations. Real-time analysis of this activity was used to build a user model of those expectations, thus representing the optimal (expected) state as perceived by the operator. Based on this model, which was continuously updated, the computer automatically adapted itself to the expectations of its operator. Further analyses showed this evoked activity to originate from the medial prefrontal cortex and to exhibit a linear correspondence to the degree of expectation violation. These findings extend our understanding of human predictive coding and provide evidence that the information used to generate the user model is task-specific and reflects goal congruency. This paper demonstrates a form of interaction without any explicit input by the operator, enabling computer systems to become neuroadaptive, that is, to automatically adapt to specific aspects of their operator's mindset. Neuroadaptive technology significantly widens the communication bottleneck and has the potential to fundamentally change the way we interact with technology.

Automating Visualization Service Generation with the WATT Compiler

NASA Astrophysics Data System (ADS)

Bollig, E. F.; Lyness, M. D.; Erlebacher, G.; Yuen, D. A.

2007-12-01

As tasks and workflows become increasingly complex, software developers are devoting increasing attention to automation tools. Among many examples, the Automator tool from Apple collects components of a workflow into a single script, with very little effort on the part of the user. Tasks are most often described as a series of instructions. The granularity of the tasks dictates the tools to use. Compilers translate fine-grained instructions to assembler code, while scripting languages (ruby, perl) are used to describe a series of tasks at a higher level. Compilers can also be viewed as transformational tools: a cross-compiler can translate executable code written on one computer to assembler code understood on another, while transformational tools can translate from one high-level language to another. We are interested in creating visualization web services automatically, starting from stand-alone VTK (Visualization Toolkit) code written in Tcl. To this end, using the OCaml programming language, we have developed a compiler that translates Tcl into C++, including all the stubs, classes and methods to interface with gSOAP, a C++ implementation of the Soap 1.1/1.2 protocols. This compiler, referred to as the Web Automation and Translation Toolkit (WATT), is the first step towards automated creation of specialized visualization web services without input from the user. The WATT compiler seeks to automate all aspects of web service generation, including the transport layer, the division of labor and the details related to interface generation. The WATT compiler is part of ongoing efforts within the NSF funded VLab consortium [1] to facilitate and automate time-consuming tasks for the science related to understanding planetary materials. Through examples of services produced by WATT for the VLab portal, we will illustrate features, limitations and the improvements necessary to achieve the ultimate goal of complete and transparent automation in the generation of web services. In particular, we will detail the generation of a charge density visualization service applicable to output from the quantum calculations of the VLab computation workflows, plus another service for mantle convection visualization. We also discuss WATT-LIVE [2], a web-based interface that allows users to interact with WATT. With WATT-LIVE users submit Tcl code, retrieve its C++ translation with various files and scripts necessary to locally install the tailor-made web service, or launch the service for a limited session on our test server. This work is supported by NSF through the ITR grant NSF-0426867. [1] Virtual Laboratory for Earth and Planetary Materials, http://vlab.msi.umn.edu, September 2007. [2] WATT-LIVE website, http://vlab2.scs.fsu.edu/watt-live, September 2007.

Automated design of infrared digital metamaterials by genetic algorithm

NASA Astrophysics Data System (ADS)

Sugino, Yuya; Ishikawa, Atsushi; Hayashi, Yasuhiko; Tsuruta, Kenji

2017-08-01

We demonstrate automatic design of infrared (IR) metamaterials using a genetic algorithm (GA) and experimentally characterize their IR properties. To implement the automated design scheme of the metamaterial structures, we adopt a digital metamaterial consisting of 7 × 7 Au nano-pixels with an area of 200 nm × 200 nm, and their placements are coded as binary genes in the GA optimization process. The GA combined with three-dimensional (3D) finite element method (FEM) simulation is developed and applied to automatically construct a digital metamaterial to exhibit pronounced plasmonic resonances at the target IR frequencies. Based on the numerical results, the metamaterials are fabricated on a Si substrate over an area of 1 mm × 1 mm by using an EB lithography, Cr/Au (2/20 nm) depositions, and liftoff process. In the FT-IR measurement, pronounced plasmonic responses of each metamaterial are clearly observed near the targeted frequencies, although the synthesized pixel arrangements of the metamaterials are seemingly random. The corresponding numerical simulations reveal the important resonant behavior of each pixel and their hybridized systems. Our approach is fully computer-aided without artificial manipulation, thus paving the way toward the novel device design for next-generation plasmonic device applications.

Using the GeoFEST Faulted Region Simulation System

NASA Technical Reports Server (NTRS)

Parker, Jay W.; Lyzenga, Gregory A.; Donnellan, Andrea; Judd, Michele A.; Norton, Charles D.; Baker, Teresa; Tisdale, Edwin R.; Li, Peggy

2004-01-01

GeoFEST (the Geophysical Finite Element Simulation Tool) simulates stress evolution, fault slip and plastic/elastic processes in realistic materials, and so is suitable for earthquake cycle studies in regions such as Southern California. Many new capabilities and means of access for GeoFEST are now supported. New abilities include MPI-based cluster parallel computing using automatic PYRAMID/Parmetis-based mesh partitioning, automatic mesh generation for layered media with rectangular faults, and results visualization that is integrated with remote sensing data. The parallel GeoFEST application has been successfully run on over a half-dozen computers, including Intel Xeon clusters, Itanium II and Altix machines, and the Apple G5 cluster. It is not separately optimized for different machines, but relies on good domain partitioning for load-balance and low communication, and careful writing of the parallel diagonally preconditioned conjugate gradient solver to keep communication overhead low. Demonstrated thousand-step solutions for over a million finite elements on 64 processors require under three hours, and scaling tests show high efficiency when using more than (order of) 4000 elements per processor. The source code and documentation for GeoFEST is available at no cost from Open Channel Foundation. In addition GeoFEST may be used through a browser-based portal environment available to approved users. That environment includes semi-automated geometry creation and mesh generation tools, GeoFEST, and RIVA-based visualization tools that include the ability to generate a flyover animation showing deformations and topography. Work is in progress to support simulation of a region with several faults using 16 million elements, using a strain energy metric to adapt the mesh to faithfully represent the solution in a region of widely varying strain.

Intelligent MONitoring System for antiviral pharmacotherapy in patients with chronic hepatitis C (SiMON-VC).

PubMed

Margusino-Framiñán, Luis; Cid-Silva, Purificación; Mena-de-Cea, Álvaro; Sanclaudio-Luhía, Ana Isabel; Castro-Castro, José Antonio; Vázquez-González, Guillermo; Martín-Herranz, Isabel

2017-01-01

Two out of six strategic axes of pharmaceutical care in our hospital are quality and safety of care, and the incorporation of information technologies. Based on this, an information system was developed in the outpatient setting for pharmaceutical care of patients with chronic hepatitis C, SiMON-VC, which would improve the quality and safety of their pharmacotherapy. The objective of this paper is to describe requirements, structure and features of Si- MON-VC. Requirements demanded were that the information system would enter automatically all critical data from electronic clinical records at each of the visits to the Outpatient Pharmacy Unit, allowing the generation of events and alerts, documenting the pharmaceutical care provided, and allowing the use of data for research purposes. In order to meet these requirements, 5 sections were structured for each patient in SiMON-VC: Main Record, Events, Notes, Monitoring Graphs and Tables, and Follow-up. Each section presents a number of tabs with those coded data needed to monitor patients in the outpatient unit. The system automatically generates alerts for assisted prescription validation, efficacy and safety of using antivirals for the treatment of this disease. It features a completely versatile Indicator Control Panel, where temporary monitoring standards and alerts can be set. It allows the generation of reports, and their export to the electronic clinical record. It also allows data to be exported to the usual operating systems, through Big Data and Business Intelligence. Summing up, we can state that SiMON-VC improves the quality of pharmaceutical care provided in the outpatient pharmacy unit to patients with chronic hepatitis C, increasing the safety of antiviral therapy. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

[Case-Mix of hospital emergencies in the Andalusian Health Service based on the 2012 Minimum Data Set. Spain].

PubMed

Goicoechea Salazar, Juan Antonio; Nieto García, María Adoración; Laguna Téllez, Antonio; Larrocha Mata, Daniel; Canto Casasola, Vicente David; Murillo Cabezas, Francisco

2013-01-01

The implementation of digital health records in emergency departments (ED) in hospitals in the Andalusian Health Service and the development of an automatic encoder for this area have allowed us to establish a Minimum Data Set for Emergencies (MDS-ED). The aim of this article is to describe the case mix of hospital EDs using various dimensions contained in the MDS-ED. 3.235.600 hospital emergency records in 2012 were classified in clinical categories from the ICD-9-CM codes generated by the automatic encoder. Operating rules to obtain response time and length of stay were defined. A descriptive analysis was carried out to obtain demographic and chronological indicators as well as hospitalization, return and death rates and response time and length of stay in the Eds. Women generated 54,26% of all occurrences and their average age (39,98 years) was higher than men's (37,61). Paediatric emergencies accounted for 21,49% of the total. The peak hours were from 10:00 to 13:00 and from 16:00 to 17:00. Patients who did not undergo observation (92,67%) remained in the ED an average of 153 minutes. Injuries and poisoning, respiratory diseases, musculoskeletal diseases and symptoms and signs generated over 50% of all visits. 79.191 cases of chest pain, 28.741 episodes of heart failure and 27.989 episodes of serious infections were identified among the most relevant disorders. The MDS-ED makes it possible to address systematically the analysis of hospital emergencies by identifying the activity developed, the case-mix attended, the response times, the time spent in ED and the quality of the care.

Acquisition Of Rainfall Dataset And The Application For The Automatic Harvester In The Chesapeake Bay Region

NASA Astrophysics Data System (ADS)

Choi, Y.; Piasecki, M.

2008-12-01

The objective of this study is the preparation and indexing of rainfall data products for ingestion into the Chesapeake Bay Environmental Observatory (CBEO) node of the CUAHSI/WATERs network. Rainfall products (which are obtained and then processed based on the WSR-88D NEXRAD network) are obtained from the NOAA/NWS Advanced Hydrologic Prediction Service that combines the Multi-sensor Precipitation Estimate (MPE) data generated by the Regional River Forecast Centers and Hydro-NEXRAD rainfall data generated as a service by the University of Iowa. The former is collected on 4*4 km grid (HRAP) with a daily average temporal resolution and the latter on a 1minute*1minute degree grid with hourly values. We have generated a cut-out for the Chesapeake Bay Basin that contains about 9,300 nodes (sites) for the MPE data and about 300,000 nodes (sites) for the Hydro-NEXRAD product. Automated harvesting services have been implemented for both data products. The MPE data is harvested from its download site using ArcGIS which in turn is used to extract the data for the Chesapeake Bay watershed before a scripting program is used to scatter the data into the ODM. The Hydro-NEXRAD is downloaded from a web-based system at the University of Iowa which permits downloads for large scale watersheds organized by Hydraulic Unit Codes (HUC). The resulting ASCII is then automatically parsed and the information stored alongside the MPE data. The two data products stored side-by-side then allows a comparison between them addressing the accuracy and agreement between the methods used to arrive at rainfall data as both use the raw reflectivity data from the WSD-88D system.

GIS Data Based Automatic High-Fidelity 3D Road Network Modeling

NASA Technical Reports Server (NTRS)

Wang, Jie; Shen, Yuzhong

2011-01-01

3D road models are widely used in many computer applications such as racing games and driving simulations_ However, almost all high-fidelity 3D road models were generated manually by professional artists at the expense of intensive labor. There are very few existing methods for automatically generating 3D high-fidelity road networks, especially those existing in the real world. This paper presents a novel approach thai can automatically produce 3D high-fidelity road network models from real 2D road GIS data that mainly contain road. centerline in formation. The proposed method first builds parametric representations of the road centerlines through segmentation and fitting . A basic set of civil engineering rules (e.g., cross slope, superelevation, grade) for road design are then selected in order to generate realistic road surfaces in compliance with these rules. While the proposed method applies to any types of roads, this paper mainly addresses automatic generation of complex traffic interchanges and intersections which are the most sophisticated elements in the road networks

Tuned grid generation with ICEM CFD

NASA Technical Reports Server (NTRS)

Wulf, Armin; Akdag, Vedat

1995-01-01

ICEM CFD is a CAD based grid generation package that supports multiblock structured, unstructured tetrahedral and unstructured hexahedral grids. Major development efforts have been spent to extend ICEM CFD's multiblock structured and hexahedral unstructured grid generation capabilities. The modules added are: a parametric grid generation module and a semi-automatic hexahedral grid generation module. A fully automatic version of the hexahedral grid generation module for around a set of predefined objects in rectilinear enclosures has been developed. These modules will be presented and the procedures used will be described, and examples will be discussed.

The automatic neutron guide optimizer guide_bot

NASA Astrophysics Data System (ADS)

Bertelsen, Mads

2017-09-01

The guide optimization software guide_bot is introduced, the main purpose of which is to reduce the time spent programming when performing numerical optimization of neutron guides. A limited amount of information on the overall guide geometry and a figure of merit describing the desired beam is used to generate the code necessary to solve the problem. A generated McStas instrument file performs the Monte Carlo ray-tracing, which is controlled by iFit optimization scripts. The resulting optimal guide is thoroughly characterized, both in terms of brilliance transfer from an idealized source and on a more realistic source such as the ESS Butterfly moderator. Basic MATLAB knowledge is required from the user, but no experience with McStas or iFit is necessary. This paper briefly describes how guide_bot is used and some important aspects of the code. A short validation against earlier work is performed which shows the expected agreement. In addition a scan over the vertical divergence requirement, where individual guide optimizations are performed for each corresponding figure of merit, provides valuable data on the consequences of this parameter. The guide_bot software package is best suited for the start of an instrument design project as it excels at comparing a large amount of different guide alternatives for a specific set of instrument requirements, but is still applicable in later stages as constraints can be used to optimize more specific guides.

Transiting exoplanet candidates from K2 Campaigns 5 and 6

NASA Astrophysics Data System (ADS)

Pope, Benjamin J. S.; Parviainen, Hannu; Aigrain, Suzanne

2016-10-01

We introduce a new transit search and vetting pipeline for observations from the K2 mission, and present the candidate transiting planets identified by this pipeline out of the targets in Campaigns 5 and 6. Our pipeline uses the Gaussian process-based K2SC code to correct for the K2 pointing systematics and simultaneously model stellar variability. The systematics-corrected, variability-detrended light curves are searched for transits with the box-least-squares method, and a period-dependent detection threshold is used to generate a preliminary candidate list. Two or three individuals vet each candidate manually to produce the final candidate list, using a set of automatically generated transit fits and assorted diagnostic tests to inform the vetting. We detect 145 single-planet system candidates and 5 multi-planet systems, independently recovering the previously published hot Jupiters EPIC 212110888b, WASP-55b (EPIC 212300977b) and Qatar-2b (EPIC 212756297b). We also report the outcome of reconnaissance spectroscopy carried out for all candidates with Kepler magnitude Kp ≤ 13, identifying 12 targets as likely false positives. We compare our results to those of other K2 transit search pipelines, noting that ours performs particularly well for variable and/or active stars, but that the results are very similar overall. All the light curves and code used in the transit search and vetting process are publicly available, as are the follow-up spectra.

Self-recovery reversible image watermarking algorithm

PubMed Central

Sun, He; Gao, Shangbing; Jin, Shenghua

2018-01-01

The integrity of image content is essential, although most watermarking algorithms can achieve image authentication but not automatically repair damaged areas or restore the original image. In this paper, a self-recovery reversible image watermarking algorithm is proposed to recover the tampered areas effectively. First of all, the original image is divided into homogeneous blocks and non-homogeneous blocks through multi-scale decomposition, and the feature information of each block is calculated as the recovery watermark. Then, the original image is divided into 4×4 non-overlapping blocks classified into smooth blocks and texture blocks according to image textures. Finally, the recovery watermark generated by homogeneous blocks and error-correcting codes is embedded into the corresponding smooth block by mapping; watermark information generated by non-homogeneous blocks and error-correcting codes is embedded into the corresponding non-embedded smooth block and the texture block via mapping. The correlation attack is detected by invariant moments when the watermarked image is attacked. To determine whether a sub-block has been tampered with, its feature is calculated and the recovery watermark is extracted from the corresponding block. If the image has been tampered with, it can be recovered. The experimental results show that the proposed algorithm can effectively recover the tampered areas with high accuracy and high quality. The algorithm is characterized by sound visual quality and excellent image restoration. PMID:29920528

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

PubMed

Swertz, Morris A; De Brock, E O; Van Hijum, Sacha A F T; De Jong, Anne; Buist, Girbe; Baerends, Richard J S; Kok, Jan; Kuipers, Oscar P; Jansen, Ritsert C

2004-09-01

Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. http://www.molgenis.nl

Specifications and programs for computer software validation

NASA Technical Reports Server (NTRS)

Browne, J. C.; Kleir, R.; Davis, T.; Henneman, M.; Haller, A.; Lasseter, G. L.

1973-01-01

Three software products developed during the study are reported and include: (1) FORTRAN Automatic Code Evaluation System, (2) the Specification Language System, and (3) the Array Index Validation System.

Automatic Data Distribution for CFD Applications on Structured Grids

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Yan, Jerry

2000-01-01

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAFT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAFT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

Association rule mining on grid monitoring data to detect error sources

NASA Astrophysics Data System (ADS)

Maier, Gerhild; Schiffers, Michael; Kranzlmueller, Dieter; Gaidioz, Benjamin

2010-04-01

Error handling is a crucial task in an infrastructure as complex as a grid. There are several monitoring tools put in place, which report failing grid jobs including exit codes. However, the exit codes do not always denote the actual fault, which caused the job failure. Human time and knowledge is required to manually trace back errors to the real fault underlying an error. We perform association rule mining on grid job monitoring data to automatically retrieve knowledge about the grid components' behavior by taking dependencies between grid job characteristics into account. Therewith, problematic grid components are located automatically and this information - expressed by association rules - is visualized in a web interface. This work achieves a decrease in time for fault recovery and yields an improvement of a grid's reliability.

Automatic Data Distribution for CFD Applications on Structured Grids

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Yan, Jerry

1999-01-01

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAPT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAPT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

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.

An Experiment in Scientific Program Understanding

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.; Owen, Karl (Technical Monitor)

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. Results are shown for three intensively studied codes and seven blind test cases; all test cases are state of the art scientific codes. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Gaussian curvature analysis allows for automatic block placement in multi-block hexahedral meshing.

PubMed

Ramme, Austin J; Shivanna, Kiran H; Magnotta, Vincent A; Grosland, Nicole M

2011-10-01

Musculoskeletal finite element analysis (FEA) has been essential to research in orthopaedic biomechanics. The generation of a volumetric mesh is often the most challenging step in a FEA. Hexahedral meshing tools that are based on a multi-block approach rely on the manual placement of building blocks for their mesh generation scheme. We hypothesise that Gaussian curvature analysis could be used to automatically develop a building block structure for multi-block hexahedral mesh generation. The Automated Building Block Algorithm incorporates principles from differential geometry, combinatorics, statistical analysis and computer science to automatically generate a building block structure to represent a given surface without prior information. We have applied this algorithm to 29 bones of varying geometries and successfully generated a usable mesh in all cases. This work represents a significant advancement in automating the definition of building blocks.

Development of an Unstructured Mesh Code for Flows About Complete Vehicles

NASA Technical Reports Server (NTRS)

Peraire, Jaime; Gupta, K. K. (Technical Monitor)

2001-01-01

This report describes the research work undertaken at the Massachusetts Institute of Technology, under NASA Research Grant NAG4-157. The aim of this research is to identify effective algorithms and methodologies for the efficient and routine solution of flow simulations about complete vehicle configurations. For over ten years we have received support from NASA to develop unstructured mesh methods for Computational Fluid Dynamics. As a result of this effort a methodology based on the use of unstructured adapted meshes of tetrahedra and finite volume flow solvers has been developed. A number of gridding algorithms, flow solvers, and adaptive strategies have been proposed. The most successful algorithms developed from the basis of the unstructured mesh system FELISA. The FELISA system has been extensively for the analysis of transonic and hypersonic flows about complete vehicle configurations. The system is highly automatic and allows for the routine aerodynamic analysis of complex configurations starting from CAD data. The code has been parallelized and utilizes efficient solution algorithms. For hypersonic flows, a version of the code which incorporates real gas effects, has been produced. The FELISA system is also a component of the STARS aeroservoelastic system developed at NASA Dryden. One of the latest developments before the start of this grant was to extend the system to include viscous effects. This required the development of viscous generators, capable of generating the anisotropic grids required to represent boundary layers, and viscous flow solvers. We show some sample hypersonic viscous computations using the developed viscous generators and solvers. Although this initial results were encouraging it became apparent that in order to develop a fully functional capability for viscous flows, several advances in solution accuracy, robustness and efficiency were required. In this grant we set out to investigate some novel methodologies that could lead to the required improvements. In particular we focused on two fronts: (1) finite element methods and (2) iterative algebraic multigrid solution techniques.

Learning-Based Just-Noticeable-Quantization- Distortion Modeling for Perceptual Video Coding.

PubMed

Ki, Sehwan; Bae, Sung-Ho; Kim, Munchurl; Ko, Hyunsuk

2018-07-01

Conventional predictive video coding-based approaches are reaching the limit of their potential coding efficiency improvements, because of severely increasing computation complexity. As an alternative approach, perceptual video coding (PVC) has attempted to achieve high coding efficiency by eliminating perceptual redundancy, using just-noticeable-distortion (JND) directed PVC. The previous JNDs were modeled by adding white Gaussian noise or specific signal patterns into the original images, which were not appropriate in finding JND thresholds due to distortion with energy reduction. In this paper, we present a novel discrete cosine transform-based energy-reduced JND model, called ERJND, that is more suitable for JND-based PVC schemes. Then, the proposed ERJND model is extended to two learning-based just-noticeable-quantization-distortion (JNQD) models as preprocessing that can be applied for perceptual video coding. The two JNQD models can automatically adjust JND levels based on given quantization step sizes. One of the two JNQD models, called LR-JNQD, is based on linear regression and determines the model parameter for JNQD based on extracted handcraft features. The other JNQD model is based on a convolution neural network (CNN), called CNN-JNQD. To our best knowledge, our paper is the first approach to automatically adjust JND levels according to quantization step sizes for preprocessing the input to video encoders. In experiments, both the LR-JNQD and CNN-JNQD models were applied to high efficiency video coding (HEVC) and yielded maximum (average) bitrate reductions of 38.51% (10.38%) and 67.88% (24.91%), respectively, with little subjective video quality degradation, compared with the input without preprocessing applied.

ADMAP (automatic data manipulation program)

NASA Technical Reports Server (NTRS)

Mann, F. I.

1971-01-01

Instructions are presented on the use of ADMAP, (automatic data manipulation program) an aerospace data manipulation computer program. The program was developed to aid in processing, reducing, plotting, and publishing electric propulsion trajectory data generated by the low thrust optimization program, HILTOP. The program has the option of generating SC4020 electric plots, and therefore requires the SC4020 routines to be available at excution time (even if not used). Several general routines are present, including a cubic spline interpolation routine, electric plotter dash line drawing routine, and single parameter and double parameter sorting routines. Many routines are tailored for the manipulation and plotting of electric propulsion data, including an automatic scale selection routine, an automatic curve labelling routine, and an automatic graph titling routine. Data are accepted from either punched cards or magnetic tape.

2D Automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

2D automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

Installation and Testing Instructions for the Sandia Automatic Report Generator (ARG).

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

Clay, Robert L.

Robert L. CLAY Sandia National Laboratories P.O. Box 969 Livermore, CA 94551, U.S.A. rlclay@sandia.gov In this report, we provide detailed and reproducible installation instructions of the Automatic Report Generator (ARG), for both Linux and macOS target platforms.

Validity of registration of ICD codes and prescriptions in a research database in Swedish primary care: a cross-sectional study in Skaraborg primary care database

PubMed Central

2010-01-01

Background In recent years, several primary care databases recording information from computerized medical records have been established and used for quality assessment of medical care and research. However, to be useful for research purposes, the data generated routinely from every day practice require registration of high quality. In this study we aimed to investigate (i) the frequency and validity of ICD code and drug prescription registration in the new Skaraborg primary care database (SPCD) and (ii) to investigate the sources of variation in this registration. Methods SPCD contains anonymous electronic medical records (ProfDoc III) automatically retrieved from all 24 public health care centres (HCC) in Skaraborg, Sweden. The frequencies of ICD code registration for the selected diagnoses diabetes mellitus, hypertension and chronic cardiovascular disease and the relevant drug prescriptions in the time period between May 2002 and October 2003 were analysed. The validity of data registration in the SPCD was assessed in a random sample of 50 medical records from each HCC (n = 1200 records) using the medical record text as gold standard. The variance of ICD code registration was studied with multi-level logistic regression analysis and expressed as median odds ratio (MOR). Results For diabetes mellitus and hypertension ICD codes were registered in 80-90% of cases, while for congestive heart failure and ischemic heart disease ICD codes were registered more seldom (60-70%). Drug prescription registration was overall high (88%). A correlation between the frequency of ICD coded visits and the sensitivity of the ICD code registration was found for hypertension and congestive heart failure but not for diabetes or ischemic heart disease. The frequency of ICD code registration varied from 42 to 90% between HCCs, and the greatest variation was found at the physician level (MORPHYSICIAN = 4.2 and MORHCC = 2.3). Conclusions Since the frequency of ICD code registration varies between different diagnoses, each diagnosis must be separately validated. Improved frequency and quality of ICD code registration might be achieved by interventions directed towards the physicians where the greatest amount of variation was found. PMID:20416069

Validity of registration of ICD codes and prescriptions in a research database in Swedish primary care: a cross-sectional study in Skaraborg primary care database.

PubMed

Hjerpe, Per; Merlo, Juan; Ohlsson, Henrik; Bengtsson Boström, Kristina; Lindblad, Ulf

2010-04-23

In recent years, several primary care databases recording information from computerized medical records have been established and used for quality assessment of medical care and research. However, to be useful for research purposes, the data generated routinely from every day practice require registration of high quality. In this study we aimed to investigate (i) the frequency and validity of ICD code and drug prescription registration in the new Skaraborg primary care database (SPCD) and (ii) to investigate the sources of variation in this registration. SPCD contains anonymous electronic medical records (ProfDoc III) automatically retrieved from all 24 public health care centres (HCC) in Skaraborg, Sweden. The frequencies of ICD code registration for the selected diagnoses diabetes mellitus, hypertension and chronic cardiovascular disease and the relevant drug prescriptions in the time period between May 2002 and October 2003 were analysed. The validity of data registration in the SPCD was assessed in a random sample of 50 medical records from each HCC (n = 1200 records) using the medical record text as gold standard. The variance of ICD code registration was studied with multi-level logistic regression analysis and expressed as median odds ratio (MOR). For diabetes mellitus and hypertension ICD codes were registered in 80-90% of cases, while for congestive heart failure and ischemic heart disease ICD codes were registered more seldom (60-70%). Drug prescription registration was overall high (88%). A correlation between the frequency of ICD coded visits and the sensitivity of the ICD code registration was found for hypertension and congestive heart failure but not for diabetes or ischemic heart disease.The frequency of ICD code registration varied from 42 to 90% between HCCs, and the greatest variation was found at the physician level (MORPHYSICIAN = 4.2 and MORHCC = 2.3). Since the frequency of ICD code registration varies between different diagnoses, each diagnosis must be separately validated. Improved frequency and quality of ICD code registration might be achieved by interventions directed towards the physicians where the greatest amount of variation was found.

XML-Based Generator of C++ Code for Integration With GUIs

NASA Technical Reports Server (NTRS)

Hua, Hook; Oyafuso, Fabiano; Klimeck, Gerhard

2003-01-01

An open source computer program has been developed to satisfy a need for simplified organization of structured input data for scientific simulation programs. Typically, such input data are parsed in from a flat American Standard Code for Information Interchange (ASCII) text file into computational data structures. Also typically, when a graphical user interface (GUI) is used, there is a need to completely duplicate the input information while providing it to a user in a more structured form. Heretofore, the duplication of the input information has entailed duplication of software efforts and increases in susceptibility to software errors because of the concomitant need to maintain two independent input-handling mechanisms. The present program implements a method in which the input data for a simulation program are completely specified in an Extensible Markup Language (XML)-based text file. The key benefit for XML is storing input data in a structured manner. More importantly, XML allows not just storing of data but also describing what each of the data items are. That XML file contains information useful for rendering the data by other applications. It also then generates data structures in the C++ language that are to be used in the simulation program. In this method, all input data are specified in one place only, and it is easy to integrate the data structures into both the simulation program and the GUI. XML-to-C is useful in two ways: 1. As an executable, it generates the corresponding C++ classes and 2. As a library, it automatically fills the objects with the input data values.

Higher-order automatic differentiation of mathematical functions

NASA Astrophysics Data System (ADS)

Charpentier, Isabelle; Dal Cappello, Claude

2015-04-01

Functions of mathematical physics such as the Bessel functions, the Chebyshev polynomials, the Gauss hypergeometric function and so forth, have practical applications in many scientific domains. On the one hand, differentiation formulas provided in reference books apply to real or complex variables. These do not account for the chain rule. On the other hand, based on the chain rule, the automatic differentiation has become a natural tool in numerical modeling. Nevertheless automatic differentiation tools do not deal with the numerous mathematical functions. This paper describes formulas and provides codes for the higher-order automatic differentiation of mathematical functions. The first method is based on Faà di Bruno's formula that generalizes the chain rule. The second one makes use of the second order differential equation they satisfy. Both methods are exemplified with the aforementioned functions.

Analysis of Content Shared in Online Cancer Communities: Systematic Review

PubMed Central

van de Poll-Franse, Lonneke V; Krahmer, Emiel; Verberne, Suzan; Mols, Floortje

2018-01-01

Background The content that cancer patients and their relatives (ie, posters) share in online cancer communities has been researched in various ways. In the past decade, researchers have used automated analysis methods in addition to manual coding methods. Patients, providers, researchers, and health care professionals can learn from experienced patients, provided that their experience is findable. Objective The aim of this study was to systematically review all relevant literature that analyzes user-generated content shared within online cancer communities. We reviewed the quality of available research and the kind of content that posters share with each other on the internet. Methods A computerized literature search was performed via PubMed (MEDLINE), PsycINFO (5 and 4 stars), Cochrane Central Register of Controlled Trials, and ScienceDirect. The last search was conducted in July 2017. Papers were selected if they included the following terms: (cancer patient) and (support group or health communities) and (online or internet). We selected 27 papers and then subjected them to a 14-item quality checklist independently scored by 2 investigators. Results The methodological quality of the selected studies varied: 16 were of high quality and 11 were of adequate quality. Of those 27 studies, 15 were manually coded, 7 automated, and 5 used a combination of methods. The best results can be seen in the papers that combined both analytical methods. The number of analyzed posts ranged from 200 to 1,500,000; the number of analyzed posters ranged from 75 to 90,000. The studies analyzing large numbers of posts mainly related to breast cancer, whereas those analyzing small numbers were related to other types of cancers. A total of 12 studies involved some or entirely automatic analysis of the user-generated content. All the authors referred to two main content categories: informational support and emotional support. In all, 15 studies reported only on the content, 6 studies explicitly reported on content and social aspects, and 6 studies focused on emotional changes. Conclusions In the future, increasing amounts of user-generated content will become available on the internet. The results of content analysis, especially of the larger studies, give detailed insights into patients’ concerns and worries, which can then be used to improve cancer care. To make the results of such analyses as usable as possible, automatic content analysis methods will need to be improved through interdisciplinary collaboration. PMID:29615384

Efficient RPG detection in noisy 3D image data

NASA Astrophysics Data System (ADS)

Pipitone, Frank

2011-06-01

We address the automatic detection of Ambush weapons such as rocket propelled grenades (RPGs) from range data which might be derived from multiple camera stereo with textured illumination or by other means. We describe our initial work in a new project involving the efficient acquisition of 3D scene data as well as discrete point invariant techniques to perform real time search for threats to a convoy. The shapes of the jump boundaries in the scene are exploited in this paper, rather than on-surface points, due to the large error typical of depth measurement at long range and the relatively high resolution obtainable in the transverse direction. We describe examples of the generation of a novel range-scaled chain code for detecting and matching jump boundaries.

Numerical investigation of hub clearance flow in a Kaplan turbine

NASA Astrophysics Data System (ADS)

Wu, H.; Feng, J. J.; Wu, G. K.; Luo, X. Q.

2012-11-01

In this paper, the flow field considering the hub clearance flow in a Kaplan turbine has been investigated through using the commercial CFD code ANSYS CFX based on high-quality structured grids generated by ANSYS ICEM CFD. The turbulence is simulated by k-ω based shear stress transport (SST) turbulence model together with automatic near wall treatments. Four kinds of simulations have been conducted for the runner geometry without hub clearance, with only the hub front clearance, with only the rear hub clearance, and with both front and rear clearance. The analysis of the obtained results is focused on the flow structure of the hub clearance flow, the effect on the turbine performance including hydraulic efficiency and cavitation performance, which can improve the understanding on the flow field in a Kaplan turbine.

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

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

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

Kostuk, M.; Uram, T. D.; Evans, T.

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

DOE PAGES

Kostuk, M.; Uram, T. D.; Evans, T.; ...

2018-02-01

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

Autonomously generating operations sequences for a Mars Rover using AI-based planning

NASA Technical Reports Server (NTRS)

Sherwood, Rob; Mishkin, Andrew; Estlin, Tara; Chien, Steve; Backes, Paul; Cooper, Brian; Maxwell, Scott; Rabideau, Gregg

2001-01-01

This paper discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from highlevel science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This Artificial Intelligence (AI) based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules.

The Effect of Different Types of Perceptual Manipulations on the Dimensionality of Automatically Generated Figural Matrices

ERIC Educational Resources Information Center

Arendasy, M.; Sommer, M.

2005-01-01

Two pilot studies (n"1=155, n"2=451) are presented in this article, which were carried out within the development of an item generator for the automatic generation of figural matrices items. The focus of the presented studies was to compare two types of item designs with regard to the effect of variations of the property ''perceptual…

SU-G-TeP1-05: Development and Clinical Introduction of Automated Radiotherapy Treatment Planning for Prostate Cancer

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

Winkel, D; Bol, GH; Asselen, B van

Purpose: To develop an automated radiotherapy treatment planning and optimization workflow for prostate cancer in order to generate clinical treatment plans. Methods: A fully automated radiotherapy treatment planning and optimization workflow was developed based on the treatment planning system Monaco (Elekta AB, Stockholm, Sweden). To evaluate our method, a retrospective planning study (n=100) was performed on patients treated for prostate cancer with 5 field intensity modulated radiotherapy, receiving a dose of 35×2Gy to the prostate and vesicles and a simultaneous integrated boost of 35×0.2Gy to the prostate only. A comparison was made between the dosimetric values of the automatically andmore » manually generated plans. Operator time to generate a plan and plan efficiency was measured. Results: A comparison of the dosimetric values show that automatically generated plans yield more beneficial dosimetric values. In automatic plans reductions of 43% in the V72Gy of the rectum and 13% in the V72Gy of the bladder are observed when compared to the manually generated plans. Smaller variance in dosimetric values is seen, i.e. the intra- and interplanner variability is decreased. For 97% of the automatically generated plans and 86% of the clinical plans all criteria for target coverage and organs at risk constraints are met. The amount of plan segments and monitor units is reduced by 13% and 9% respectively. Automated planning requires less than one minute of operator time compared to over an hour for manual planning. Conclusion: The automatically generated plans are highly suitable for clinical use. The plans have less variance and a large gain in time efficiency has been achieved. Currently, a pilot study is performed, comparing the preference of the clinician and clinical physicist for the automatic versus manual plan. Future work will include expanding our automated treatment planning method to other tumor sites and develop other automated radiotherapy workflows.« less

iGen: An automated generator of simplified models with provable error bounds.

NASA Astrophysics Data System (ADS)

Tang, D.; Dobbie, S.

2009-04-01

Climate models employ various simplifying assumptions and parameterisations in order to increase execution speed. However, in order to draw conclusions about the Earths climate from the results of a climate simulation it is necessary to have information about the error that these assumptions and parameterisations introduce. A novel computer program, called iGen, is being developed which automatically generates fast, simplified models by analysing the source code of a slower, high resolution model. The resulting simplified models have provable bounds on error compared to the high resolution model and execute at speeds that are typically orders of magnitude faster. iGen's input is a definition of the prognostic variables of the simplified model, a set of bounds on acceptable error and the source code of a model that captures the behaviour of interest. In the case of an atmospheric model, for example, this would be a global cloud resolving model with very high resolution. Although such a model would execute far too slowly to be used directly in a climate model, iGen never executes it. Instead, it converts the code of the resolving model into a mathematical expression which is then symbolically manipulated and approximated to form a simplified expression. This expression is then converted back into a computer program and output as a simplified model. iGen also derives and reports formal bounds on the error of the simplified model compared to the resolving model. These error bounds are always maintained below the user-specified acceptable error. Results will be presented illustrating the success of iGen's analysis of a number of example models. These extremely encouraging results have lead on to work which is currently underway to analyse a cloud resolving model and so produce an efficient parameterisation of moist convection with formally bounded error.

The Pan-STARRS PS1 Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Magnier, E.

The Pan-STARRS PS1 Image Processing Pipeline (IPP) performs the image processing and data analysis tasks needed to enable the scientific use of the images obtained by the Pan-STARRS PS1 prototype telescope. The primary goals of the IPP are to process the science images from the Pan-STARRS telescopes and make the results available to other systems within Pan-STARRS. It also is responsible for combining all of the science images in a given filter into a single representation of the non-variable component of the night sky defined as the "Static Sky". To achieve these goals, the IPP also performs other analysis functions to generate the calibrations needed in the science image processing, and to occasionally use the derived data to generate improved astrometric and photometric reference catalogs. It also provides the infrastructure needed to store the incoming data and the resulting data products. The IPP inherits lessons learned, and in some cases code and prototype code, from several other astronomy image analysis systems, including Imcat (Kaiser), the Sloan Digital Sky Survey (REF), the Elixir system (Magnier & Cuillandre), and Vista (Tonry). Imcat and Vista have a large number of robust image processing functions. SDSS has demonstrated a working analysis pipeline and large-scale databasesystem for a dedicated project. The Elixir system has demonstrated an automatic image processing system and an object database system for operational usage. This talk will present an overview of the IPP architecture, functional flow, code development structure, and selected analysis algorithms. Also discussed is the HW highly parallel HW configuration necessary to support PS1 operational requirements. Finally, results are presented of the processing of images collected during PS1 early commissioning tasks utilizing the Pan-STARRS Test Camera #3.

Unsupervised MDP Value Selection for Automating ITS Capabilities

ERIC Educational Resources Information Center

Stamper, John; Barnes, Tiffany

2009-01-01

We seek to simplify the creation of intelligent tutors by using student data acquired from standard computer aided instruction (CAI) in conjunction with educational data mining methods to automatically generate adaptive hints. In our previous work, we have automatically generated hints for logic tutoring by constructing a Markov Decision Process…

Automatic Digital Content Generation System for Real-Time Distance Lectures

ERIC Educational Resources Information Center

Iwatsuki, Masami; Takeuchi, Norio; Kobayashi, Hisato; Yana, Kazuo; Takeda, Hiroshi; Yaginuma, Hisashi; Kiyohara, Hajime; Tokuyasu, Akira

2007-01-01

This article describes a new automatic digital content generation system we have developed. Recently some universities, including Hosei University, have been offering students opportunities to take distance interactive classes over the Internet from overseas. When such distance lectures are delivered in English to Japanese students, there is a…

Automatic Calibration of Stereo-Cameras Using Ordinary Chess-Board Patterns

NASA Astrophysics Data System (ADS)

Prokos, A.; Kalisperakis, I.; Petsa, E.; Karras, G.

2012-07-01

Automation of camera calibration is facilitated by recording coded 2D patterns. Our toolbox for automatic camera calibration using images of simple chess-board patterns is freely available on the Internet. But it is unsuitable for stereo-cameras whose calibration implies recovering camera geometry and their true-to-scale relative orientation. In contrast to all reported methods requiring additional specific coding to establish an object space coordinate system, a toolbox for automatic stereo-camera calibration relying on ordinary chess-board patterns is presented here. First, the camera calibration algorithm is applied to all image pairs of the pattern to extract nodes of known spacing, order them in rows and columns, and estimate two independent camera parameter sets. The actual node correspondences on stereo-pairs remain unknown. Image pairs of a textured 3D scene are exploited for finding the fundamental matrix of the stereo-camera by applying RANSAC to point matches established with the SIFT algorithm. A node is then selected near the centre of the left image; its match on the right image is assumed as the node closest to the corresponding epipolar line. This yields matches for all nodes (since these have already been ordered), which should also satisfy the 2D epipolar geometry. Measures for avoiding mismatching are taken. With automatically estimated initial orientation values, a bundle adjustment is performed constraining all pairs on a common (scaled) relative orientation. Ambiguities regarding the actual exterior orientations of the stereo-camera with respect to the pattern are irrelevant. Results from this automatic method show typical precisions not above 1/4 pixels for 640×480 web cameras.

Automated generation of lattice QCD Feynman rules

NASA Astrophysics Data System (ADS)

Hart, A.; von Hippel, G. M.; Horgan, R. R.; Müller, E. H.

2009-12-01

The derivation of the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially for highly improved actions such as HISQ. This task is, however, both important and particularly suitable for automation. We describe a suite of software to generate and evaluate Feynman rules for a wide range of lattice field theories with gluons and (relativistic and/or heavy) quarks. Our programs are capable of dealing with actions as complicated as (m)NRQCD and HISQ. Automated differentiation methods are used to calculate also the derivatives of Feynman diagrams. Program summaryProgram title: HiPPY, HPsrc Catalogue identifier: AEDX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 (see Additional comments below) No. of lines in distributed program, including test data, etc.: 513 426 No. of bytes in distributed program, including test data, etc.: 4 893 707 Distribution format: tar.gz Programming language: Python, Fortran95 Computer: HiPPy: Single-processor workstations. HPsrc: Single-processor workstations and MPI-enabled multi-processor systems Operating system: HiPPy: Any for which Python v2.5.x is available. HPsrc: Any for which a standards-compliant Fortran95 compiler is available Has the code been vectorised or parallelised?: Yes RAM: Problem specific, typically less than 1 GB for either code Classification: 4.4, 11.5 Nature of problem: Derivation and use of perturbative Feynman rules for complicated lattice QCD actions. Solution method: An automated expansion method implemented in Python (HiPPy) and code to use expansions to generate Feynman rules in Fortran95 (HPsrc). Restrictions: No general restrictions. Specific restrictions are discussed in the text. Additional comments: The HiPPy and HPsrc codes are released under the second version of the GNU General Public Licence (GPL v2). Therefore anyone is free to use or modify the code for their own calculations. As part of the licensing, we ask that any publications including results from the use of this code or of modifications of it cite Refs. [1,2] as well as this paper. Finally, we also ask that details of these publications, as well as of any bugs or required or useful improvements of this core code, would be communicated to us. Running time: Very problem specific, depending on the complexity of the Feynman rules and the number of integration points. Typically between a few minutes and several weeks. The installation tests provided with the program code take only a few seconds to run. References:A. Hart, G.M. von Hippel, R.R. Horgan, L.C. Storoni, Automatically generating Feynman rules for improved lattice eld theories, J. Comput. Phys. 209 (2005) 340-353, doi:10.1016/j.jcp.2005.03.010, arXiv:hep-lat/0411026. M. Lüscher, P. Weisz, Efficient Numerical Techniques for Perturbative Lattice Gauge Theory Computations, Nucl. Phys. B 266 (1986) 309, doi:10.1016/0550-3213(86)90094-5.

Periodic, On-Demand, and User-Specified Information Reconciliation

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

Automated sequence generation (autogen) signifies both a process and software used to automatically generate sequences of commands to operate various spacecraft. Autogen requires fewer workers than are needed for older manual sequence-generation processes and reduces sequence-generation times from weeks to minutes. The autogen software comprises the autogen script plus the Activity Plan Generator (APGEN) program. APGEN can be used for planning missions and command sequences. APGEN includes a graphical user interface that facilitates scheduling of activities on a time line and affords a capability to automatically expand, decompose, and schedule activities.

Cost Reporting Elements and Activity Cost Tradeoffs for Defense System Software. Volume I. Study Results.

DTIC Science & Technology

1977-05-01

C31) programs; (4) simulator/ trainer programs ; and (5) automatic test equipment software. Each of these five types of software represents a problem...coded in the same source language, say JOVIAL, then source—language statements would be a better measure, since that would automatically compensate...whether done at no (visible) cost or by renegotiation of the contract. Fig. 2.3 illustrates these with solid lines. It is conjec- tured that the change

Applying automatic item generation to create cohesive physics testlets

NASA Astrophysics Data System (ADS)

Mindyarto, B. N.; Nugroho, S. E.; Linuwih, S.

2018-03-01

Computer-based testing has created the demand for large numbers of items. This paper discusses the production of cohesive physics testlets using an automatic item generation concepts and procedures. The testlets were composed by restructuring physics problems to reveal deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based testlet generator was used to generate the testlet variants. Using this methodology, 1248 testlet variants were effectively generated from 25 testlet templates. Some issues related to the effective application of the generated physics testlets in practical assessments were discussed.

GSE, data management system programmers/User' manual

NASA Technical Reports Server (NTRS)

Schlagheck, R. A.; Dolerhie, B. D., Jr.; Ghiglieri, F. J.

1974-01-01

The GSE data management system is a computerized program which provides for a central storage source for key data associated with the mechanical ground support equipment (MGSE). Eight major sort modes can be requested by the user. Attributes that are printed automatically with each sort include the GSE end item number, description, class code, functional code, fluid media, use location, design responsibility, weight, cost, quantity, dimensions, and applicable documents. Multiple subsorts are available for the class code, functional code, fluid media, use location, design responsibility, and applicable document categories. These sorts and how to use them are described. The program and GSE data bank may be easily updated and expanded.

Automatic Processing of Reactive Polymers

NASA Technical Reports Server (NTRS)

Roylance, D.

1985-01-01

A series of process modeling computer codes were examined. The codes use finite element techniques to determine the time-dependent process parameters operative during nonisothermal reactive flows such as can occur in reaction injection molding or composites fabrication. The use of these analytical codes to perform experimental control functions is examined; since the models can determine the state of all variables everywhere in the system, they can be used in a manner similar to currently available experimental probes. A small but well instrumented reaction vessel in which fiber-reinforced plaques are cured using computer control and data acquisition was used. The finite element codes were also extended to treat this particular process.

Validation of the Operating and Support Cost Model for Avionics Automatic Test Equipment (OSCATE).

DTIC Science & Technology

1980-06-01

AFLCR 65-1 (56) DOD 4140 -32 (74) CODES DATA LISTED BY. ALC code, Division Code, Equipment Specialist Code, NSN DATA ORDERING SEQUENCEs This data is...PAJ6A 4140 -01-043-5035 .... IL0UERft1TfR 1002 1 319.55 22720 1 0 0 1003 0 14.55 0 0 0 10.00 0 0 1004 0 0 32.454 16.42 0 0 0 0 0 0 0 127 1101 PAJHA 4920...5320 480 CONTINUE 5330 60 To 150 5340 5350C *...*~****.*.s*..** 5360C *****eOUTPUT OPTION 7 5370C e**ss*** sae ******* 5380 500 PRINT 510 5390 510

Strengths and limitations of the NATALI code for aerosol typing from multiwavelength Raman lidar observations

NASA Astrophysics Data System (ADS)

Nicolae, Doina; Talianu, Camelia; Vasilescu, Jeni; Nicolae, Victor; Stachlewska, Iwona S.

2018-04-01

A Python code was developed to automatically retrieve the aerosol type (and its predominant component in the mixture) from EARLINET's 3 backscatter and 2 extinction data. The typing relies on Artificial Neural Networks which are trained to identify the most probable aerosol type from a set of mean-layer intensive optical parameters. This paper presents the use and limitations of the code with respect to the quality of the inputed lidar profiles, as well as with the assumptions made in the aerosol model.

Automatic generation of natural language nursing shift summaries in neonatal intensive care: BT-Nurse.

PubMed

Hunter, James; Freer, Yvonne; Gatt, Albert; Reiter, Ehud; Sripada, Somayajulu; Sykes, Cindy

2012-11-01

Our objective was to determine whether and how a computer system could automatically generate helpful natural language nursing shift summaries solely from an electronic patient record system, in a neonatal intensive care unit (NICU). A system was developed which automatically generates partial NICU shift summaries (for the respiratory and cardiovascular systems), using data-to-text technology. It was evaluated for 2 months in the NICU at the Royal Infirmary of Edinburgh, under supervision. In an on-ward evaluation, a substantial majority of the summaries was found by outgoing and incoming nurses to be understandable (90%), and a majority was found to be accurate (70%), and helpful (59%). The evaluation also served to identify some outstanding issues, especially with regard to extra content the nurses wanted to see in the computer-generated summaries. It is technically possible automatically to generate limited natural language NICU shift summaries from an electronic patient record. However, it proved difficult to handle electronic data that was intended primarily for display to the medical staff, and considerable engineering effort would be required to create a deployable system from our proof-of-concept software. Copyright © 2012 Elsevier B.V. All rights reserved.

Automatic Query Formulations in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1983-01-01

Introduces methods designed to reduce role of search intermediaries by generating Boolean search formulations automatically using term frequency considerations from natural language statements provided by system patrons. Experimental results are supplied and methods are described for applying automatic query formulation process in practice.…

PUS Services Software Building Block Automatic Generation for Space Missions

NASA Astrophysics Data System (ADS)

Candia, S.; Sgaramella, F.; Mele, G.

2008-08-01

The Packet Utilization Standard (PUS) has been specified by the European Committee for Space Standardization (ECSS) and issued as ECSS-E-70-41A to define the application-level interface between Ground Segments and Space Segments. The ECSS-E- 70-41A complements the ECSS-E-50 and the Consultative Committee for Space Data Systems (CCSDS) recommendations for packet telemetry and telecommand. The ECSS-E-70-41A characterizes the identified PUS Services from a functional point of view and the ECSS-E-70-31 standard specifies the rules for their mission-specific tailoring. The current on-board software design for a space mission implies the production of several PUS terminals, each providing a specific tailoring of the PUS services. The associated on-board software building blocks are developed independently, leading to very different design choices and implementations even when the mission tailoring requires very similar services (from the Ground operative perspective). In this scenario, the automatic production of the PUS services building blocks for a mission would be a way to optimize the overall mission economy and improve the robusteness and reliability of the on-board software and of the Ground-Space interactions. This paper presents the Space Software Italia (SSI) activities for the development of an integrated environment to support: the PUS services tailoring activity for a specific mission. the mission-specific PUS services configuration. the generation the UML model of the software building block implementing the mission-specific PUS services and the related source code, support documentation (software requirements, software architecture, test plans/procedures, operational manuals), and the TM/TC database. The paper deals with: (a) the project objectives, (b) the tailoring, configuration, and generation process, (c) the description of the environments supporting the process phases, (d) the characterization of the meta-model used for the generation, (e) the characterization of the reference avionics architecture and of the reference on- board software high-level architecture.

MeSH indexing based on automatically generated summaries.

PubMed

Jimeno-Yepes, Antonio J; Plaza, Laura; Mork, James G; Aronson, Alan R; Díaz, Alberto

2013-06-26

MEDLINE citations are manually indexed at the U.S. National Library of Medicine (NLM) using as reference the Medical Subject Headings (MeSH) controlled vocabulary. For this task, the human indexers read the full text of the article. Due to the growth of MEDLINE, the NLM Indexing Initiative explores indexing methodologies that can support the task of the indexers. Medical Text Indexer (MTI) is a tool developed by the NLM Indexing Initiative to provide MeSH indexing recommendations to indexers. Currently, the input to MTI is MEDLINE citations, title and abstract only. Previous work has shown that using full text as input to MTI increases recall, but decreases precision sharply. We propose using summaries generated automatically from the full text for the input to MTI to use in the task of suggesting MeSH headings to indexers. Summaries distill the most salient information from the full text, which might increase the coverage of automatic indexing approaches based on MEDLINE. We hypothesize that if the results were good enough, manual indexers could possibly use automatic summaries instead of the full texts, along with the recommendations of MTI, to speed up the process while maintaining high quality of indexing results. We have generated summaries of different lengths using two different summarizers, and evaluated the MTI indexing on the summaries using different algorithms: MTI, individual MTI components, and machine learning. The results are compared to those of full text articles and MEDLINE citations. Our results show that automatically generated summaries achieve similar recall but higher precision compared to full text articles. Compared to MEDLINE citations, summaries achieve higher recall but lower precision. Our results show that automatic summaries produce better indexing than full text articles. Summaries produce similar recall to full text but much better precision, which seems to indicate that automatic summaries can efficiently capture the most important contents within the original articles. The combination of MEDLINE citations and automatically generated summaries could improve the recommendations suggested by MTI. On the other hand, indexing performance might be dependent on the MeSH heading being indexed. Summarization techniques could thus be considered as a feature selection algorithm that might have to be tuned individually for each MeSH heading.

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.

Source Lines Counter (SLiC) Version 4.0

NASA Technical Reports Server (NTRS)

Monson, Erik W.; Smith, Kevin A.; Newport, Brian J.; Gostelow, Roli D.; Hihn, Jairus M.; Kandt, Ronald K.

2011-01-01

Source Lines Counter (SLiC) is a software utility designed to measure software source code size using logical source statements and other common measures for 22 of the programming languages commonly used at NASA and the aerospace industry. Such metrics can be used in a wide variety of applications, from parametric cost estimation to software defect analysis. SLiC has a variety of unique features such as automatic code search, automatic file detection, hierarchical directory totals, and spreadsheet-compatible output. SLiC was written for extensibility; new programming language support can be added with minimal effort in a short amount of time. SLiC runs on a variety of platforms including UNIX, Windows, and Mac OSX. Its straightforward command-line interface allows for customization and incorporation into the software build process for tracking development metrics. T

Segmentation, dynamic storage, and variable loading on CDC equipment

NASA Technical Reports Server (NTRS)

Tiffany, S. H.

1980-01-01

Techniques for varying the segmented load structure of a program and for varying the dynamic storage allocation, depending upon whether a batch type or interactive type run is desired, are explained and demonstrated. All changes are based on a single data input to the program. The techniques involve: code within the program to suppress scratch pad input/output (I/O) for a batch run or translate the in-core data storage area from blank common to the end-of-code+1 address of a particular segment for an interactive run; automatic editing of the segload directives prior to loading, based upon data input to the program, to vary the structure of the load for interactive and batch runs; and automatic editing of the load map to determine the initial addresses for in core data storage for an interactive run.

Joint three-dimensional inversion of coupled groundwater flow and heat transfer based on automatic differentiation: sensitivity calculation, verification, and synthetic examples

NASA Astrophysics Data System (ADS)

Rath, V.; Wolf, A.; Bücker, H. M.

2006-10-01

Inverse methods are useful tools not only for deriving estimates of unknown parameters of the subsurface, but also for appraisal of the thus obtained models. While not being neither the most general nor the most efficient methods, Bayesian inversion based on the calculation of the Jacobian of a given forward model can be used to evaluate many quantities useful in this process. The calculation of the Jacobian, however, is computationally expensive and, if done by divided differences, prone to truncation error. Here, automatic differentiation can be used to produce derivative code by source transformation of an existing forward model. We describe this process for a coupled fluid flow and heat transport finite difference code, which is used in a Bayesian inverse scheme to estimate thermal and hydraulic properties and boundary conditions form measured hydraulic potentials and temperatures. The resulting derivative code was validated by comparison to simple analytical solutions and divided differences. Synthetic examples from different flow regimes demonstrate the use of the inverse scheme, and its behaviour in different configurations.