Software Architecture for a Virtual Environment for Nano Scale Assembly (VENSA)

PubMed Central

Lee, Yong-Gu; Lyons, Kevin W.; Feng, Shaw C.

2004-01-01

A Virtual Environment (VE) uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. The information flow between the user and the VE is bidirectional and the user can influence the environment. The software development of a VE requires orchestrating multiple peripherals and computers in a synchronized way in real time. Although a multitude of useful software components for VEs exists, many of these are packaged within a complex framework and can not be used separately. In this paper, an architecture is presented which is designed to let multiple frameworks work together while being shielded from the application program. This architecture, which is called the Virtual Environment for Nano Scale Assembly (VENSA), has been constructed for interfacing with an optical tweezers instrument for nanotechnology development. However, this approach can be generalized for most virtual environments. Through the use of VENSA, the programmer can rely on existing solutions and concentrate more on the application software design. PMID:27366610

PACS/information systems interoperability using Enterprise Communication Framework.

PubMed

alSafadi, Y; Lord, W P; Mankovich, N J

1998-06-01

Interoperability among healthcare applications goes beyond connectivity to allow components to exchange structured information and work together in a predictable, coordinated fashion. To facilitate building an interoperability infrastructure, an Enterprise Communication Framework (ECF) was developed by the members of the Andover Working Group for Healthcare Interoperability (AWG-OHI). The ECF consists of four models: 1) Use Case Model, 2) Domain Information Model (DIM), 3) Interaction Model, and 4) Message Model. To realize this framework, a software component called the Enterprise Communicator (EC) is used. In this paper, we will demonstrate the use of the framework in interoperating a picture archiving and communication system (PACS) with a radiology information system (RIS).

Multidisciplinary Optimization Branch Experience Using iSIGHT Software

NASA Technical Reports Server (NTRS)

Padula, S. L.; Korte, J. J.; Dunn, H. J.; Salas, A. O.

1999-01-01

The Multidisciplinary Optimization (MDO) Branch at NASA Langley Research Center is investigating frameworks for supporting multidisciplinary analysis and optimization research. An optimization framework call improve the design process while reducing time and costs. A framework provides software and system services to integrate computational tasks and allows the researcher to concentrate more on the application and less on the programming details. A framework also provides a common working environment and a full range of optimization tools, and so increases the productivity of multidisciplinary research teams. Finally, a framework enables staff members to develop applications for use by disciplinary experts in other organizations. Since the release of version 4.0, the MDO Branch has gained experience with the iSIGHT framework developed by Engineous Software, Inc. This paper describes experiences with four aerospace applications: (1) reusable launch vehicle sizing, (2) aerospike nozzle design, (3) low-noise rotorcraft trajectories, and (4) acoustic liner design. All applications have been successfully tested using the iSIGHT framework, except for the aerospike nozzle problem, which is in progress. Brief overviews of each problem are provided. The problem descriptions include the number and type of disciplinary codes, as well as all estimate of the multidisciplinary analysis execution time. In addition, the optimization methods, objective functions, design variables, and design constraints are described for each problem. Discussions on the experience gained and lessons learned are provided for each problem. These discussions include the advantages and disadvantages of using the iSIGHT framework for each case as well as the ease of use of various advanced features. Potential areas of improvement are identified.

The Offline Software Framework of the NA61/SHINE Experiment

NASA Astrophysics Data System (ADS)

Sipos, Roland; Laszlo, Andras; Marcinek, Antoni; Paul, Tom; Szuba, Marek; Unger, Michael; Veberic, Darko; Wyszynski, Oskar

2012-12-01

NA61/SHINE (SHINE = SPS Heavy Ion and Neutrino Experiment) is an experiment at the CERN SPS using the upgraded NA49 hadron spectrometer. Among its physics goals are precise hadron production measurements for improving calculations of the neutrino beam flux in the T2K neutrino oscillation experiment as well as for more reliable simulations of cosmic-ray air showers. Moreover, p+p, p+Pb and nucleus+nucleus collisions will be studied extensively to allow for a study of properties of the onset of deconfinement and search for the critical point of strongly interacting matter. Currently NA61/SHINE uses the old NA49 software framework for reconstruction, simulation and data analysis. The core of this legacy framework was developed in the early 1990s. It is written in different programming and scripting languages (C, pgi-Fortran, shell) and provides several concurrent data formats for the event data model, which includes also obsolete parts. In this contribution we will introduce the new software framework, called Shine, that is written in C++ and designed to comprise three principal parts: a collection of processing modules which can be assembled and sequenced by the user via XML files, an event data model which contains all simulation and reconstruction information based on STL and ROOT streaming, and a detector description which provides data on the configuration and state of the experiment. To assure a quick migration to the Shine framework, wrappers were introduced that allow to run legacy code parts as modules in the new framework and we will present first results on the cross validation of the two frameworks.

Automated software system for checking the structure and format of ACM SIG documents

NASA Astrophysics Data System (ADS)

Mirza, Arsalan Rahman; Sah, Melike

2017-04-01

Microsoft (MS) Office Word is one of the most commonly used software tools for creating documents. MS Word 2007 and above uses XML to represent the structure of MS Word documents. Metadata about the documents are automatically created using Office Open XML (OOXML) syntax. We develop a new framework, which is called ADFCS (Automated Document Format Checking System) that takes the advantage of the OOXML metadata, in order to extract semantic information from MS Office Word documents. In particular, we develop a new ontology for Association for Computing Machinery (ACM) Special Interested Group (SIG) documents for representing the structure and format of these documents by using OWL (Web Ontology Language). Then, the metadata is extracted automatically in RDF (Resource Description Framework) according to this ontology using the developed software. Finally, we generate extensive rules in order to infer whether the documents are formatted according to ACM SIG standards. This paper, introduces ACM SIG ontology, metadata extraction process, inference engine, ADFCS online user interface, system evaluation and user study evaluations.

Proposed software system for atomic-structure calculation

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

Fischer, C.F.

1981-07-01

Atomic structure calculations are understood well enough that, at a routine level, an atomic structure software package can be developed. At the Atomic Physics Conference in Riga, 1978 L.V. Chernysheva and M.Y. Amusia of Leningrad University, presented a paper on Software for Atomic Calculations. Their system, called ATOM is based on the Hartree-Fock approximation and correlation is included within the framework of RPAE. Energy level calculations, transition probabilities, photo-ionization cross-sections, electron scattering cross-sections are some of the physical properties that can be evaluated by their system. The MCHF method, together with CI techniques and the Breit-Pauli approximation also provides amore » sound theoretical basis for atomic structure calculations.« less

NASA Data Acquisition System Software Development for Rocket Propulsion Test Facilities

NASA Technical Reports Server (NTRS)

Herbert, Phillip W., Sr.; Elliot, Alex C.; Graves, Andrew R.

2015-01-01

Current NASA propulsion test facilities include Stennis Space Center in Mississippi, Marshall Space Flight Center in Alabama, Plum Brook Station in Ohio, and White Sands Test Facility in New Mexico. Within and across these centers, a diverse set of data acquisition systems exist with different hardware and software platforms. The NASA Data Acquisition System (NDAS) is a software suite designed to operate and control many critical aspects of rocket engine testing. The software suite combines real-time data visualization, data recording to a variety formats, short-term and long-term acquisition system calibration capabilities, test stand configuration control, and a variety of data post-processing capabilities. Additionally, data stream conversion functions exist to translate test facility data streams to and from downstream systems, including engine customer systems. The primary design goals for NDAS are flexibility, extensibility, and modularity. Providing a common user interface for a variety of hardware platforms helps drive consistency and error reduction during testing. In addition, with an understanding that test facilities have different requirements and setups, the software is designed to be modular. One engine program may require real-time displays and data recording; others may require more complex data stream conversion, measurement filtering, or test stand configuration management. The NDAS suite allows test facilities to choose which components to use based on their specific needs. The NDAS code is primarily written in LabVIEW, a graphical, data-flow driven language. Although LabVIEW is a general-purpose programming language; large-scale software development in the language is relatively rare compared to more commonly used languages. The NDAS software suite also makes extensive use of a new, advanced development framework called the Actor Framework. The Actor Framework provides a level of code reuse and extensibility that has previously been difficult to achieve using LabVIEW. The

Technical design and system implementation of region-line primitive association framework

NASA Astrophysics Data System (ADS)

Wang, Min; Xing, Jinjin; Wang, Jie; Lv, Guonian

2017-08-01

Apart from regions, image edge lines are an important information source, and they deserve more attention in object-based image analysis (OBIA) than they currently receive. In the region-line primitive association framework (RLPAF), we promote straight-edge lines as line primitives to achieve powerful OBIAs. Along with regions, straight lines become basic units for subsequent extraction and analysis of OBIA features. This study develops a new software system called remote-sensing knowledge finder (RSFinder) to implement RLPAF for engineering application purposes. This paper introduces the extended technical framework, a comprehensively designed feature set, key technology, and software implementation. To our knowledge, RSFinder is the world's first OBIA system based on two types of primitives, namely, regions and lines. It is fundamentally different from other well-known region-only-based OBIA systems, such as eCogntion and ENVI feature extraction module. This paper has important reference values for the development of similarly structured OBIA systems and line-involved extraction algorithms of remote sensing information.

Remote control of astronomical instruments via the Internet

NASA Astrophysics Data System (ADS)

Ashley, M. C. B.; Brooks, P. W.; Lloyd, J. P.

1996-01-01

A software package called ERIC is described that provides a framework for allowing scientific instruments to be remotely controlled via the Internet. The package has been used to control four diverse astronomical instruments, and is now being made freely available to the community. For a description of ERIC's capabilities, and how to obtain a copy, see the conclusion to this paper.

A theoretical basis for the analysis of multiversion software subject to coincident errors

NASA Technical Reports Server (NTRS)

Eckhardt, D. E., Jr.; Lee, L. D.

1985-01-01

Fundamental to the development of redundant software techniques (known as fault-tolerant software) is an understanding of the impact of multiple joint occurrences of errors, referred to here as coincident errors. A theoretical basis for the study of redundant software is developed which: (1) provides a probabilistic framework for empirically evaluating the effectiveness of a general multiversion strategy when component versions are subject to coincident errors, and (2) permits an analytical study of the effects of these errors. An intensity function, called the intensity of coincident errors, has a central role in this analysis. This function describes the propensity of programmers to introduce design faults in such a way that software components fail together when executing in the application environment. A condition under which a multiversion system is a better strategy than relying on a single version is given.

Ant-Based Cyber Defense (also known as

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

Glenn Fink, PNNL

2015-09-29

ABCD is a four-level hierarchy with human supervisors at the top, a top-level agent called a Sergeant controlling each enclave, Sentinel agents located at each monitored host, and mobile Sensor agents that swarm through the enclaves to detect cyber malice and misconfigurations. The code comprises four parts: (1) the core agent framework, (2) the user interface and visualization, (3) test-range software to create a network of virtual machines including a simulated Internet and user and host activity emulation scripts, and (4) a test harness to allow the safe running of adversarial code within the framework of monitored virtual machines.

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

David, O.

2011-12-01

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

GCS component development cycle

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Theoretical Foundation of Copernicus: A Unified System for Trajectory Design and Optimization

NASA Technical Reports Server (NTRS)

Ocampo, Cesar; Senent, Juan S.; Williams, Jacob

2010-01-01

The fundamental methods are described for the general spacecraft trajectory design and optimization software system called Copernicus. The methods rely on a unified framework that is used to model, design, and optimize spacecraft trajectories that may operate in complex gravitational force fields, use multiple propulsion systems, and involve multiple spacecraft. The trajectory model, with its associated equations of motion and maneuver models, are discussed.

National Cycle Program (NCP) Common Analysis Tool for Aeropropulsion

NASA Technical Reports Server (NTRS)

Follen, G.; Naiman, C.; Evans, A.

1999-01-01

Through the NASA/Industry Cooperative Effort (NICE) agreement, NASA Lewis and industry partners are developing a new engine simulation, called the National Cycle Program (NCP), which is the initial framework of NPSS. NCP is the first phase toward achieving the goal of NPSS. This new software supports the aerothermodynamic system simulation process for the full life cycle of an engine. The National Cycle Program (NCP) was written following the Object Oriented Paradigm (C++, CORBA). The software development process used was also based on the Object Oriented paradigm. Software reviews, configuration management, test plans, requirements, design were all apart of the process used in developing NCP. Due to the many contributors to NCP, the stated software process was mandatory for building a common tool intended for use by so many organizations. The U.S. aircraft and airframe companies recognize NCP as the future industry standard for propulsion system modeling.

Activity-Centric Approach to Distributed Programming

NASA Technical Reports Server (NTRS)

Levy, Renato; Satapathy, Goutam; Lang, Jun

2004-01-01

The first phase of an effort to develop a NASA version of the Cybele software system has been completed. To give meaning to even a highly abbreviated summary of the modifications to be embodied in the NASA version, it is necessary to present the following background information on Cybele: Cybele is a proprietary software infrastructure for use by programmers in developing agent-based application programs [complex application programs that contain autonomous, interacting components (agents)]. Cybele provides support for event handling from multiple sources, multithreading, concurrency control, migration, and load balancing. A Cybele agent follows a programming paradigm, called activity-centric programming, that enables an abstraction over system-level thread mechanisms. Activity centric programming relieves application programmers of the complex tasks of thread management, concurrency control, and event management. In order to provide such functionality, activity-centric programming demands support of other layers of software. This concludes the background information. In the first phase of the present development, a new architecture for Cybele was defined. In this architecture, Cybele follows a modular service-based approach to coupling of the programming and service layers of software architecture. In a service-based approach, the functionalities supported by activity-centric programming are apportioned, according to their characteristics, among several groups called services. A well-defined interface among all such services serves as a path that facilitates the maintenance and enhancement of such services without adverse effect on the whole software framework. The activity-centric application-program interface (API) is part of a kernel. The kernel API calls the services by use of their published interface. This approach makes it possible for any application code written exclusively under the API to be portable for any configuration of Cybele.

A Verification System for Distributed Objects with Asynchronous Method Calls

NASA Astrophysics Data System (ADS)

Ahrendt, Wolfgang; Dylla, Maximilian

We present a verification system for Creol, an object-oriented modeling language for concurrent distributed applications. The system is an instance of KeY, a framework for object-oriented software verification, which has so far been applied foremost to sequential Java. Building on KeY characteristic concepts, like dynamic logic, sequent calculus, explicit substitutions, and the taclet rule language, the system presented in this paper addresses functional correctness of Creol models featuring local cooperative thread parallelism and global communication via asynchronous method calls. The calculus heavily operates on communication histories which describe the interfaces of Creol units. Two example scenarios demonstrate the usage of the system.

Integrating Formal Methods and Testing 2002

NASA Technical Reports Server (NTRS)

Cukic, Bojan

2002-01-01

Traditionally, qualitative program verification methodologies and program testing are studied in separate research communities. None of them alone is powerful and practical enough to provide sufficient confidence in ultra-high reliability assessment when used exclusively. Significant advances can be made by accounting not only tho formal verification and program testing. but also the impact of many other standard V&V techniques, in a unified software reliability assessment framework. The first year of this research resulted in the statistical framework that, given the assumptions on the success of the qualitative V&V and QA procedures, significantly reduces the amount of testing needed to confidently assess reliability at so-called high and ultra-high levels (10-4 or higher). The coming years shall address the methodologies to realistically estimate the impacts of various V&V techniques to system reliability and include the impact of operational risk to reliability assessment. Combine formal correctness verification, process and product metrics, and other standard qualitative software assurance methods with statistical testing with the aim of gaining higher confidence in software reliability assessment for high-assurance applications. B) Quantify the impact of these methods on software reliability. C) Demonstrate that accounting for the effectiveness of these methods reduces the number of tests needed to attain certain confidence level. D) Quantify and justify the reliability estimate for systems developed using various methods.

Adaptive awareness for personal and small group decision making.

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

Perano, Kenneth J.; Tucker, Steve; Pancerella, Carmen M.

2003-12-01

Many situations call for the use of sensors monitoring physiological and environmental data. In order to use the large amounts of sensor data to affect decision making, we are coupling heterogeneous sensors with small, light-weight processors, other powerful computers, wireless communications, and embedded intelligent software. The result is an adaptive awareness and warning tool, which provides both situation awareness and personal awareness to individuals and teams. Central to this tool is a sensor-independent architecture, which combines both software agents and a reusable core software framework that manages the available hardware resources and provides services to the agents. Agents can recognizemore » cues from the data, warn humans about situations, and act as decision-making aids. Within the agents, self-organizing maps (SOMs) are used to process physiological data in order to provide personal awareness. We have employed a novel clustering algorithm to train the SOM to discern individual body states and activities. This awareness tool has broad applicability to emergency teams, military squads, military medics, individual exercise and fitness monitoring, health monitoring for sick and elderly persons, and environmental monitoring in public places. This report discusses our hardware decisions, software framework, and a pilot awareness tool, which has been developed at Sandia National Laboratories.« less

The Human-Robot Interaction Operating System

NASA Technical Reports Server (NTRS)

Fong, Terrence; Kunz, Clayton; Hiatt, Laura M.; Bugajska, Magda

2006-01-01

In order for humans and robots to work effectively together, they need to be able to converse about abilities, goals and achievements. Thus, we are developing an interaction infrastructure called the "Human-Robot Interaction Operating System" (HRI/OS). The HRI/OS provides a structured software framework for building human-robot teams, supports a variety of user interfaces, enables humans and robots to engage in task-oriented dialogue, and facilitates integration of robots through an extensible API.

From expert-derived user needs to user-perceived ease of use and usefulness: a two-phase mixed-methods evaluation framework.

PubMed

Boland, Mary Regina; Rusanov, Alexander; So, Yat; Lopez-Jimenez, Carlos; Busacca, Linda; Steinman, Richard C; Bakken, Suzanne; Bigger, J Thomas; Weng, Chunhua

2014-12-01

Underspecified user needs and frequent lack of a gold standard reference are typical barriers to technology evaluation. To address this problem, this paper presents a two-phase evaluation framework involving usability experts (phase 1) and end-users (phase 2). In phase 1, a cross-system functionality alignment between expert-derived user needs and system functions was performed to inform the choice of "the best available" comparison system to enable a cognitive walkthrough in phase 1 and a comparative effectiveness evaluation in phase 2. During phase 2, five quantitative and qualitative evaluation methods are mixed to assess usability: time-motion analysis, software log, questionnaires - System Usability Scale and the Unified Theory of Acceptance of Use of Technology, think-aloud protocols, and unstructured interviews. Each method contributes data for a unique measure (e.g., time motion analysis contributes task-completion-time; software log contributes action transition frequency). The measures are triangulated to yield complementary insights regarding user-perceived ease-of-use, functionality integration, anxiety during use, and workflow impact. To illustrate its use, we applied this framework in a formative evaluation of a software called Integrated Model for Patient Care and Clinical Trials (IMPACT). We conclude that this mixed-methods evaluation framework enables an integrated assessment of user needs satisfaction and user-perceived usefulness and usability of a novel design. This evaluation framework effectively bridges the gap between co-evolving user needs and technology designs during iterative prototyping and is particularly useful when it is difficult for users to articulate their needs for technology support due to the lack of a baseline. Copyright © 2013 Elsevier Inc. All rights reserved.

SparkMed: a framework for dynamic integration of multimedia medical data into distributed m-Health systems.

PubMed

Constantinescu, Liviu; Kim, Jinman; Feng, David Dagan

2012-01-01

With the advent of 4G and other long-term evolution (LTE) wireless networks, the traditional boundaries of patient record propagation are diminishing as networking technologies extend the reach of hospital infrastructure and provide on-demand mobile access to medical multimedia data. However, due to legacy and proprietary software, storage and decommissioning costs, and the price of centralization and redevelopment, it remains complex, expensive, and often unfeasible for hospitals to deploy their infrastructure for online and mobile use. This paper proposes the SparkMed data integration framework for mobile healthcare (m-Health), which significantly benefits from the enhanced network capabilities of LTE wireless technologies, by enabling a wide range of heterogeneous medical software and database systems (such as the picture archiving and communication systems, hospital information system, and reporting systems) to be dynamically integrated into a cloud-like peer-to-peer multimedia data store. Our framework allows medical data applications to share data with mobile hosts over a wireless network (such as WiFi and 3G), by binding to existing software systems and deploying them as m-Health applications. SparkMed integrates techniques from multimedia streaming, rich Internet applications (RIA), and remote procedure call (RPC) frameworks to construct a Self-managing, Pervasive Automated netwoRK for Medical Enterprise Data (SparkMed). Further, it is resilient to failure, and able to use mobile and handheld devices to maintain its network, even in the absence of dedicated server devices. We have developed a prototype of the SparkMed framework for evaluation on a radiological workflow simulation, which uses SparkMed to deploy a radiological image viewer as an m-Health application for telemedical use by radiologists and stakeholders. We have evaluated our prototype using ten devices over WiFi and 3G, verifying that our framework meets its two main objectives: 1) interactive delivery of medical multimedia data to mobile devices; and 2) attaching to non-networked medical software processes without significantly impacting their performance. Consistent response times of under 500 ms and graphical frame rates of over 5 frames per second were observed under intended usage conditions. Further, overhead measurements displayed linear scalability and low resource requirements.

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

NASA Astrophysics Data System (ADS)

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

2011-09-01

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

Software platform for managing the classification of error- related potentials of observers

NASA Astrophysics Data System (ADS)

Asvestas, P.; Ventouras, E.-C.; Kostopoulos, S.; Sidiropoulos, K.; Korfiatis, V.; Korda, A.; Uzunolglu, A.; Karanasiou, I.; Kalatzis, I.; Matsopoulos, G.

2015-09-01

Human learning is partly based on observation. Electroencephalographic recordings of subjects who perform acts (actors) or observe actors (observers), contain a negative waveform in the Evoked Potentials (EPs) of the actors that commit errors and of observers who observe the error-committing actors. This waveform is called the Error-Related Negativity (ERN). Its detection has applications in the context of Brain-Computer Interfaces. The present work describes a software system developed for managing EPs of observers, with the aim of classifying them into observations of either correct or incorrect actions. It consists of an integrated platform for the storage, management, processing and classification of EPs recorded during error-observation experiments. The system was developed using C# and the following development tools and frameworks: MySQL, .NET Framework, Entity Framework and Emgu CV, for interfacing with the machine learning library of OpenCV. Up to six features can be computed per EP recording per electrode. The user can select among various feature selection algorithms and then proceed to train one of three types of classifiers: Artificial Neural Networks, Support Vector Machines, k-nearest neighbour. Next the classifier can be used for classifying any EP curve that has been inputted to the database.

Framework for architecture-independent run-time reconfigurable applications

NASA Astrophysics Data System (ADS)

Lehn, David I.; Hudson, Rhett D.; Athanas, Peter M.

2000-10-01

Configurable Computing Machines (CCMs) have emerged as a technology with the computational benefits of custom ASICs as well as the flexibility and reconfigurability of general-purpose microprocessors. Significant effort from the research community has focused on techniques to move this reconfigurability from a rapid application development tool to a run-time tool. This requires the ability to change the hardware design while the application is executing and is known as Run-Time Reconfiguration (RTR). Widespread acceptance of run-time reconfigurable custom computing depends upon the existence of high-level automated design tools. Such tools must reduce the designers effort to port applications between different platforms as the architecture, hardware, and software evolves. A Java implementation of a high-level application framework, called Janus, is presented here. In this environment, developers create Java classes that describe the structural behavior of an application. The framework allows hardware and software modules to be freely mixed and interchanged. A compilation phase of the development process analyzes the structure of the application and adapts it to the target platform. Janus is capable of structuring the run-time behavior of an application to take advantage of the memory and computational resources available.

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

Background High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/. PMID:23327565

Mining collections of compounds with Screening Assistant 2.

PubMed

Guilloux, Vincent Le; Arrault, Alban; Colliandre, Lionel; Bourg, Stéphane; Vayer, Philippe; Morin-Allory, Luc

2012-08-31

High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

Damage tolerance in filament-wound graphite/epoxy pressure vessels

NASA Technical Reports Server (NTRS)

Simon, William E.; Ngueyen, Vinh D.; Chenna, Ravi K.

1995-01-01

Graphite/epoxy composites are extensively used in the aerospace and sporting goods industries due to their superior engineering properties compared to those of metals. However, graphite/epoxy is extremely susceptible to impact damage which can cause considerable and sometimes undetected reduction in strength. An inelastic impact model was developed to predict damage due to low-velocity impact. A transient dynamic finite element formulation was used in conjunction with the 3D Tsai-Wu failure criterion to determine and incorporate failure in the materials during impact. Material degradation can be adjusted from no degradation to partial degradation to full degradation. The developed software is based on an object-oriented implementation framework called Extensible Implementation Framework for Finite Elements (EIFFE).

Use of Annotations for Component and Framework Interoperability

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Framework Programmable Platform for the advanced software development workstation: Framework processor design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, Wes; Sanders, Les

1991-01-01

The design of the Framework Processor (FP) component of the Framework Programmable Software Development Platform (FFP) is described. The FFP is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by the model, this Framework Processor will take advantage of an integrated operating environment to provide automated support for the management and control of the software development process so that costly mistakes during the development phase can be eliminated.

Automated systems for the analysis of meteor spectra: The SMART Project

NASA Astrophysics Data System (ADS)

Madiedo, José M.

2017-09-01

This work analyzes a meteor spectroscopy survey called SMART (Spectroscopy of Meteoroids in the Atmosphere by means of Robotic Technologies), which is being conducted since 2006. In total, 55 spectrographs have been deployed at 10 different locations in Spain with the aim to obtain information about the chemical nature of meteoroids ablating in the atmosphere. The main improvements in the hardware and the software developed in the framework of this project are described, and some results obtained by these automatic devices are also discussed.

StakeMeter: value-based stakeholder identification and quantification framework for value-based software systems.

PubMed

Babar, Muhammad Imran; Ghazali, Masitah; Jawawi, Dayang N A; Bin Zaheer, Kashif

2015-01-01

Value-based requirements engineering plays a vital role in the development of value-based software (VBS). Stakeholders are the key players in the requirements engineering process, and the selection of critical stakeholders for the VBS systems is highly desirable. Based on the stakeholder requirements, the innovative or value-based idea is realized. The quality of the VBS system is associated with the concrete set of valuable requirements, and the valuable requirements can only be obtained if all the relevant valuable stakeholders participate in the requirements elicitation phase. The existing value-based approaches focus on the design of the VBS systems. However, the focus on the valuable stakeholders and requirements is inadequate. The current stakeholder identification and quantification (SIQ) approaches are neither state-of-the-art nor systematic for the VBS systems. The existing approaches are time-consuming, complex and inconsistent which makes the initiation process difficult. Moreover, the main motivation of this research is that the existing SIQ approaches do not provide the low level implementation details for SIQ initiation and stakeholder metrics for quantification. Hence, keeping in view the existing SIQ problems, this research contributes in the form of a new SIQ framework called 'StakeMeter'. The StakeMeter framework is verified and validated through case studies. The proposed framework provides low-level implementation guidelines, attributes, metrics, quantification criteria and application procedure as compared to the other methods. The proposed framework solves the issues of stakeholder quantification or prioritization, higher time consumption, complexity, and process initiation. The framework helps in the selection of highly critical stakeholders for the VBS systems with less judgmental error.

A Comparison of Authoring Software for Developing Mathematics Self-Learning Software Packages.

ERIC Educational Resources Information Center

Suen, Che-yin; Pok, Yang-ming

Four years ago, the authors started to develop a self-paced mathematics learning software called NPMaths by using an authoring package called Tencore. However, NPMaths had some weak points. A development team was hence formed to develop similar software called Mathematics On Line. This time the team used another development language called…

Framework Programmable Platform for the Advanced Software Development Workstation (FPP/ASDW). Demonstration framework document. Volume 1: Concepts and activity descriptions

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Dewitte, Paul S.; Crump, John W.; Ackley, Keith A.

1992-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at effectively combining tool and data integration mechanisms with a model of the software development process to provide an intelligent integrated software development environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The Advanced Software Development Workstation (ASDW) program is conducting research into development of advanced technologies for Computer Aided Software Engineering (CASE).

Genotyping in the cloud with Crossbow.

PubMed

Gurtowski, James; Schatz, Michael C; Langmead, Ben

2012-09-01

Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. It is built on Apache Hadoop, an implementation of the MapReduce software framework. Hadoop allows Crossbow to distribute read alignment and SNP calling subtasks over a cluster of commodity computers. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores. Through protocol examples, this unit will demonstrate the use of Crossbow for identifying variations in three different operating modes: on a Hadoop cluster, on a single computer, and on the Amazon Elastic MapReduce cloud computing service.

Discovering objects in a blood recipient information system.

PubMed

Qiu, D; Junghans, G; Marquardt, K; Kroll, H; Mueller-Eckhardt, C; Dudeck, J

1995-01-01

Application of object-oriented (OO) methodologies has been generally considered as a solution to the problem of improving the software development process and managing the so-called software crisis. Among them, object-oriented analysis (OOA) is the most essential and is a vital prerequisite for the successful use of other OO methodologies. Though there are already a good deal of OOA methods published, the most important aspect common to all these methods: discovering objects classes truly relevant to the given problem domain, has remained a subject to be intensively researched. In this paper, using the successful development of a blood recipient information system as an example, we present our approach which is based on the conceptual framework of responsibility-driven OOA. In the discussion, we also suggest that it may be inadequate to simply attribute the software crisis to the waterfall model of the software development life-cycle. We are convinced that the real causes for the failure of some software and information systems should be sought in the methodologies used in some crucial phases of the software development process. Furthermore, a software system can also fail if object classes essential to the problem domain are not discovered, implemented and visualized, so that the real-world situation cannot be faithfully traced by it.

Integration Framework of Process Planning based on Resource Independent Operation Summary to Support Collaborative Manufacturing

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

Kulvatunyou, Boonserm; Wysk, Richard A.; Cho, Hyunbo

2004-06-01

In today's global manufacturing environment, manufacturing functions are distributed as never before. Design, engineering, fabrication, and assembly of new products are done routinely in many different enterprises scattered around the world. Successful business transactions require the sharing of design and engineering data on an unprecedented scale. This paper describes a framework that facilitates the collaboration of engineering tasks, particularly process planning and analysis, to support such globalized manufacturing activities. The information models of data and the software components that integrate those information models are described. The integration framework uses an Integrated Product and Process Data (IPPD) representation called a Resourcemore » Independent Operation Summary (RIOS) to facilitate the communication of business and manufacturing requirements. Hierarchical process modeling, process planning decomposition and an augmented AND/OR directed graph are used in this representation. The Resource Specific Process Planning (RSPP) module assigns required equipment and tools, selects process parameters, and determines manufacturing costs based on two-level hierarchical RIOS data. The shop floor knowledge (resource and process knowledge) and a hybrid approach (heuristic and linear programming) to linearize the AND/OR graph provide the basis for the planning. Finally, a prototype system is developed and demonstrated with an exemplary part. Java and XML (Extensible Markup Language) are used to ensure software and information portability.« less

Knowledge assistant: A sensor fusion framework for robotic environmental characterization

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

Feddema, J.T.; Rivera, J.J.; Tucker, S.D.

1996-12-01

A prototype sensor fusion framework called the {open_quotes}Knowledge Assistant{close_quotes} has been developed and tested on a gantry robot at Sandia National Laboratories. This Knowledge Assistant guides the robot operator during the planning, execution, and post analysis stages of the characterization process. During the planning stage, the Knowledge Assistant suggests robot paths and speeds based on knowledge of sensors available and their physical characteristics. During execution, the Knowledge Assistant coordinates the collection of data through a data acquisition {open_quotes}specialist.{close_quotes} During execution and post analysis, the Knowledge Assistant sends raw data to other {open_quotes}specialists,{close_quotes} which include statistical pattern recognition software, a neuralmore » network, and model-based search software. After the specialists return their results, the Knowledge Assistant consolidates the information and returns a report to the robot control system where the sensed objects and their attributes (e.g. estimated dimensions, weight, material composition, etc.) are displayed in the world model. This paper highlights the major components of this system.« less

RGG: A general GUI Framework for R scripts

PubMed Central

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

2009-01-01

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

Pedagogy and Related Criteria: The Selection of Software for Computer Assisted Language Learning

ERIC Educational Resources Information Center

Samuels, Jeffrey D.

2013-01-01

Computer-Assisted Language Learning (CALL) is an established field of academic inquiry with distinct applications for second language teaching and learning. Many CALL professionals direct language labs or language resource centers (LRCs) in which CALL software applications and generic software applications support language learning programs and…

A semiparametric Bayesian proportional hazards model for interval censored data with frailty effects.

PubMed

Henschel, Volkmar; Engel, Jutta; Hölzel, Dieter; Mansmann, Ulrich

2009-02-10

Multivariate analysis of interval censored event data based on classical likelihood methods is notoriously cumbersome. Likelihood inference for models which additionally include random effects are not available at all. Developed algorithms bear problems for practical users like: matrix inversion, slow convergence, no assessment of statistical uncertainty. MCMC procedures combined with imputation are used to implement hierarchical models for interval censored data within a Bayesian framework. Two examples from clinical practice demonstrate the handling of clustered interval censored event times as well as multilayer random effects for inter-institutional quality assessment. The software developed is called survBayes and is freely available at CRAN. The proposed software supports the solution of complex analyses in many fields of clinical epidemiology as well as health services research.

GERICOS: A Generic Framework for the Development of On-Board Software

NASA Astrophysics Data System (ADS)

Plasson, P.; Cuomo, C.; Gabriel, G.; Gauthier, N.; Gueguen, L.; Malac-Allain, L.

2016-08-01

This paper presents an overview of the GERICOS framework (GEneRIC Onboard Software), its architecture, its various layers and its future evolutions. The GERICOS framework, developed and qualified by LESIA, offers a set of generic, reusable and customizable software components for the rapid development of payload flight software. The GERICOS framework has a layered structure. The first layer (GERICOS::CORE) implements the concept of active objects and forms an abstraction layer over the top of real-time kernels. The second layer (GERICOS::BLOCKS) offers a set of reusable software components for building flight software based on generic solutions to recurrent functionalities. The third layer (GERICOS::DRIVERS) implements software drivers for several COTS IP cores of the LEON processor ecosystem.

Informatics in radiology: web-based preliminary reporting system for radiology residents with PACS integration.

PubMed

O'Connell, Timothy; Chang, Debra

2012-01-01

While on call, radiology residents review imaging studies and issue preliminary reports to referring clinicians. In the absence of an integrated reporting system at the training sites of the authors' institution, residents were typing and faxing preliminary reports. To partially automate the on-call resident workflow, a Web-based system for resident reporting was developed by using the free open-source xAMP Web application framework and an open-source DICOM (Digital Imaging and Communications in Medicine) software toolkit, with the goals of reducing errors and lowering barriers to education. This reporting system integrates with the picture archiving and communication system to display a worklist of studies. Patient data are automatically entered in the preliminary report to prevent identification errors and simplify the report creation process. When the final report for a resident's on-call study is available, the reporting system queries the report broker for the final report, and then displays the preliminary report side by side with the final report, thus simplifying the review process and encouraging review of all of the resident's reports. The xAMP Web application framework should be considered for development of radiology department informatics projects owing to its zero cost, minimal hardware requirements, ease of programming, and large support community.

CaveMan Enterprise version 1.0 Software Validation and Verification.

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

Hart, David

The U.S. Department of Energy Strategic Petroleum Reserve stores crude oil in caverns solution-mined in salt domes along the Gulf Coast of Louisiana and Texas. The CaveMan software program has been used since the late 1990s as one tool to analyze pressure mea- surements monitored at each cavern. The purpose of this monitoring is to catch potential cavern integrity issues as soon as possible. The CaveMan software was written in Microsoft Visual Basic, and embedded in a Microsoft Excel workbook; this method of running the CaveMan software is no longer sustainable. As such, a new version called CaveMan Enter- prisemore » has been developed. CaveMan Enterprise version 1.0 does not have any changes to the CaveMan numerical models. CaveMan Enterprise represents, instead, a change from desktop-managed work- books to an enterprise framework, moving data management into coordinated databases and porting the numerical modeling codes into the Python programming language. This document provides a report of the code validation and verification testing.« less

StakeMeter: Value-Based Stakeholder Identification and Quantification Framework for Value-Based Software Systems

PubMed Central

Babar, Muhammad Imran; Ghazali, Masitah; Jawawi, Dayang N. A.; Zaheer, Kashif Bin

2015-01-01

Value-based requirements engineering plays a vital role in the development of value-based software (VBS). Stakeholders are the key players in the requirements engineering process, and the selection of critical stakeholders for the VBS systems is highly desirable. Based on the stakeholder requirements, the innovative or value-based idea is realized. The quality of the VBS system is associated with the concrete set of valuable requirements, and the valuable requirements can only be obtained if all the relevant valuable stakeholders participate in the requirements elicitation phase. The existing value-based approaches focus on the design of the VBS systems. However, the focus on the valuable stakeholders and requirements is inadequate. The current stakeholder identification and quantification (SIQ) approaches are neither state-of-the-art nor systematic for the VBS systems. The existing approaches are time-consuming, complex and inconsistent which makes the initiation process difficult. Moreover, the main motivation of this research is that the existing SIQ approaches do not provide the low level implementation details for SIQ initiation and stakeholder metrics for quantification. Hence, keeping in view the existing SIQ problems, this research contributes in the form of a new SIQ framework called ‘StakeMeter’. The StakeMeter framework is verified and validated through case studies. The proposed framework provides low-level implementation guidelines, attributes, metrics, quantification criteria and application procedure as compared to the other methods. The proposed framework solves the issues of stakeholder quantification or prioritization, higher time consumption, complexity, and process initiation. The framework helps in the selection of highly critical stakeholders for the VBS systems with less judgmental error. PMID:25799490

CSM Testbed Development and Large-Scale Structural Applications

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Gillian, R. E.; Mccleary, Susan L.; Lotts, C. G.; Poole, E. L.; Overman, A. L.; Macy, S. C.

1989-01-01

A research activity called Computational Structural Mechanics (CSM) conducted at the NASA Langley Research Center is described. This activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM Testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM Testbed methods development environment is presented and some new numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software

PubMed Central

Mejías, Andrés; Herrera, Reyes S.; Márquez, Marco A.; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-01

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)—this one designed using the intuitive graphical system of EJS—located on the user’s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented. PMID:28067801

Easy Handling of Sensors and Actuators over TCP/IP Networks by Open Source Hardware/Software.

PubMed

Mejías, Andrés; Herrera, Reyes S; Márquez, Marco A; Calderón, Antonio José; González, Isaías; Andújar, José Manuel

2017-01-05

There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user's computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.

Status report of the SRT radiotelescope control software: the DISCOS project

NASA Astrophysics Data System (ADS)

Orlati, A.; Bartolini, M.; Buttu, M.; Fara, A.; Migoni, C.; Poppi, S.; Righini, S.

2016-08-01

The Sardinia Radio Telescope (SRT) is a 64-m fully-steerable radio telescope. It is provided with an active surface to correct for gravitational deformations, allowing observations from 300 MHz to 100 GHz. At present, three receivers are available: a coaxial LP-band receiver (305-410 MHz and 1.5-1.8 GHz), a C-band receiver (5.7-7.7 GHz) and a 7-feed K-band receiver (18-26.5 GHz). Several back-ends are also available in order to perform the different data acquisition and analysis procedures requested by scientific projects. The design and development of the SRT control software started in 2004, and now belongs to a wider project called DISCOS (Development of the Italian Single-dish COntrol System), which provides a common infrastructure to the three Italian radio telescopes (Medicina, Noto and SRT dishes). DISCOS is based on the Alma Common Software (ACS) framework, and currently consists of more than 500k lines of code. It is organized in a common core and three specific product lines, one for each telescope. Recent developments, carried out after the conclusion of the technical commissioning of the instrument (October 2013), consisted in the addition of several new features in many parts of the observing pipeline, spanning from the motion control to the digital back-ends for data acquisition and data formatting; we brie y describe such improvements. More importantly, in the last two years we have supported the astronomical validation of the SRT radio telescope, leading to the opening of the first public call for proposals in late 2015. During this period, while assisting both the engineering and the scientific staff, we massively employed the control software and were able to test all of its features: in this process we received our first feedback from the users and we could verify how the system performed in a real-life scenario, drawing the first conclusions about the overall system stability and performance. We examine how the system behaves in terms of network load and system load, how it reacts to failures and errors, and what components and services seem to be the most critical parts of our architecture, showing how the ACS framework impacts on these aspects. Moreover, the exposure to public utilization has highlighted the major flaws in our development and software management process, which had to be tuned and improved in order to achieve faster release cycles in response to user feedback, and safer deploy operations. In this regard we show how the introduction of testing practices, along with continuous integration, helped us to meet higher quality standards. Having identified the most critical aspects of our software, we conclude showing our intentions for the future development of DISCOS, both in terms of software features and software infrastructures.

Future Standardization of Space Telecommunications Radio System with Core Flight System

NASA Technical Reports Server (NTRS)

Hickey, Joseph P.; Briones, Janette C.; Roche, Rigoberto; Handler, Louis M.; Hall, Steven

2016-01-01

NASA Glenn Research Center (GRC) is integrating the NASA Space Telecommunications Radio System (STRS) Standard with the Core Flight System (cFS). The STRS standard provides a common, consistent framework to develop, qualify, operate and maintain complex, reconfigurable and reprogrammable radio systems. The cFS is a flexible, open architecture that features a plug-and-play software executive called the Core Flight Executive (cFE), a reusable library of software components for flight and space missions and an integrated tool suite. Together, STRS and cFS create a development environment that allows for STRS compliant applications to reference the STRS APIs through the cFS infrastructure. These APis are used to standardize the communication protocols on NASAs space SDRs. The cFE-STRS Operating Environment (OE) is a portable cFS library, which adds the ability to run STRS applications on existing cFS platforms. The purpose of this paper is to discuss the cFE-STRS OE prototype, preliminary experimental results performed using the Advanced Space Radio Platform (ASRP), the GRC Sband Ground Station and the SCaN (Space Communication and Navigation) Testbed currently flying onboard the International Space Station. Additionally, this paper presents a demonstration of the Consultative Committee for Space Data Systems (CCSDS) Spacecraft Onboard Interface Services (SOIS) using electronic data sheets inside cFE. This configuration allows for the data sheets to specify binary formats for data exchange between STRS applications. The integration of STRS with cFS leverages mission-proven platform functions and mitigates barriers to integration with future missions. This reduces flight software development time and the costs of software-defined radio (SDR) platforms. Furthermore, the combined benefits of STRS standardization with the flexibility of cFS provide an effective, reliable and modular framework to minimize software development efforts for spaceflight missions.

Framework programmable platform for the advanced software development workstation. Integration mechanism design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Reddy, Uday; Ackley, Keith; Futrell, Mike

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by this model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated.

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: Earth System Modeling Software Framework Survey

NASA Technical Reports Server (NTRS)

Talbot, Bryan; Zhou, Shu-Jia; Higgins, Glenn; Zukor, Dorothy (Technical Monitor)

2002-01-01

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task, both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation. while maintaining high performance across numerous supercomputer and workstation architectures. This document surveys numerous software frameworks for potential use in Earth science modeling. Several frameworks are evaluated in depth, including Parallel Object-Oriented Methods and Applications (POOMA), Cactus (from (he relativistic physics community), Overture, Goddard Earth Modeling System (GEMS), the National Center for Atmospheric Research Flux Coupler, and UCLA/UCB Distributed Data Broker (DDB). Frameworks evaluated in less detail include ROOT, Parallel Application Workspace (PAWS), and Advanced Large-Scale Integrated Computational Environment (ALICE). A host of other frameworks and related tools are referenced in this context. The frameworks are evaluated individually and also compared with each other.

MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data

PubMed Central

Hu, Jiyuan; Li, Tengfei; Xiu, Zidi; Zhang, Hong

2015-01-01

Most existing statistical methods developed for calling single nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS) data are based on Bayesian frameworks, and there does not exist any SNP caller that produces p-values for calling SNPs in a frequentist framework. To fill in this gap, we develop a new method MAFsnp, a Multiple-sample based Accurate and Flexible algorithm for calling SNPs with NGS data. MAFsnp is based on an estimated likelihood ratio test (eLRT) statistic. In practical situation, the involved parameter is very close to the boundary of the parametric space, so the standard large sample property is not suitable to evaluate the finite-sample distribution of the eLRT statistic. Observing that the distribution of the test statistic is a mixture of zero and a continuous part, we propose to model the test statistic with a novel two-parameter mixture distribution. Once the parameters in the mixture distribution are estimated, p-values can be easily calculated for detecting SNPs, and the multiple-testing corrected p-values can be used to control false discovery rate (FDR) at any pre-specified level. With simulated data, MAFsnp is shown to have much better control of FDR than the existing SNP callers. Through the application to two real datasets, MAFsnp is also shown to outperform the existing SNP callers in terms of calling accuracy. An R package “MAFsnp” implementing the new SNP caller is freely available at http://homepage.fudan.edu.cn/zhangh/softwares/. PMID:26309201

An integrated development framework for rapid development of platform-independent and reusable satellite on-board software

NASA Astrophysics Data System (ADS)

Ziemke, Claas; Kuwahara, Toshinori; Kossev, Ivan

2011-09-01

Even in the field of small satellites, the on-board data handling subsystem has become complex and powerful. With the introduction of powerful CPUs and the availability of considerable amounts of memory on-board a small satellite it has become possible to utilize the flexibility and power of contemporary platform-independent real-time operating systems. Especially the non-commercial sector such like university institutes and community projects such as AMSAT or SSETI are characterized by the inherent lack of financial as well as manpower resources. The opportunity to utilize such real-time operating systems will contribute significantly to achieve a successful mission. Nevertheless the on-board software of a satellite is much more than just an operating system. It has to fulfill a multitude of functional requirements such as: Telecommand interpretation and execution, execution of control loops, generation of telemetry data and frames, failure detection isolation and recovery, the communication with peripherals and so on. Most of the aforementioned tasks are of generic nature and have to be conducted on any satellite with only minor modifications. A general set of functional requirements as well as a protocol for communication is defined in the SA ECSS-E-70-41A standard "Telemetry and telecommand packet utilization". This standard not only defines the communication protocol of the satellite-ground link but also defines a set of so called services which have to be available on-board of every compliant satellite and which are of generic nature. In this paper, a platform-independent and reusable framework is described which is implementing not only the ECSS-E-70-41A standard but also functionalities for interprocess communication, scheduling and a multitude of tasks commonly performed on-board of a satellite. By making use of the capabilities of the high-level programming language C/C++, the powerful open source library BOOST, the real-time operating system RTEMS and finally by providing generic functionalities compliant to the ECSS-E-70-41A standard the proposed framework can provide a great boost in productivity. Together with open source tools such like the GNU tool-chain, Eclipse SDK, the simulation framework OpenSimKit, the emulator QEMU, the proposed on-board software framework forms an integrated development framework. It is possible to design, code and build the on-board software together with the operating system and then run it on a simulated satellite for performance analysis and debugging purposes. This makes it possible to rapidly develop and deploy a full-fledged satellite on-board software with minimal cost and in a limited time frame.

An evolutionary morphological approach for software development cost estimation.

PubMed

Araújo, Ricardo de A; Oliveira, Adriano L I; Soares, Sergio; Meira, Silvio

2012-08-01

In this work we present an evolutionary morphological approach to solve the software development cost estimation (SDCE) problem. The proposed approach consists of a hybrid artificial neuron based on framework of mathematical morphology (MM) with algebraic foundations in the complete lattice theory (CLT), referred to as dilation-erosion perceptron (DEP). Also, we present an evolutionary learning process, called DEP(MGA), using a modified genetic algorithm (MGA) to design the DEP model, because a drawback arises from the gradient estimation of morphological operators in the classical learning process of the DEP, since they are not differentiable in the usual way. Furthermore, an experimental analysis is conducted with the proposed model using five complex SDCE problems and three well-known performance metrics, demonstrating good performance of the DEP model to solve SDCE problems. Copyright © 2012 Elsevier Ltd. All rights reserved.

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

Objective To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG™) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. Measurements The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. Conclusions While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community. PMID:18096909

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.

Molpher: a software framework for systematic chemical space exploration

PubMed Central

2014-01-01

Background Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. Results In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term ‘molecular morphing’, Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called ‘morphing operators’ that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Conclusions Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline. PMID:24655571

Molpher: a software framework for systematic chemical space exploration.

PubMed

Hoksza, David; Skoda, Petr; Voršilák, Milan; Svozil, Daniel

2014-03-21

Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

Future Standardization of Space Telecommunications Radio System with Core Flight System

NASA Technical Reports Server (NTRS)

Briones, Janette C.; Hickey, Joseph P.; Roche, Rigoberto; Handler, Louis M.; Hall, Charles S.

2016-01-01

NASA Glenn Research Center (GRC) is integrating the NASA Space Telecommunications Radio System (STRS) Standard with the Core Flight System (cFS), an avionics software operating environment. The STRS standard provides a common, consistent framework to develop, qualify, operate and maintain complex, reconfigurable and reprogrammable radio systems. The cFS is a flexible, open architecture that features a plugand- play software executive called the Core Flight Executive (cFE), a reusable library of software components for flight and space missions and an integrated tool suite. Together, STRS and cFS create a development environment that allows for STRS compliant applications to reference the STRS application programmer interfaces (APIs) that use the cFS infrastructure. These APIs are used to standardize the communication protocols on NASAs space SDRs. The cFS-STRS Operating Environment (OE) is a portable cFS library, which adds the ability to run STRS applications on existing cFS platforms. The purpose of this paper is to discuss the cFS-STRS OE prototype, preliminary experimental results performed using the Advanced Space Radio Platform (ASRP), the GRC S- band Ground Station and the SCaN (Space Communication and Navigation) Testbed currently flying onboard the International Space Station (ISS). Additionally, this paper presents a demonstration of the Consultative Committee for Space Data Systems (CCSDS) Spacecraft Onboard Interface Services (SOIS) using electronic data sheets (EDS) inside cFE. This configuration allows for the data sheets to specify binary formats for data exchange between STRS applications. The integration of STRS with cFS leverages mission-proven platform functions and mitigates barriers to integration with future missions. This reduces flight software development time and the costs of software-defined radio (SDR) platforms. Furthermore, the combined benefits of STRS standardization with the flexibility of cFS provide an effective, reliable and modular framework to minimize software development efforts for spaceflight missions.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

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

Framework Programmable Platform for the Advanced Software Development Workstation: Preliminary system design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, John W., IV; Henderson, Richard; Futrell, Michael T.

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The focus here is on the design of components that make up the FPP. These components serve as supporting systems for the Integration Mechanism and the Framework Processor and provide the 'glue' that ties the FPP together. Also discussed are the components that allow the platform to operate in a distributed, heterogeneous environment and to manage the development and evolution of software system artifacts.

Virtual Levels and Role Models: N-Level Structural Equations Model of Reciprocal Ratings Data.

PubMed

Mehta, Paras D

2018-01-01

A general latent variable modeling framework called n-Level Structural Equations Modeling (NL-SEM) for dependent data-structures is introduced. NL-SEM is applicable to a wide range of complex multilevel data-structures (e.g., cross-classified, switching membership, etc.). Reciprocal dyadic ratings obtained in round-robin design involve complex set of dependencies that cannot be modeled within Multilevel Modeling (MLM) or Structural Equations Modeling (SEM) frameworks. The Social Relations Model (SRM) for round robin data is used as an example to illustrate key aspects of the NL-SEM framework. NL-SEM introduces novel constructs such as 'virtual levels' that allows a natural specification of latent variable SRMs. An empirical application of an explanatory SRM for personality using xxM, a software package implementing NL-SEM is presented. Results show that person perceptions are an integral aspect of personality. Methodological implications of NL-SEM for the analyses of an emerging class of contextual- and relational-SEMs are discussed.

OpenSeesPy: Python library for the OpenSees finite element framework

NASA Astrophysics Data System (ADS)

Zhu, Minjie; McKenna, Frank; Scott, Michael H.

2018-01-01

OpenSees, an open source finite element software framework, has been used broadly in the earthquake engineering community for simulating the seismic response of structural and geotechnical systems. The framework allows users to perform finite element analysis with a scripting language and for developers to create both serial and parallel finite element computer applications as interpreters. For the last 15 years, Tcl has been the primary scripting language to which the model building and analysis modules of OpenSees are linked. To provide users with different scripting language options, particularly Python, the OpenSees interpreter interface was refactored to provide multi-interpreter capabilities. This refactoring, resulting in the creation of OpenSeesPy as a Python module, is accomplished through an abstract interface for interpreter calls with concrete implementations for different scripting languages. Through this approach, users are able to develop applications that utilize the unique features of several scripting languages while taking advantage of advanced finite element analysis models and algorithms.

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

PubMed Central

Baik, Jongmoon

2014-01-01

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

Simulink/PARS Integration Support

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

Vacaliuc, B.; Nakhaee, N.

2013-12-18

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

Tcl as a Software Environment for a TCS

NASA Astrophysics Data System (ADS)

Terrett, David L.

2002-12-01

This paper describes how the Tcl scripting language and C API has been used as the software environment for a telescope pointing kernel so that new pointing algorithms and software architectures can be developed and tested without needing a real-time operating system or real-time software environment. It has enabled development to continue outside the framework of a specific telescope project while continuing to build a system that is sufficiently complete to be capable of controlling real hardware but expending minimum effort on replacing the services that would normally by provided by a real-time software environment. Tcl is used as a scripting language for configuring the system at startup and then as the command interface for controlling the running system; the Tcl C language API is used to provided a system independent interface to file and socket I/O and other operating system services. The pointing algorithms themselves are implemented as a set of C++ objects calling C library functions that implement the algorithms described in [2]. Although originally designed as a test and development environment, the system, running as a soft real-time process on Linux, has been used to test the SOAR mount control system and will be used as the pointing kernel of the SOAR telescope control system

MAPI: a software framework for distributed biomedical applications

PubMed Central

2013-01-01

Background The amount of web-based resources (databases, tools etc.) in biomedicine has increased, but the integrated usage of those resources is complex due to differences in access protocols and data formats. However, distributed data processing is becoming inevitable in several domains, in particular in biomedicine, where researchers face rapidly increasing data sizes. This big data is difficult to process locally because of the large processing, memory and storage capacity required. Results This manuscript describes a framework, called MAPI, which provides a uniform representation of resources available over the Internet, in particular for Web Services. The framework enhances their interoperability and collaborative use by enabling a uniform and remote access. The framework functionality is organized in modules that can be combined and configured in different ways to fulfil concrete development requirements. Conclusions The framework has been tested in the biomedical application domain where it has been a base for developing several clients that are able to integrate different web resources. The MAPI binaries and documentation are freely available at http://www.bitlab-es.com/mapi under the Creative Commons Attribution-No Derivative Works 2.5 Spain License. The MAPI source code is available by request (GPL v3 license). PMID:23311574

An integrated model to simulate the scattering of ultrasounds by inclusions in steels.

PubMed

Darmon, Michel; Calmon, Pierre; Bèle, Bertrand

2004-04-01

We present a study performed to model and predict the ultrasonic response of alumina inclusions in steels. The Born and the extended quasistatic approximations have been applied and modified to improve their accuracy in the framework of this application. The modified Born approximation, called "doubly distorted wave (D(2)W) Born approximation" allowing to deal with various inclusion shapes, has been selected to be implemented in the CIVA software. The model reliability has been evaluated by comparison with Ying and Truell's exact analytical solution. In parallel, measurements have been carried out upon both natural and artificial alumina inclusions.

Analysis of Bioprocesses. Dynamic Modeling is a Must.

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

Ramkrishna, Doraiswami; Song, Hyun-Seob

2016-01-01

The goal of this paper is to report on the performance of a promising dynamic framework based on the cybernetic concepts which have evolved over three decades. We present case studies of successful dynamic simulations of wild-type strains as well as specific KO mutants on bacteria and yeast. An extensive metabolic engineering effort, including genome scale networks, is called for to secure the methodology and realize its full potential. Towards this end, the software AUMIC is under active further development to enable speedy applications. Its wide use will be enabled by a publication that is shortly due.

An Interoperability Framework and Capability Profiling for Manufacturing Software

NASA Astrophysics Data System (ADS)

Matsuda, M.; Arai, E.; Nakano, N.; Wakai, H.; Takeda, H.; Takata, M.; Sasaki, H.

ISO/TC184/SC5/WG4 is working on ISO16100: Manufacturing software capability profiling for interoperability. This paper reports on a manufacturing software interoperability framework and a capability profiling methodology which were proposed and developed through this international standardization activity. Within the context of manufacturing application, a manufacturing software unit is considered to be capable of performing a specific set of function defined by a manufacturing software system architecture. A manufacturing software interoperability framework consists of a set of elements and rules for describing the capability of software units to support the requirements of a manufacturing application. The capability profiling methodology makes use of the domain-specific attributes and methods associated with each specific software unit to describe capability profiles in terms of unit name, manufacturing functions, and other needed class properties. In this methodology, manufacturing software requirements are expressed in terns of software unit capability profiles.

Fostering Multirepresentational Levels of Chemical Concepts: A Framework to Develop Educational Software

ERIC Educational Resources Information Center

Marson, Guilherme A.; Torres, Bayardo B.

2011-01-01

This work presents a convenient framework for developing interactive chemical education software to facilitate the integration of macroscopic, microscopic, and symbolic dimensions of chemical concepts--specifically, via the development of software for gel permeation chromatography. The instructional role of the software was evaluated in a study…

Software Engineering Frameworks: Textbooks vs. Student Perceptions

ERIC Educational Resources Information Center

McMaster, Kirby; Hadfield, Steven; Wolthuis, Stuart; Sambasivam, Samuel

2012-01-01

This research examines the frameworks used by Computer Science and Information Systems students at the conclusion of their first semester of study of Software Engineering. A questionnaire listing 64 Software Engineering concepts was given to students upon completion of their first Software Engineering course. This survey was given to samples of…

Software framework for the upcoming MMT Observatory primary mirror re-aluminization

NASA Astrophysics Data System (ADS)

Gibson, J. Duane; Clark, Dusty; Porter, Dallan

2014-07-01

Details of the software framework for the upcoming in-situ re-aluminization of the 6.5m MMT Observatory (MMTO) primary mirror are presented. This framework includes: 1) a centralized key-value store and data structure server for data exchange between software modules, 2) a newly developed hardware-software interface for faster data sampling and better hardware control, 3) automated control algorithms that are based upon empirical testing, modeling, and simulation of the aluminization process, 4) re-engineered graphical user interfaces (GUI's) that use state-of-the-art web technologies, and 5) redundant relational databases for data logging. Redesign of the software framework has several objectives: 1) automated process control to provide more consistent and uniform mirror coatings, 2) optional manual control of the aluminization process, 3) modular design to allow flexibility in process control and software implementation, 4) faster data sampling and logging rates to better characterize the approximately 100-second aluminization event, and 5) synchronized "real-time" web application GUI's to provide all users with exactly the same data. The framework has been implemented as four modules interconnected by a data store/server. The four modules are integrated into two Linux system services that start automatically at boot-time and remain running at all times. Performance of the software framework is assessed through extensive testing within 2.0 meter and smaller coating chambers at the Sunnyside Test Facility. The redesigned software framework helps ensure that a better performing and longer lasting coating will be achieved during the re-aluminization of the MMTO primary mirror.

Evaluation of copy number variation detection for a SNP array platform

PubMed Central

2014-01-01

Background Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform. We selected four publicly available software packages designed for CNV calling from an Affymetrix SNP array, including Birdsuite, dChip, Genotyping Console (GTC) and PennCNV. The publicly available dataset generated by Array-based Comparative Genomic Hybridization (CGH), with a resolution of 24 million probes per sample, was considered to be the “gold standard”. Compared with the CGH-based dataset, the success rate, average stability rate, sensitivity, consistence and reproducibility of these four software packages were assessed compared with the “gold standard”. Specially, we also compared the efficiency of detecting CNVs simultaneously by two, three and all of the software packages with that by a single software package. Results Simply from the quantity of the detected CNVs, Birdsuite detected the most while GTC detected the least. We found that Birdsuite and dChip had obvious detecting bias. And GTC seemed to be inferior because of the least amount of CNVs it detected. Thereafter we investigated the detection consistency produced by one certain software package and the rest three software suits. We found that the consistency of dChip was the lowest while GTC was the highest. Compared with the CNVs detecting result of CGH, in the matching group, GTC called the most matching CNVs, PennCNV-Affy ranked second. In the non-overlapping group, GTC called the least CNVs. With regards to the reproducibility of CNV calling, larger CNVs were usually replicated better. PennCNV-Affy shows the best consistency while Birdsuite shows the poorest. Conclusion We found that PennCNV outperformed the other three packages in the sensitivity and specificity of CNV calling. Obviously, each calling method had its own limitations and advantages for different data analysis. Therefore, the optimized calling methods might be identified using multiple algorithms to evaluate the concordance and discordance of SNP array-based CNV calling. PMID:24555668

Framework Support For Knowledge-Based Software Development

NASA Astrophysics Data System (ADS)

Huseth, Steve

1988-03-01

The advent of personal engineering workstations has brought substantial information processing power to the individual programmer. Advanced tools and environment capabilities supporting the software lifecycle are just beginning to become generally available. However, many of these tools are addressing only part of the software development problem by focusing on rapid construction of self-contained programs by a small group of talented engineers. Additional capabilities are required to support the development of large programming systems where a high degree of coordination and communication is required among large numbers of software engineers, hardware engineers, and managers. A major player in realizing these capabilities is the framework supporting the software development environment. In this paper we discuss our research toward a Knowledge-Based Software Assistant (KBSA) framework. We propose the development of an advanced framework containing a distributed knowledge base that can support the data representation needs of tools, provide environmental support for the formalization and control of the software development process, and offer a highly interactive and consistent user interface.

Using Software Design Methods in CALL

ERIC Educational Resources Information Center

Ward, Monica

2006-01-01

The phrase "software design" is not one that arouses the interest of many CALL practitioners, particularly those from a humanities background. However, software design essentials are simply logical ways of going about designing a system. The fundamentals include modularity, anticipation of change, generality and an incremental approach. While CALL…

A general observatory control software framework design for existing small and mid-size telescopes

NASA Astrophysics Data System (ADS)

Ge, Liang; Lu, Xiao-Meng; Jiang, Xiao-Jun

2015-07-01

A general framework for observatory control software would help to improve the efficiency of observation and operation of telescopes, and would also be advantageous for remote and joint observations. We describe a general framework for observatory control software, which considers principles of flexibility and inheritance to meet the expectations from observers and technical personnel. This framework includes observation scheduling, device control and data storage. The design is based on a finite state machine that controls the whole process.

Instrument Control (iC) – An Open-Source Software to Automate Test Equipment

PubMed Central

Pernstich, K. P.

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming. PMID:26900522

An Ontology-based Architecture for Integration of Clinical Trials Management Applications

PubMed Central

Shankar, Ravi D.; Martins, Susana B.; O’Connor, Martin; Parrish, David B.; Das, Amar K.

2007-01-01

Management of complex clinical trials involves coordinated-use of a myriad of software applications by trial personnel. The applications typically use distinct knowledge representations and generate enormous amount of information during the course of a trial. It becomes vital that the applications exchange trial semantics in order for efficient management of the trials and subsequent analysis of clinical trial data. Existing model-based frameworks do not address the requirements of semantic integration of heterogeneous applications. We have built an ontology-based architecture to support interoperation of clinical trial software applications. Central to our approach is a suite of clinical trial ontologies, which we call Epoch, that define the vocabulary and semantics necessary to represent information on clinical trials. We are continuing to demonstrate and validate our approach with different clinical trials management applications and with growing number of clinical trials. PMID:18693919

Architecture of distributed picture archiving and communication systems for storing and processing high resolution medical images

NASA Astrophysics Data System (ADS)

Tokareva, Victoria

2018-04-01

New generation medicine demands a better quality of analysis increasing the amount of data collected during checkups, and simultaneously decreasing the invasiveness of a procedure. Thus it becomes urgent not only to develop advanced modern hardware, but also to implement special software infrastructure for using it in everyday clinical practice, so-called Picture Archiving and Communication Systems (PACS). Developing distributed PACS is a challenging task for nowadays medical informatics. The paper discusses the architecture of distributed PACS server for processing large high-quality medical images, with respect to technical specifications of modern medical imaging hardware, as well as international standards in medical imaging software. The MapReduce paradigm is proposed for image reconstruction by server, and the details of utilizing the Hadoop framework for this task are being discussed in order to provide the design of distributed PACS as ergonomic and adapted to the needs of end users as possible.

Instrument Control (iC) - An Open-Source Software to Automate Test Equipment.

PubMed

Pernstich, K P

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming.

THE EPA MULTIMEDIA INTEGRATED MODELING SYSTEM SOFTWARE SUITE

EPA Science Inventory

The U.S. EPA is developing a Multimedia Integrated Modeling System (MIMS) framework that will provide a software infrastructure or environment to support constructing, composing, executing, and evaluating complex modeling studies. The framework will include (1) common software ...

Content Documents Management

NASA Technical Reports Server (NTRS)

Muniz, R.; Hochstadt, J.; Boelke J.; Dalton, A.

2011-01-01

The Content Documents are created and managed under the System Software group with. Launch Control System (LCS) project. The System Software product group is lead by NASA Engineering Control and Data Systems branch (NEC3) at Kennedy Space Center. The team is working on creating Operating System Images (OSI) for different platforms (i.e. AIX, Linux, Solaris and Windows). Before the OSI can be created, the team must create a Content Document which provides the information of a workstation or server, with the list of all the software that is to be installed on it and also the set where the hardware belongs. This can be for example in the LDS, the ADS or the FR-l. The objective of this project is to create a User Interface Web application that can manage the information of the Content Documents, with all the correct validations and filters for administrator purposes. For this project we used one of the most excellent tools in agile development applications called Ruby on Rails. This tool helps pragmatic programmers develop Web applications with Rails framework and Ruby programming language. It is very amazing to see how a student can learn about OOP features with the Ruby language, manage the user interface with HTML and CSS, create associations and queries with gems, manage databases and run a server with MYSQL, run shell commands with command prompt and create Web frameworks with Rails. All of this in a real world project and in just fifteen weeks!

Software Design Challenges in Time Series Prediction Systems Using Parallel Implementation of Artificial Neural Networks.

PubMed

Manikandan, Narayanan; Subha, Srinivasan

2016-01-01

Software development life cycle has been characterized by destructive disconnects between activities like planning, analysis, design, and programming. Particularly software developed with prediction based results is always a big challenge for designers. Time series data forecasting like currency exchange, stock prices, and weather report are some of the areas where an extensive research is going on for the last three decades. In the initial days, the problems with financial analysis and prediction were solved by statistical models and methods. For the last two decades, a large number of Artificial Neural Networks based learning models have been proposed to solve the problems of financial data and get accurate results in prediction of the future trends and prices. This paper addressed some architectural design related issues for performance improvement through vectorising the strengths of multivariate econometric time series models and Artificial Neural Networks. It provides an adaptive approach for predicting exchange rates and it can be called hybrid methodology for predicting exchange rates. This framework is tested for finding the accuracy and performance of parallel algorithms used.

Software Design Challenges in Time Series Prediction Systems Using Parallel Implementation of Artificial Neural Networks

PubMed Central

Manikandan, Narayanan; Subha, Srinivasan

2016-01-01

Software development life cycle has been characterized by destructive disconnects between activities like planning, analysis, design, and programming. Particularly software developed with prediction based results is always a big challenge for designers. Time series data forecasting like currency exchange, stock prices, and weather report are some of the areas where an extensive research is going on for the last three decades. In the initial days, the problems with financial analysis and prediction were solved by statistical models and methods. For the last two decades, a large number of Artificial Neural Networks based learning models have been proposed to solve the problems of financial data and get accurate results in prediction of the future trends and prices. This paper addressed some architectural design related issues for performance improvement through vectorising the strengths of multivariate econometric time series models and Artificial Neural Networks. It provides an adaptive approach for predicting exchange rates and it can be called hybrid methodology for predicting exchange rates. This framework is tested for finding the accuracy and performance of parallel algorithms used. PMID:26881271

General Aviation Data Framework

NASA Technical Reports Server (NTRS)

Blount, Elaine M.; Chung, Victoria I.

2006-01-01

The Flight Research Services Directorate at the NASA Langley Research Center (LaRC) provides development and operations services associated with three general aviation (GA) aircraft used for research experiments. The GA aircraft includes a Cessna 206X Stationair, a Lancair Colombia 300X, and a Cirrus SR22X. Since 2004, the GA Data Framework software was designed and implemented to gather data from a varying set of hardware and software sources as well as enable transfer of the data to other computers or devices. The key requirements for the GA Data Framework software include platform independence, the ability to reuse the framework for different projects without changing the framework code, graphics display capabilities, and the ability to vary the interfaces and their performance. Data received from the various devices is stored in shared memory. This paper concentrates on the object oriented software design patterns within the General Aviation Data Framework, and how they enable the construction of project specific software without changing the base classes. The issues of platform independence and multi-threading which enable interfaces to run at different frame rates are also discussed in this paper.

System Software Framework for System of Systems Avionics

NASA Technical Reports Server (NTRS)

Ferguson, Roscoe C.; Peterson, Benjamin L; Thompson, Hiram C.

2005-01-01

Project Constellation implements NASA's vision for space exploration to expand human presence in our solar system. The engineering focus of this project is developing a system of systems architecture. This architecture allows for the incremental development of the overall program. Systems can be built and connected in a "Lego style" manner to generate configurations supporting various mission objectives. The development of the avionics or control systems of such a massive project will result in concurrent engineering. Also, each system will have software and the need to communicate with other (possibly heterogeneous) systems. Fortunately, this design problem has already been solved during the creation and evolution of systems such as the Internet and the Department of Defense's successful effort to standardize distributed simulation (now IEEE 1516). The solution relies on the use of a standard layered software framework and a communication protocol. A standard framework and communication protocol is suggested for the development and maintenance of Project Constellation systems. The ARINC 653 standard is a great start for such a common software framework. This paper proposes a common system software framework that uses the Real Time Publish/Subscribe protocol for framework-to-framework communication to extend ARINC 653. It is highly recommended that such a framework be established before development. This is important for the success of concurrent engineering. The framework provides an infrastructure for general system services and is designed for flexibility to support a spiral development effort.

Experimentation in software engineering

NASA Technical Reports Server (NTRS)

Basili, V. R.; Selby, R. W.; Hutchens, D. H.

1986-01-01

Experimentation in software engineering supports the advancement of the field through an iterative learning process. In this paper, a framework for analyzing most of the experimental work performed in software engineering over the past several years is presented. A variety of experiments in the framework is described and their contribution to the software engineering discipline is discussed. Some useful recommendations for the application of the experimental process in software engineering are included.

Towards Model-Driven End-User Development in CALL

ERIC Educational Resources Information Center

Farmer, Rod; Gruba, Paul

2006-01-01

The purpose of this article is to introduce end-user development (EUD) processes to the CALL software development community. EUD refers to the active participation of end-users, as non-professional developers, in the software development life cycle. Unlike formal software engineering approaches, the focus in EUD on means/ends development is…

Successful Use of CALL Software: An Investigation from the User's Perspective

ERIC Educational Resources Information Center

Scagnoli, Norma; Yontz, Ruth; Choo, Jinhee

2014-01-01

This study explores the use and implementation of computer-assisted language learning (CALL) software in graduate professional education. The investigation looked into self-reported information on graduate students' use of ESL (English as a Second Language) software to improve language skills and their competencies in professional English…

A Prototype for the Support of Integrated Software Process Development and Improvement

NASA Astrophysics Data System (ADS)

Porrawatpreyakorn, Nalinpat; Quirchmayr, Gerald; Chutimaskul, Wichian

An efficient software development process is one of key success factors for quality software. Not only can the appropriate establishment but also the continuous improvement of integrated project management and of the software development process result in efficiency. This paper hence proposes a software process maintenance framework which consists of two core components: an integrated PMBOK-Scrum model describing how to establish a comprehensive set of project management and software engineering processes and a software development maturity model advocating software process improvement. Besides, a prototype tool to support the framework is introduced.

EAGLE: 'EAGLE'Is an' Algorithmic Graph Library for Exploration

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

2015-01-16

The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. Today there is no tools to conduct "graph mining" on RDF standard data sets. We address that need through implementation of popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, degree distribution,more » diversity degree, PageRank, etc.). We implement these algorithms as SPARQL queries, wrapped within Python scripts and call our software tool as EAGLE. In RDF style, EAGLE stands for "EAGLE 'Is an' algorithmic graph library for exploration. EAGLE is like 'MATLAB' for 'Linked Data.'« less

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

PubMed

Buske, Fabian A; French, Hugh J; Smith, Martin A; Clark, Susan J; Bauer, Denis C

2014-05-15

The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. Denis.Bauer@csiro.au Supplementary data are available at Bioinformatics online.

Framework Based Guidance Navigation and Control Flight Software Development

NASA Technical Reports Server (NTRS)

McComas, David

2007-01-01

This viewgraph presentation describes NASA's guidance navigation and control flight software development background. The contents include: 1) NASA/Goddard Guidance Navigation and Control (GN&C) Flight Software (FSW) Development Background; 2) GN&C FSW Development Improvement Concepts; and 3) GN&C FSW Application Framework.

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: An Earth Modeling System Software Framework Strawman Design that Integrates Cactus and UCLA/UCB Distributed Data Broker

NASA Technical Reports Server (NTRS)

Talbot, Bryan; Zhou, Shu-Jia; Higgins, Glenn

2002-01-01

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task. both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation, while maintaining high performance across numerous supercomputer and workstation architectures. This document proposes a strawman framework design for the climate community based on the integration of Cactus, from the relativistic physics community, and UCLA/UCB Distributed Data Broker (DDB) from the climate community. This design is the result of an extensive survey of climate models and frameworks in the climate community as well as frameworks from many other scientific communities. The design addresses fundamental development and runtime needs using Cactus, a framework with interfaces for FORTRAN and C-based languages, and high-performance model communication needs using DDB. This document also specifically explores object-oriented design issues in the context of climate modeling as well as climate modeling issues in terms of object-oriented design.

A Validation Framework for the Long Term Preservation of High Energy Physics Data

NASA Astrophysics Data System (ADS)

Ozerov, Dmitri; South, David M.

2014-06-01

The study group on data preservation in high energy physics, DPHEP, is moving to a new collaboration structure, which will focus on the implementation of preservation projects, such as those described in the group's large scale report published in 2012. One such project is the development of a validation framework, which checks the compatibility of evolving computing environments and technologies with the experiments software for as long as possible, with the aim of substantially extending the lifetime of the analysis software, and hence of the usability of the data. The framework is designed to automatically test and validate the software and data of an experiment against changes and upgrades to the computing environment, as well as changes to the experiment software itself. Technically, this is realised using a framework capable of hosting a number of virtual machine images, built with different configurations of operating systems and the relevant software, including any necessary external dependencies.

The Health Service Bus: an architecture and case study in achieving interoperability in healthcare.

PubMed

Ryan, Amanda; Eklund, Peter

2010-01-01

Interoperability in healthcare is a requirement for effective communication between entities, to ensure timely access to up to-date patient information and medical knowledge, and thus facilitate consistent patient care. An interoperability framework called the Health Service Bus (HSB), based on the Enterprise Service Bus (ESB) middleware software architecture is presented here as a solution to all three levels of interoperability as defined by the HL7 EHR Interoperability Work group in their definitive white paper "Coming to Terms". A prototype HSB system was implemented based on the Mule Open-Source ESB and is outlined and discussed, followed by a clinically-based example.

An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

PubMed

Zhang, Zhe; Fenstermacher, David

2005-01-01

Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

Practical use of a framework for network science experimentation

NASA Astrophysics Data System (ADS)

Toth, Andrew; Bergamaschi, Flavio

2014-06-01

In 2006, the US Army Research Laboratory (ARL) and the UK Ministry of Defence (MoD) established a collaborative research alliance with academia and industry, called the International Technology Alliance (ITA)1 In Network and Information Sciences, to address fundamental issues concerning Network and Information Sciences that will enhance decision making for coalition operations and enable rapid, secure formation of ad hoc teams in coalition environments and enhance US and UK capabilities to conduct coalition warfare. Research conducted under the ITA was extended through collaboration between ARL and IBM UK to characterize and dene a software stack and tooling that has become the reference framework for network science experimentation in support for validation of theoretical research. This paper discusses the composition of the reference framework for experimentation resulting from the ARL/IBM UK collaboration and its use, by the Network Science Collaborative Technology Alliance (NS CTA)2 , in a recent network science experiment conducted at ARL. It also discusses how the experiment was modeled using the reference framework, the integration of two new components, the Apollo Fact-Finder3 tool and the Medusa Crowd Sensing4 application, the limitations identified and how they shall be addressed in future work.

Distributed Computing Framework for Synthetic Radar Application

NASA Technical Reports Server (NTRS)

Gurrola, Eric M.; Rosen, Paul A.; Aivazis, Michael

2006-01-01

We are developing an extensible software framework, in response to Air Force and NASA needs for distributed computing facilities for a variety of radar applications. The objective of this work is to develop a Python based software framework, that is the framework elements of the middleware that allows developers to control processing flow on a grid in a distributed computing environment. Framework architectures to date allow developers to connect processing functions together as interchangeable objects, thereby allowing a data flow graph to be devised for a specific problem to be solved. The Pyre framework, developed at the California Institute of Technology (Caltech), and now being used as the basis for next-generation radar processing at JPL, is a Python-based software framework. We have extended the Pyre framework to include new facilities to deploy processing components as services, including components that monitor and assess the state of the distributed network for eventual real-time control of grid resources.

VCFR: A package to manipulate and visualize variant call format data in R

USDA-ARS?s Scientific Manuscript database

Software to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (vcf) as their output format of choice. This has created a need for tools to work with vcf files. While an increasing number of software exists to read vcf data, many of them only ex...

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

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

Oster, S.; Langella, S.; Hastings, S.

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design: An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG{trademark}) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including (1) discovery, (2) integrated and large-scale data analysis, and (3) coordinated study. Measurements: The caGrid is built as a Grid software infrastructure andmore » leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results: The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: .« less

A software framework for real-time multi-modal detection of microsleeps.

PubMed

Knopp, Simon J; Bones, Philip J; Weddell, Stephen J; Jones, Richard D

2017-09-01

A software framework is described which was designed to process EEG, video of one eye, and head movement in real time, towards achieving early detection of microsleeps for prevention of fatal accidents, particularly in transport sectors. The framework is based around a pipeline structure with user-replaceable signal processing modules. This structure can encapsulate a wide variety of feature extraction and classification techniques and can be applied to detecting a variety of aspects of cognitive state. Users of the framework can implement signal processing plugins in C++ or Python. The framework also provides a graphical user interface and the ability to save and load data to and from arbitrary file formats. Two small studies are reported which demonstrate the capabilities of the framework in typical applications: monitoring eye closure and detecting simulated microsleeps. While specifically designed for microsleep detection/prediction, the software framework can be just as appropriately applied to (i) other measures of cognitive state and (ii) development of biomedical instruments for multi-modal real-time physiological monitoring and event detection in intensive care, anaesthesiology, cardiology, neurosurgery, etc. The software framework has been made freely available for researchers to use and modify under an open source licence.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Nemesis Autonomous Test System

NASA Technical Reports Server (NTRS)

Barltrop, Kevin J.; Lee, Cin-Young; Horvath, Gregory A,; Clement, Bradley J.

2012-01-01

A generalized framework has been developed for systems validation that can be applied to both traditional and autonomous systems. The framework consists of an automated test case generation and execution system called Nemesis that rapidly and thoroughly identifies flaws or vulnerabilities within a system. By applying genetic optimization and goal-seeking algorithms on the test equipment side, a "war game" is conducted between a system and its complementary nemesis. The end result of the war games is a collection of scenarios that reveals any undesirable behaviors of the system under test. The software provides a reusable framework to evolve test scenarios using genetic algorithms using an operation model of the system under test. It can automatically generate and execute test cases that reveal flaws in behaviorally complex systems. Genetic algorithms focus the exploration of tests on the set of test cases that most effectively reveals the flaws and vulnerabilities of the system under test. It leverages advances in state- and model-based engineering, which are essential in defining the behavior of autonomous systems. It also uses goal networks to describe test scenarios.

INITIATE: An Intelligent Adaptive Alert Environment.

PubMed

Jafarpour, Borna; Abidi, Samina Raza; Ahmad, Ahmad Marwan; Abidi, Syed Sibte Raza

2015-01-01

Exposure to a large volume of alerts generated by medical Alert Generating Systems (AGS) such as drug-drug interaction softwares or clinical decision support systems over-whelms users and causes alert fatigue in them. Some of alert fatigue effects are ignoring crucial alerts and longer response times. A common approach to avoid alert fatigue is to devise mechanisms in AGS to stop them from generating alerts that are deemed irrelevant. In this paper, we present a novel framework called INITIATE: an INtellIgent adapTIve AlerT Environment to avoid alert fatigue by managing alerts generated by one or more AGS. We have identified and categories the lifecycle of different alerts and have developed alert management logic as per the alerts' lifecycle. Our framework incorporates an ontology that represents the alert management strategy and an alert management engine that executes this strategy. Our alert management framework offers the following features: (1) Adaptability based on users' feedback; (2) Personalization and aggregation of messages; and (3) Connection to Electronic Medical Records by implementing a HL7 Clinical Document Architecture parser.

BioContainers: an open-source and community-driven framework for software standardization.

PubMed

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

BioContainers: an open-source and community-driven framework for software standardization

PubMed Central

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

Surgical model-view-controller simulation software framework for local and collaborative applications

PubMed Central

Sankaranarayanan, Ganesh; Halic, Tansel; Arikatla, Venkata Sreekanth; Lu, Zhonghua; De, Suvranu

2010-01-01

Purpose Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. Methods A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. Results The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. Conclusion A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users. PMID:20714933

Surgical model-view-controller simulation software framework for local and collaborative applications.

PubMed

Maciel, Anderson; Sankaranarayanan, Ganesh; Halic, Tansel; Arikatla, Venkata Sreekanth; Lu, Zhonghua; De, Suvranu

2011-07-01

Surgical simulations require haptic interactions and collaboration in a shared virtual environment. A software framework for decoupled surgical simulation based on a multi-controller and multi-viewer model-view-controller (MVC) pattern was developed and tested. A software framework for multimodal virtual environments was designed, supporting both visual interactions and haptic feedback while providing developers with an integration tool for heterogeneous architectures maintaining high performance, simplicity of implementation, and straightforward extension. The framework uses decoupled simulation with updates of over 1,000 Hz for haptics and accommodates networked simulation with delays of over 1,000 ms without performance penalty. The simulation software framework was implemented and was used to support the design of virtual reality-based surgery simulation systems. The framework supports the high level of complexity of such applications and the fast response required for interaction with haptics. The efficacy of the framework was tested by implementation of a minimally invasive surgery simulator. A decoupled simulation approach can be implemented as a framework to handle simultaneous processes of the system at the various frame rates each process requires. The framework was successfully used to develop collaborative virtual environments (VEs) involving geographically distributed users connected through a network, with the results comparable to VEs for local users.

Introducing Python tools for magnetotellurics: MTpy

NASA Astrophysics Data System (ADS)

Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

2013-12-01

Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South Australia. Workflow of MT data processing. Within the structural diagram, the MTpy sub-packages are shown in red (time series data processing), green (handling of EDI files and impedance tensor data), yellow (connection to modelling/inversion algorithms), black (impedance tensor interpretation, e.g. by Phase Tensor calculations), and blue (generation of visual representations, e.g pseudo sections or resistivity models).

HPC Software Stack Testing Framework

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

Garvey, Cormac

The HPC Software stack testing framework (hpcswtest) is used in the INL Scientific Computing Department to test the basic sanity and integrity of the HPC Software stack (Compilers, MPI, Numerical libraries and Applications) and to quickly discover hard failures, and as a by-product it will indirectly check the HPC infrastructure (network, PBS and licensing servers).

What Does CALL Have to Offer Computer Science and What Does Computer Science Have to Offer CALL?

ERIC Educational Resources Information Center

Cushion, Steve

2006-01-01

We will argue that CALL can usefully be viewed as a subset of computer software engineering and can profit from adopting some of the recent progress in software development theory. The unified modelling language has become the industry standard modelling technique and the accompanying unified process is rapidly gaining acceptance. The manner in…

ATLAS offline software performance monitoring and optimization

NASA Astrophysics Data System (ADS)

Chauhan, N.; Kabra, G.; Kittelmann, T.; Langenberg, R.; Mandrysch, R.; Salzburger, A.; Seuster, R.; Ritsch, E.; Stewart, G.; van Eldik, N.; Vitillo, R.; Atlas Collaboration

2014-06-01

In a complex multi-developer, multi-package software environment, such as the ATLAS offline framework Athena, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide the optimization work. The first tool we used to instrument the code is PAPI, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles, instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event results in a good understanding of the algorithm level performance of ATLAS code. Further data can be obtained using Pin, a dynamic binary instrumentation tool. Pin tools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is also possible. Pin tools can additionally interrogate the arguments to functions, like those in linear algebra libraries, so that a detailed usage profile can be obtained. These tools have characterized the extensive use of vector and matrix operations in ATLAS tracking. Currently, CLHEP is used here, which is not an optimal choice. To help evaluate replacement libraries a testbed has been setup allowing comparison of the performance of different linear algebra libraries (including CLHEP, Eigen and SMatrix/SVector). Results are then presented via the ATLAS Performance Management Board framework, which runs daily with the current development branch of the code and monitors reconstruction and Monte-Carlo jobs. This framework analyses the CPU and memory performance of algorithms and an overview of results are presented on a web page. These tools have provided the insight necessary to plan and implement performance enhancements in ATLAS code by identifying the most common operations, with the call parameters well understood, and allowing improvements to be quantified in detail.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

PubMed Central

Degenhart, Alan D.; Kelly, John W.; Ashmore, Robin C.; Collinger, Jennifer L.; Tyler-Kabara, Elizabeth C.; Weber, Douglas J.; Wang, Wei

2011-01-01

This paper presents “Craniux,” an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development. PMID:21687575

Craniux: a LabVIEW-based modular software framework for brain-machine interface research.

PubMed

Degenhart, Alan D; Kelly, John W; Ashmore, Robin C; Collinger, Jennifer L; Tyler-Kabara, Elizabeth C; Weber, Douglas J; Wang, Wei

2011-01-01

This paper presents "Craniux," an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development.

Problem Solving Frameworks for Mathematics and Software Development

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Blake, Ashley

2012-01-01

In this research, we examine how problem solving frameworks differ between Mathematics and Software Development. Our methodology is based on the assumption that the words used frequently in a book indicate the mental framework of the author. We compared word frequencies in a sample of 139 books that discuss problem solving. The books were grouped…

PVM Wrapper

NASA Technical Reports Server (NTRS)

Katz, Daniel

2004-01-01

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

Abstraction and Assume-Guarantee Reasoning for Automated Software Verification

NASA Technical Reports Server (NTRS)

Chaki, S.; Clarke, E.; Giannakopoulou, D.; Pasareanu, C. S.

2004-01-01

Compositional verification and abstraction are the key techniques to address the state explosion problem associated with model checking of concurrent software. A promising compositional approach is to prove properties of a system by checking properties of its components in an assume-guarantee style. This article proposes a framework for performing abstraction and assume-guarantee reasoning of concurrent C code in an incremental and fully automated fashion. The framework uses predicate abstraction to extract and refine finite state models of software and it uses an automata learning algorithm to incrementally construct assumptions for the compositional verification of the abstract models. The framework can be instantiated with different assume-guarantee rules. We have implemented our approach in the COMFORT reasoning framework and we show how COMFORT out-performs several previous software model checking approaches when checking safety properties of non-trivial concurrent programs.

Parallels in Computer-Aided Design Framework and Software Development Environment Efforts.

DTIC Science & Technology

1992-05-01

de - sign kits, and tool and design management frameworks. Also, books about software engineer- ing environments [Long 91] and electronic design...tool integration [Zarrella 90], and agreement upon a universal de - sign automation framework, such as the CAD Framework Initiative (CFI) [Malasky 91...ments: identification, control, status accounting, and audit and review. The paper by Dart ex- tracts 15 CM concepts from existing SDEs and tools

Applying a Framework to Evaluate Assignment Marking Software: A Case Study on Lightwork

ERIC Educational Resources Information Center

Heinrich, Eva; Milne, John

2012-01-01

This article presents the findings of a qualitative evaluation on the effect of a specialised software tool on the efficiency and quality of assignment marking. The software, Lightwork, combines with the Moodle learning management system and provides support through marking rubrics and marker allocations. To enable the evaluation a framework has…

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

Model Diagnostics for the Department of Energy's Accelerated Climate Modeling for Energy (ACME) Project

NASA Astrophysics Data System (ADS)

Smith, B.

2015-12-01

In 2014, eight Department of Energy (DOE) national laboratories, four academic institutions, one company, and the National Centre for Atmospheric Research combined forces in a project called Accelerated Climate Modeling for Energy (ACME) with the goal to speed Earth system model development for climate and energy. Over the planned 10-year span, the project will conduct simulations and modeling on DOE's most powerful high-performance computing systems at Oak Ridge, Argonne, and Lawrence Berkeley Leadership Compute Facilities. A key component of the ACME project is the development of an interactive test bed for the advanced Earth system model. Its execution infrastructure will accelerate model development and testing cycles. The ACME Workflow Group is leading the efforts to automate labor-intensive tasks, provide intelligent support for complex tasks and reduce duplication of effort through collaboration support. As part of this new workflow environment, we have created a diagnostic, metric, and intercomparison Python framework, called UVCMetrics, to aid in the testing-to-production execution of the ACME model. The framework exploits similarities among different diagnostics to compactly support diagnosis of new models. It presently focuses on atmosphere and land but is designed to support ocean and sea ice model components as well. This framework is built on top of the existing open-source software framework known as the Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT). Because of its flexible framework design, scientists and modelers now can generate thousands of possible diagnostic outputs. These diagnostics can compare model runs, compare model vs. observation, or simply verify a model is physically realistic. Additional diagnostics are easily integrated into the framework, and our users have already added several. Diagnostics can be generated, viewed, and manipulated from the UV-CDAT graphical user interface, Python command line scripts and programs, and web browsers. The framework is designed to be scalable to large datasets, yet easy to use and familiar to scientists using previous tools. Integration in the ACME overall user interface facilitates data publication, further analysis, and quick feedback to model developers and scientists making component or coupled model runs.

Knowledge assistant for robotic environmental characterization

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

Feddema, J.; Rivera, J.; Tucker, S.

1996-08-01

A prototype sensor fusion framework called the {open_quotes}Knowledge Assistant{close_quotes} has been developed and tested on a gantry robot at Sandia National Laboratories. This Knowledge Assistant guides the robot operator during the planning, execution, and post analysis stages of the characterization process. During the planning stage, the Knowledge Assistant suggests robot paths and speeds based on knowledge of sensors available and their physical characteristics. During execution, the Knowledge Assistant coordinates the collection of data through a data acquisition {open_quotes}specialist.{close_quotes} During execution and postanalysis, the Knowledge Assistant sends raw data to other {open_quotes}specialists,{close_quotes} which include statistical pattern recognition software, a neural network,more » and model-based search software. After the specialists return their results, the Knowledge Assistant consolidates the information and returns a report to the robot control system where the sensed objects and their attributes (e.g., estimated dimensions, weight, material composition, etc.) are displayed in the world model. This report highlights the major components of this system.« less

jmzTab: a java interface to the mzTab data standard.

PubMed

Xu, Qing-Wei; Griss, Johannes; Wang, Rui; Jones, Andrew R; Hermjakob, Henning; Vizcaíno, Juan Antonio

2014-06-01

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches. We here present an open-source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files. In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com. © 2014 The Authors PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Federated software defined network operations for LHC experiments

NASA Astrophysics Data System (ADS)

Kim, Dongkyun; Byeon, Okhwan; Cho, Kihyeon

2013-09-01

The most well-known high-energy physics collaboration, the Large Hadron Collider (LHC), which is based on e-Science, has been facing several challenges presented by its extraordinary instruments in terms of the generation, distribution, and analysis of large amounts of scientific data. Currently, data distribution issues are being resolved by adopting an advanced Internet technology called software defined networking (SDN). Stability of the SDN operations and management is demanded to keep the federated LHC data distribution networks reliable. Therefore, in this paper, an SDN operation architecture based on the distributed virtual network operations center (DvNOC) is proposed to enable LHC researchers to assume full control of their own global end-to-end data dissemination. This may achieve an enhanced data delivery performance based on data traffic offloading with delay variation. The evaluation results indicate that the overall end-to-end data delivery performance can be improved over multi-domain SDN environments based on the proposed federated SDN/DvNOC operation framework.

Achieving Agility and Stability in Large-Scale Software Development

DTIC Science & Technology

2013-01-16

temporary team is assigned to prepare layers and frameworks for future feature teams. Presentation Layer Domain Layer Data Access Layer Framework...http://www.sei.cmu.edu/training/ elearning ~ Software Engineering Institute CarnegieMellon

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

NASA Technical Reports Server (NTRS)

Ordaz, Irian

2011-01-01

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

A Software Rejuvenation Framework for Distributed Computing

NASA Technical Reports Server (NTRS)

Chau, Savio

2009-01-01

A performability-oriented conceptual framework for software rejuvenation has been constructed as a means of increasing levels of reliability and performance in distributed stateful computing. As used here, performability-oriented signifies that the construction of the framework is guided by the concept of analyzing the ability of a given computing system to deliver services with gracefully degradable performance. The framework is especially intended to support applications that involve stateful replicas of server computers.

A software framework for developing measurement applications under variable requirements.

PubMed

Arpaia, Pasquale; Buzio, Marco; Fiscarelli, Lucio; Inglese, Vitaliano

2012-11-01

A framework for easily developing software for measurement and test applications under highly and fast-varying requirements is proposed. The framework allows the software quality, in terms of flexibility, usability, and maintainability, to be maximized. Furthermore, the development effort is reduced and finalized, by relieving the test engineer of development details. The framework can be configured for satisfying a large set of measurement applications in a generic field for an industrial test division, a test laboratory, or a research center. As an experimental case study, the design, the implementation, and the assessment inside the application to a measurement scenario of magnet testing at the European Organization for Nuclear Research is reported.

A Methodological Framework for Enterprise Information System Requirements Derivation

NASA Astrophysics Data System (ADS)

Caplinskas, Albertas; Paškevičiūtė, Lina

Current information systems (IS) are enterprise-wide systems supporting strategic goals of the enterprise and meeting its operational business needs. They are supported by information and communication technologies (ICT) and other software that should be fully integrated. To develop software responding to real business needs, we need requirements engineering (RE) methodology that ensures the alignment of requirements for all levels of enterprise system. The main contribution of this chapter is a requirement-oriented methodological framework allowing to transform business requirements level by level into software ones. The structure of the proposed framework reflects the structure of Zachman's framework. However, it has other intentions and is purposed to support not the design but the RE issues.

A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints.

PubMed

Sundharam, Sakthivel Manikandan; Navet, Nicolas; Altmeyer, Sebastian; Havet, Lionel

2018-02-20

Model-Driven Engineering (MDE) is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS). The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller), he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency). This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language), an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system.

A Model-Driven Co-Design Framework for Fusing Control and Scheduling Viewpoints

PubMed Central

Navet, Nicolas; Havet, Lionel

2018-01-01

Model-Driven Engineering (MDE) is widely applied in the industry to develop new software functions and integrate them into the existing run-time environment of a Cyber-Physical System (CPS). The design of a software component involves designers from various viewpoints such as control theory, software engineering, safety, etc. In practice, while a designer from one discipline focuses on the core aspects of his field (for instance, a control engineer concentrates on designing a stable controller), he neglects or considers less importantly the other engineering aspects (for instance, real-time software engineering or energy efficiency). This may cause some of the functional and non-functional requirements not to be met satisfactorily. In this work, we present a co-design framework based on timing tolerance contract to address such design gaps between control and real-time software engineering. The framework consists of three steps: controller design, verified by jitter margin analysis along with co-simulation, software design verified by a novel schedulability analysis, and the run-time verification by monitoring the execution of the models on target. This framework builds on CPAL (Cyber-Physical Action Language), an MDE design environment based on model-interpretation, which enforces a timing-realistic behavior in simulation through timing and scheduling annotations. The application of our framework is exemplified in the design of an automotive cruise control system. PMID:29461489

A Buyer Behaviour Framework for the Development and Design of Software Agents in E-Commerce.

ERIC Educational Resources Information Center

Sproule, Susan; Archer, Norm

2000-01-01

Software agents are computer programs that run in the background and perform tasks autonomously as delegated by the user. This paper blends models from marketing research and findings from the field of decision support systems to build a framework for the design of software agents to support in e-commerce buying applications. (Contains 35…

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

IMIS desktop & smartphone software solutions for monitoring spacecrafts' payload from anywhere

NASA Astrophysics Data System (ADS)

Baroukh, J.; Queyrut, O.; Airaud, J.

In the past years, the demand for satellite remote operations has increased guided by on one hand, the will to reduce operations cost (on-call operators out of business hours), and on the other hand, the development of cooperation space missions resulting in a world wide distribution of engineers and science team members. Only a few off-the-shelf solutions exist to fulfill the need of remote payload monitoring, and they mainly use proprietary devices. The recent advent of mobile technologies (laptops, smartphones and tablets) as well as the worldwide deployment of broadband networks (3G, Wi-Fi hotspots), has opened up a technical window that brings new options. As part of the Mars Science Laboratory (MSL) mission, the Centre National D'Etudes Spatiales (CNES, the French space agency) has developed a new software solution for monitoring spacecraft payloads. The Instrument Monitoring Interactive Software (IMIS) offers state-of-the-art operational features for payload monitoring, and can be accessed remotely. It was conceived as a generic tool that can be used for heterogeneous payloads and missions. IMIS was designed as a classical client/server architecture. The server is hosted at CNES and acts as a data provider while two different kinds of clients are available depending on the level of mobility required. The first one is a rich client application, built on Eclipse framework, which can be installed on usual operating systems and communicates with the server through the Internet. The second one is a smartphone application for any Android platform, connected to the server thanks to the mobile broadband network or a Wi-Fi connection. This second client is mainly devoted to on-call operations and thus only contains a subset of the IMIS functionalities. This paper describes the operational context, including security aspects, that led IMIS development, presents the selected software architecture and details the various features of both clients: the desktop and the sm- rtphone application.

ControlShell - A real-time software framework

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Software Framework for Peer Data-Management Services

NASA Technical Reports Server (NTRS)

Hughes, John; Hardman, Sean; Crichton, Daniel; Hyon, Jason; Kelly, Sean; Tran, Thuy

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-to-peer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

Are cellular phone blocking applications effective for novice teen drivers?

PubMed

Creaser, Janet I; Edwards, Christopher J; Morris, Nichole L; Donath, Max

2015-09-01

Distracted driving is a significant concern for novice teen drivers. Although cellular phone bans are applied in many jurisdictions to restrict cellular phone use, teen drivers often report making calls and texts while driving. The Minnesota Teen Driver Study incorporated cellular phone blocking functions via a software application for 182 novice teen drivers in two treatment conditions. The first condition included 92 teens who ran a driver support application on a smartphone that also blocked phone usage. The second condition included 90 teens who ran the same application with phone blocking but which also reported back to parents about monitored risky behaviors (e.g., speeding). A third control group consisting of 92 novice teen drivers had the application and phone-based software installed on the phones to record cellular phone (but not block it) use while driving. The two treatment groups made significantly fewer calls and texts per mile driven compared to the control group. The control group data also demonstrated a higher propensity to text while driving rather than making calls. Software that blocks cellular phone use (except 911) while driving can be effective at mitigating calling and texting for novice teen drivers. However, subjective data indicates that some teens were motivated to find ways around the software, as well as to use another teen's phone while driving when they were unable to use theirs. Cellular phone bans for calling and texting are the first step to changing behaviors associated with texting and driving, particularly among novice teen drivers. Blocking software has the additional potential to reduce impulsive calling and texting while driving among novice teen drivers who might logically know the risks, but for whom it is difficult to ignore calling or texting while driving. Copyright © 2015 Elsevier Ltd and National Safety Council. All rights reserved.

Architecture of a framework for providing information services for public transport.

PubMed

García, Carmelo R; Pérez, Ricardo; Lorenzo, Alvaro; Quesada-Arencibia, Alexis; Alayón, Francisco; Padrón, Gabino

2012-01-01

This paper presents OnRoute, a framework for developing and running ubiquitous software that provides information services to passengers of public transportation, including payment systems and on-route guidance services. To achieve a high level of interoperability, accessibility and context awareness, OnRoute uses the ubiquitous computing paradigm. To guarantee the quality of the software produced, the reliable software principles used in critical contexts, such as automotive systems, are also considered by the framework. The main components of its architecture (run-time, system services, software components and development discipline) and how they are deployed in the transportation network (stations and vehicles) are described in this paper. Finally, to illustrate the use of OnRoute, the development of a guidance service for travellers is explained.

A Software Framework for Aircraft Simulation

NASA Technical Reports Server (NTRS)

Curlett, Brian P.

2008-01-01

The National Aeronautics and Space Administration Dryden Flight Research Center has a long history in developing simulations of experimental fixed-wing aircraft from gliders to suborbital vehicles on platforms ranging from desktop simulators to pilot-in-the-loop/aircraft-in-the-loop simulators. Regardless of the aircraft or simulator hardware, much of the software framework is common to all NASA Dryden simulators. Some of this software has withstood the test of time, but in recent years the push toward high-fidelity user-friendly simulations has resulted in some significant changes. This report presents an overview of the current NASA Dryden simulation software framework and capabilities with an emphasis on the new features that have permitted NASA to develop more capable simulations while maintaining the same staffing levels.

Property-Based Software Engineering Measurement

NASA Technical Reports Server (NTRS)

Briand, Lionel; Morasca, Sandro; Basili, Victor R.

1995-01-01

Little theory exists in the field of software system measurement. Concepts such as complexity, coupling, cohesion or even size are very often subject to interpretation and appear to have inconsistent definitions in the literature. As a consequence, there is little guidance provided to the analyst attempting to define proper measures for specific problems. Many controversies in the literature are simply misunderstandings and stem from the fact that some people talk about different measurement concepts under the same label (complexity is the most common case). There is a need to define unambiguously the most important measurement concepts used in the measurement of software products. One way of doing so is to define precisely what mathematical properties characterize these concepts regardless of the specific software artifacts to which these concepts are applied. Such a mathematical framework could generate a consensus in the software engineering community and provide a means for better communication among researchers, better guidelines for analysis, and better evaluation methods for commercial static analyzers for practitioners. In this paper, we propose a mathematical framework which is generic, because it is not specific to any particular software artifact, and rigorous, because it is based on precise mathematical concepts. This framework defines several important measurement concepts (size, length, complexity, cohesion, coupling). It is not intended to be complete or fully objective; other frameworks could have been proposed and different choices could have been made. However, we believe that the formalism and properties we introduce are convenient and intuitive. In addition, we have reviewed the literature on this subject and compared it with our work. This framework contributes constructively to a firmer theoretical ground of software measurement.

Property-Based Software Engineering Measurement

NASA Technical Reports Server (NTRS)

Briand, Lionel C.; Morasca, Sandro; Basili, Victor R.

1997-01-01

Little theory exists in the field of software system measurement. Concepts such as complexity, coupling, cohesion or even size are very often subject to interpretation and appear to have inconsistent definitions in the literature. As a consequence, there is little guidance provided to the analyst attempting to define proper measures for specific problems. Many controversies in the literature are simply misunderstandings and stem from the fact that some people talk about different measurement concepts under the same label (complexity is the most common case). There is a need to define unambiguously the most important measurement concepts used in the measurement of software products. One way of doing so is to define precisely what mathematical properties characterize these concepts, regardless of the specific software artifacts to which these concepts are applied. Such a mathematical framework could generate a consensus in the software engineering community and provide a means for better communication among researchers, better guidelines for analysts, and better evaluation methods for commercial static analyzers for practitioners. In this paper, we propose a mathematical framework which is generic, because it is not specific to any particular software artifact and rigorous, because it is based on precise mathematical concepts. We use this framework to propose definitions of several important measurement concepts (size, length, complexity, cohesion, coupling). It does not intend to be complete or fully objective; other frameworks could have been proposed and different choices could have been made. However, we believe that the formalisms and properties we introduce are convenient and intuitive. This framework contributes constructively to a firmer theoretical ground of software measurement.

Matriarch: A Python Library for Materials Architecture.

PubMed

Giesa, Tristan; Jagadeesan, Ravi; Spivak, David I; Buehler, Markus J

2015-10-12

Biological materials, such as proteins, often have a hierarchical structure ranging from basic building blocks at the nanoscale (e.g., amino acids) to assembled structures at the macroscale (e.g., fibers). Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric arrangement of unequilibrated structures. Given some knowledge of a larger-scale structure, instructing the software to create it can be very difficult and time-intensive. To this end, the present paper reports a mathematical language, using category theory, to describe the architecture of a material, i.e., its set of building blocks and instructions for combining them. While this framework applies to any hierarchical material, here we concentrate on proteins. We implement this mathematical language as an open-source Python library called Matriarch. It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality. As a case study, we use our software to alter both building blocks and building instructions for tropocollagen, and determine their effect on its structure and mechanical properties.

MTpy: A Python toolbox for magnetotellurics

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared R.

2014-11-01

We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

MAPI: towards the integrated exploitation of bioinformatics Web Services.

PubMed

Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

2011-10-27

Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

Construction of integrated case environments.

PubMed

Losavio, Francisca; Matteo, Alfredo; Pérez, María

2003-01-01

The main goal of Computer-Aided Software Engineering (CASE) technology is to improve the entire software system development process. The CASE approach is not merely a technology; it involves a fundamental change in the process of software development. The tendency of the CASE approach, technically speaking, is the integration of tools that assist in the application of specific methods. In this sense, the environment architecture, which includes the platform and the system's hardware and software, constitutes the base of the CASE environment. The problem of tools integration has been proposed for two decades. Current integration efforts emphasize the interoperability of tools, especially in distributed environments. In this work we use the Brown approach. The environment resulting from the application of this model is called a federative environment, focusing on the fact that this architecture pays special attention to the connections among the components of the environment. This approach is now being used in component-based design. This paper describes a concrete experience in civil engineering and architecture fields, for the construction of an integrated CASE environment. A generic architectural framework based on an intermediary architectural pattern is applied to achieve the integration of the different tools. This intermediary represents the control perspective of the PAC (Presentation-Abstraction-Control) style, which has been implemented as a Mediator pattern and it has been used in the interactive systems domain. In addition, a process is given to construct the integrated CASE.

ESPC Common Model Architecture Earth System Modeling Framework (ESMF) Software and Application Development

DTIC Science & Technology

2015-09-30

originate from NASA , NOAA , and community modeling efforts, and support for creation of the suite was shared by sponsors from other agencies. ESPS...Framework (ESMF) Software and Application Development Cecelia Deluca NESII/CIRES/ NOAA Earth System Research Laboratory 325 Broadway Boulder, CO...Capability (NUOPC) was established between NOAA and Navy to develop a common software architecture for easy and efficient interoperability. The

Diagnosis and Prognosis of Weapon Systems

NASA Technical Reports Server (NTRS)

Nolan, Mary; Catania, Rebecca; deMare, Gregory

2005-01-01

The Prognostics Framework is a set of software tools with an open architecture that affords a capability to integrate various prognostic software mechanisms and to provide information for operational and battlefield decision-making and logistical planning pertaining to weapon systems. The Prognostics NASA Tech Briefs, February 2005 17 Framework is also a system-level health -management software system that (1) receives data from performance- monitoring and built-in-test sensors and from other prognostic software and (2) processes the received data to derive a diagnosis and a prognosis for a weapon system. This software relates the diagnostic and prognostic information to the overall health of the system, to the ability of the system to perform specific missions, and to needed maintenance actions and maintenance resources. In the development of the Prognostics Framework, effort was focused primarily on extending previously developed model-based diagnostic-reasoning software to add prognostic reasoning capabilities, including capabilities to perform statistical analyses and to utilize information pertaining to deterioration of parts, failure modes, time sensitivity of measured values, mission criticality, historical data, and trends in measurement data. As thus extended, the software offers an overall health-monitoring capability.

A vision and strategy for the virtual physiological human in 2010 and beyond.

PubMed

Hunter, Peter; Coveney, Peter V; de Bono, Bernard; Diaz, Vanessa; Fenner, John; Frangi, Alejandro F; Harris, Peter; Hose, Rod; Kohl, Peter; Lawford, Pat; McCormack, Keith; Mendes, Miriam; Omholt, Stig; Quarteroni, Alfio; Skår, John; Tegner, Jesper; Randall Thomas, S; Tollis, Ioannis; Tsamardinos, Ioannis; van Beek, Johannes H G M; Viceconti, Marco

2010-06-13

European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.

A Functional Data Model Realized: LaTiS Deployments

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Logistics Process Analysis ToolProcess Analysis Tool

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

2008-03-31

LPAT is the resulting integrated system between ANL-developed Enhanced Logistics Intra Theater Support Tool (ELIST) sponsored by SDDC-TEA and the Fort Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the process Anlysis Tool (PAT) which evolved into a stand=-along tool for detailed process analysis at a location. Combined with ELIST, an inter-installation logistics component was added to enable users to define large logistical agent-based models without having to program. PAT is the evolution of an ANL-developed software system called Fortmore » Future Virtual Installation Tool (sponsored by CERL). The Fort Future Simulation Engine was an application written in the ANL Repast Simphony framework and used as the basis for the Process Analysis Tool(PAT) which evolved into a stand-alone tool for detailed process analysis at a location (sponsored by the SDDC-TEA).« less

A vision and strategy for the virtual physiological human in 2010 and beyond

PubMed Central

Hunter, Peter; Coveney, Peter V.; de Bono, Bernard; Diaz, Vanessa; Fenner, John; Frangi, Alejandro F.; Harris, Peter; Hose, Rod; Kohl, Peter; Lawford, Pat; McCormack, Keith; Mendes, Miriam; Omholt, Stig; Quarteroni, Alfio; Skår, John; Tegner, Jesper; Randall Thomas, S.; Tollis, Ioannis; Tsamardinos, Ioannis; van Beek, Johannes H. G. M.; Viceconti, Marco

2010-01-01

European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE. PMID:20439264

3D virtual character reconstruction from projections: a NURBS-based approach

NASA Astrophysics Data System (ADS)

Triki, Olfa; Zaharia, Titus B.; Preteux, Francoise J.

2004-05-01

This work has been carried out within the framework of the industrial project, so-called TOON, supported by the French government. TOON aims at developing tools for automating the traditional 2D cartoon content production. This paper presents preliminary results of the TOON platform. The proposed methodology concerns the issues of 2D/3D reconstruction from a limited number of drawn projections, and 2D/3D manipulation/deformation/refinement of virtual characters. Specifically, we show that the NURBS-based modeling approach developed here offers a well-suited framework for generating deformable 3D virtual characters from incomplete 2D information. Furthermore, crucial functionalities such as animation and non-rigid deformation can be also efficiently handled and solved. Note that user interaction is enabled exclusively in 2D by achieving a multiview constraint specification method. This is fully consistent and compliant with the cartoon creator traditional practice and makes it possible to avoid the use of 3D modeling software packages which are generally complex to manipulate.

Bridging CALL & HCI: Input from Participatory Design

ERIC Educational Resources Information Center

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

2010-01-01

Participatory design (PD), or the collaboration between software engineers and end users throughout the design process, may help improve CALL design practices. In this case study, four ESL learners, a software designer, and a language teacher created and evaluated a series of paper prototypes concerning help options in computer-based second…

Teacher Resistance to CALL.

ERIC Educational Resources Information Center

Eastment, David

Despite the evolution of software for computer-assisted language learning (CALL), teacher resistance remains high. Early software for language instruction was almost exclusively designed for drill and practice. That approach was later replaced by a model in which the computer provided a stimulus for students, most often as a partner in games.…

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

Eighteen-Month Outcomes of Titanium Frameworks Using Computer-Aided Design and Computer-Aided Manufacturing Method.

PubMed

Turkyilmaz, Ilser; Asar, Neset Volkan

2017-06-01

The aim of the report is to introduce a new software and a new scanner with a noncontact laser probe and to present outcomes of computer-aided design and computer-aided manufacturing titanium frameworks using this new software and scanner with a laser probe. Seven patients received 40 implants placed using a 1-stage protocol. After all implants were planned using an implant planning software (NobelClinician), either 5 or 6 implants were placed in each edentulous arch. Each edentulous arch was treated with a fixed dental prosthesis using implant-supported complete-arch milled-titanium framework using the software (NobelProcera) and the scanner. All patients were followed up for 18 ± 3 months. Implant survival, prosthesis survival, framework fit, marginal bone levels, and maintenance requirements were evaluated. One implant was lost during the follow-up period, giving the implant survival rate of 97.5%; 0.4 ± 0.2 mm marginal bone loss was noted for all implants after 18 ± 3 months. None of the prostheses needed a replacement, indicating the prosthesis success rate of 100%. The results of this clinical study suggest that titanium frameworks fabricated using the software and scanner presented in this study fit accurately and may be a viable option to restore edentulous arches.

[Construction of educational software about personality disorders].

PubMed

Botti, Nadja Cristiane Lappann; Carneiro, Ana Luíza Marques; Almeida, Camila Souza; Pereira, Cíntia Braga Silva

2011-01-01

The study describes the experience of building educational software in the area of mental health. The software was developed to enable the nursing student identify personality disorders. In this process, we applied the pedagogical framework of Vygotsky and the theoretical framework of the diagnostic criteria defined by DSM-IV. From these references were identified personality disorders characters in stories and / or children's movies. The software development bank was built with multimedia graphics data, sound and explanatory. The software developed like educational game like questions with increasing levels of difficulty. The software was developed with Microsoft Office PowerPoint 2007. It is believed in the validity of this strategy for teaching-learning to the area of mental health nursing.

State-and-transition simulation models: a framework for forecasting landscape change

USGS Publications Warehouse

Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

2016-01-01

SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.

GeoSciGraph: An Ontological Framework for EarthCube Semantic Infrastructure

NASA Astrophysics Data System (ADS)

Gupta, A.; Schachne, A.; Condit, C.; Valentine, D.; Richard, S.; Zaslavsky, I.

2015-12-01

The CINERGI (Community Inventory of EarthCube Resources for Geosciences Interoperability) project compiles an inventory of a wide variety of earth science resources including documents, catalogs, vocabularies, data models, data services, process models, information repositories, domain-specific ontologies etc. developed by research groups and data practitioners. We have developed a multidisciplinary semantic framework called GeoSciGraph semantic ingration of earth science resources. An integrated ontology is constructed with Basic Formal Ontology (BFO) as its upper ontology and currently ingests multiple component ontologies including the SWEET ontology, GeoSciML's lithology ontology, Tematres controlled vocabulary server, GeoNames, GCMD vocabularies on equipment, platforms and institutions, software ontology, CUAHSI hydrology vocabulary, the environmental ontology (ENVO) and several more. These ontologies are connected through bridging axioms; GeoSciGraph identifies lexically close terms and creates equivalence class or subclass relationships between them after human verification. GeoSciGraph allows a community to create community-specific customizations of the integrated ontology. GeoSciGraph uses the Neo4J,a graph database that can hold several billion concepts and relationships. GeoSciGraph provides a number of REST services that can be called by other software modules like the CINERGI information augmentation pipeline. 1) Vocabulary services are used to find exact and approximate terms, term categories (community-provided clusters of terms e.g., measurement-related terms or environmental material related terms), synonyms, term definitions and annotations. 2) Lexical services are used for text parsing to find entities, which can then be included into the ontology by a domain expert. 3) Graph services provide the ability to perform traversal centric operations e.g., finding paths and neighborhoods which can be used to perform ontological operations like computing transitive closure (e.g., finding all subclasses of rocks). 4) Annotation services are used to adorn an arbitrary block of text (e.g., from a NOAA catalog record) with ontology terms. The system has been used to ontologically integrate diverse sources like Science-base, NOAA records, PETDB.

NASA Software Documentation Standard

NASA Technical Reports Server (NTRS)

1991-01-01

The NASA Software Documentation Standard (hereinafter referred to as "Standard") is designed to support the documentation of all software developed for NASA; its goal is to provide a framework and model for recording the essential information needed throughout the development life cycle and maintenance of a software system. The NASA Software Documentation Standard can be applied to the documentation of all NASA software. The Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. The basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

Architecture of a Framework for Providing Information Services for Public Transport

PubMed Central

García, Carmelo R.; Pérez, Ricardo; Lorenzo, Álvaro; Quesada-Arencibia, Alexis; Alayón, Francisco; Padrón, Gabino

2012-01-01

This paper presents OnRoute, a framework for developing and running ubiquitous software that provides information services to passengers of public transportation, including payment systems and on-route guidance services. To achieve a high level of interoperability, accessibility and context awareness, OnRoute uses the ubiquitous computing paradigm. To guarantee the quality of the software produced, the reliable software principles used in critical contexts, such as automotive systems, are also considered by the framework. The main components of its architecture (run-time, system services, software components and development discipline) and how they are deployed in the transportation network (stations and vehicles) are described in this paper. Finally, to illustrate the use of OnRoute, the development of a guidance service for travellers is explained. PMID:22778585

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Speech Recognition Software for Language Learning: Toward an Evaluation of Validity and Student Perceptions

ERIC Educational Resources Information Center

Cordier, Deborah

2009-01-01

A renewed focus on foreign language (FL) learning and speech for communication has resulted in computer-assisted language learning (CALL) software developed with Automatic Speech Recognition (ASR). ASR features for FL pronunciation (Lafford, 2004) are functional components of CALL designs used for FL teaching and learning. The ASR features…

Generic Software Architecture for Prognostics (GSAP) User Guide

NASA Technical Reports Server (NTRS)

Teubert, Christopher Allen; Daigle, Matthew John; Watkins, Jason; Sankararaman, Shankar; Goebel, Kai

2016-01-01

The Generic Software Architecture for Prognostics (GSAP) is a framework for applying prognostics. It makes applying prognostics easier by implementing many of the common elements across prognostic applications. The standard interface enables reuse of prognostic algorithms and models across systems using the GSAP framework.

The NOvA software testing framework

NASA Astrophysics Data System (ADS)

Tamsett, M.; C Group

2015-12-01

The NOvA experiment at Fermilab is a long-baseline neutrino experiment designed to study vε appearance in a vμ beam. NOvA has already produced more than one million Monte Carlo and detector generated files amounting to more than 1 PB in size. This data is divided between a number of parallel streams such as far and near detector beam spills, cosmic ray backgrounds, a number of data-driven triggers and over 20 different Monte Carlo configurations. Each of these data streams must be processed through the appropriate steps of the rapidly evolving, multi-tiered, interdependent NOvA software framework. In total there are greater than 12 individual software tiers, each of which performs a different function and can be configured differently depending on the input stream. In order to regularly test and validate that all of these software stages are working correctly NOvA has designed a powerful, modular testing framework that enables detailed validation and benchmarking to be performed in a fast, efficient and accessible way with minimal expert knowledge. The core of this system is a novel series of python modules which wrap, monitor and handle the underlying C++ software framework and then report the results to a slick front-end web-based interface. This interface utilises modern, cross-platform, visualisation libraries to render the test results in a meaningful way. They are fast and flexible, allowing for the easy addition of new tests and datasets. In total upwards of 14 individual streams are regularly tested amounting to over 70 individual software processes, producing over 25 GB of output files. The rigour enforced through this flexible testing framework enables NOvA to rapidly verify configurations, results and software and thus ensure that data is available for physics analysis in a timely and robust manner.

A Framework of the Use of Information in Software Testing

ERIC Educational Resources Information Center

Kaveh, Payman

2010-01-01

With the increasing role that software systems play in our daily lives, software quality has become extremely important. Software quality is impacted by the efficiency of the software testing process. There are a growing number of software testing methodologies, models, and initiatives to satisfy the need to improve software quality. The main…

ICW eHealth Framework.

PubMed

Klein, Karsten; Wolff, Astrid C; Ziebold, Oliver; Liebscher, Thomas

2008-01-01

The ICW eHealth Framework (eHF) is a powerful infrastructure and platform for the development of service-oriented solutions in the health care business. It is the culmination of many years of experience of ICW in the development and use of in-house health care solutions and represents the foundation of ICW product developments based on the Java Enterprise Edition (Java EE). The ICW eHealth Framework has been leveraged to allow development by external partners - enabling adopters a straightforward integration into ICW solutions. The ICW eHealth Framework consists of reusable software components, development tools, architectural guidelines and conventions defining a full software-development and product lifecycle. From the perspective of a partner, the framework provides services and infrastructure capabilities for integrating applications within an eHF-based solution. This article introduces the ICW eHealth Framework's basic architectural concepts and technologies. It provides an overview of its module and component model, describes the development platform that supports the complete software development lifecycle of health care applications and outlines technological aspects, mainly focusing on application development frameworks and open standards.

Evolution of the ATLAS Software Framework towards Concurrency

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

ENKI - An Open Source environmental modelling platfom

NASA Astrophysics Data System (ADS)

Kolberg, S.; Bruland, O.

2012-04-01

The ENKI software framework for implementing spatio-temporal models is now released under the LGPL license. Originally developed for evaluation and comparison of distributed hydrological model compositions, ENKI can be used for simulating any time-evolving process over a spatial domain. The core approach is to connect a set of user specified subroutines into a complete simulation model, and provide all administrative services needed to calibrate and run that model. This includes functionality for geographical region setup, all file I/O, calibration and uncertainty estimation etc. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines and various model compositions in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational water resource management. ENKI uses a plug-in structure to invoke separately compiled subroutines, separately built as dynamic-link libraries (dlls). The source code of an ENKI routine is highly compact, with a narrow framework-routine interface allowing the main program to recognise the number, types, and names of the routine's variables. The framework then exposes these variables to the user within the proper context, ensuring that distributed maps coincide spatially, time series exist for input variables, states are initialised, GIS data sets exist for static map data, manually or automatically calibrated values for parameters etc. By using function calls and memory data structures to invoke routines and facilitate information flow, ENKI provides good performance. For a typical distributed hydrological model setup in a spatial domain of 25000 grid cells, 3-4 time steps simulated per second should be expected. Future adaptation to parallel processing may further increase this speed. New modifications to ENKI include a full separation of API and user interface, making it possible to run ENKI from GIS programs and other software environments. ENKI currently compiles under Windows and Visual Studio only, but ambitions exist to remove the platform and compiler dependencies.

Towards Archetypes-Based Software Development

NASA Astrophysics Data System (ADS)

Piho, Gunnar; Roost, Mart; Perkins, David; Tepandi, Jaak

We present a framework for the archetypes based engineering of domains, requirements and software (Archetypes-Based Software Development, ABD). An archetype is defined as a primordial object that occurs consistently and universally in business domains and in business software systems. An archetype pattern is a collaboration of archetypes. Archetypes and archetype patterns are used to capture conceptual information into domain specific models that are utilized by ABD. The focus of ABD is on software factories - family-based development artefacts (domain specific languages, patterns, frameworks, tools, micro processes, and others) that can be used to build the family members. We demonstrate the usage of ABD for developing laboratory information management system (LIMS) software for the Clinical and Biomedical Proteomics Group, at the Leeds Institute of Molecular Medicine, University of Leeds.

Software Reviews Since Acquisition Reform - The Artifact Perspective

DTIC Science & Technology

2004-01-01

Risk Management OLD NEW Slide 13Acquisition of Software Intensive Systems 2004 – Peter Hantos Single, basic software paradigm Single processor Low...software risk mitigation related trade-offs must be done together Integral Software Engineering Activities Process Maturity and Quality Frameworks Quality

Improving communication among nurses and patients.

PubMed

Unluturk, Mehmet S; Ozcanhan, Mehmet H; Dalkilic, Gokhan

2015-07-01

Patients use nurse call systems to signal nurses for medical help. Traditional push button-flashing lamp call systems are not integrated with other hospital automation systems. Therefore, nurse response time becomes a matter of personal discretion. The improvement obtained by integrating a pager system into the nurse call systems does not increase care efficiency, because unnecessary visits are still not eliminated. To obtain an immediate response and a purposeful visit by a nurse; regardless of the location of nurse in hospital, traditional systems have to be improved by intelligent telephone system integration. The results of the developed Nurse Call System Software (NCSS), the Wireless Phone System Software (WPSS), the Location System Software (LSS) and the communication protocol are provided, together with detailed XML message structures. The benefits of the proposed system are also discussed and the direction of future work is presented. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Shao, Hongbing

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

Coupled dam safety analysis using WinDAM

USDA-ARS?s Scientific Manuscript database

Windows® Dam Analysis Modules (WinDAM) is a set of modular software components that can be used to analyze overtopping and internal erosion of embankment dams. Dakota is an extensive software framework for design exploration and simulation. These tools can be coupled to create a powerful framework...

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

Development and use of mathematical models and software frameworks for integrated analysis of agricultural systems and associated water use impacts

USGS Publications Warehouse

Fowler, K. R.; Jenkins, E.W.; Parno, M.; Chrispell, J.C.; Colón, A. I.; Hanson, Randall T.

2016-01-01

The development of appropriate water management strategies requires, in part, a methodology for quantifying and evaluating the impact of water policy decisions on regional stakeholders. In this work, we describe the framework we are developing to enhance the body of resources available to policy makers, farmers, and other community members in their e orts to understand, quantify, and assess the often competing objectives water consumers have with respect to usage. The foundation for the framework is the construction of a simulation-based optimization software tool using two existing software packages. In particular, we couple a robust optimization software suite (DAKOTA) with the USGS MF-OWHM water management simulation tool to provide a flexible software environment that will enable the evaluation of one or multiple (possibly competing) user-defined (or stakeholder) objectives. We introduce the individual software components and outline the communication strategy we defined for the coupled development. We present numerical results for case studies related to crop portfolio management with several defined objectives. The objectives are not optimally satisfied for any single user class, demonstrating the capability of the software tool to aid in the evaluation of a variety of competing interests.

The development of an artificial organic networks toolkit for LabVIEW.

PubMed

Ponce, Hiram; Ponce, Pedro; Molina, Arturo

2015-03-15

Two of the most challenging problems that scientists and researchers face when they want to experiment with new cutting-edge algorithms are the time-consuming for encoding and the difficulties for linking them with other technologies and devices. In that sense, this article introduces the artificial organic networks toolkit for LabVIEW™ (AON-TL) from the implementation point of view. The toolkit is based on the framework provided by the artificial organic networks technique, giving it the potential to add new algorithms in the future based on this technique. Moreover, the toolkit inherits both the rapid prototyping and the easy-to-use characteristics of the LabVIEW™ software (e.g., graphical programming, transparent usage of other softwares and devices, built-in programming event-driven for user interfaces), to make it simple for the end-user. In fact, the article describes the global architecture of the toolkit, with particular emphasis in the software implementation of the so-called artificial hydrocarbon networks algorithm. Lastly, the article includes two case studies for engineering purposes (i.e., sensor characterization) and chemistry applications (i.e., blood-brain barrier partitioning data model) to show the usage of the toolkit and the potential scalability of the artificial organic networks technique. © 2015 Wiley Periodicals, Inc.

Application of the Golden Software Surfer mapping software for automation of visualisation of meteorological and oceanographic data in IMGW Maritime Branch.

NASA Astrophysics Data System (ADS)

Piliczewski, B.

2003-04-01

The Golden Software Surfer has been used in IMGW Maritime Branch for more than ten years. This tool provides ActiveX Automation objects, which allow scripts to control practically every feature of Surfer. These objects can be accessed from any Automation-enabled environment, such as Visual Basic or Excel. Several applications based on Surfer has been developed in IMGW. The first example is an on-line oceanographic service, which presents forecasts of the water temperature, sea level and currents originating from the HIROMB model and is automatically updated every day. Surfer was also utilised in MERMAID, an international project supported by EC under the 5th Framework Programme. The main aim of this project was to create a prototype of the Internet-based data brokerage system, which would enable to search, extract, buy and download datasets containing meteorological or oceanographic data. During the project IMGW developed an online application, called Mermaid Viewer, which enables communication with the data broker and automatic visualisation of the downloaded data using Surfer. Both the above mentioned applications were developed in Visual Basic. Currently it is considered to adopt Surfer for the monitoring service, which provides access to the data collected in the monitoring of the Baltic Sea environment.

EpHLA: an innovative and user-friendly software automating the HLAMatchmaker algorithm for antibody analysis.

PubMed

Sousa, Luiz Cláudio Demes da Mata; Filho, Herton Luiz Alves Sales; Von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; Neto, Pedro de Alcântara dos Santos; de Castro, José Adail Fonseca; do Monte, Semíramis Jamil Hadad

2011-12-01

The global challenge for solid organ transplantation programs is to distribute organs to the highly sensitized recipients. The purpose of this work is to describe and test the functionality of the EpHLA software, a program that automates the analysis of acceptable and unacceptable HLA epitopes on the basis of the HLAMatchmaker algorithm. HLAMatchmaker considers small configurations of polymorphic residues referred to as eplets as essential components of HLA-epitopes. Currently, the analyses require the creation of temporary files and the manual cut and paste of laboratory tests results between electronic spreadsheets, which is time-consuming and prone to administrative errors. The EpHLA software was developed in Object Pascal programming language and uses the HLAMatchmaker algorithm to generate histocompatibility reports. The automated generation of reports requires the integration of files containing the results of laboratory tests (HLA typing, anti-HLA antibody signature) and public data banks (NMDP, IMGT). The integration and the access to this data were accomplished by means of the framework called eDAFramework. The eDAFramework was developed in Object Pascal and PHP and it provides data access functionalities for software developed in these languages. The tool functionality was successfully tested in comparison to actual, manually derived reports of patients from a renal transplantation program with related donors. We successfully developed software, which enables the automated definition of the epitope specificities of HLA antibodies. This new tool will benefit the management of recipient/donor pairs selection for highly sensitized patients. Copyright © 2011 Elsevier B.V. All rights reserved.

A Practical Guide to the Technology and Adoption of Software Process Automation

DTIC Science & Technology

1994-03-01

IDE’s integration of Software through Pictures, CodeCenter, and FrameMaker ). However, successful use of in- tegrated tools, as reflected in actual...tool for a specific platform. Thus, when a Work Context calls for a word processor, the weaver.tis file can be set up to call FrameMaker for the Sun4

Overview of Current Activities in Combustion Instability

DTIC Science & Technology

2015-10-02

and avoid liquid rocket engine combustion stability problems Approach:  1) Develop a  SOA  combustion stability software package  called Stable...phase II will invest in Multifidelity Tools and Methodologies – CSTD will develop a SOA combustion stability software package called Stable Combustion

Integrated Language Skills CALL Course Design

ERIC Educational Resources Information Center

Watson, Kevin; Agawa, Grant

2013-01-01

The importance of a structured learning framework or interrelated frameworks is the cornerstone of a solid English as a foreign language (EFL) computer-assisted language learning (CALL) curriculum. While the benefits of CALL are widely promoted in the literature, there is often an endemic discord separating theory and practice. Oftentimes the…

Towards a comprehensive framework for reuse: A reuse-enabling software evolution environment

NASA Technical Reports Server (NTRS)

Basili, V. R.; Rombach, H. D.

1988-01-01

Reuse of products, processes and knowledge will be the key to enable the software industry to achieve the dramatic improvement in productivity and quality required to satisfy the anticipated growing demand. Although experience shows that certain kinds of reuse can be successful, general success has been elusive. A software life-cycle technology which allows broad and extensive reuse could provide the means to achieving the desired order-of-magnitude improvements. The scope of a comprehensive framework for understanding, planning, evaluating and motivating reuse practices and the necessary research activities is outlined. As a first step towards such a framework, a reuse-enabling software evolution environment model is introduced which provides a basis for the effective recording of experience, the generalization and tailoring of experience, the formalization of experience, and the (re-)use of experience.

A Framework for Teaching Software Development Methods

ERIC Educational Resources Information Center

Dubinsky, Yael; Hazzan, Orit

2005-01-01

This article presents a study that aims at constructing a teaching framework for software development methods in higher education. The research field is a capstone project-based course, offered by the Technion's Department of Computer Science, in which Extreme Programming is introduced. The research paradigm is an Action Research that involves…

Frameworks Coordinate Scientific Data Management

NASA Technical Reports Server (NTRS)

2012-01-01

Jet Propulsion Laboratory computer scientists developed a unique software framework to help NASA manage its massive amounts of science data. Through a partnership with the Apache Software Foundation of Forest Hill, Maryland, the technology is now available as an open-source solution and is in use by cancer researchers and pediatric hospitals.

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

PubMed Central

Stamataki, Evangelia; Harich, Benjamin; Guignard, Léo; Preibisch, Stephan; Shorte, Spencer; Keller, Philipp J

2018-01-01

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic. PMID:29595475

Design and Effects of Scenario Educational Software.

ERIC Educational Resources Information Center

Keegan, Mark

1993-01-01

Describes the development of educational computer software called scenario software that was designed to incorporate advances in cognitive, affective, and physiological research. Instructional methods are outlined; the need to change from didactic methods to discovery learning is explained; and scenario software design features are discussed. (24…

ICCE Policy Statement on Network and Multiple Machine Software.

ERIC Educational Resources Information Center

International Council for Computers in Education, Eugene, OR.

Designed to provide educators with guidance for the lawful reproduction of computer software, this document contains suggested guidelines, sample forms, and several short articles concerning software copyright and license agreements. The initial policy statement calls for educators to provide software developers (or their agents) with a…

Trajectory Software With Upper Atmosphere Model

NASA Technical Reports Server (NTRS)

Barrett, Charles

2012-01-01

The Trajectory Software Applications 6.0 for the Dec Alpha platform has an implementation of the Jacchia-Lineberry Upper Atmosphere Density Model used in the Mission Control Center for International Space Station support. Previous trajectory software required an upper atmosphere to support atmosphere drag calculations in the Mission Control Center. The Functional operation will differ depending on the end-use of the module. In general, the calling routine will use function-calling arguments to specify input to the processor. The atmosphere model will then compute and return atmospheric density at the time of interest.

KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain

PubMed Central

2013-01-01

Background Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there are so many diverse methods and methodologies available, that for biomedical researchers who are inexperienced in the use of even relatively popular knowledge discovery methods, it can be very difficult to select the most appropriate method for their particular research problem. Results A web application, called KNODWAT (KNOwledge Discovery With Advanced Techniques) has been developed, using Java on Spring framework 3.1. and following a user-centered approach. The software runs on Java 1.6 and above and requires a web server such as Apache Tomcat and a database server such as the MySQL Server. For frontend functionality and styling, Twitter Bootstrap was used as well as jQuery for interactive user interface operations. Conclusions The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework. PMID:23763826

KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain.

PubMed

Holzinger, Andreas; Zupan, Mario

2013-06-13

Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there are so many diverse methods and methodologies available, that for biomedical researchers who are inexperienced in the use of even relatively popular knowledge discovery methods, it can be very difficult to select the most appropriate method for their particular research problem. A web application, called KNODWAT (KNOwledge Discovery With Advanced Techniques) has been developed, using Java on Spring framework 3.1. and following a user-centered approach. The software runs on Java 1.6 and above and requires a web server such as Apache Tomcat and a database server such as the MySQL Server. For frontend functionality and styling, Twitter Bootstrap was used as well as jQuery for interactive user interface operations. The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework.

Generic, Extensible, Configurable Push-Pull Framework for Large-Scale Science Missions

NASA Technical Reports Server (NTRS)

Foster, Brian M.; Chang, Albert Y.; Freeborn, Dana J.; Crichton, Daniel J.; Woollard, David M.; Mattmann, Chris A.

2011-01-01

The push-pull framework was developed in hopes that an infrastructure would be created that could literally connect to any given remote site, and (given a set of restrictions) download files from that remote site based on those restrictions. The Cataloging and Archiving Service (CAS) has recently been re-architected and re-factored in its canonical services, including file management, workflow management, and resource management. Additionally, a generic CAS Crawling Framework was built based on motivation from Apache s open-source search engine project called Nutch. Nutch is an Apache effort to provide search engine services (akin to Google), including crawling, parsing, content analysis, and indexing. It has produced several stable software releases, and is currently used in production services at companies such as Yahoo, and at NASA's Planetary Data System. The CAS Crawling Framework supports many of the Nutch Crawler's generic services, including metadata extraction, crawling, and ingestion. However, one service that was not ported over from Nutch is a generic protocol layer service that allows the Nutch crawler to obtain content using protocol plug-ins that download content using implementations of remote protocols, such as HTTP, FTP, WinNT file system, HTTPS, etc. Such a generic protocol layer would greatly aid in the CAS Crawling Framework, as the layer would allow the framework to generically obtain content (i.e., data products) from remote sites using protocols such as FTP and others. Augmented with this capability, the Orbiting Carbon Observatory (OCO) and NPP (NPOESS Preparatory Project) Sounder PEATE (Product Evaluation and Analysis Tools Elements) would be provided with an infrastructure to support generic FTP-based pull access to remote data products, obviating the need for any specialized software outside of the context of their existing process control systems. This extensible configurable framework was created in Java, and allows the use of different underlying communication middleware (at present, both XMLRPC, and RMI). In addition, the framework is entirely suitable in a multi-mission environment and is supporting both NPP Sounder PEATE and the OCO Mission. Both systems involve tasks such as high-throughput job processing, terabyte-scale data management, and science computing facilities. NPP Sounder PEATE is already using the push-pull framework to accept hundreds of gigabytes of IASI (infrared atmospheric sounding interferometer) data, and is in preparation to accept CRIMS (Cross-track Infrared Microwave Sounding Suite) data. OCO will leverage the framework to download MODIS, CloudSat, and other ancillary data products for use in the high-performance Level 2 Science Algorithm. The National Cancer Institute is also evaluating the framework for use in sharing and disseminating cancer research data through its Early Detection Research Network (EDRN).

A clinically viable capsule endoscopy video analysis platform for automatic bleeding detection

NASA Astrophysics Data System (ADS)

Yi, Steven; Jiao, Heng; Xie, Jean; Mui, Peter; Leighton, Jonathan A.; Pasha, Shabana; Rentz, Lauri; Abedi, Mahmood

2013-02-01

In this paper, we present a novel and clinically valuable software platform for automatic bleeding detection on gastrointestinal (GI) tract from Capsule Endoscopy (CE) videos. Typical CE videos for GI tract run about 8 hours and are manually reviewed by physicians to locate diseases such as bleedings and polyps. As a result, the process is time consuming and is prone to disease miss-finding. While researchers have made efforts to automate this process, however, no clinically acceptable software is available on the marketplace today. Working with our collaborators, we have developed a clinically viable software platform called GISentinel for fully automated GI tract bleeding detection and classification. Major functional modules of the SW include: the innovative graph based NCut segmentation algorithm, the unique feature selection and validation method (e.g. illumination invariant features, color independent features, and symmetrical texture features), and the cascade SVM classification for handling various GI tract scenes (e.g. normal tissue, food particles, bubbles, fluid, and specular reflection). Initial evaluation results on the SW have shown zero bleeding instance miss-finding rate and 4.03% false alarm rate. This work is part of our innovative 2D/3D based GI tract disease detection software platform. While the overall SW framework is designed for intelligent finding and classification of major GI tract diseases such as bleeding, ulcer, and polyp from the CE videos, this paper will focus on the automatic bleeding detection functional module.

An Open Hardware seismic data recorder - a solid basis for citizen science

NASA Astrophysics Data System (ADS)

Mertl, Stefan

2015-04-01

"Ruwai" is a 24-Bit Open Hardware seismic data recorder. It is built up of four stackable printed circuit boards fitting the Arduino Mega 2560 microcontroller prototyping platform. An interface to the BeagleBone Black single-board computer enables extensive data storage, -processing and networking capabilities. The four printed circuit boards provide a uBlox Lea-6T GPS module and real-time clock (GPS Timing shield), an Texas Instruments ADS1274 24-Bit analog to digital converter (ADC main shield), an analog input section with a Texas Instruments PGA281 programmable gain amplifier and an analog anti-aliasing filter (ADC analog interface pga) and the power conditioning based on 9-36V DC input (power supply shield). The Arduino Mega 2560 is used for controlling the hardware components, timestamping sampled data using the GPS timing information and transmitting the data to the BeagleBone Black single-board computer. The BeagleBone Black provides local data storage, wireless mesh networking using the optimized link state routing daemon and differential GNSS positioning using the RTKLIB software. The complete hardware and software is published under free software - or open hardware licenses and only free software (e.g. KiCad) was used for the development to facilitate the reusability of the design and increases the sustainability of the project. "Ruwai" was developed within the framework of the "Community Environmental Observation Network (CEON)" (http://www.mertl-research.at/ceon/) which was supported by the Internet Foundation Austria (IPA) within the NetIdee 2013 call.

A Role-Playing Game for a Software Engineering Lab: Developing a Product Line

ERIC Educational Resources Information Center

Zuppiroli, Sara; Ciancarini, Paolo; Gabbrielli, Maurizio

2012-01-01

Software product line development refers to software engineering practices and techniques for creating families of similar software systems from a basic set of reusable components, called shared assets. Teaching how to deal with software product lines in a university lab course is a challenging task, because there are several practical issues that…

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

PubMed Central

Cheng, Yinhe; Tzeng, Tzy-Hwa Kathy

2016-01-01

This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156–186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory. PMID:27861637

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

PubMed

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

2018-02-23

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

Continuous integration for concurrent MOOSE framework and application development on GitHub

DOE PAGES

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.; ...

2015-11-20

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Continuous integration for concurrent MOOSE framework and application development on GitHub

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

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Patient Safety—Incorporating Drawing Software into Root Cause Analysis Software

PubMed Central

Williams, Linda; Grayson, Diana; Gosbee, John

2001-01-01

Drawing software from Lassalle Technologies1 (France) designed for Visual Basic is the tool we used to standardize the creation, storage, and retrieval of flow diagrams containing information about adverse events and close calls.

Patient Safety—Incorporating Drawing Software into Root Cause Analysis Software

PubMed Central

Williams, Linda; Grayson, Diana; Gosbee, John

2002-01-01

Drawing software from Lassalle Technologies1 (France) designed for Visual Basic is the tool we used to standardize the creation, storage, and retrieval of flow diagrams containing information about adverse events and close calls.

An Ontology and a Software Framework for Competency Modeling and Management

ERIC Educational Resources Information Center

Paquette, Gilbert

2007-01-01

The importance given to competency management is well justified. Acquiring new competencies is the central goal of any education or knowledge management process. Thus, it must be embedded in any software framework as an instructional engineering tool, to inform the runtime environment of the knowledge that is processed by actors, and their…

ALFA: The new ALICE-FAIR software framework

NASA Astrophysics Data System (ADS)

Al-Turany, M.; Buncic, P.; Hristov, P.; Kollegger, T.; Kouzinopoulos, C.; Lebedev, A.; Lindenstruth, V.; Manafov, A.; Richter, M.; Rybalchenko, A.; Vande Vyvre, P.; Winckler, N.

2015-12-01

The commonalities between the ALICE and FAIR experiments and their computing requirements led to the development of large parts of a common software framework in an experiment independent way. The FairRoot project has already shown the feasibility of such an approach for the FAIR experiments and extending it beyond FAIR to experiments at other facilities[1, 2]. The ALFA framework is a joint development between ALICE Online- Offline (O2) and FairRoot teams. ALFA is designed as a flexible, elastic system, which balances reliability and ease of development with performance using multi-processing and multithreading. A message- based approach has been adopted; such an approach will support the use of the software on different hardware platforms, including heterogeneous systems. Each process in ALFA assumes limited communication and reliance on other processes. Such a design will add horizontal scaling (multiple processes) to vertical scaling provided by multiple threads to meet computing and throughput demands. ALFA does not dictate any application protocols. Potentially, any content-based processor or any source can change the application protocol. The framework supports different serialization standards for data exchange between different hardware and software languages.

Software cost/resource modeling: Software quality tradeoff measurement

NASA Technical Reports Server (NTRS)

Lawler, R. W.

1980-01-01

A conceptual framework for treating software quality from a total system perspective is developed. Examples are given to show how system quality objectives may be allocated to hardware and software; to illustrate trades among quality factors, both hardware and software, to achieve system performance objectives; and to illustrate the impact of certain design choices on software functionality.

Designing Educational Software for Tomorrow.

ERIC Educational Resources Information Center

Harvey, Wayne

Designed to address the management and use of computer software in education and training, this paper explores both good and poor software design, calling for improvements in the quality of educational software by attending to design considerations that are based on general principles of learning rather than specific educational objectives. This…

Third-Party Software's Trust Quagmire.

PubMed

Voas, J; Hurlburt, G

2015-12-01

Current software development has trended toward the idea of integrating independent software sub-functions to create more complete software systems. Software sub-functions are often not homegrown - instead they are developed by unknown 3 rd party organizations and reside in software marketplaces owned or controlled by others. Such software sub-functions carry plausible concern in terms of quality, origins, functionality, security, interoperability, to name a few. This article surveys key technical difficulties in confidently building systems from acquired software sub-functions by calling out the principle software supply chain actors.

Architecture for autonomy

NASA Astrophysics Data System (ADS)

Broten, Gregory S.; Monckton, Simon P.; Collier, Jack; Giesbrecht, Jared

2006-05-01

In 2002 Defence R&D Canada changed research direction from pure tele-operated land vehicles to general autonomy for land, air, and sea craft. The unique constraints of the military environment coupled with the complexity of autonomous systems drove DRDC to carefully plan a research and development infrastructure that would provide state of the art tools without restricting research scope. DRDC's long term objectives for its autonomy program address disparate unmanned ground vehicle (UGV), unattended ground sensor (UGS), air (UAV), and subsea and surface (UUV and USV) vehicles operating together with minimal human oversight. Individually, these systems will range in complexity from simple reconnaissance mini-UAVs streaming video to sophisticated autonomous combat UGVs exploiting embedded and remote sensing. Together, these systems can provide low risk, long endurance, battlefield services assuming they can communicate and cooperate with manned and unmanned systems. A key enabling technology for this new research is a software architecture capable of meeting both DRDC's current and future requirements. DRDC built upon recent advances in the computing science field while developing its software architecture know as the Architecture for Autonomy (AFA). Although a well established practice in computing science, frameworks have only recently entered common use by unmanned vehicles. For industry and government, the complexity, cost, and time to re-implement stable systems often exceeds the perceived benefits of adopting a modern software infrastructure. Thus, most persevere with legacy software, adapting and modifying software when and wherever possible or necessary -- adopting strategic software frameworks only when no justifiable legacy exists. Conversely, academic programs with short one or two year projects frequently exploit strategic software frameworks but with little enduring impact. The open-source movement radically changes this picture. Academic frameworks, open to public scrutiny and modification, now rival commercial frameworks in both quality and economic impact. Further, industry now realizes that open source frameworks can reduce cost and risk of systems engineering. This paper describes the Architecture for Autonomy implemented by DRDC and how this architecture meets DRDC's current needs. It also presents an argument for why this architecture should also satisfy DRDC's future requirements as well.

Development of software for computing forming information using a component based approach

NASA Astrophysics Data System (ADS)

Ko, Kwang Hee; Park, Jiing Seo; Kim, Jung; Kim, Young Bum; Shin, Jong Gye

2009-12-01

In shipbuilding industry, the manufacturing technology> has advanced at an unprecedented pace for the last decade. As a result, many automatic systems for cutting, welding, etc. have been developed and employed in the manufacturing process and accordingly the productivity has been increased drastically. Despite such improvement in the manufacturing technology', however, development of an automatic system for fabricating a curved hull plate remains at the beginning stage since hardware and software for the automation of the curved hull fabrication process should be developed differently depending on the dimensions of plates, forming methods and manufacturing processes of each shipyard. To deal with this problem, it is necessary> to create a "plug-in ''framework, which can adopt various kinds of hardware and software to construct a full automatic fabrication system. In this paper, a frame-work for automatic fabrication of curved hull plates is proposed, which consists of four components and related software. In particular the software module for computing fabrication information is developed by using the ooCBD development methodology; which can interface with other hardware and software with minimum effort. Examples of the proposed framework applied to medium and large shipyards are presented.

A Framework for Performing Verification and Validation in Reuse Based Software Engineering

NASA Technical Reports Server (NTRS)

Addy, Edward A.

1997-01-01

Verification and Validation (V&V) is currently performed during application development for many systems, especially safety-critical and mission- critical systems. The V&V process is intended to discover errors, especially errors related to critical processing, as early as possible during the development process. The system application provides the context under which the software artifacts are validated. This paper describes a framework that extends V&V from an individual application system to a product line of systems that are developed within an architecture-based software engineering environment. This framework includes the activities of traditional application-level V&V, and extends these activities into domain engineering and into the transition between domain engineering and application engineering. The framework includes descriptions of the types of activities to be performed during each of the life-cycle phases, and provides motivation for the activities.

Research and Design of the Three-tier Distributed Network Management System Based on COM / COM + and DNA

NASA Astrophysics Data System (ADS)

Liang, Likai; Bi, Yushen

Considered on the distributed network management system's demand of high distributives, extensibility and reusability, a framework model of Three-tier distributed network management system based on COM/COM+ and DNA is proposed, which adopts software component technology and N-tier application software framework design idea. We also give the concrete design plan of each layer of this model. Finally, we discuss the internal running process of each layer in the distributed network management system's framework model.

ActiveTutor: Towards More Adaptive Features in an E-Learning Framework

ERIC Educational Resources Information Center

Fournier, Jean-Pierre; Sansonnet, Jean-Paul

2008-01-01

Purpose: This paper aims to sketch the emerging notion of auto-adaptive software when applied to e-learning software. Design/methodology/approach: The study and the implementation of the auto-adaptive architecture are based on the operational framework "ActiveTutor" that is used for teaching the topic of computer science programming in first-grade…

Developing a Pedagogical-Technical Framework to Improve Creative Writing

ERIC Educational Resources Information Center

Chong, Stefanie Xinyi; Lee, Chien-Sing

2012-01-01

There are many evidences of motivational and educational benefits from the use of learning software. However, there is a lack of study with regards to the teaching of creative writing. This paper aims to bridge the following gaps: first, the need for a proper framework for scaffolding creative writing through learning software; second, the lack of…

Applying Hypertext Structures to Software Documentation.

ERIC Educational Resources Information Center

French, James C.; And Others

1997-01-01

Describes a prototype system for software documentation management called SLEUTH (Software Literacy Enhancing Usefulness to Humans) being developed at the University of Virginia. Highlights include information retrieval techniques, hypertext links that are installed automatically, a WAIS (Wide Area Information Server) search engine, user…

Biomathematical Description of Synthetic Peptide Libraries

PubMed Central

Trepel, Martin

2015-01-01

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

Discrete Fourier Transform Analysis in a Complex Vector Space

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2009-01-01

Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.

Creating a Software Framework for Simulating Satellite Geolocation

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

Koch, Daniel B

2011-01-01

It is hard to imagine life these days without having some sort of electronic indication of one's current location. Whether the purpose is for business, personal, or emergency use, utilizing smart cell phones, in-vehicle navigation systems, or location beacons, dependence on the Global Positioning System (GPS) is pervasive. Yet the availability of the GPS should not be taken for granted. Both environmental (e.g., terrain, weather) and intentional interference (i.e., jamming) can reduce or deny satellite access. In order to investigate these and other issues, as well as to explore possible alternative satellite constellations, an application called the Satellite Simulation Toolkitmore » (SatSim) was created. This paper presents a high-level overview of SatSim and an example of how it may be used to study geolocation.« less

An Integrated Framework Advancing Membrane Protein Modeling and Design

PubMed Central

Weitzner, Brian D.; Duran, Amanda M.; Tilley, Drew C.; Elazar, Assaf; Gray, Jeffrey J.

2015-01-01

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design. PMID:26325167

Computer-aided drug design at Boehringer Ingelheim

NASA Astrophysics Data System (ADS)

Muegge, Ingo; Bergner, Andreas; Kriegl, Jan M.

2017-03-01

Computer-Aided Drug Design (CADD) is an integral part of the drug discovery endeavor at Boehringer Ingelheim (BI). CADD contributes to the evaluation of new therapeutic concepts, identifies small molecule starting points for drug discovery, and develops strategies for optimizing hit and lead compounds. The CADD scientists at BI benefit from the global use and development of both software platforms and computational services. A number of computational techniques developed in-house have significantly changed the way early drug discovery is carried out at BI. In particular, virtual screening in vast chemical spaces, which can be accessed by combinatorial chemistry, has added a new option for the identification of hits in many projects. Recently, a new framework has been implemented allowing fast, interactive predictions of relevant on and off target endpoints and other optimization parameters. In addition to the introduction of this new framework at BI, CADD has been focusing on the enablement of medicinal chemists to independently perform an increasing amount of molecular modeling and design work. This is made possible through the deployment of MOE as a global modeling platform, allowing computational and medicinal chemists to freely share ideas and modeling results. Furthermore, a central communication layer called the computational chemistry framework provides broad access to predictive models and other computational services.

[Utility of Smartphone in Home Care Medicine - First Trial].

PubMed

Takeshige, Toshiyuki; Hirano, Chiho; Nakagawa, Midori; Yoshioka, Rentaro

2015-12-01

The use of video calls for home care can reduce anxiety and offer patients peace of mind. The most suitable terminals at facilities to support home care have been iPad Air and iPhone with FaceTime software. However, usage has been limited to specific terminals. In order to eliminate the need for special terminals and software, we have developed a program that has been customized to meet the needs of facilities using Web Real Time Communication(WebRTC)in cooperation with the University of Aizu. With this software, video calls can accommodate the large number of home care patients.

Luigi Gentile Polese | NREL

Science.gov Websites

software development of next-generation whole-building energy modeling, analysis, and simulation tools technical positions in networking protocol specifications, call control software, and requirements

PyPWA: A partial-wave/amplitude analysis software framework

NASA Astrophysics Data System (ADS)

Salgado, Carlos

2016-05-01

The PyPWA project aims to develop a software framework for Partial Wave and Amplitude Analysis of data; providing the user with software tools to identify resonances from multi-particle final states in photoproduction. Most of the code is written in Python. The software is divided into two main branches: one general-shell where amplitude's parameters (or any parametric model) are to be estimated from the data. This branch also includes software to produce simulated data-sets using the fitted amplitudes. A second branch contains a specific realization of the isobar model (with room to include Deck-type and other isobar model extensions) to perform PWA with an interface into the computer resources at Jefferson Lab. We are currently implementing parallelism and vectorization using the Intel's Xeon Phi family of coprocessors.

Use of a quality improvement tool, the prioritization matrix, to identify and prioritize triage software algorithm enhancement.

PubMed

North, Frederick; Varkey, Prathiba; Caraballo, Pedro; Vsetecka, Darlene; Bartel, Greg

2007-10-11

Complex decision support software can require significant effort in maintenance and enhancement. A quality improvement tool, the prioritization matrix, was successfully used to guide software enhancement of algorithms in a symptom assessment call center.

EMMA: a new paradigm in configurable software

DOE PAGES

Nogiec, J. M.; Trombly-Freytag, K.

2017-11-23

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. As a result, it provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: A New Paradigm in Configurable Software

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

Nogiec, J. M.; Trombly-Freytag, K.

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. It provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: a new paradigm in configurable software

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

Nogiec, J. M.; Trombly-Freytag, K.

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. As a result, it provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

EMMA: a new paradigm in configurable software

NASA Astrophysics Data System (ADS)

Nogiec, J. M.; Trombly-Freytag, K.

2017-10-01

EMMA is a framework designed to create a family of configurable software systems, with emphasis on extensibility and flexibility. It is based on a loosely coupled, event driven architecture. The EMMA framework has been built upon the premise of composing software systems from independent components. It opens up opportunities for reuse of components and their functionality and composing them together in many different ways. It provides the developer of test and measurement applications with a lightweight alternative to microservices, while sharing their various advantages, including composability, loose coupling, encapsulation, and reuse.

Geospatial Data Stream Processing in Python Using FOSS4G Components

NASA Astrophysics Data System (ADS)

McFerren, G.; van Zyl, T.

2016-06-01

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

A Unified Framework for Periodic, On-Demand, and User-Specified Software Information

NASA Technical Reports Server (NTRS)

Kolano, Paul Z.

2004-01-01

Although grid computing can increase the number of resources available to a user; not all resources on the grid may have a software environment suitable for running a given application. To provide users with the necessary assistance for selecting resources with compatible software environments and/or for automatically establishing such environments, it is necessary to have an accurate source of information about the software installed across the grid. This paper presents a new OGSI-compliant software information service that has been implemented as part of NASA's Information Power Grid project. This service is built on top of a general framework for reconciling information from periodic, on-demand, and user-specified sources. Information is retrieved using standard XPath queries over a single unified namespace independent of the information's source. Two consumers of the provided software information, the IPG Resource Broker and the IPG Neutralization Service, are briefly described.

Dynamic Weather Routes Architecture Overview

NASA Technical Reports Server (NTRS)

Eslami, Hassan; Eshow, Michelle

2014-01-01

Dynamic Weather Routes Architecture Overview, presents the high level software architecture of DWR, based on the CTAS software framework and the Direct-To automation tool. The document also covers external and internal data flows, required dataset, changes to the Direct-To software for DWR, collection of software statistics, and the code structure.

DoD Application Store: Enabling C2 Agility?

DTIC Science & Technology

2014-06-01

Framework, will include automated delivery of software patches, web applications, widgets and mobile application packages. The envisioned DoD...Marketplace within the Ozone Widget Framework, will include automated delivery of software patches, web applications, widgets and mobile application...current needs. DoD has started to make inroads within this environment with several Programs of Record (PoR) embracing widgets and other mobile

An application framework for computer-aided patient positioning in radiation therapy.

PubMed

Liebler, T; Hub, M; Sanner, C; Schlegel, W

2003-09-01

The importance of exact patient positioning in radiation therapy increases with the ongoing improvements in irradiation planning and treatment. Therefore, new ways to overcome precision limitations of current positioning methods in fractionated treatment have to be found. The Department of Medical Physics at the German Cancer Research Centre (DKFZ) follows different video-based approaches to increase repositioning precision. In this context, the modular software framework FIVE (Fast Integrated Video-based Environment) has been designed and implemented. It is both hardware- and platform-independent and supports merging position data by integrating various computer-aided patient positioning methods. A highly precise optical tracking system and several subtraction imaging techniques have been realized as modules to supply basic video-based repositioning techniques. This paper describes the common framework architecture, the main software modules and their interfaces. An object-oriented software engineering process has been applied using the UML, C + + and the Qt library. The significance of the current framework prototype for the application in patient positioning as well as the extension to further application areas will be discussed. Particularly in experimental research, where special system adjustments are often necessary, the open design of the software allows problem-oriented extensions and adaptations.

GammaLib and ctools. A software framework for the analysis of astronomical gamma-ray data

NASA Astrophysics Data System (ADS)

Knödlseder, J.; Mayer, M.; Deil, C.; Cayrou, J.-B.; Owen, E.; Kelley-Hoskins, N.; Lu, C.-C.; Buehler, R.; Forest, F.; Louge, T.; Siejkowski, H.; Kosack, K.; Gerard, L.; Schulz, A.; Martin, P.; Sanchez, D.; Ohm, S.; Hassan, T.; Brau-Nogué, S.

2016-08-01

The field of gamma-ray astronomy has seen important progress during the last decade, yet to date no common software framework has been developed for the scientific analysis of gamma-ray telescope data. We propose to fill this gap by means of the GammaLib software, a generic library that we have developed to support the analysis of gamma-ray event data. GammaLib was written in C++ and all functionality is available in Python through an extension module. Based on this framework we have developed the ctools software package, a suite of software tools that enables flexible workflows to be built for the analysis of Imaging Air Cherenkov Telescope event data. The ctools are inspired by science analysis software available for existing high-energy astronomy instruments, and they follow the modular ftools model developed by the High Energy Astrophysics Science Archive Research Center. The ctools were written in Python and C++, and can be either used from the command line via shell scripts or directly from Python. In this paper we present the GammaLib and ctools software versions 1.0 that were released at the end of 2015. GammaLib and ctools are ready for the science analysis of Imaging Air Cherenkov Telescope event data, and also support the analysis of Fermi-LAT data and the exploitation of the COMPTEL legacy data archive. We propose using ctools as the science tools software for the Cherenkov Telescope Array Observatory.

Abstracted Workow Framework with a Structure from Motion Application

NASA Astrophysics Data System (ADS)

Rossi, Adam J.

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

Automated and Scalable Data Reduction in the textsc{Sofia} Data Processing System

NASA Astrophysics Data System (ADS)

Krzaczek, R.; Shuping, R.; Charcos-Llorens, M.; Alles, R.; Vacca, W.

2015-09-01

In order to provide suitable data products to general investigators and other end users in a timely manner, the Stratospheric Observatory for Infrared Astronomy SOFIA) has developed a framework supporting the automated execution of data processing pipelines for the various instruments, called the Data Processing System (DPS), see Shuping et al. (2014) for overview). The primary requirement is to process all data collected from a flight within eight hours, allowing data quality assessments and inspections to be made the following day. The raw data collected during a flight requires processing by a number of different software packages and tools unique to each combination of instrument and mode of operation, much of it developed in-house, in order to create data products for use by investigators and other end-users. The requirement to deliver these data products in a consistent, predictable, and performant manner presents a significant challenge for the observatory. Herein we present aspects of the DPS that help to achieve these goals. We discuss how it supports data reduction software written in a variety of languages and environments, its support for new versions and live upgrades to that software and other necessary resources (e.g., calibrations), its accommodation of sudden processing loads through the addition (and eventual removal) of computing resources, and close with an observation of the performance achieved in the first two observing cycles of SOFIA.

The Validation of a Software Evaluation Instrument.

ERIC Educational Resources Information Center

Schmitt, Dorren Rafael

This study, conducted at six southern universities, analyzed the validity and reliability of a researcher developed instrument designed to evaluate educational software in secondary mathematics. The instrument called the Instrument for Software Evaluation for Educators uses measurement scales, presents a summary section of the evaluation, and…

NASA software documentation standard software engineering program

NASA Technical Reports Server (NTRS)

1991-01-01

The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

Recent developments in the CCP-EM software suite.

PubMed

Burnley, Tom; Palmer, Colin M; Winn, Martyn

2017-06-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

Recent developments in the CCP-EM software suite

PubMed Central

Burnley, Tom

2017-01-01

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail. PMID:28580908

Authentic Oral Language Production and Interaction in CALL: An Evolving Conceptual Framework for the Use of Learning Analytics within the SpeakApps Project

ERIC Educational Resources Information Center

Nic Giolla Mhichíl, Mairéad; van Engen, Jeroen; Ó Ciardúbháin, Colm; Ó Cléircín, Gearóid; Appel, Christine

2014-01-01

This paper sets out to construct and present the evolving conceptual framework of the SpeakApps projects to consider the application of learning analytics to facilitate synchronous and asynchronous oral language skills within this CALL context. Drawing from both the CALL and wider theoretical and empirical literature of learner analytics, the…

Distributed software framework and continuous integration in hydroinformatics systems

NASA Astrophysics Data System (ADS)

Zhou, Jianzhong; Zhang, Wei; Xie, Mengfei; Lu, Chengwei; Chen, Xiao

2017-08-01

When encountering multiple and complicated models, multisource structured and unstructured data, complex requirements analysis, the platform design and integration of hydroinformatics systems become a challenge. To properly solve these problems, we describe a distributed software framework and it’s continuous integration process in hydroinformatics systems. This distributed framework mainly consists of server cluster for models, distributed database, GIS (Geographic Information System) servers, master node and clients. Based on it, a GIS - based decision support system for joint regulating of water quantity and water quality of group lakes in Wuhan China is established.

A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies

PubMed Central

Ochs, Christopher; Geller, James; Perl, Yehoshua; Musen, Mark A.

2016-01-01

Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving “live partial-area taxonomies” is demonstrated. PMID:27345947

The Diamond Beamline Controls and Data Acquisition Software Architecture

NASA Astrophysics Data System (ADS)

Rees, N.

2010-06-01

The software for the Diamond Light Source beamlines[1] is based on two complementary software frameworks: low level control is provided by the Experimental Physics and Industrial Control System (EPICS) framework[2][3] and the high level user interface is provided by the Java based Generic Data Acquisition or GDA[4][5]. EPICS provides a widely used, robust, generic interface across a wide range of hardware where the user interfaces are focused on serving the needs of engineers and beamline scientists to obtain detailed low level views of all aspects of the beamline control systems. The GDA system provides a high-level system that combines an understanding of scientific concepts, such as reciprocal lattice coordinates, a flexible python syntax scripting interface for the scientific user to control their data acquisition, and graphical user interfaces where necessary. This paper describes the beamline software architecture in more detail, highlighting how these complementary frameworks provide a flexible system that can accommodate a wide range of requirements.

A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

PubMed

Ochs, Christopher; Geller, James; Perl, Yehoshua; Musen, Mark A

2016-08-01

Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving "live partial-area taxonomies" is demonstrated. Copyright © 2016 Elsevier Inc. All rights reserved.

Framework for Integrating Science Data Processing Algorithms Into Process Control Systems

NASA Technical Reports Server (NTRS)

Mattmann, Chris A.; Crichton, Daniel J.; Chang, Albert Y.; Foster, Brian M.; Freeborn, Dana J.; Woollard, David M.; Ramirez, Paul M.

2011-01-01

A software framework called PCS Task Wrapper is responsible for standardizing the setup, process initiation, execution, and file management tasks surrounding the execution of science data algorithms, which are referred to by NASA as Product Generation Executives (PGEs). PGEs codify a scientific algorithm, some step in the overall scientific process involved in a mission science workflow. The PCS Task Wrapper provides a stable operating environment to the underlying PGE during its execution lifecycle. If the PGE requires a file, or metadata regarding the file, the PCS Task Wrapper is responsible for delivering that information to the PGE in a manner that meets its requirements. If the PGE requires knowledge of upstream or downstream PGEs in a sequence of executions, that information is also made available. Finally, if information regarding disk space, or node information such as CPU availability, etc., is required, the PCS Task Wrapper provides this information to the underlying PGE. After this information is collected, the PGE is executed, and its output Product file and Metadata generation is managed via the PCS Task Wrapper framework. The innovation is responsible for marshalling output Products and Metadata back to a PCS File Management component for use in downstream data processing and pedigree. In support of this, the PCS Task Wrapper leverages the PCS Crawler Framework to ingest (during pipeline processing) the output Product files and Metadata produced by the PGE. The architectural components of the PCS Task Wrapper framework include PGE Task Instance, PGE Config File Builder, Config File Property Adder, Science PGE Config File Writer, and PCS Met file Writer. This innovative framework is really the unifying bridge between the execution of a step in the overall processing pipeline, and the available PCS component services as well as the information that they collectively manage.

Towards an Open, Distributed Software Architecture for UxS Operations

NASA Technical Reports Server (NTRS)

Cross, Charles D.; Motter, Mark A.; Neilan, James H.; Qualls, Garry D.; Rothhaar, Paul M.; Tran, Loc; Trujillo, Anna C.; Allen, B. Danette

2015-01-01

To address the growing need to evaluate, test, and certify an ever expanding ecosystem of UxS platforms in preparation of cultural integration, NASA Langley Research Center's Autonomy Incubator (AI) has taken on the challenge of developing a software framework in which UxS platforms developed by third parties can be integrated into a single system which provides evaluation and testing, mission planning and operation, and out-of-the-box autonomy and data fusion capabilities. This software framework, named AEON (Autonomous Entity Operations Network), has two main goals. The first goal is the development of a cross-platform, extensible, onboard software system that provides autonomy at the mission execution and course-planning level, a highly configurable data fusion framework sensitive to the platform's available sensor hardware, and plug-and-play compatibility with a wide array of computer systems, sensors, software, and controls hardware. The second goal is the development of a ground control system that acts as a test-bed for integration of the proposed heterogeneous fleet, and allows for complex mission planning, tracking, and debugging capabilities. The ground control system should also be highly extensible and allow plug-and-play interoperability with third party software systems. In order to achieve these goals, this paper proposes an open, distributed software architecture which utilizes at its core the Data Distribution Service (DDS) standards, established by the Object Management Group (OMG), for inter-process communication and data flow. The design decisions proposed herein leverage the advantages of existing robotics software architectures and the DDS standards to develop software that is scalable, high-performance, fault tolerant, modular, and readily interoperable with external platforms and software.

Software And Systems Engineering Risk Management

DTIC Science & Technology

2010-04-01

RSKM 2004 COSO Enterprise RSKM Framework 2006 ISO/IEC 16085 Risk Management Process 2008 ISO/IEC 12207 Software Lifecycle Processes 2009 ISO/IEC...1 Software And Systems Engineering Risk Management John Walz VP Technical and Conferences Activities, IEEE Computer Society Vice-Chair Planning...Software & Systems Engineering Standards Committee, IEEE Computer Society US TAG to ISO TMB Risk Management Working Group Systems and Software

The Software Architecture of the Upgraded ESA DRAMA Software Suite

NASA Astrophysics Data System (ADS)

Kebschull, Christopher; Flegel, Sven; Gelhaus, Johannes; Mockel, Marek; Braun, Vitali; Radtke, Jonas; Wiedemann, Carsten; Vorsmann, Peter; Sanchez-Ortiz, Noelia; Krag, Holger

2013-08-01

In the beginnings of man's space flight activities there was the belief that space is so big that everybody could use it without any repercussions. However during the last six decades the increasing use of Earth's orbits has lead to a rapid growth in the space debris environment, which has a big influence on current and future space missions. For this reason ESA issued the "Requirements on Space Debris Mitigation for ESA Projects" [1] in 2008, which apply to all ESA missions henceforth. The DRAMA (Debris Risk Assessment and Mitigation Analysis) software suite had been developed to support the planning of space missions to comply with these requirements. During the last year the DRAMA software suite has been upgraded under ESA contract by TUBS and DEIMOS to include additional tools and increase the performance of existing ones. This paper describes the overall software architecture of the ESA DRAMA software suite. Specifically the new graphical user interface, which manages the five main tools ARES (Assessment of Risk Event Statistics), MIDAS (MASTER-based Impact Flux and Damage Assessment Software), OSCAR (Orbital Spacecraft Active Removal), CROC (Cross Section of Complex Bodies) and SARA (Re-entry Survival and Risk Analysis) is being discussed. The advancements are highlighted as well as the challenges that arise from the integration of the five tool interfaces. A framework had been developed at the ILR and was used for MASTER-2009 and PROOF-2009. The Java based GUI framework, enables the cross-platform deployment, and its underlying model-view-presenter (MVP) software pattern, meet strict design requirements necessary to ensure a robust and reliable method of operation in an environment where the GUI is separated from the processing back-end. While the GUI framework evolved with each project, allowing an increasing degree of integration of services like validators for input fields, it has also increased in complexity. The paper will conclude with an outlook on the future development of the GUI framework, where the potential for advancements will be shown.

A multi-GPU real-time dose simulation software framework for lung radiotherapy.

PubMed

Santhanam, A P; Min, Y; Neelakkantan, H; Papp, N; Meeks, S L; Kupelian, P A

2012-09-01

Medical simulation frameworks facilitate both the preoperative and postoperative analysis of the patient's pathophysical condition. Of particular importance is the simulation of radiation dose delivery for real-time radiotherapy monitoring and retrospective analyses of the patient's treatment. In this paper, a software framework tailored for the development of simulation-based real-time radiation dose monitoring medical applications is discussed. A multi-GPU-based computational framework coupled with inter-process communication methods is introduced for simulating the radiation dose delivery on a deformable 3D volumetric lung model and its real-time visualization. The model deformation and the corresponding dose calculation are allocated among the GPUs in a task-specific manner and is performed in a pipelined manner. Radiation dose calculations are computed on two different GPU hardware architectures. The integration of this computational framework with a front-end software layer and back-end patient database repository is also discussed. Real-time simulation of the dose delivered is achieved at once every 120 ms using the proposed framework. With a linear increase in the number of GPU cores, the computational time of the simulation was linearly decreased. The inter-process communication time also improved with an increase in the hardware memory. Variations in the delivered dose and computational speedup for variations in the data dimensions are investigated using D70 and D90 as well as gEUD as metrics for a set of 14 patients. Computational speed-up increased with an increase in the beam dimensions when compared with a CPU-based commercial software while the error in the dose calculation was <1%. Our analyses show that the framework applied to deformable lung model-based radiotherapy is an effective tool for performing both real-time and retrospective analyses.

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

Stoiber, Marcus H.; Brown, James B.

This software implements the first base caller for nanopore data that calls bases directly from raw data. The basecRAWller algorithm has two major advantages over current nanopore base calling software: (1) streaming base calling and (2) base calling from information rich raw signal. The ability to perform truly streaming base calling as signal is received from the sequencer can be very powerful as this is one of the major advantages of this technology as compared to other sequencing technologies. As such enabling as much streaming potential as possible will be incredibly important as this technology continues to become more widelymore » applied in biosciences. All other base callers currently employ the Viterbi algorithm which requires the whole sequence to employ the complete base calling procedure and thus precludes a natural streaming base calling procedure. The other major advantage of the basecRAWller algorithm is the prediction of bases from raw signal which contains much richer information than the segmented chunks that current algorithms employ. This leads to the potential for much more accurate base calls which would make this technology much more valuable to all of the growing user base for this technology.« less

Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

PubMed

Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

2015-01-01

DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA gel electrophoresis images, called GELect, which was written in Java and made available through the imageJ framework. With a novel automated image processing workflow, the tool can accurately segment lanes from a gel matrix, intelligently extract distorted and even doublet bands that are difficult to identify by existing image processing tools. Consequently, genotyping from DNA gel electrophoresis can be performed automatically allowing users to efficiently conduct large scale DNA fingerprinting via DNA gel electrophoresis. The software is freely available from http://www.biotec.or.th/gi/tools/gelect.

Structural Analysis and Design Software

NASA Technical Reports Server (NTRS)

1997-01-01

Collier Research and Development Corporation received a one-of-a-kind computer code for designing exotic hypersonic aircraft called ST-SIZE in the first ever Langley Research Center software copyright license agreement. Collier transformed the NASA computer code into a commercial software package called HyperSizer, which integrates with other Finite Element Modeling and Finite Analysis private-sector structural analysis program. ST-SIZE was chiefly conceived as a means to improve and speed the structural design of a future aerospace plane for Langley Hypersonic Vehicles Office. Including the NASA computer code into HyperSizer has enabled the company to also apply the software to applications other than aerospace, including improved design and construction for offices, marine structures, cargo containers, commercial and military aircraft, rail cars, and a host of everyday consumer products.

Upper Secondary and Vocational Level Teachers at Social Software

ERIC Educational Resources Information Center

Valtonen, Teemu; Kontkanen, Sini; Dillon, Patrick; Kukkonen, Jari; Väisänen, Pertti

2014-01-01

This study focuses on upper secondary and vocational level teachers as users of social software i.e. what software they use during their leisure and work and for what purposes they use software in teaching. The study is theorised within a technological pedagogical content knowledge framework, the emphasis is especially on technological knowledge…

GeoFramework: A Modeling Framework for Solid Earth Geophysics

NASA Astrophysics Data System (ADS)

Gurnis, M.; Aivazis, M.; Tromp, J.; Tan, E.; Thoutireddy, P.; Liu, Q.; Choi, E.; Dicaprio, C.; Chen, M.; Simons, M.; Quenette, S.; Appelbe, B.; Aagaard, B.; Williams, C.; Lavier, L.; Moresi, L.; Law, H.

2003-12-01

As data sets in geophysics become larger and of greater relevance to other earth science disciplines, and as earth science becomes more interdisciplinary in general, modeling tools are being driven in new directions. There is now a greater need to link modeling codes to one another, link modeling codes to multiple datasets, and to make modeling software available to non modeling specialists. Coupled with rapid progress in computer hardware (including the computational speed afforded by massively parallel computers), progress in numerical algorithms, and the introduction of software frameworks, these lofty goals of merging software in geophysics are now possible. The GeoFramework project, a collaboration between computer scientists and geoscientists, is a response to these needs and opportunities. GeoFramework is based on and extends Pyre, a Python-based modeling framework, recently developed to link solid (Lagrangian) and fluid (Eulerian) models, as well as mesh generators, visualization packages, and databases, with one another for engineering applications. The utility and generality of Pyre as a general purpose framework in science is now being recognized. Besides its use in engineering and geophysics, it is also being used in particle physics and astronomy. Geology and geophysics impose their own unique requirements on software frameworks which are not generally available in existing frameworks and so there is a need for research in this area. One of the special requirements is the way Lagrangian and Eulerian codes will need to be linked in time and space within a plate tectonics context. GeoFramework has grown beyond its initial goal of linking a limited number of exiting codes together. The following codes are now being reengineered within the context of Pyre: Tecton, 3-D FE Visco-elastic code for lithospheric relaxation; CitComS, a code for spherical mantle convection; SpecFEM3D, a SEM code for global and regional seismic waves; eqsim, a FE code for dynamic earthquake rupture; SNAC, a developing 3-D coded based on the FLAC method for visco-elastoplastic deformation; SNARK, a 3-D FE-PIC method for viscoplastic deformation; and gPLATES an open source paleogeographic/plate tectonics modeling package. We will demonstrate how codes can be linked with themselves, such as a regional and global model of mantle convection and a visco-elastoplastic representation of the crust within viscous mantle flow. Finally, we will describe how http://GeoFramework.org has become a distribution site for a suite of modeling software in geophysics.

Onyx-Advanced Aeropropulsion Simulation Framework Created

NASA Technical Reports Server (NTRS)

Reed, John A.

2001-01-01

The Numerical Propulsion System Simulation (NPSS) project at the NASA Glenn Research Center is developing a new software environment for analyzing and designing aircraft engines and, eventually, space transportation systems. Its purpose is to dramatically reduce the time, effort, and expense necessary to design and test jet engines by creating sophisticated computer simulations of an aerospace object or system (refs. 1 and 2). Through a university grant as part of that effort, researchers at the University of Toledo have developed Onyx, an extensible Java-based (Sun Micro-systems, Inc.), objectoriented simulation framework, to investigate how advanced software design techniques can be successfully applied to aeropropulsion system simulation (refs. 3 and 4). The design of Onyx's architecture enables users to customize and extend the framework to add new functionality or adapt simulation behavior as required. It exploits object-oriented technologies, such as design patterns, domain frameworks, and software components, to develop a modular system in which users can dynamically replace components with others having different functionality.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

The ALICE data quality monitoring system

NASA Astrophysics Data System (ADS)

von Haller, B.; Telesca, A.; Chapeland, S.; Carena, F.; Carena, W.; Chibante Barroso, V.; Costa, F.; Denes, E.; Divià, R.; Fuchs, U.; Simonetti, G.; Soós, C.; Vande Vyvre, P.; ALICE Collaboration

2011-12-01

ALICE (A Large Ion Collider Experiment) is the heavy-ion detector designed to study the physics of strongly interacting matter and the quark-gluon plasma at the CERN Large Hadron Collider (LHC). The online Data Quality Monitoring (DQM) is a key element of the Data Acquisition's software chain. It provide shifters with precise and complete information to quickly identify and overcome problems, and as a consequence to ensure acquisition of high quality data. DQM typically involves the online gathering, the analysis by user-defined algorithms and the visualization of monitored data. This paper describes the final design of ALICE'S DQM framework called AMORE (Automatic MOnitoRing Environment), as well as its latest and coming features like the integration with the offline analysis and reconstruction framework, a better use of multi-core processors by a parallelization effort, and its interface with the eLogBook. The concurrent collection and analysis of data in an online environment requires the framework to be highly efficient, robust and scalable. We will describe what has been implemented to achieve these goals and the procedures we follow to ensure appropriate robustness and performance. We finally review the wide range of usages people make of this framework, from the basic monitoring of a single sub-detector to the most complex ones within the High Level Trigger farm or using the Prompt Reconstruction and we describe the various ways of accessing the monitoring results. We conclude with our experience, before and after the LHC startup, when monitoring the data quality in a challenging environment.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Evaluating a Service-Oriented Architecture

DTIC Science & Technology

2007-09-01

See the description on page 13. SaaS Software as a service ( SaaS ) is a software delivery model where customers don’t own a copy of the application... serviceability REST Representational State Transfer RIA rich internet application RPC remote procedure call SaaS software as a service SAML Security...Evaluating a Service -Oriented Architecture Phil Bianco, Software Engineering Institute Rick Kotermanski, Summa Technologies Paulo Merson

multi-dice: r package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes.

PubMed

Xue, Alexander T; Hickerson, Michael J

2017-11-01

Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis. This approach has been applied to classical phylogeographic data sets such as mitochondrial barcodes as well as reduced-genome polymorphism data sets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest and composite likelihood optimization. Here, we introduce the r package multi-dice, a wrapper program that exploits existing simulation software for flexible execution of hierarchical model-based inference using the aSFS, which is derived from reduced genome data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding co-demographic pulses and specifying flexible hyperprior distributions. In sum, multi-dice provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a tool for comparative phylogeography and population genomics. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Low Cost Real Time Autonomous Remote Monitoring Platform

NASA Astrophysics Data System (ADS)

Rodríguez, J. R.; Maldonado, P. M.; Pierson, J. J.; Harris, L.

2016-02-01

Environmental scientists have a need for gathering multiple parameters during specific time periods to answer their research questions. Most available monitoring systems are very expensive and closed systems, which limits the potential to scale up research projects. We developed a low cost, autonomous, real-time monitoring platform that is both open hardware/software and easy to build, deploy, manage and maintain. The hardware is built with off-the-shelf components and a credit card sized computer called Raspberry Pi, running an open source operating (Raspbian). The system runs off a set of batteries and a solar panel, which makes it ideal for remote locations. The software is divided into three parts: 1) a framework for abstracting the sensors (initializing, pooling and communications) designed in python and using a fully object-oriented design, making it easy for new sensor to be added with minimal code changes, 2) a web front end for managing the entire system, 3) a data store (database) framework for local and remote data retrieval and reporting services. Connectivity to the system can be accomplished through a Wi-Fi or cellular Internet connection. Scientists are being forced to do more with less, in response our platform will provide them with a flexible system that can improve the process of data gathering with an accessible, modular, low-cost, and efficient monitoring system. Currently, we have the required permits from the Department of Natural Resources in Puerto Rico to deploy the platform at the Laguna Grande Bioluminescence Lagoon in Fajardo, PR. This station will include probes for pH, DO, Conductivity and water temperature.

Timing is everything :

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

Kobos, Peter Holmes; Walker, La Tonya Nicole; Malczynski, Leonard A.

People save for retirement throughout their career because it is virtually impossible to save all youll need in retirement the year before you retire. Similarly, without installing incremental amounts of clean fossil, renewable or transformative energy technologies throughout the coming decades, a radical and immediate change will be near impossible the year before a policy goal is set to be in place. Therefore, our research question is, To meet our desired technical and policy goals, what are the factors that affect the rate we must install technology to achieve these goals in the coming decades? Existing models do not includemore » full regulatory constraints due to their often complex, and inflexible approaches to solve for optimal engineering instead of robust and multidisciplinary solutions. This project outlines the theory and then develops an applied software tool to model the laboratory-to-market transition using the traditional technology readiness level (TRL) framework, but develops subsequent and a novel regulatory readiness level (RRL) and market readiness level (MRL). This tool uses the ideally-suited system dynamics framework to incorporate feedbacks and time delays. Future energy-economic-environment models, regardless of their programming platform, may adapt this software model component framework or module to further vet the likelihood of new or innovative technology moving through the laboratory, regulatory and market space. The prototype analytical framework and tool, called the Technology, Regulatory and Market Readiness Level simulation model (TRMsim) illustrates the interaction between technology research, application, policy and market dynamics as they relate to a new or innovative technology moving from the theoretical stage to full market deployment. The initial results that illustrate the models capabilities indicate for a hypothetical technology, that increasing the key driver behind each of the TRL, RRL and MRL components individually decreases the time required for the technology to progress through each component by 63, 68 and 64%, respectively. Therefore, under the current working assumptions, to decrease the time it may take for a technology to move from the conceptual stage to full scale market adoption one might consider expending additional effort to secure regulatory approval and reducing the uncertainty of the technologys demand in the marketplace.« less

Exploring the Use of a Test Automation Framework

NASA Technical Reports Server (NTRS)

Cervantes, Alex

2009-01-01

It is known that software testers, more often than not, lack the time needed to fully test the delivered software product within the time period allotted to them. When problems in the implementation phase of a development project occur, it normally causes the software delivery date to slide. As a result, testers either need to work longer hours, or supplementary resources need to be added to the test team in order to meet aggressive test deadlines. One solution to this problem is to provide testers with a test automation framework to facilitate the development of automated test solutions.

GEOSTATISTICS FOR WASTE MANAGEMENT: A USER'S MANUEL FOR THE GEOPACK (VERSION 1.0) GEOSTATISTICAL SOFTWARE SYSTEM

EPA Science Inventory

A comprehensive, user-friendly geostatistical software system called GEOPACk has been developed. The purpose of this software is to make available the programs necessary to undertake a geostatistical analysis of spatially correlated data. The programs were written so that they ...

A Call for Bioimaging Software Usability

PubMed Central

Carpenter, Anne E.; Kamentsky, Lee; Eliceiri, Kevin W.

2013-01-01

Bioimaging software developed in a research setting often fails to be widely used by the scientific community. We suggest that, to maximize both the public’s and researchers’ investments, usability should be a more highly valued goal. We describe specific characteristics of usability towards which bioimaging software projects should aim. PMID:22743771

Software Engineering Basics: A Primer for the Project Manager.

DTIC Science & Technology

1982-06-01

computer software (45, 46]. It is named after Ada Augusta who is generally credited as having been the first programmer as an assistant to Charles ... Babbage , and is called, appropriately enough, ADA. The development of one common programming language for tactical software clearly has the p-.tential for

Methodology for Software Reliability Prediction. Volume 1.

DTIC Science & Technology

1987-11-01

SPACECRAFT 0 MANNED SPACECRAFT B ATCH SYSTEM AIRBORNE AVIONICS 0 UNMANNED EVENT C014TROL a REAL TIME CLOSED 0 UNMANNED SPACECRAFT LOOP OPERATINS SPACECRAFT...software reliability. A Software Reliability Measurement Framework was established which spans the life cycle of a software system and includes the...specification, prediction, estimation, and assessment of software reliability. Data from 59 systems , representing over 5 million lines of code, were

Coordinated Fault-Tolerance for High-Performance Computing Final Project Report

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

Panda, Dhabaleswar Kumar; Beckman, Pete

2011-07-28

With the Coordinated Infrastructure for Fault Tolerance Systems (CIFTS, as the original project came to be called) project, our aim has been to understand and tackle the following broad research questions, the answers to which will help the HEC community analyze and shape the direction of research in the field of fault tolerance and resiliency on future high-end leadership systems. Will availability of global fault information, obtained by fault information exchange between the different HEC software on a system, allow individual system software to better detect, diagnose, and adaptively respond to faults? If fault-awareness is raised throughout the system throughmore » fault information exchange, is it possible to get all system software working together to provide a more comprehensive end-to-end fault management on the system? What are the missing fault-tolerance features that widely used HEC system software lacks today that would inhibit such software from taking advantage of systemwide global fault information? What are the practical limitations of a systemwide approach for end-to-end fault management based on fault awareness and coordination? What mechanisms, tools, and technologies are needed to bring about fault awareness and coordination of responses on a leadership-class system? What standards, outreach, and community interaction are needed for adoption of the concept of fault awareness and coordination for fault management on future systems? Keeping our overall objectives in mind, the CIFTS team has taken a parallel fourfold approach. Our central goal was to design and implement a light-weight, scalable infrastructure with a simple, standardized interface to allow communication of fault-related information through the system and facilitate coordinated responses. This work led to the development of the Fault Tolerance Backplane (FTB) publish-subscribe API specification, together with a reference implementation and several experimental implementations on top of existing publish-subscribe tools. We enhanced the intrinsic fault tolerance capabilities representative implementations of a variety of key HPC software subsystems and integrated them with the FTB. Targeting software subsystems included: MPI communication libraries, checkpoint/restart libraries, resource managers and job schedulers, and system monitoring tools. Leveraging the aforementioned infrastructure, as well as developing and utilizing additional tools, we have examined issues associated with expanded, end-to-end fault response from both system and application viewpoints. From the standpoint of system operations, we have investigated log and root cause analysis, anomaly detection and fault prediction, and generalized notification mechanisms. Our applications work has included libraries for fault-tolerance linear algebra, application frameworks for coupled multiphysics applications, and external frameworks to support the monitoring and response for general applications. Our final goal was to engage the high-end computing community to increase awareness of tools and issues around coordinated end-to-end fault management.« less

Living Design Memory: Framework, Implementation, Lessons Learned.

ERIC Educational Resources Information Center

Terveen, Loren G.; And Others

1995-01-01

Discusses large-scale software development and describes the development of the Designer Assistant to improve software development effectiveness. Highlights include the knowledge management problem; related work, including artificial intelligence and expert systems, software process modeling research, and other approaches to organizational memory;…

Data fusion for automated non-destructive inspection

PubMed Central

Brierley, N.; Tippetts, T.; Cawley, P.

2014-01-01

In industrial non-destructive evaluation (NDE), it is increasingly common for data acquisition to be automated, driving a recent substantial increase in the availability of data. The collected data need to be analysed, typically necessitating the painstaking manual labour of a skilled operator. Moreover, in automated NDE a region of an inspected component is typically interrogated several times, be it within a single data channel due to multiple probe passes, across several channels acquired simultaneously or over the course of repeated inspections. The systematic combination of these diverse readings is recognized to offer an opportunity to improve the reliability of the inspection, but is not achievable in a manual analysis. This paper describes a data-fusion-based software framework providing a partial automation capability, allowing component regions to be declared defect-free to a very high probability while readily identifying defect indications, thereby optimizing the use of the operator's time. The system is designed to applicable to a wide range of automated NDE scenarios, but the processing is exemplified using the industrial ultrasonic immersion inspection of aerospace turbine discs. Results obtained for industrial datasets demonstrate an orders-of-magnitude reduction in false-call rates, for a given probability of detection, achievable using the developed software system. PMID:25002828

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

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

Application of Metamorphic Testing to Supervised Classifiers

PubMed Central

Xie, Xiaoyuan; Ho, Joshua; Kaiser, Gail; Xu, Baowen; Chen, Tsong Yueh

2010-01-01

Many applications in the field of scientific computing - such as computational biology, computational linguistics, and others - depend on Machine Learning algorithms to provide important core functionality to support solutions in the particular problem domains. However, it is difficult to test such applications because often there is no “test oracle” to indicate what the correct output should be for arbitrary input. To help address the quality of such software, in this paper we present a technique for testing the implementations of supervised machine learning classification algorithms on which such scientific computing software depends. Our technique is based on an approach called “metamorphic testing”, which has been shown to be effective in such cases. More importantly, we demonstrate that our technique not only serves the purpose of verification, but also can be applied in validation. In addition to presenting our technique, we describe a case study we performed on a real-world machine learning application framework, and discuss how programmers implementing machine learning algorithms can avoid the common pitfalls discovered in our study. We also discuss how our findings can be of use to other areas outside scientific computing, as well. PMID:21243103

Object-Oriented Multi-Disciplinary Design, Analysis, and Optimization Tool

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2011-01-01

An Object-Oriented Optimization (O3) tool was developed that leverages existing tools and practices, and allows the easy integration and adoption of new state-of-the-art software. At the heart of the O3 tool is the Central Executive Module (CEM), which can integrate disparate software packages in a cross platform network environment so as to quickly perform optimization and design tasks in a cohesive, streamlined manner. This object-oriented framework can integrate the analysis codes for multiple disciplines instead of relying on one code to perform the analysis for all disciplines. The CEM was written in FORTRAN and the script commands for each performance index were submitted through the use of the FORTRAN Call System command. In this CEM, the user chooses an optimization methodology, defines objective and constraint functions from performance indices, and provides starting and side constraints for continuous as well as discrete design variables. The structural analysis modules such as computations of the structural weight, stress, deflection, buckling, and flutter and divergence speeds have been developed and incorporated into the O3 tool to build an object-oriented Multidisciplinary Design, Analysis, and Optimization (MDAO) tool.

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

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

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

The Need for V&V in Reuse-Based Software Engineering

NASA Technical Reports Server (NTRS)

Addy, Edward A.

1997-01-01

V&V is currently performed during application development for many systems, especially safety-critical and mission-critical systems. The V&V process is intended to discover errors, especially errors related to entire' domain or product line rather than a critical processing, as early as possible during the development process. The system application provides the context under which the software artifacts are validated. engineering. This paper describes a framework that extends V&V from an individual application system to a product line of systems that are developed within an architecture-based software engineering environment. This framework includes the activities of traditional application-level V&V, and extends these activities into the transition between domain engineering and application engineering. The framework includes descriptions of the types of activities to be performed during each of the life-cycle phases, and provides motivation for activities.

Hybrid Optimization Parallel Search PACKage

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

2009-11-10

HOPSPACK is open source software for solving optimization problems without derivatives. Application problems may have a fully nonlinear objective function, bound constraints, and linear and nonlinear constraints. Problem variables may be continuous, integer-valued, or a mixture of both. The software provides a framework that supports any derivative-free type of solver algorithm. Through the framework, solvers request parallel function evaluation, which may use MPI (multiple machines) or multithreading (multiple processors/cores on one machine). The framework provides a Cache and Pending Cache of saved evaluations that reduces execution time and facilitates restarts. Solvers can dynamically create other algorithms to solve subproblems, amore » useful technique for handling multiple start points and integer-valued variables. HOPSPACK ships with the Generating Set Search (GSS) algorithm, developed at Sandia as part of the APPSPACK open source software project.« less

HelioScan: a software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility.

PubMed

Langer, Dominik; van 't Hoff, Marcel; Keller, Andreas J; Nagaraja, Chetan; Pfäffli, Oliver A; Göldi, Maurice; Kasper, Hansjörg; Helmchen, Fritjof

2013-04-30

Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid Development of Custom Software Architecture Design Environments

DTIC Science & Technology

1999-08-01

the tools themselves. This dissertation describes a new approach to capturing and using architectural design expertise in software architecture design environments...A language and tools are presented for capturing and encapsulating software architecture design expertise within a conceptual framework...of architectural styles and design rules. The design expertise thus captured is supported with an incrementally configurable software architecture

Proceedings of the Systems Reengineering Technology Workshop (4th) held in Monterey, California on February 8 - 10, 1994

DTIC Science & Technology

1994-09-01

report for the Properties of User Interface Software Architetures ", draft DISCUS Working Group, Programmers Tutorial, MITRE paper, SEI. Carnegie...execution that we have defined called asynchronous remote procedure call (ARPC) [15], which allows concurrency in amounts proportional to the amount of...demonstration project to use STARS DoD software budget and the proportion concepts. IBM is one of the prime is expected to be increased during the contractors

Drowsy driver mobile application: Development of a novel scleral-area detection method.

PubMed

Mohammad, Faisal; Mahadas, Kausalendra; Hung, George K

2017-10-01

A reliable and practical app for mobile devices was developed to detect driver drowsiness. It consisted of two main components: a Haar cascade classifier, provided by a computer vision framework called OpenCV, for face/eye detection; and a dedicated JAVA software code for image processing that was applied over a masked region circumscribing the eye. A binary threshold was performed over the masked region to provide a quantitative measure of the number of white pixels in the sclera, which represented the state of eye opening. A continuously low white-pixel count would indicate drowsiness, thereby triggering an alarm to alert the driver. This system was successfully implemented on: (1) a static face image, (2) two subjects under laboratory conditions, and (3) a subject in a vehicle environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Pachuilo, Andrew R; Ragan, Eric; Goodall, John R

Visualization tools can take advantage of multiple coordinated views to support analysis of large, multidimensional data sets. Effective design of such views and layouts can be challenging, but understanding users analysis strategies can inform design improvements. We outline an approach for intelligent design configuration of visualization tools with multiple coordinated views, and we discuss a proposed software framework to support the approach. The proposed software framework could capture and learn from user interaction data to automate new compositions of views and widgets. Such a framework could reduce the time needed for meta analysis of the visualization use and lead tomore » more effective visualization design.« less

A Mechanized Decision Support System for Academic Scheduling.

DTIC Science & Technology

1986-03-01

an operational system called software. The first step in the development phase is Design . Designers destribute software control by factoring the Data...SUBJECT TERMS (Continue on reverse if necessary and identify by block number) ELD GROUP SUB-GROUP Scheduling, Decision Support System , Software Design ...scheduling system . It will also examine software - design techniques to identify the most appropriate method- ology for this problem. " - Chapter 3 will

Software For Genetic Algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steve E.

1992-01-01

SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.

Connecting the person with dementia and family: a feasibility study of a telepresence robot

PubMed Central

2014-01-01

Background Maintenance of communication is important for people with dementia living in long-term care. The purpose of this study was to assess the feasibility of using “Giraff”, a telepresence robot to enhance engagement between family and a person with dementia living in long-term care. Methods A mixed-methods approach involving semi-structured interviews, call records and video observational data was used. Five people with dementia and their family member participated in a discussion via the Giraff robot for a minimum of six times over a six-week period. A feasibility framework was used to assess feasibility and included video analysis of emotional response and engagement. Results Twenty-six calls with an average duration of 23 mins took place. Residents showed a general state of positive emotions across the calls with a high level of engagement and a minimal level of negative emotions. Participants enjoyed the experience and families reported that the Giraff robot offered the opportunity to reduce social isolation. A number of software and hardware challenges were encountered. Conclusions Participants perceived this novel approach to engage families and people with dementia as a feasible option. Participants were observed and also reported to enjoy the experience. The technical challenges identified have been improved in a newer version of the robot. Future research should include a feasibility trial of longer duration, with a larger sample and a cost analysis. PMID:24456417

Long-term recall accuracy for mobile phone calls in young Japanese people: A follow-up validation study using software-modified phones.

PubMed

Kiyohara, Kosuke; Wake, Kanako; Watanabe, Soichi; Arima, Takuji; Sato, Yasuto; Kojimahara, Noriko; Taki, Masao; Cardis, Elisabeth; Yamaguchi, Naohito

2018-03-01

This study examined changes in recall accuracy for mobile phone calls over a long period. Japanese students' actual call statuses were monitored for 1 month using software-modified phones (SMPs). Three face-to-face interviews were conducted to obtain information regarding self-reported call status during the monitoring period: first interview: immediately after the monitoring period; second interview: after 10-12 months; third interview: after 48-55 months. Using the SMP records as the "gold standard", phone call recall accuracy was assessed for each interview. Data for 94 participants were analyzed. The number of calls made was underestimated considerably and the duration of calls was overestimated slightly in all interviews. Agreement between self-report and SMP records regarding the number of calls, duration of calls and laterality (i.e., use of the dominant ear while making calls) gradually deteriorated with the increase in the interval following the monitoring period (number of calls: first interview: Pearson's r=0.641, third interview: 0.396; duration of calls: first interview: Pearson's r=0.763, third interview: 0.356; laterality: first interview: weighted-κ=0.677, third interview: 0.448). Thus, recall accuracy for mobile phone calls would be consistently imperfect over a long period, and the results of related epidemiological studies should be interpreted carefully.

Integrating software architectures for distributed simulations and simulation analysis communities.

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

Goldsby, Michael E.; Fellig, Daniel; Linebarger, John Michael

2005-10-01

The one-year Software Architecture LDRD (No.79819) was a cross-site effort between Sandia California and Sandia New Mexico. The purpose of this research was to further develop and demonstrate integrating software architecture frameworks for distributed simulation and distributed collaboration in the homeland security domain. The integrated frameworks were initially developed through the Weapons of Mass Destruction Decision Analysis Center (WMD-DAC), sited at SNL/CA, and the National Infrastructure Simulation & Analysis Center (NISAC), sited at SNL/NM. The primary deliverable was a demonstration of both a federation of distributed simulations and a federation of distributed collaborative simulation analysis communities in the context ofmore » the same integrated scenario, which was the release of smallpox in San Diego, California. To our knowledge this was the first time such a combination of federations under a single scenario has ever been demonstrated. A secondary deliverable was the creation of the standalone GroupMeld{trademark} collaboration client, which uses the GroupMeld{trademark} synchronous collaboration framework. In addition, a small pilot experiment that used both integrating frameworks allowed a greater range of crisis management options to be performed and evaluated than would have been possible without the use of the frameworks.« less

DEVELOP MULTI-STRESSOR, OPEN ARCHITECTURE MODELING FRAMEWORK FOR ECOLOGICAL EXPOSURE FROM SITE TO WATERSHED SCALE

EPA Science Inventory

A number of multimedia modeling frameworks are currently being developed. The Multimedia Integrated Modeling System (MIMS) is one of these frameworks. A framework should be seen as more of a multimedia modeling infrastructure than a single software system. This infrastructure do...

Advance Directives and Do Not Resuscitate Orders

MedlinePlus

... a form. Call a lawyer. Use a computer software package for legal documents. Advance directives and living ... you write by yourself or with a computer software package should follow your state laws. You may ...

UAF: a generic OPC unified architecture framework

NASA Astrophysics Data System (ADS)

Pessemier, Wim; Deconinck, Geert; Raskin, Gert; Saey, Philippe; Van Winckel, Hans

2012-09-01

As an emerging Service Oriented Architecture (SOA) specically designed for industrial automation and process control, the OPC Unied Architecture specication should be regarded as an attractive candidate for controlling scientic instrumentation. Even though an industry-backed standard such as OPC UA can oer substantial added value to these projects, its inherent complexity poses an important obstacle for adopting the technology. Building OPC UA applications requires considerable eort, even when taking advantage of a COTS Software Development Kit (SDK). The OPC Unied Architecture Framework (UAF) attempts to reduce this burden by introducing an abstraction layer between the SDK and the application code in order to achieve a better separation of the technical and the functional concerns. True to its industrial origin, the primary requirement of the framework is to maintain interoperability by staying close to the standard specications, and by expecting the minimum compliance from other OPC UA servers and clients. UAF can therefore be regarded as a software framework to quickly and comfortably develop and deploy OPC UA-based applications, while remaining compatible to third party OPC UA-compliant toolkits, servers (such as PLCs) and clients (such as SCADA software). In the rst phase, as covered by this paper, only the client-side of UAF has been tackled in order to transparently handle discovery, session management, subscriptions, monitored items etc. We describe the design principles and internal architecture of our open-source software project, the rst results of the framework running at the Mercator Telescope, and we give a preview of the planned server-side implementation.

Automating Software Design Metrics.

DTIC Science & Technology

1984-02-01

INTRODUCTION 1 ", ... 0..1 1.2 HISTORICAL PERSPECTIVE High quality software is of interest to both the software engineering com- munity and its users. As...contributions of many other software engineering efforts, most notably [MCC 77] and [Boe 83b], which have defined and refined a framework for quantifying...AUTOMATION OF DESIGN METRICS Software metrics can be useful within the context of an integrated soft- ware engineering environment. The purpose of this

Cognitive issues in autonomous spacecraft-control operations: An investigation of software-mediated decision making in a scaled environment

NASA Astrophysics Data System (ADS)

Murphy, Elizabeth Drummond

As advances in technology are applied in complex, semi-automated domains, human controllers are distanced from the controlled process. This physical and psychological distance may both facilitate and degrade human performance. To investigate cognitive issues in spacecraft ground-control operations, the present experimental research was undertaken. The primary issue concerned the ability of operations analysts who do not monitor operations to make timely, accurate decisions when autonomous software calls for human help. Another key issue involved the potential effects of spatial-visualization ability (SVA) in environments that present data in graphical formats. Hypotheses were derived largely from previous findings and predictions in the literature. Undergraduate psychology students were assigned at random to a monitoring condition or an on-call condition in a scaled environment. The experimental task required subjects to decide on the veracity of a problem diagnosis delivered by a software process on-board a simulated spacecraft. To support decision-making, tabular and graphical data displays presented information on system status. A level of software confidence in the problem diagnosis was displayed, and subjects reported their own level of confidence in their decisions. Contrary to expectations, the performance of on-call subjects did not differ significantly from that of continuous monitors. Analysis yielded a significant interaction of sex and condition: Females in the on-call condition had the lowest mean accuracy. Results included a preference for bar charts over line graphs and faster performance with tables than with line graphs. A significant correlation was found between subjective confidence and decision accuracy. SVA was found to be predictive of accuracy but not speed; and SVA was found to be a stronger predictor of performance for males than for females. Low-SVA subjects reported that they relied more on software confidence than did medium- or high-SVA subjects. These and other findings have implications for the design of user interfaces to support human decision-making in on-call situations and to accommodate low-SVA users.

Do We Really Know What Makes Educational Software Effective? A Call for Empirical Research on Effectiveness.

ERIC Educational Resources Information Center

Jolicoeur, Karen; Berger, Dale E.

1986-01-01

Examination of methods used by two software review services in evaluating microcomputer courseware--EPIE (Educational Products Information Exchange) and MicroSIFT (Microcomputer Software and Information for Teachers)--found low correlations between their recommendations for 82 programs. This lack of agreement casts doubts on the usefulness of…

Lessons from 30 Years of Flight Software

NASA Technical Reports Server (NTRS)

McComas, David C.

2015-01-01

This presentation takes a brief historical look at flight software over the past 30 years, extracts lessons learned and shows how many of the lessons learned are embodied in the Flight Software product line called the core Flight System (cFS). It also captures the lessons learned from developing and applying the cFS.

Active Learning through Modeling: Introduction to Software Development in the Business Curriculum

ERIC Educational Resources Information Center

Roussev, Boris; Rousseva, Yvonna

2004-01-01

Modern software practices call for the active involvement of business people in the software process. Therefore, programming has become an indispensable part of the information systems component of the core curriculum at business schools. In this paper, we present a model-based approach to teaching introduction to programming to general business…

Software Application for Computer Aided Vocabulary Learning in a Blended Learning Environment

ERIC Educational Resources Information Center

Essam, Rasha

2010-01-01

This study focuses on the effect of computer-aided vocabulary learning software called "ArabCAVL" on students' vocabulary acquisition. It was hypothesized that students who use the ArabCAVL software in blended learning environment will surpass students who use traditional vocabulary learning strategies in face-to-face learning…

PARTONS: PARtonic Tomography Of Nucleon Software. A computing framework for the phenomenology of Generalized Parton Distributions

NASA Astrophysics Data System (ADS)

Berthou, B.; Binosi, D.; Chouika, N.; Colaneri, L.; Guidal, M.; Mezrag, C.; Moutarde, H.; Rodríguez-Quintero, J.; Sabatié, F.; Sznajder, P.; Wagner, J.

2018-06-01

We describe the architecture and functionalities of a C++ software framework, coined PARTONS, dedicated to the phenomenology of Generalized Parton Distributions. These distributions describe the three-dimensional structure of hadrons in terms of quarks and gluons, and can be accessed in deeply exclusive lepto- or photo-production of mesons or photons. PARTONS provides a necessary bridge between models of Generalized Parton Distributions and experimental data collected in various exclusive production channels. We outline the specification of the PARTONS framework in terms of practical needs, physical content and numerical capacity. This framework will be useful for physicists - theorists or experimentalists - not only to develop new models, but also to interpret existing measurements and even design new experiments.

FRAMES-2.0 Software System: Frames 2.0 Pest Integration (F2PEST)

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

Castleton, Karl J.; Meyer, Philip D.

2009-06-17

The implementation of the FRAMES 2.0 F2PEST module is described, including requirements, design, and specifications of the software. This module integrates the PEST parameter estimation software within the FRAMES 2.0 environmental modeling framework. A test case is presented.

Framework for Risk Analysis in Multimedia Environmental Systems: Modeling Individual Steps of a Risk Assessment Process

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

Shah, Anuj; Castleton, Karl J.; Hoopes, Bonnie L.

2004-06-01

The study of the release and effects of chemicals in the environment and their associated risks to humans is central to public and private decision making. FRAMES 1.X, Framework for Risk Analysis in Multimedia Environmental Systems, is a systems modeling software platform, developed by PNNL, Pacific Northwest National Laboratory, that helps scientists study the release and effects of chemicals on a source to outcome basis, create environmental models for similar risk assessment and management problems. The unique aspect of FRAMES is to dynamically introduce software modules representing individual components of a risk assessment (e.g., source release of contaminants, fate andmore » transport in various environmental media, exposure, etc.) within a software framework, manipulate their attributes and run simulations to obtain results. This paper outlines the fundamental constituents of FRAMES 2.X, an enhanced version of FRAMES 1.X, that greatly improve the ability of the module developers to “plug” their self-developed software modules into the system. The basic design, the underlying principles and a discussion of the guidelines for module developers are presented.« less

Incorporating Manual and Autonomous Code Generation

NASA Technical Reports Server (NTRS)

McComas, David

1998-01-01

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

Integrated Systems Health Management (ISHM) Toolkit

NASA Technical Reports Server (NTRS)

Venkatesh, Meera; Kapadia, Ravi; Walker, Mark; Wilkins, Kim

2013-01-01

A framework of software components has been implemented to facilitate the development of ISHM systems according to a methodology based on Reliability Centered Maintenance (RCM). This framework is collectively referred to as the Toolkit and was developed using General Atomics' Health MAP (TM) technology. The toolkit is intended to provide assistance to software developers of mission-critical system health monitoring applications in the specification, implementation, configuration, and deployment of such applications. In addition to software tools designed to facilitate these objectives, the toolkit also provides direction to software developers in accordance with an ISHM specification and development methodology. The development tools are based on an RCM approach for the development of ISHM systems. This approach focuses on defining, detecting, and predicting the likelihood of system functional failures and their undesirable consequences.

A Generic Software Architecture For Prognostics

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Daigle, Matthew J.; Sankararaman, Shankar; Goebel, Kai; Watkins, Jason

2017-01-01

Prognostics is a systems engineering discipline focused on predicting end-of-life of components and systems. As a relatively new and emerging technology, there are few fielded implementations of prognostics, due in part to practitioners perceiving a large hurdle in developing the models, algorithms, architecture, and integration pieces. As a result, no open software frameworks for applying prognostics currently exist. This paper introduces the Generic Software Architecture for Prognostics (GSAP), an open-source, cross-platform, object-oriented software framework and support library for creating prognostics applications. GSAP was designed to make prognostics more accessible and enable faster adoption and implementation by industry, by reducing the effort and investment required to develop, test, and deploy prognostics. This paper describes the requirements, design, and testing of GSAP. Additionally, a detailed case study involving battery prognostics demonstrates its use.

Student Evaluation of CALL Tools during the Design Process

ERIC Educational Resources Information Center

Nesbitt, Dallas

2013-01-01

This article discusses the comparative effectiveness of student input at different times during the design of CALL tools for learning kanji, the Japanese characters of Chinese origin. The CALL software "package" consisted of tools to facilitate the writing, reading and practising of kanji characters in context. A pre-design questionnaire…

Improving the Operations of the Earth Observing One Mission via Automated Mission Planning

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel; Rabideau, Gregg; Schaffer, Steve; Mandl, Daniel; Frye, Stuart

2010-01-01

We describe the modeling and reasoning about operations constraints in an automated mission planning system for an earth observing satellite - EO-1. We first discuss the large number of elements that can be naturally represented in an expressive planning and scheduling framework. We then describe a number of constraints that challenge the current state of the art in automated planning systems and discuss how we modeled these constraints as well as discuss tradeoffs in representation versus efficiency. Finally we describe the challenges in efficiently generating operations plans for this mission. These discussions involve lessons learned from an operations model that has been in use since Fall 2004 (called R4) as well as a newer more accurate operations model operational since June 2009 (called R5). We present analysis of the R5 software documenting a significant (greater than 50%) increase in the number of weekly observations scheduled by the EO-1 mission. We also show that the R5 mission planning system produces schedules within 15% of an upper bound on optimal schedules. This operational enhancement has created value of millions of dollars US over the projected remaining lifetime of the EO-1 mission.

Composable Framework Support for Software-FMEA Through Model Execution

NASA Astrophysics Data System (ADS)

Kocsis, Imre; Patricia, Andras; Brancati, Francesco; Rossi, Francesco

2016-08-01

Performing Failure Modes and Effect Analysis (FMEA) during software architecture design is becoming a basic requirement in an increasing number of domains; however, due to the lack of standardized early design phase model execution, classic SW-FMEA approaches carry significant risks and are human effort-intensive even in processes that use Model-Driven Engineering.Recently, modelling languages with standardized executable semantics have emerged. Building on earlier results, this paper describes framework support for generating executable error propagation models from such models during software architecture design. The approach carries the promise of increased precision, decreased risk and more automated execution for SW-FMEA during dependability- critical system development.

Layout Study and Application of Mobile App Recommendation Approach Based On Spark Streaming Framework

NASA Astrophysics Data System (ADS)

Wang, H. T.; Chen, T. T.; Yan, C.; Pan, H.

2018-05-01

For App recommended areas of mobile phone software, made while using conduct App application recommended combined weighted Slope One algorithm collaborative filtering algorithm items based on further improvement of the traditional collaborative filtering algorithm in cold start, data matrix sparseness and other issues, will recommend Spark stasis parallel algorithm platform, the introduction of real-time streaming streaming real-time computing framework to improve real-time software applications recommended.

A loosely coupled framework for terminology controlled distributed EHR search for patient cohort identification in clinical research.

PubMed

Zhao, Lei; Lim Choi Keung, Sarah N; Taweel, Adel; Tyler, Edward; Ogunsina, Ire; Rossiter, James; Delaney, Brendan C; Peterson, Kevin A; Hobbs, F D Richard; Arvanitis, Theodoros N

2012-01-01

Heterogeneous data models and coding schemes for electronic health records present challenges for automated search across distributed data sources. This paper describes a loosely coupled software framework based on the terminology controlled approach to enable the interoperation between the search interface and heterogeneous data sources. Software components interoperate via common terminology service and abstract criteria model so as to promote component reuse and incremental system evolution.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

NASA Astrophysics Data System (ADS)

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

2017-10-01

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

(Quickly) Testing the Tester via Path Coverage

NASA Technical Reports Server (NTRS)

Groce, Alex

2009-01-01

The configuration complexity and code size of an automated testing framework may grow to a point that the tester itself becomes a significant software artifact, prone to poor configuration and implementation errors. Unfortunately, testing the tester by using old versions of the software under test (SUT) may be impractical or impossible: test framework changes may have been motivated by interface changes in the tested system, or fault detection may become too expensive in terms of computing time to justify running until errors are detected on older versions of the software. We propose the use of path coverage measures as a "quick and dirty" method for detecting many faults in complex test frameworks. We also note the possibility of using techniques developed to diversify state-space searches in model checking to diversify test focus, and an associated classification of tester changes into focus-changing and non-focus-changing modifications.

The SeaHorn Verification Framework

NASA Technical Reports Server (NTRS)

Gurfinkel, Arie; Kahsai, Temesghen; Komuravelli, Anvesh; Navas, Jorge A.

2015-01-01

In this paper, we present SeaHorn, a software verification framework. The key distinguishing feature of SeaHorn is its modular design that separates the concerns of the syntax of the programming language, its operational semantics, and the verification semantics. SeaHorn encompasses several novelties: it (a) encodes verification conditions using an efficient yet precise inter-procedural technique, (b) provides flexibility in the verification semantics to allow different levels of precision, (c) leverages the state-of-the-art in software model checking and abstract interpretation for verification, and (d) uses Horn-clauses as an intermediate language to represent verification conditions which simplifies interfacing with multiple verification tools based on Horn-clauses. SeaHorn provides users with a powerful verification tool and researchers with an extensible and customizable framework for experimenting with new software verification techniques. The effectiveness and scalability of SeaHorn are demonstrated by an extensive experimental evaluation using benchmarks from SV-COMP 2015 and real avionics code.

A streamlined Python framework for AT-TPC data analysis

NASA Astrophysics Data System (ADS)

Taylor, J. Z.; Bradt, J.; Bazin, D.; Kuchera, M. P.

2017-09-01

User-friendly data analysis software has been developed for the Active-Target Time Projection Chamber (AT-TPC) experiment at the National Superconducting Cyclotron Laboratory at Michigan State University. The AT-TPC, commissioned in 2014, is a gas-filled detector that acts as both the detector and target for high-efficiency detection of low-intensity, exotic nuclear reactions. The pytpc framework is a Python package for analyzing AT-TPC data. The package was developed for the analysis of 46Ar(p, p) data. The existing software was used to analyze data produced by the 40Ar(p, p) experiment that ran in August, 2015. Usage of the package was documented in an analysis manual both to improve analysis steps and aid in the work of future AT-TPC users. Software features and analysis methods in the pytpc framework will be presented along with the 40Ar results.

Management Aspects of Software Maintenance.

DTIC Science & Technology

1984-09-01

educated in * the complex nature of software maintenance to be able to properly evaluate and manage the software maintenance effort. In this...maintenance and improvement may be called "software evolution". The soft- ware manager must be Educated in the complex nature cf soft- Iware maintenance to be...complaint of error or request for modification is also studied in order to determine what action needs tc be taken. 2. Define Objective and Approach :

Reliability Engineering for Service Oriented Architectures

DTIC Science & Technology

2013-02-01

Common Object Request Broker Architecture Ecosystem In software , an ecosystem is a set of applications and/or services that grad- ually build up over time...Enterprise Service Bus Foreign In an SOA context: Any SOA, service or software which the owners of the calling software do not have control of, either...SOA Service Oriented Architecture SRE Software Reliability Engineering System Mode Many systems exhibit different modes of operation. E.g. the cockpit

Control software and electronics architecture design in the framework of the E-ELT instrumentation

NASA Astrophysics Data System (ADS)

Di Marcantonio, P.; Coretti, I.; Cirami, R.; Comari, M.; Santin, P.; Pucillo, M.

2010-07-01

During the last years the European Southern Observatory (ESO), in collaboration with other European astronomical institutes, has started several feasibility studies for the E-ELT (European-Extremely Large Telescope) instrumentation and post-focal adaptive optics. The goal is to create a flexible suite of instruments to deal with the wide variety of scientific questions astronomers would like to see solved in the coming decades. In this framework INAF-Astronomical Observatory of Trieste (INAF-AOTs) is currently responsible of carrying out the analysis and the preliminary study of the architecture of the electronics and control software of three instruments: CODEX (control software and electronics) and OPTIMOS-EVE/OPTIMOS-DIORAMAS (control software). To cope with the increased complexity and new requirements for stability, precision, real-time latency and communications among sub-systems imposed by these instruments, new solutions have been investigated by our group. In this paper we present the proposed software and electronics architecture based on a distributed common framework centered on the Component/Container model that uses OPC Unified Architecture as a standard layer to communicate with COTS components of three different vendors. We describe three working prototypes that have been set-up in our laboratory and discuss their performances, integration complexity and ease of deployment.

NASA Software Assurance's Roles in Research and Technology

NASA Technical Reports Server (NTRS)

Wetherholt, Martha

2010-01-01

This slide presentation reviews the interactions between the scientist and engineers doing research and technology and the software developers and others who are doing software assurance. There is a discussion of the role of the Safety and Mission Assurance (SMA) in developing software to be used for research and technology, and the importance of this role as the technology moves to the higher levels of the technology readiness levels (TRLs). There is also a call to change the way the development of software is developed.

Proposing an Evidence-Based Strategy for Software Requirements Engineering.

PubMed

Lindoerfer, Doris; Mansmann, Ulrich

2016-01-01

This paper discusses an evidence-based approach to software requirements engineering. The approach is called evidence-based, since it uses publications on the specific problem as a surrogate for stakeholder interests, to formulate risks and testing experiences. This complements the idea that agile software development models are more relevant, in which requirements and solutions evolve through collaboration between self-organizing cross-functional teams. The strategy is exemplified and applied to the development of a Software Requirements list used to develop software systems for patient registries.

Assessing Tsunami Vulnerabilities of Geographies with Shallow Water Equations

NASA Technical Reports Server (NTRS)

Aras, Rifat; Shen, Yuzhong

2012-01-01

Tsunami preparedness is crucial for saving human lives in case of disasters that involve massive water movement. In this work, we develop a framework for visual assessment of tsunami preparedness of geographies. Shallow water equations (also called Saint Venant equations) are a set of hyperbolic partial differential equations that are derived by depth-integrating the Navier-Stokes equations and provide a great abstraction of water masses that have lower depths compared to their free surface area. Our specific contribution in this study is to use Microsoft's XNA Game Studio to import underwater and shore line geographies, create different tsunami scenarios, and visualize the propagation of the waves and their impact on the shore line geography. Most importantly, we utilized the computational power of graphical processing units (GPUs) as HLSL based shader files and delegated all of the heavy computations to the GPU. Finally, we also conducted a validation study, in which we have tested our model against a controlled shallow water experiment. We believe that such a framework with an easy to use interface that is based on readily available software libraries, which are widely available and easily distributable, would encourage not only researchers, but also educators to showcase ideas.

UWB Tracking Software Development

NASA Technical Reports Server (NTRS)

Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

2006-01-01

An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

Knowledge synthesis with maps of neural connectivity.

PubMed

Tallis, Marcelo; Thompson, Richard; Russ, Thomas A; Burns, Gully A P C

2011-01-01

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called "Knowledge Engineering from Experimental Design" (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features.

Potential of a suite of robot/computer-assisted motivating systems for personalized, home-based, stroke rehabilitation.

PubMed

Johnson, Michelle J; Feng, Xin; Johnson, Laura M; Winters, Jack M

2007-03-01

There is a need to improve semi-autonomous stroke therapy in home environments often characterized by low supervision of clinical experts and low extrinsic motivation. Our distributed device approach to this problem consists of an integrated suite of low-cost robotic/computer-assistive technologies driven by a novel universal access software framework called UniTherapy. Our design strategy for personalizing the therapy, providing extrinsic motivation and outcome assessment is presented and evaluated. Three studies were conducted to evaluate the potential of the suite. A conventional force-reflecting joystick, a modified joystick therapy platform (TheraJoy), and a steering wheel platform (TheraDrive) were tested separately with the UniTherapy software. Stroke subjects with hemiparesis and able-bodied subjects completed tracking activities with the devices in different positions. We quantify motor performance across subject groups and across device platforms and muscle activation across devices at two positions in the arm workspace. Trends in the assessment metrics were consistent across devices with able-bodied and high functioning strokes subjects being significantly more accurate and quicker in their motor performance than low functioning subjects. Muscle activation patterns were different for shoulder and elbow across different devices and locations. The Robot/CAMR suite has potential for stroke rehabilitation. By manipulating hardware and software variables, we can create personalized therapy environments that engage patients, address their therapy need, and track their progress. A larger longitudinal study is still needed to evaluate these systems in under-supervised environments such as the home.

SEE: improving nurse-patient communications and preventing software piracy in nurse call applications.

PubMed

Unluturk, Mehmet S

2012-06-01

Nurse call system is an electrically functioning system by which patients can call upon from a bedside station or from a duty station. An intermittent tone shall be heard and a corridor lamp located outside the room starts blinking with a slow or a faster rate depending on the call origination. It is essential to alert nurses on time so that they can offer care and comfort without any delay. There are currently many devices available for a nurse call system to improve communication between nurses and patients such as pagers, RFID (radio frequency identification) badges, wireless phones and so on. To integrate all these devices into an existing nurse call system and make they communicate with each other, we propose software client applications called bridges in this paper. We also propose a window server application called SEE (Supervised Event Executive) that delivers messages among these devices. A single hardware dongle is utilized for authentication and copy protection for SEE. Protecting SEE with securities provided by dongle only is a weak defense against hackers. In this paper, we develop some defense patterns for hackers such as calculating checksums in runtime, making calls to dongle from multiple places in code and handling errors properly by logging them into database.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Model Based Analysis and Test Generation for Flight Software

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.; Schumann, Johann M.; Mehlitz, Peter C.; Lowry, Mike R.; Karsai, Gabor; Nine, Harmon; Neema, Sandeep

2009-01-01

We describe a framework for model-based analysis and test case generation in the context of a heterogeneous model-based development paradigm that uses and combines Math- Works and UML 2.0 models and the associated code generation tools. This paradigm poses novel challenges to analysis and test case generation that, to the best of our knowledge, have not been addressed before. The framework is based on a common intermediate representation for different modeling formalisms and leverages and extends model checking and symbolic execution tools for model analysis and test case generation, respectively. We discuss the application of our framework to software models for a NASA flight mission.

Software for Data Analysis with Graphical Models

NASA Technical Reports Server (NTRS)

Buntine, Wray L.; Roy, H. Scott

1994-01-01

Probabilistic graphical models are being used widely in artificial intelligence and statistics, for instance, in diagnosis and expert systems, as a framework for representing and reasoning with probabilities and independencies. They come with corresponding algorithms for performing statistical inference. This offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper illustrates the framework with an example and then presents some basic techniques for the task: problem decomposition and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

Model-based software process improvement

NASA Technical Reports Server (NTRS)

Zettervall, Brenda T.

1994-01-01

The activities of a field test site for the Software Engineering Institute's software process definition project are discussed. Products tested included the improvement model itself, descriptive modeling techniques, the CMM level 2 framework document, and the use of process definition guidelines and templates. The software process improvement model represents a five stage cyclic approach for organizational process improvement. The cycles consist of the initiating, diagnosing, establishing, acting, and leveraging phases.

EBEX: A Balloon-Borne Telescope for Measuring Cosmic Microwave Background Polarization

NASA Astrophysics Data System (ADS)

Chapman, Daniel

2015-05-01

EBEX is a long-duration balloon-borne (LDB) telescope designed to probe polarization signals in the cosmic microwave background (CMB). It is designed to measure or place an upper limit on the inflationary B-mode signal, a signal predicted by inflationary theories to be imprinted on the CMB by gravitational waves, to detect the effects of gravitational lensing on the polarization of the CMB, and to characterize polarized Galactic foreground emission. The payload consists of a pointed gondola that houses the optics, polarimetry, detectors and detector readout systems, as well as the pointing sensors, control motors, telemetry sytems, and data acquisition and flight control computers. Polarimetry is achieved with a rotating half-wave plate and wire grid polarizer. The detectors are sensitive to frequency bands centered on 150, 250, and 410 GHz. EBEX was flown in 2009 from New Mexico as a full system test, and then flown again in December 2012 / January 2013 over Antarctica in a long-duration flight to collect scientific data. In the instrumentation part of this thesis we discuss the pointing sensors and attitude determination algorithms. We also describe the real-time map making software, "QuickLook", that was custom-designed for EBEX. We devote special attention to the design and construction of the primary pointing sensors, the star cameras, and their custom-designed flight software package, "STARS" (the Star Tracking Attitude Reconstruction Software). In the analysis part of this thesis we describe the current status of the post-flight analysis procedure. We discuss the data structures used in analysis and the pipeline stages related to attitude determination and map making. We also discuss a custom-designed software framework called "LEAP" (the LDB EBEX Analysis Pipeline) that supports most of the analysis pipeline stages.

Constructing an Evidence-Base for Future CALL Design with "Engineering Power": The Need for More Basic Research and Instrumental Replication

ERIC Educational Resources Information Center

Handley, Zöe

2014-01-01

This paper argues that the goal of Computer-Assisted Language Learning (CALL) research should be to construct a reliable evidence-base with "engineering power" and generality upon which the design of future CALL software and activities can be based. In order to establish such an evidence base for future CALL design, it suggests that CALL…

Software Metrics

DTIC Science & Technology

1988-12-01

software development scene is often charac- c. SPQR Model-Jones terized by: * schedule and cost estimates that are gross-d. COPMO-Thebaut ly inaccurate, SEI...time c. SPQR Model-Jones (in seconds) is simply derived from E by dividing T. Capers Jones has developed a software cost by the Stroud number, S...estimation model called the Software Produc- T=E/S tivity, Quality, and Reliability ( SPQR ) model. The basic approach is similar to that of Boehm’s The value

A Generic Ground Framework for Image Expertise Centres and Small-Sized Production Centres

NASA Astrophysics Data System (ADS)

Sellé, A.

2009-05-01

Initiated by the Pleiadas Earth Observation Program, the CNES (French Space Agency) has developed a generic collaborative framework for its image quality centre, highly customisable for any upcoming expertise centre. This collaborative framework has been design to be used by a group of experts or scientists that want to share data and processings and manage interfaces with external entities. Its flexible and scalable architecture complies with the core requirements: defining a user data model with no impact on the software (generic access data), integrating user processings with a GUI builder and built-in APIs, and offering a scalable architecture to fit any preformance requirement and accompany growing projects. The CNES jas given licensing grants for two software companies that will be able to redistribute this framework to any customer.

Achieving Agility and Stability in Large-Scale Software Development

DTIC Science & Technology

2013-01-16

temporary team is assigned to prepare layers and frameworks for future feature teams. Presentation Layer Domain Layer Data Access Layer...http://www.sei.cmu.edu/training/ elearning ~ Software Engineering Institute CarnegieMellon

Interim Open Source Software (OSS) Policy

EPA Pesticide Factsheets

This interim Policy establishes a framework to implement the requirements of the Office of Management and Budget's (OMB) Federal Source Code Policy to achieve efficiency, transparency and innovation through reusable and open source software.

USEEIO Framework Demo

EPA Science Inventory

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

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

The Profiles in Practice School Reporting Software.

ERIC Educational Resources Information Center

Griffin, Patrick

"The Profiles in Practice: School Reporting Software" provides a framework for reports on different aspects of performance in an assessment program. This booklet is the installation guide and user manual for the Profiles in Practice software, which is included as a CD-ROM. The chapters of the guide are: (1) "Installation"; (2) "Starting the…

Checklists for the Evaluation of Educational Software: Critical Review and Prospects.

ERIC Educational Resources Information Center

Tergan, Sigmar-Olaf

1998-01-01

Reviews strengths and weaknesses of check lists for the evaluation of computer software and outlines consequences for their practical application. Suggests an approach based on an instructional design model and a comprehensive framework to cope with problems of validity and predictive power of software evaluation. Discusses prospects of the…

Application Development Methodology Appropriateness: An Exploratory Case Study Bridging the Gap between Framework Characteristics and Selection

ERIC Educational Resources Information Center

Williams, Lawrence H., Jr.

2013-01-01

This qualitative study analyzed experiences of twenty software developers. The research showed that all software development methodologies are distinct from each other. While some, such as waterfall, focus on traditional, plan-driven approaches that allow software requirements and design to evolve; others facilitate ambiguity and uncertainty by…

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.

PubMed

Stajdohar, Miha; Rosengarten, Rafael D; Kokosar, Janez; Jeran, Luka; Blenkus, Domen; Shaulsky, Gad; Zupan, Blaz

2017-06-02

Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomics and transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights. We present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq). The application features visualization modules that include time course expression profiles, clustering, gene ontology enrichment analysis, differential expression analysis and comparison of experiments. All visualizations are interactive and interconnected, such that the selection of genes in one module propagates instantly to visualizations in other modules. dictyExpress currently stores the data from over 800 Dictyostelium experiments and is embedded within a general-purpose software framework for management of next-generation sequencing data. dictyExpress allows users to explore their data in a broader context by reciprocal linking with dictyBase-a repository of Dictyostelium genomic data. In addition, we introduce a companion application called GenBoard, an intuitive graphic user interface for data management and bioinformatics analysis. dictyExpress and GenBoard enable broad adoption of next generation sequencing based inquiries by the Dictyostelium research community. Labs without the means to undertake deep sequencing projects can mine the data available to the public. The entire information flow, from raw sequence data to hypothesis testing, can be accomplished in an efficient workspace. The software framework is generalizable and represents a useful approach for any research community. To encourage more wide usage, the backend is open-source, available for extension and further development by bioinformaticians and data scientists.

A framework for incorporating DTI Atlas Builder registration into Tract-Based Spatial Statistics and a simulated comparison to standard TBSS.

PubMed

Leming, Matthew; Steiner, Rachel; Styner, Martin

2016-02-27

Tract-based spatial statistics (TBSS) 6 is a software pipeline widely employed in comparative analysis of the white matter integrity from diffusion tensor imaging (DTI) datasets. In this study, we seek to evaluate the relationship between different methods of atlas registration for use with TBSS and different measurements of DTI (fractional anisotropy, FA, axial diffusivity, AD, radial diffusivity, RD, and medial diffusivity, MD). To do so, we have developed a novel tool that builds on existing diffusion atlas building software, integrating it into an adapted version of TBSS called DAB-TBSS (DTI Atlas Builder-Tract-Based Spatial Statistics) by using the advanced registration offered in DTI Atlas Builder 7 . To compare the effectiveness of these two versions of TBSS, we also propose a framework for simulating population differences for diffusion tensor imaging data, providing a more substantive means of empirically comparing DTI group analysis programs such as TBSS. In this study, we used 33 diffusion tensor imaging datasets and simulated group-wise changes in this data by increasing, in three different simulations, the principal eigenvalue (directly altering AD), the second and third eigenvalues (RD), and all three eigenvalues (MD) in the genu, the right uncinate fasciculus, and the left IFO. Additionally, we assessed the benefits of comparing the tensors directly using a functional analysis of diffusion tensor tract statistics (FADTTS 10 ). Our results indicate comparable levels of FA-based detection between DAB-TBSS and TBSS, with standard TBSS registration reporting a higher rate of false positives in other measurements of DTI. Within the simulated changes investigated here, this study suggests that the use of DTI Atlas Builder's registration enhances TBSS group-based studies.

Master Middle Ware: A Tool to Integrate Water Resources and Fish Population Dynamics Models

NASA Astrophysics Data System (ADS)

Yi, S.; Sandoval Solis, S.; Thompson, L. C.; Kilduff, D. P.

2017-12-01

Linking models that investigate separate components of ecosystem processes has the potential to unify messages regarding management decisions by evaluating potential trade-offs in a cohesive framework. This project aimed to improve the ability of riparian resource managers to forecast future water availability conditions and resultant fish habitat suitability, in order to better inform their management decisions. To accomplish this goal, we developed a middleware tool that is capable of linking and overseeing the operations of two existing models, a water resource planning tool Water Evaluation and Planning (WEAP) model and a habitat-based fish population dynamics model (WEAPhish). First, we designed the Master Middle Ware (MMW) software in Visual Basic for Application® in one Excel® file that provided a familiar framework for both data input and output Second, MMW was used to link and jointly operate WEAP and WEAPhish, using Visual Basic Application (VBA) macros to implement system level calls to run the models. To demonstrate the utility of this approach, hydrological, biological, and middleware model components were developed for the Butte Creek basin. This tributary of the Sacramento River, California is managed for both hydropower and the persistence of a threatened population of spring-run Chinook salmon (Oncorhynchus tschawytscha). While we have demonstrated the use of MMW for a particular watershed and fish population, MMW can be customized for use with different rivers and fish populations, assuming basic data requirements are met. This model integration improves on ad hoc linkages for managing data transfer between software programs by providing a consistent, user-friendly, and familiar interface across different model implementations. Furthermore, the data-viewing capabilities of MMW facilitate the rapid interpretation of model results by hydrologists, fisheries biologists, and resource managers, in order to accelerate learning and management decision making.

Matpar: Parallel Extensions for MATLAB

NASA Technical Reports Server (NTRS)

Springer, P. L.

1998-01-01

Matpar is a set of client/server software that allows a MATLAB user to take advantage of a parallel computer for very large problems. The user can replace calls to certain built-in MATLAB functions with calls to Matpar functions.

Distributed data mining on grids: services, tools, and applications.

PubMed

Cannataro, Mario; Congiusta, Antonio; Pugliese, Andrea; Talia, Domenico; Trunfio, Paolo

2004-12-01

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

CRPropa 2.0 - A public framework for propagating high energy nuclei, secondary gamma rays and neutrinos

NASA Astrophysics Data System (ADS)

Kampert, Karl-Heinz; Kulbartz, Jörg; Maccione, Luca; Nierstenhoefer, Nils; Schiffer, Peter; Sigl, Günter; van Vliet, Arjen René

2013-02-01

Version 2.0 of CRPropa [CRPropa is published under the 3rd version of the GNU General Public License (GPLv3). It is available, together with a detailed documentation of the code, at https://crpropa.desy.de.] is public software to model the extra-galactic propagation of ultra-high energy nuclei of atomic number Z⩽26 through structured magnetic fields and ambient photon backgrounds taking into account all relevant particle interactions. CRPropa covers the energy range 7×1016

Algorithms and software for nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.

1989-01-01

The objective of this research is to develop efficient methods for explicit time integration in nonlinear structural dynamics for computers which utilize both concurrency and vectorization. As a framework for these studies, the program WHAMS, which is described in Explicit Algorithms for the Nonlinear Dynamics of Shells (T. Belytschko, J. I. Lin, and C.-S. Tsay, Computer Methods in Applied Mechanics and Engineering, Vol. 42, 1984, pp 225 to 251), is used. There are two factors which make the development of efficient concurrent explicit time integration programs a challenge in a structural dynamics program: (1) the need for a variety of element types, which complicates the scheduling-allocation problem; and (2) the need for different time steps in different parts of the mesh, which is here called mixed delta t integration, so that a few stiff elements do not reduce the time steps throughout the mesh.

An acoustical bubble counter for superheated drop detectors.

PubMed

Taylor, Chris; Montvila, Darius; Flynn, David; Brennan, Christopher; d'Errico, Francesco

2006-01-01

A new bubble counter has been developed based on the well-established approach of detecting vaporization events acoustically in superheated drop detectors (SDDs). This counter is called the Framework Scientific ABC 1260, and it represents a major improvement over prior versions of this technology. By utilizing advanced acoustic pattern recognition software, the bubble formation event can be differentiated from ambient background noise, as well as from other acoustic signatures. Additional structural design enhancements include a relocation of the electronic components to the bottom of the device; thus allowing for greater stability, easier access to vial SDDs without exposure to system electronics. Upgrades in the electronics permit an increase in the speed of bubble detection by almost 50%, compared with earlier versions of the counters. By positioning the vial on top of the device, temperature and sound insulation can be accommodated for extreme environments. Lead shells can also be utilized for an enhanced response to high-energy neutrons.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

PubMed

Chen, Haochuan; Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

2018-06-18

Extended adaptive biasing force (eABF), a collective variable (CV)-based importance-sampling algorithm, has proven to be very robust and efficient compared with the original ABF algorithm. Its implementation in Colvars, a software addition to molecular dynamics (MD) engines, is, however, currently limited to NAMD and LAMMPS. To broaden the scope of eABF and its variants, like its generalized form (egABF), and make them available to other MD engines, e.g., GROMACS, AMBER, CP2K, and openMM, we present a PLUMED-based implementation, called extended-Lagrangian free energy calculation (ELF). This implementation can be used as a stand-alone gradient estimator for other CV-based sampling algorithms, such as temperature-accelerated MD (TAMD) and extended-Lagrangian metadynamics (MtD). ELF provides the end user with a convenient framework to help select the best-suited importance-sampling algorithm for a given application without any commitment to a particular MD engine.

Legal Issues of Ambient Intelligence in the SERENITY Project

NASA Astrophysics Data System (ADS)

Krausová, Alžběta; Dumortier, Jos

The successful functionality of the solutions proposed by the SERENITY project will only be achieved when they fit into the existing legal framework. Therefore, when developing software and hardware solutions, developers must respect requirements set out by law. The aim of this chapter is to define legal challenges that arise with the advent of the Ambient Intelligence, and to explain how SERENITY deals with the challenge of legal compliance. To do this, we will first describe how the legal requirements are translated into a machinereadable form in the SERENITY project, and introduce the concept of so called legal patterns. The application of relevant legal principles on data protection will be illustrated using two particular scenarios. We will then focus on practical legal problems related to daily operations of SERENITY technical solutions. Finally, we conclude with an evaluation of the SERENITY approach and its outcomes

ATLAS particle detector CSC ROD software design and implementation, and, Addition of K physics to chi-squared analysis of FDQM

NASA Astrophysics Data System (ADS)

Hawkins, Donovan Lee

In this thesis I present a software framework for use on the ATLAS muon CSC readout driver. This C++ framework uses plug-in Decoders incorporating hand-optimized assembly language routines to perform sparsification and data formatting. The software is designed with both flexibility and performance in mind, and runs on a custom 9U VME board using Texas Instruments TMS360C6203 digital signal processors. I describe the requirements of the software, the methods used in its design, and the results of testing the software with simulated data. I also present modifications to a chi-squared analysis of the Standard Model and Four Down Quark Model (FDQM) originally done by Dr. Dennis Silverman. The addition of four new experiments to the analysis has little effect on the Standard Model but provides important new restrictions on the FDQM. The method used to incorporate these new experiments is presented, and the consequences of their addition are reviewed.

Happy software developers solve problems better: psychological measurements in empirical software engineering

PubMed Central

Wang, Xiaofeng; Abrahamsson, Pekka

2014-01-01

For more than thirty years, it has been claimed that a way to improve software developers’ productivity and software quality is to focus on people and to provide incentives to make developers satisfied and happy. This claim has rarely been verified in software engineering research, which faces an additional challenge in comparison to more traditional engineering fields: software development is an intellectual activity and is dominated by often-neglected human factors (called human aspects in software engineering research). Among the many skills required for software development, developers must possess high analytical problem-solving skills and creativity for the software construction process. According to psychology research, affective states—emotions and moods—deeply influence the cognitive processing abilities and performance of workers, including creativity and analytical problem solving. Nonetheless, little research has investigated the correlation between the affective states, creativity, and analytical problem-solving performance of programmers. This article echoes the call to employ psychological measurements in software engineering research. We report a study with 42 participants to investigate the relationship between the affective states, creativity, and analytical problem-solving skills of software developers. The results offer support for the claim that happy developers are indeed better problem solvers in terms of their analytical abilities. The following contributions are made by this study: (1) providing a better understanding of the impact of affective states on the creativity and analytical problem-solving capacities of developers, (2) introducing and validating psychological measurements, theories, and concepts of affective states, creativity, and analytical-problem-solving skills in empirical software engineering, and (3) raising the need for studying the human factors of software engineering by employing a multidisciplinary viewpoint. PMID:24688866

Happy software developers solve problems better: psychological measurements in empirical software engineering.

PubMed

Graziotin, Daniel; Wang, Xiaofeng; Abrahamsson, Pekka

2014-01-01

For more than thirty years, it has been claimed that a way to improve software developers' productivity and software quality is to focus on people and to provide incentives to make developers satisfied and happy. This claim has rarely been verified in software engineering research, which faces an additional challenge in comparison to more traditional engineering fields: software development is an intellectual activity and is dominated by often-neglected human factors (called human aspects in software engineering research). Among the many skills required for software development, developers must possess high analytical problem-solving skills and creativity for the software construction process. According to psychology research, affective states-emotions and moods-deeply influence the cognitive processing abilities and performance of workers, including creativity and analytical problem solving. Nonetheless, little research has investigated the correlation between the affective states, creativity, and analytical problem-solving performance of programmers. This article echoes the call to employ psychological measurements in software engineering research. We report a study with 42 participants to investigate the relationship between the affective states, creativity, and analytical problem-solving skills of software developers. The results offer support for the claim that happy developers are indeed better problem solvers in terms of their analytical abilities. The following contributions are made by this study: (1) providing a better understanding of the impact of affective states on the creativity and analytical problem-solving capacities of developers, (2) introducing and validating psychological measurements, theories, and concepts of affective states, creativity, and analytical-problem-solving skills in empirical software engineering, and (3) raising the need for studying the human factors of software engineering by employing a multidisciplinary viewpoint.

Elements of strategic capability for software outsourcing enterprises based on the resource

NASA Astrophysics Data System (ADS)

Shi, Wengeng

2011-10-01

Software outsourcing enterprises as an emerging high-tech enterprises, the rise of the speed and the number was very amazing. In addition to Chinese software outsourcing for giving preferential policies, the software outsourcing business has its ability to upgrade, and in general the software companies have not had the related characteristics. View from the resource base of the theory, the analysis software outsourcing companies have the ability and resources of rare and valuable and non-mimic, we try to give an initial framework for theoretical analysis based on this.

Press Calls | NOAA Gulf Spill Restoration

Science.gov Websites

Projects Near You Strategic Frameworks Monitoring and Adaptive Management Restoration Areas Alabama Florida Archive Home Press Calls Press Calls Gulf Spill Restoration Menu Home Restoration Areas About Us Data How

Incorporating cost-benefit analyses into software assurance planning

NASA Technical Reports Server (NTRS)

Feather, M. S.; Sigal, B.; Cornford, S. L.; Hutchinson, P.

2001-01-01

The objective is to use cost-benefit analyses to identify, for a given project, optimal sets of software assurance activities. Towards this end we have incorporated cost-benefit calculations into a risk management framework.

Final Technical Report - Center for Technology for Advanced Scientific Component Software (TASCS)

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

Sussman, Alan

2014-10-21

This is a final technical report for the University of Maryland work in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS). The Maryland work focused on software tools for coupling parallel software components built using the Common Component Architecture (CCA) APIs. Those tools are based on the Maryland InterComm software framework that has been used in multiple computational science applications to build large-scale simulations of complex physical systems that employ multiple separately developed codes.

Wake Turbulence Mitigation for Departures (WTMD) Prototype System - Software Design Document

NASA Technical Reports Server (NTRS)

Sturdy, James L.

2008-01-01

This document describes the software design of a prototype Wake Turbulence Mitigation for Departures (WTMD) system that was evaluated in shadow mode operation at the Saint Louis (KSTL) and Houston (KIAH) airports. This document describes the software that provides the system framework, communications, user displays, and hosts the Wind Forecasting Algorithm (WFA) software developed by the M.I.T. Lincoln Laboratory (MIT-LL). The WFA algorithms and software are described in a separate document produced by MIT-LL.

Neutron imaging data processing using the Mantid framework

NASA Astrophysics Data System (ADS)

Pouzols, Federico M.; Draper, Nicholas; Nagella, Sri; Yang, Erica; Sajid, Ahmed; Ross, Derek; Ritchie, Brian; Hill, John; Burca, Genoveva; Minniti, Triestino; Moreton-Smith, Christopher; Kockelmann, Winfried

2016-09-01

Several imaging instruments are currently being constructed at neutron sources around the world. The Mantid software project provides an extensible framework that supports high-performance computing for data manipulation, analysis and visualisation of scientific data. At ISIS, IMAT (Imaging and Materials Science & Engineering) will offer unique time-of-flight neutron imaging techniques which impose several software requirements to control the data reduction and analysis. Here we outline the extensions currently being added to Mantid to provide specific support for neutron imaging requirements.

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

PubMed

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

2015-04-01

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

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

PubMed Central

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

2015-01-01

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

Verification of Java Programs using Symbolic Execution and Invariant Generation

NASA Technical Reports Server (NTRS)

Pasareanu, Corina; Visser, Willem

2004-01-01

Software verification is recognized as an important and difficult problem. We present a norel framework, based on symbolic execution, for the automated verification of software. The framework uses annotations in the form of method specifications an3 loop invariants. We present a novel iterative technique that uses invariant strengthening and approximation for discovering these loop invariants automatically. The technique handles different types of data (e.g. boolean and numeric constraints, dynamically allocated structures and arrays) and it allows for checking universally quantified formulas. Our framework is built on top of the Java PathFinder model checking toolset and it was used for the verification of several non-trivial Java programs.

A database for TMT interface control documents

NASA Astrophysics Data System (ADS)

Gillies, Kim; Roberts, Scott; Brighton, Allan; Rogers, John

2016-08-01

The TMT Software System consists of software components that interact with one another through a software infrastructure called TMT Common Software (CSW). CSW consists of software services and library code that is used by developers to create the subsystems and components that participate in the software system. CSW also defines the types of components that can be constructed and their roles. The use of common component types and shared middleware services allows standardized software interfaces for the components. A software system called the TMT Interface Database System was constructed to support the documentation of the interfaces for components based on CSW. The programmer describes a subsystem and each of its components using JSON-style text files. A command interface file describes each command a component can receive and any commands a component sends. The event interface files describe status, alarms, and events a component publishes and status and events subscribed to by a component. A web application was created to provide a user interface for the required features. Files are ingested into the software system's database. The user interface allows browsing subsystem interfaces, publishing versions of subsystem interfaces, and constructing and publishing interface control documents that consist of the intersection of two subsystem interfaces. All published subsystem interfaces and interface control documents are versioned for configuration control and follow the standard TMT change control processes. Subsystem interfaces and interface control documents can be visualized in the browser or exported as PDF files.

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

DTIC Science & Technology

2015-08-13

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

Framework for multi-resolution analyses of advanced traffic management strategies [summary].

DOT National Transportation Integrated Search

2017-01-01

Transportation planning relies extensively on software that can simulate and predict travel behavior in response to alternative transportation networks. However, different software packages view traffic at different scales. Some programs are based on...

A GIS-based generic real-time risk assessment framework and decision tools for chemical spills in the river basin.

PubMed

Jiang, Jiping; Wang, Peng; Lung, Wu-seng; Guo, Liang; Li, Mei

2012-08-15

This paper presents a generic framework and decision tools of real-time risk assessment on Emergency Environmental Decision Support System for response to chemical spills in river basin. The generic "4-step-3-model" framework is able to delineate the warning area and the impact on vulnerable receptors considering four types of hazards referring to functional area, societal impact, and human health and ecology system. Decision tools including the stand-alone system and software components were implemented on GIS platform. A detailed case study on the Songhua River nitrobenzene spill illustrated the goodness of the framework and tool Spill first responders and decision makers of catchment management will benefit from the rich, visual and dynamic hazard information output from the software. Copyright © 2012 Elsevier B.V. All rights reserved.

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

PubMed

Cavuşoğlu, M Cenk; Göktekin, Tolga G; Tendick, Frank

2006-04-01

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

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

PubMed

Sarpe, Vladimir; Schriemer, David C

2017-02-01

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

A general framework for parametric survival analysis.

PubMed

Crowther, Michael J; Lambert, Paul C

2014-12-30

Parametric survival models are being increasingly used as an alternative to the Cox model in biomedical research. Through direct modelling of the baseline hazard function, we can gain greater understanding of the risk profile of patients over time, obtaining absolute measures of risk. Commonly used parametric survival models, such as the Weibull, make restrictive assumptions of the baseline hazard function, such as monotonicity, which is often violated in clinical datasets. In this article, we extend the general framework of parametric survival models proposed by Crowther and Lambert (Journal of Statistical Software 53:12, 2013), to incorporate relative survival, and robust and cluster robust standard errors. We describe the general framework through three applications to clinical datasets, in particular, illustrating the use of restricted cubic splines, modelled on the log hazard scale, to provide a highly flexible survival modelling framework. Through the use of restricted cubic splines, we can derive the cumulative hazard function analytically beyond the boundary knots, resulting in a combined analytic/numerical approach, which substantially improves the estimation process compared with only using numerical integration. User-friendly Stata software is provided, which significantly extends parametric survival models available in standard software. Copyright © 2014 John Wiley & Sons, Ltd.

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

A Framework for Performing V&V within Reuse-Based Software Engineering

NASA Technical Reports Server (NTRS)

Addy, Edward A.

1996-01-01

Verification and validation (V&V) is performed during application development for many systems, especially safety-critical and mission-critical systems. The V&V process is intended to discover errors, especially errors related to critical processing, as early as possible during the development process. Early discovery is important in order to minimize the cost and other impacts of correcting these errors. In order to provide early detection of errors, V&V is conducted in parallel with system development, often beginning with the concept phase. In reuse-based software engineering, however, decisions on the requirements, design and even implementation of domain assets can be made prior to beginning development of a specific system. In this case, V&V must be performed during domain engineering in order to have an impact on system development. This paper describes a framework for performing V&V within architecture-centric, reuse-based software engineering. This framework includes the activities of traditional application-level V&V, and extends these activities into domain engineering and into the transition between domain engineering and application engineering. The framework includes descriptions of the types of activities to be performed during each of the life-cycle phases, and provides motivation for the activities.

SACA: Software Assisted Call Analysis--an interactive tool supporting content exploration, online guidance and quality improvement of counseling dialogues.

PubMed

Trinkaus, Hans L; Gaisser, Andrea E

2010-09-01

Nearly 30,000 individual inquiries are answered annually by the telephone cancer information service (CIS, KID) of the German Cancer Research Center (DKFZ). The aim was to develop a tool for evaluating these calls, and to support the complete counseling process interactively. A novel software tool is introduced, based on a structure similar to a music score. Treating the interaction as a "duet", guided by the CIS counselor, the essential contents of the dialogue are extracted automatically. For this, "trained speech recognition" is applied to the (known) counselor's part, and "keyword spotting" is used on the (unknown) client's part to pick out specific items from the "word streams". The outcomes fill an abstract score representing the dialogue. Pilot tests performed on a prototype of SACA (Software Assisted Call Analysis) resulted in a basic proof of concept: Demographic data as well as information regarding the situation of the caller could be identified. The study encourages following up on the vision of an integrated SACA tool for supporting calls online and performing statistics on its knowledge database offline. Further research perspectives are to check SACA's potential in comparison with established interaction analysis systems like RIAS. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

A Practical Software Architecture for Virtual Universities

ERIC Educational Resources Information Center

Xiang, Peifeng; Shi, Yuanchun; Qin, Weijun

2006-01-01

This article introduces a practical software architecture called CUBES, which focuses on system integration and evolvement for online virtual universities. The key of CUBES is a supporting platform that helps to integrate and evolve heterogeneous educational applications developed by different organizations. Both standardized educational…

Framework for End-User Programming of Cross-Smart Space Applications

PubMed Central

Palviainen, Marko; Kuusijärvi, Jarkko; Ovaska, Eila

2012-01-01

Cross-smart space applications are specific types of software services that enable users to share information, monitor the physical and logical surroundings and control it in a way that is meaningful for the user's situation. For developing cross-smart space applications, this paper makes two main contributions: it introduces (i) a component design and scripting method for end-user programming of cross-smart space applications and (ii) a backend framework of components that interwork to support the brunt of the RDFScript translation, and the use and execution of ontology models. Before end-user programming activities, the software professionals must develop easy-to-apply Driver components for the APIs of existing software systems. Thereafter, end-users are able to create applications from the commands of the Driver components with the help of the provided toolset. The paper also introduces the reference implementation of the framework, tools for the Driver component development and end-user programming of cross-smart space applications and the first evaluation results on their application. PMID:23202169

EarthCube's Assessment Framework: Ensuring Return on Investment

NASA Astrophysics Data System (ADS)

Lehnert, K.

2016-12-01

EarthCube is a community-governed, NSF-funded initiative to transform geoscience research by developing cyberinfrastructure that improves access, sharing, visualization, and analysis of all forms of geosciences data and related resources. EarthCube's goal is to enable geoscientists to tackle the challenges of understanding and predicting a complex and evolving solid Earth, hydrosphere, atmosphere, and space environment systems. EarthCube's infrastructure needs capabilities around data, software, and systems. It is essential for EarthCube to determine the value of new capabilities for the community and the progress of the overall effort to demonstrate its value to the science community and Return on Investment for the NSF. EarthCube is therefore developing an assessment framework for research proposals, projects funded by EarthCube, and the overall EarthCube program. As a first step, a software assessment framework has been developed that addresses the EarthCube Strategic Vision by promoting best practices in software development, complete and useful documentation, interoperability, standards adherence, open science, and education and training opportunities for research developers.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

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

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks.more » Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.« less

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

PubMed Central

2009-01-01

Background Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange. Results This paper presents a database application called MP-PBmice (insertional mutation mapping system of PB Mutagenesis Information Center), which is developed to serve the on-going large-scale PB insertional mutagenesis project. A lightweight enterprise-level development framework Struts-Spring-Hibernate is used here to ensure constructive and flexible support to the application. The MP-PBmice database system has three major features: strict access-control, efficient workflow control, and good expandability. It supports the collaboration among different groups that enter data and exchange information on daily basis, and is capable of providing real time progress reports for the whole project. MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice. Conclusion MP-PBmice is a web-based application for large-scale insertional mutation mapping onto the mouse genome, implemented with the widely used framework Struts-Spring-Hibernate. This system is already in use by the on-going genome-wide PB insertional mutation mapping project at IDM, Fudan University. PMID:19958505

PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.

PubMed

Hanke, Michael; Halchenko, Yaroslav O; Sederberg, Per B; Hanson, Stephen José; Haxby, James V; Pollmann, Stefan

2009-01-01

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data

PubMed Central

Hanke, Michael; Halchenko, Yaroslav O.; Sederberg, Per B.; Hanson, Stephen José; Haxby, James V.; Pollmann, Stefan

2009-01-01

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine-learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability. PMID:19184561

Transportability, distributability and rehosting experience with a kernel operating system interface set

NASA Technical Reports Server (NTRS)

Blumberg, F. C.; Reedy, A.; Yodis, E.

1986-01-01

For the past two years, PRC has been transporting and installing a software engineering environment framework, the Automated Product control Environment (APCE), at a number of PRC and government sites on a variety of different hardware. The APCE was designed using a layered architecture which is based on a standardized set of interfaces to host system services. This interface set called the APCE Interface Set (AIS), was designed to support many of the same goals as the Common Ada Programming Support Environment (APSE) Interface Set (CAIS). The APCE was developed to provide support for the full software lifecycle. Specific requirements of the APCE design included: automation of labor intensive administrative and logistical tasks: freedom for project team members to use existing tools: maximum transportability for APCE programs, interoperability of APCE database data, and distributability of both processes and data: and maximum performance on a wide variety of operating systems. A brief description is given of the APCE and AIS, a comparison of the AIS and CAIS both in terms of functionality and of philosophy and approach and a presentation of PRC's experience in rehosting AIS and transporting APCE programs and project data. Conclusions are drawn from this experience with respect to both the CAIS efforts and Space Station plans.

MYRaf: A new Approach with IRAF for Astronomical Photometric Reduction

NASA Astrophysics Data System (ADS)

Kilic, Y.; Shameoni Niaei, M.; Özeren, F. F.; Yesilyaprak, C.

2016-12-01

In this study, the design and some developments of MYRaf software for astronomical photometric reduction are presented. MYRaf software is an easy to use, reliable, and has a fast IRAF aperture photometry GUI tools. MYRaf software is an important step for the automated software process of robotic telescopes, and uses IRAF, PyRAF, matplotlib, ginga, alipy, and Sextractor with the general-purpose and high-level programming language Python and uses the QT framework.

Development of a Next Generation Concurrent Framework for the ATLAS Experiment

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Measuring and improving patient safety through health information technology: The Health IT Safety Framework

PubMed Central

Singh, Hardeep

2016-01-01

Health information technology (health IT) has potential to improve patient safety but its implementation and use has led to unintended consequences and new safety concerns. A key challenge to improving safety in health IT-enabled healthcare systems is to develop valid, feasible strategies to measure safety concerns at the intersection of health IT and patient safety. In response to the fundamental conceptual and methodological gaps related to both defining and measuring health IT-related patient safety, we propose a new framework, the Health IT Safety (HITS) measurement framework, to provide a conceptual foundation for health IT-related patient safety measurement, monitoring, and improvement. The HITS framework follows both Continuous Quality Improvement (CQI) and sociotechnical approaches and calls for new measures and measurement activities to address safety concerns in three related domains: 1) concerns that are unique and specific to technology (e.g., to address unsafe health IT related to unavailable or malfunctioning hardware or software); 2) concerns created by the failure to use health IT appropriately or by misuse of health IT (e.g. to reduce nuisance alerts in the electronic health record (EHR)), and 3) the use of health IT to monitor risks, health care processes and outcomes and identify potential safety concerns before they can harm patients (e.g. use EHR-based algorithms to identify patients at risk for medication errors or care delays). The framework proposes to integrate both retrospective and prospective measurement of HIT safety with an organization's existing clinical risk management and safety programs. It aims to facilitate organizational learning, comprehensive 360 degree assessment of HIT safety that includes vendor involvement, refinement of measurement tools and strategies, and shared responsibility to identify problems and implement solutions. A long term framework goal is to enable rigorous measurement that helps achieve the safety benefits of health IT in real-world clinical settings. PMID:26369894

Application of a COTS Resource Optimization Framework to the SSN Sensor Tasking Domain - Part I: Problem Definition

NASA Astrophysics Data System (ADS)

Tran, T.

With the onset of the SmallSat era, the RSO catalog is expected to see continuing growth in the near future. This presents a significant challenge to the current sensor tasking of the SSN. The Air Force is in need of a sensor tasking system that is robust, efficient, scalable, and able to respond in real-time to interruptive events that can change the tracking requirements of the RSOs. Furthermore, the system must be capable of using processed data from heterogeneous sensors to improve tasking efficiency. The SSN sensor tasking can be regarded as an economic problem of supply and demand: the amount of tracking data needed by each RSO represents the demand side while the SSN sensor tasking represents the supply side. As the number of RSOs to be tracked grows, demand exceeds supply. The decision-maker is faced with the problem of how to allocate resources in the most efficient manner. Braxton recently developed a framework called Multi-Objective Resource Optimization using Genetic Algorithm (MOROUGA) as one of its modern COTS software products. This optimization framework took advantage of the maturing technology of evolutionary computation in the last 15 years. This framework was applied successfully to address the resource allocation of an AFSCN-like problem. In any resource allocation problem, there are five key elements: (1) the resource pool, (2) the tasks using the resources, (3) a set of constraints on the tasks and the resources, (4) the objective functions to be optimized, and (5) the demand levied on the resources. In this paper we explain in detail how the design features of this optimization framework are directly applicable to address the SSN sensor tasking domain. We also discuss our validation effort as well as present the result of the AFSCN resource allocation domain using a prototype based on this optimization framework.

Analysis of key technologies for virtual instruments metrology

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

[Software as medical devices/medical apps : Tasks, requirements, and experiences from the point of view of a competent authority].

PubMed

Terhechte, Arno

2018-03-01

Software can be classified as a medical device according to the Medical Device Directive 93/42/EEC. The number of software products and medical apps is continuously increasing and so too is the use in health institutions (e. g., in hospitals and doctors' surgeries) for diagnosis and therapy.Different aspects of standalone software and medical apps from the perspective of the authority responsible are presented. The quality system implemented to establish a risk-based systematic inspection and supervision of manufacturers is discussed. The legal framework, as well as additional standards that are the basis for inspection, are outlined. The article highlights special aspects that occur during inspection like verification of software and interfaces, and the clinical evaluation of software. The Bezirksregierung, as the local government authority responsible in North Rhine-Westphalia, is also in charge of inspection of health institutions. Therefore this article is not limited to the manufacturers placing the software on the market, but in addition it describes the management and use of software as a medical device in hospitals.The future legal framework, the Medical Device Regulation, will strengthen the requirements and engage notified bodies more than today in the conformity assessment of software as a medical device.Manufacturers, health institutions, notified bodies and the authorities responsible are in charge of intensifying their efforts towards software as a medical device. Mutual information, improvement of skills, and inspections will lead to compliance with regulatory requirements.

Software Accelerates Computing Time for Complex Math

NASA Technical Reports Server (NTRS)

2014-01-01

Ames Research Center awarded Newark, Delaware-based EM Photonics Inc. SBIR funding to utilize graphic processing unit (GPU) technology- traditionally used for computer video games-to develop high-computing software called CULA. The software gives users the ability to run complex algorithms on personal computers with greater speed. As a result of the NASA collaboration, the number of employees at the company has increased 10 percent.

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Computational methods in sequence and structure prediction

NASA Astrophysics Data System (ADS)

Lang, Caiyi

This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed a software package which is capable of designing novel protein structures at the atomic resolution. This software package allows us to perform protein structure design with a flexible backbone. The backbone flexibility includes loop region relaxation as well as a secondary structure collective mode relaxation scheme. (Abstract shortened by UMI.)

Formal verification of mathematical software

NASA Technical Reports Server (NTRS)

Sutherland, D.

1984-01-01

Methods are investigated for formally specifying and verifying the correctness of mathematical software (software which uses floating point numbers and arithmetic). Previous work in the field was reviewed. A new model of floating point arithmetic called the asymptotic paradigm was developed and formalized. Two different conceptual approaches to program verification, the classical Verification Condition approach and the more recently developed Programming Logic approach, were adapted to use the asymptotic paradigm. These approaches were then used to verify several programs; the programs chosen were simplified versions of actual mathematical software.

An Evaluation of the Availability and Application of Microcomputer Software Programs for Use in Air Force Ground Transportation Squadrons

DTIC Science & Technology

1988-09-01

software programs capable of being used on a microcomputer will be considered for analysis. No software intended for use on a miniframe or mainframe...Dial-A-Log consists of a program written in a computer language called L-10 that is run on a DEC-20 miniframe . The combination of the specific...proliferation of software dealing with microcomputers. Instead, they were geared more towards managing the use of miniframe or mainframe computer

Investing in Software Sustainment

DTIC Science & Technology

2015-04-30

colored arrows simply represent a reinforcing  loop called the “ Bandwagon   Effect ”.  This  effect   simply means that a series of successful missions will...the Software Engineering Institute (SEI) developed a simulation model for analyzing the effects of changes in demand for software sustainment and the...developed a simulation model for analyzing the effects of changes in demand for software sustainment and the corresponding funding decisions. The model

Test Driven Development: Lessons from a Simple Scientific Model

NASA Astrophysics Data System (ADS)

Clune, T. L.; Kuo, K.

2010-12-01

In the commercial software industry, unit testing frameworks have emerged as a disruptive technology that has permanently altered the process by which software is developed. Unit testing frameworks significantly reduce traditional barriers, both practical and psychological, to creating and executing tests that verify software implementations. A new development paradigm, known as test driven development (TDD), has emerged from unit testing practices, in which low-level tests (i.e. unit tests) are created by developers prior to implementing new pieces of code. Although somewhat counter-intuitive, this approach actually improves developer productivity. In addition to reducing the average time for detecting software defects (bugs), the requirement to provide procedure interfaces that enable testing frequently leads to superior design decisions. Although TDD is widely accepted in many software domains, its applicability to scientific modeling still warrants reasonable skepticism. While the technique is clearly relevant for infrastructure layers of scientific models such as the Earth System Modeling Framework (ESMF), numerical and scientific components pose a number of challenges to TDD that are not often encountered in commercial software. Nonetheless, our experience leads us to believe that the technique has great potential not only for developer productivity, but also as a tool for understanding and documenting the basic scientific assumptions upon which our models are implemented. We will provide a brief introduction to test driven development and then discuss our experience in using TDD to implement a relatively simple numerical model that simulates the growth of snowflakes. Many of the lessons learned are directly applicable to larger scientific models.

A Software Framework for Remote Patient Monitoring by Using Multi-Agent Systems Support.

PubMed

Fernandes, Chrystinne Oliveira; Lucena, Carlos José Pereira De

2017-03-27

Although there have been significant advances in network, hardware, and software technologies, the health care environment has not taken advantage of these developments to solve many of its inherent problems. Research activities in these 3 areas make it possible to apply advanced technologies to address many of these issues such as real-time monitoring of a large number of patients, particularly where a timely response is critical. The objective of this research was to design and develop innovative technological solutions to offer a more proactive and reliable medical care environment. The short-term and primary goal was to construct IoT4Health, a flexible software framework to generate a range of Internet of things (IoT) applications, containing components such as multi-agent systems that are designed to perform Remote Patient Monitoring (RPM) activities autonomously. An investigation into its full potential to conduct such patient monitoring activities in a more proactive way is an expected future step. A framework methodology was selected to evaluate whether the RPM domain had the potential to generate customized applications that could achieve the stated goal of being responsive and flexible within the RPM domain. As a proof of concept of the software framework's flexibility, 3 applications were developed with different implementations for each framework hot spot to demonstrate potential. Agents4Health was selected to illustrate the instantiation process and IoT4Health's operation. To develop more concrete indicators of the responsiveness of the simulated care environment, an experiment was conducted while Agents4Health was operating, to measure the number of delays incurred in monitoring the tasks performed by agents. IoT4Health's construction can be highlighted as our contribution to the development of eHealth solutions. As a software framework, IoT4Health offers extensibility points for the generation of applications. Applications can extend the framework in the following ways: identification, collection, storage, recovery, visualization, monitoring, anomalies detection, resource notification, and dynamic reconfiguration. Based on other outcomes involving observation of the resulting applications, it was noted that its design contributed toward more proactive patient monitoring. Through these experimental systems, anomalies were detected in real time, with agents sending notifications instantly to the health providers. We conclude that the cost-benefit of the construction of a more generic and complex system instead of a custom-made software system demonstrated the worth of the approach, making it possible to generate applications in this domain in a more timely fashion. ©Chrystinne Oliveira Fernandes, Carlos José Pereira De Lucena. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 27.03.2017.

LCG Persistency Framework (CORAL, COOL, POOL): Status and Outlook

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

Valassi, A.; /CERN; Clemencic, M.

2012-04-19

The Persistency Framework consists of three software packages (CORAL, COOL and POOL) addressing the data access requirements of the LHC experiments in different areas. It is the result of the collaboration between the CERN IT Department and the three experiments (ATLAS, CMS and LHCb) that use this software to access their data. POOL is a hybrid technology store for C++ objects, metadata catalogs and collections. CORAL is a relational database abstraction layer with an SQL-free API. COOL provides specific software tools and components for the handling of conditions data. This paper reports on the status and outlook of the projectmore » and reviews in detail the usage of each package in the three experiments.« less

Software Review: Welcome to the World of Delta Drawing.

ERIC Educational Resources Information Center

King, Charles

1983-01-01

Provided is a review of an educational software program called "Delta Drawing." Included are comments on how the graphics program works, programing features, comparison with LOGO, educational value, and availability. Indicates that as a powerful learning program, it is innovative and imaginative. (JN)

RAPTR-SV: a hybrid method for the detection of structural variants

USDA-ARS?s Scientific Manuscript database

Motivation: Identification of Structural Variants (SV) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. Results: Simulations using RAPTR-SV and another software package that uses a similar algorithm for SV detection...

An expert system as applied to bridges : software development phase.

DOT National Transportation Integrated Search

1989-01-01

This report describes the results of the third of a four-part study dealing with the use of a computerized expert system to assist bridge engineers in their structures management program. In this phase of the study, software (called DOBES) was writte...

"Test" is a Four Letter Word

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

Pope, G M

2005-05-03

For a number of years I had the pleasure of teaching Testing Seminars all over the world and meeting and learning from others in our field. Over a twelve year period, I always asked the following questions to Software Developers, Test Engineers, and Managers who took my two or three day seminar on Software Testing: 'When was the first time you heard the word test'? 'Where were you when you first heard the word test'? 'Who said the word test'? 'How did the word test make you feel'? Most of the thousands of responses were similar to 'It was mymore » third grade teacher at school, and I felt nervous and afraid'. Now there were a few exceptions like 'It was my third grade teacher, and I was happy and excited to show how smart I was'. But by and large, my informal survey found that 'testing' is a word to which most people attach negative meanings, based on its historical context. So why is this important to those of us in the software development business? Because I have found that a preponderance of software developers do not get real excited about hearing that the software they just wrote is going to be 'tested' by the Test Group. Typical reactions I have heard over the years run from: 'I'm sure there is nothing wrong with the software, so go ahead and test it, better you find defects than our customers'. to these extremes: 'There is no need to test my software because there is nothing wrong with it'. 'You are not qualified to test my software because you don't know as much as I do about it'. 'If any Test Engineers come into our office again to test our software we will throw them through the third floor window'. So why is there such a strong negative reaction to testing? It is primitive. It goes back to grade school for many of us. It is a negative word that congers up negative emotions. In other words, 'test' is a four letter word. How many of us associate 'Joy' with 'Test'? Not many. It is hard for most of us to reprogram associations learned at an early age. So what can we do about it (short of hypnotic therapy for software developers)? Well one concept I have used (and still use) is to not call testing 'testing'. Call it something else. Ever wonder why most of the Independent Software Testing groups are called Software Quality Assurance groups? Now you know. Software Quality Assurance is not such a negatively charged phrase, even though Software Quality Assurance is much more than simply testing. It was a real blessing when the concept of Validation and Verification came about for software. Now I define Validation to mean assuring that the product produced does the right thing (usually what the customer wants it to do), and verification means that the product was built the right way (in accordance with some good design principles and practices). So I have deliberately called the System Test Group the Verification and Validation Group, or V&V Group, as a way of avoiding the negative image problem. I remember once having a conversation with a developer colleague who said, in the heat of battle, that it was fine to V&V his code, just don't test it! Once again V&V includes many things besides testing, but it just doesn't sound like an onerous thing to do to software. In my current job, working at a highly regarded national laboratory with world renowned physicists, I have again encountered the negativity about testing software. Except here they don't take kindly to Software Quality Assurance or Software Verification and Validation either. After all, software is just a trivial tool to automate algorithms that implement physics models. Testing, SQA, and V&V take time and get in the way of completing ground breaking science experiments. So I have again had to change the name of software testing to something less negative in the physics world. I found (the hard way) that if I requested more time to do software experimentation, the physicist's resistance melted. And so the conversation continues, 'We have time to run more software experiments. Just don't waste any time testing the software'! In case the concept of not calling testing 'testing' appeals to you, and there may be an opportunity for you to take the sting out of the name at your place of employment, I have compiled a table of things that testing could be called besides 'testing'. Of course we can embellish this by adding some good sounding prefixes and suffixes also. To come up with alternate names for testing, pick a word from columns A, B, and C in the table below. For instance Unified Acceptance Trials (A2,B7,C3) or Tailored Observational Demonstration (A6,B5,C5) or Agile Criteria Scoring (A3,B8,C8) or Rapid Requirement Proof (A1,B9,C7) or Satisfaction Assurance (B10,C1). You can probably think of some additional combinations appropriate for your industry.« less

A Software Framework for Remote Patient Monitoring by Using Multi-Agent Systems Support

PubMed Central

2017-01-01

Background Although there have been significant advances in network, hardware, and software technologies, the health care environment has not taken advantage of these developments to solve many of its inherent problems. Research activities in these 3 areas make it possible to apply advanced technologies to address many of these issues such as real-time monitoring of a large number of patients, particularly where a timely response is critical. Objective The objective of this research was to design and develop innovative technological solutions to offer a more proactive and reliable medical care environment. The short-term and primary goal was to construct IoT4Health, a flexible software framework to generate a range of Internet of things (IoT) applications, containing components such as multi-agent systems that are designed to perform Remote Patient Monitoring (RPM) activities autonomously. An investigation into its full potential to conduct such patient monitoring activities in a more proactive way is an expected future step. Methods A framework methodology was selected to evaluate whether the RPM domain had the potential to generate customized applications that could achieve the stated goal of being responsive and flexible within the RPM domain. As a proof of concept of the software framework’s flexibility, 3 applications were developed with different implementations for each framework hot spot to demonstrate potential. Agents4Health was selected to illustrate the instantiation process and IoT4Health’s operation. To develop more concrete indicators of the responsiveness of the simulated care environment, an experiment was conducted while Agents4Health was operating, to measure the number of delays incurred in monitoring the tasks performed by agents. Results IoT4Health’s construction can be highlighted as our contribution to the development of eHealth solutions. As a software framework, IoT4Health offers extensibility points for the generation of applications. Applications can extend the framework in the following ways: identification, collection, storage, recovery, visualization, monitoring, anomalies detection, resource notification, and dynamic reconfiguration. Based on other outcomes involving observation of the resulting applications, it was noted that its design contributed toward more proactive patient monitoring. Through these experimental systems, anomalies were detected in real time, with agents sending notifications instantly to the health providers. Conclusions We conclude that the cost-benefit of the construction of a more generic and complex system instead of a custom-made software system demonstrated the worth of the approach, making it possible to generate applications in this domain in a more timely fashion. PMID:28347973

CAreDroid: Adaptation Framework for Android Context-Aware Applications

PubMed Central

Elmalaki, Salma; Wanner, Lucas; Srivastava, Mani

2015-01-01

Context-awareness is the ability of software systems to sense and adapt to their physical environment. Many contemporary mobile applications adapt to changing locations, connectivity states, available computational and energy resources, and proximity to other users and devices. Nevertheless, there is little systematic support for context-awareness in contemporary mobile operating systems. Because of this, application developers must build their own context-awareness adaptation engines, dealing directly with sensors and polluting application code with complex adaptation decisions. In this paper, we introduce CAreDroid, which is a framework that is designed to decouple the application logic from the complex adaptation decisions in Android context-aware applications. In this framework, developers are required— only—to focus on the application logic by providing a list of methods that are sensitive to certain contexts along with the permissible operating ranges under those contexts. At run time, CAreDroid monitors the context of the physical environment and intercepts calls to sensitive methods, activating only the blocks of code that best fit the current physical context. CAreDroid is implemented as part of the Android runtime system. By pushing context monitoring and adaptation into the runtime system, CAreDroid eases the development of context-aware applications and increases their efficiency. In particular, case study applications implemented using CAre-Droid are shown to have: (1) at least half lines of code fewer and (2) at least 10× more efficient in execution time compared to equivalent context-aware applications that use only standard Android APIs. PMID:26834512

A framework for testing and comparing binaural models.

PubMed

Dietz, Mathias; Lestang, Jean-Hugues; Majdak, Piotr; Stern, Richard M; Marquardt, Torsten; Ewert, Stephan D; Hartmann, William M; Goodman, Dan F M

2018-03-01

Auditory research has a rich history of combining experimental evidence with computational simulations of auditory processing in order to deepen our theoretical understanding of how sound is processed in the ears and in the brain. Despite significant progress in the amount of detail and breadth covered by auditory models, for many components of the auditory pathway there are still different model approaches that are often not equivalent but rather in conflict with each other. Similarly, some experimental studies yield conflicting results which has led to controversies. This can be best resolved by a systematic comparison of multiple experimental data sets and model approaches. Binaural processing is a prominent example of how the development of quantitative theories can advance our understanding of the phenomena, but there remain several unresolved questions for which competing model approaches exist. This article discusses a number of current unresolved or disputed issues in binaural modelling, as well as some of the significant challenges in comparing binaural models with each other and with the experimental data. We introduce an auditory model framework, which we believe can become a useful infrastructure for resolving some of the current controversies. It operates models over the same paradigms that are used experimentally. The core of the proposed framework is an interface that connects three components irrespective of their underlying programming language: The experiment software, an auditory pathway model, and task-dependent decision stages called artificial observers that provide the same output format as the test subject. Copyright © 2017 Elsevier B.V. All rights reserved.

CAreDroid: Adaptation Framework for Android Context-Aware Applications.

PubMed

Elmalaki, Salma; Wanner, Lucas; Srivastava, Mani

2015-09-01

Context-awareness is the ability of software systems to sense and adapt to their physical environment. Many contemporary mobile applications adapt to changing locations, connectivity states, available computational and energy resources, and proximity to other users and devices. Nevertheless, there is little systematic support for context-awareness in contemporary mobile operating systems. Because of this, application developers must build their own context-awareness adaptation engines, dealing directly with sensors and polluting application code with complex adaptation decisions. In this paper, we introduce CAreDroid, which is a framework that is designed to decouple the application logic from the complex adaptation decisions in Android context-aware applications. In this framework, developers are required- only-to focus on the application logic by providing a list of methods that are sensitive to certain contexts along with the permissible operating ranges under those contexts. At run time, CAreDroid monitors the context of the physical environment and intercepts calls to sensitive methods, activating only the blocks of code that best fit the current physical context. CAreDroid is implemented as part of the Android runtime system. By pushing context monitoring and adaptation into the runtime system, CAreDroid eases the development of context-aware applications and increases their efficiency. In particular, case study applications implemented using CAre-Droid are shown to have: (1) at least half lines of code fewer and (2) at least 10× more efficient in execution time compared to equivalent context-aware applications that use only standard Android APIs.

Lessons Learned From Developing A Streaming Data Framework for Scientific Analysis

NASA Technical Reports Server (NTRS)

Wheeler. Kevin R.; Allan, Mark; Curry, Charles

2003-01-01

We describe the development and usage of a streaming data analysis software framework. The framework is used for three different applications: Earth science hyper-spectral imaging analysis, Electromyograph pattern detection, and Electroencephalogram state determination. In each application the framework was used to answer a series of science questions which evolved with each subsequent answer. This evolution is summarized in the form of lessons learned.

A Framework for the Evaluation of CASE Tool Learnability in Educational Environments

ERIC Educational Resources Information Center

Senapathi, Mali

2005-01-01

The aim of the research is to derive a framework for the evaluation of Computer Aided Software Engineering (CASE) tool learnability in educational environments. Drawing from the literature of Human Computer Interaction and educational research, a framework for evaluating CASE tool learnability in educational environments is derived. The two main…

Improving component interoperability and reusability with the java connection framework (JCF): overview and application to the ages-w environmental model

USDA-ARS?s Scientific Manuscript database

Environmental modeling framework (EMF) design goals are multi-dimensional and often include many aspects of general software framework development. Many functional capabilities offered by current EMFs are closely related to interoperability and reuse aspects. For example, an EMF needs to support dev...

Carpet: Adaptive Mesh Refinement for the Cactus Framework

NASA Astrophysics Data System (ADS)

Schnetter, Erik; Hawley, Scott; Hawke, Ian

2016-11-01

Carpet is an adaptive mesh refinement and multi-patch driver for the Cactus Framework (ascl:1102.013). Cactus is a software framework for solving time-dependent partial differential equations on block-structured grids, and Carpet acts as driver layer providing adaptive mesh refinement, multi-patch capability, as well as parallelization and efficient I/O.

Using software-modified smartphones to validate self-reported mobile phone use in young people: A pilot study.

PubMed

Goedhart, Geertje; Vrijheid, Martine; Wiart, Joe; Hours, Martine; Kromhout, Hans; Cardis, Elisabeth; Eastman Langer, Chelsea; de Llobet Viladoms, Patricia; Massardier-Pilonchery, Amelie; Vermeulen, Roel

2015-10-01

A newly developed smartphone application was piloted to characterize and validate mobile phone use in young people. Twenty-six volunteers (mean age 17.3 years) from France, Spain, and the Netherlands used a software-modified smartphone for 4 weeks; the application installed on the phone recorded number and duration of calls, data use, laterality, hands-free device usage, and communication system used for both voice calls and data transfer. Upon returning the phone, participants estimated their mobile phone use during those 4 weeks via an interviewer-administered questionnaire. Results indicated that participants on average underestimated the number of calls they made, while they overestimated total call duration. Participants held the phone for about 90% of total call time near the head, mainly on the side of the head they reported as dominant. Some limitations were encountered when comparing reported and recorded data use and speaker use. When applied in a larger sample, information recorded by the smartphone application will be very useful to improve radiofrequency (RF) exposure modeling from mobile phones to be used in epidemiological research. © 2015 Wiley Periodicals, Inc.

SIM_EXPLORE: Software for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

A General Water Resources Regulation Software System in China

NASA Astrophysics Data System (ADS)

LEI, X.

2017-12-01

To avoid iterative development of core modules in water resource normal regulation and emergency regulation and improve the capability of maintenance and optimization upgrading of regulation models and business logics, a general water resources regulation software framework was developed based on the collection and analysis of common demands for water resources regulation and emergency management. It can provide a customizable, secondary developed and extensible software framework for the three-level platform "MWR-Basin-Province". Meanwhile, this general software system can realize business collaboration and information sharing of water resources regulation schemes among the three-level platforms, so as to improve the decision-making ability of national water resources regulation. There are four main modules involved in the general software system: 1) A complete set of general water resources regulation modules allows secondary developer to custom-develop water resources regulation decision-making systems; 2) A complete set of model base and model computing software released in the form of Cloud services; 3) A complete set of tools to build the concept map and model system of basin water resources regulation, as well as a model management system to calibrate and configure model parameters; 4) A database which satisfies business functions and functional requirements of general water resources regulation software can finally provide technical support for building basin or regional water resources regulation models.

The Effects of the Use of Activity-Based Costing Software in the Learning Process: An Empirical Analysis

ERIC Educational Resources Information Center

Tan, Andrea; Ferreira, Aldónio

2012-01-01

This study investigates the influence of the use of accounting software in teaching activity-based costing (ABC) on the learning process. It draws upon the Theory of Planned Behaviour and uses the end-user computer satisfaction (EUCS) framework to examine students' satisfaction with the ABC software. The study examines students' satisfaction with…

Software Framework for Controlling Unsupervised Scientific Instruments.

PubMed

Schmid, Benjamin; Jahr, Wiebke; Weber, Michael; Huisken, Jan

2016-01-01

Science outreach and communication are gaining more and more importance for conveying the meaning of today's research to the general public. Public exhibitions of scientific instruments can provide hands-on experience with technical advances and their applications in the life sciences. The software of such devices, however, is oftentimes not appropriate for this purpose. In this study, we describe a software framework and the necessary computer configuration that is well suited for exposing a complex self-built and software-controlled instrument such as a microscope to laymen under limited supervision, e.g. in museums or schools. We identify several aspects that must be met by such software, and we describe a design that can simultaneously be used to control either (i) a fully functional instrument in a robust and fail-safe manner, (ii) an instrument that has low-cost or only partially working hardware attached for illustration purposes or (iii) a completely virtual instrument without hardware attached. We describe how to assess the educational success of such a device, how to monitor its operation and how to facilitate its maintenance. The introduced concepts are illustrated using our software to control eduSPIM, a fluorescent light sheet microscope that we are currently exhibiting in a technical museum.

Software for MR image overlay guided needle insertions: the clinical translation process

NASA Astrophysics Data System (ADS)

Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

2013-03-01

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

A Framework for Software Reuse in Safety-Critical System of Systems

DTIC Science & Technology

2008-03-01

environment.8 Pressman , on the other hand, defines a software component as a unit of composition with contractually specified and explicit context...2005, p654. 9 R.S. Pressman ., Software Engineering A Practitioner’s Approach, Sixth Edition, New York, NY.: McGraw-Hill, 2005, p817. 10 W.C. Lim...index.php. 79 Pressman , R.S., Software Engineering A Practitioner’s Approach, Sixth Edition, New York, NY.: McGraw-Hill, 2005. Radio Technical

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

DTIC Science & Technology

2011-01-01

open-source BMI software solu- tions are currently available, we feel that the Craniux software package fills a specific need in the realm of BMI...data, such as cortical source imaging using EEG or MEG recordings. It is with these characteristics in mind that we feel the Craniux software package...S. Adee, “Dean Kamen’s ‘luke arm’ prosthesis readies for clinical trials,” IEEE Spectrum, February 2008, http://spectrum .ieee.org/biomedical

ELPSA as a Lesson Design Framework

ERIC Educational Resources Information Center

Lowrie, Tom; Patahuddin, Sitti Maesuri

2015-01-01

This paper offers a framework for a mathematics lesson design that is consistent with the way we learn about, and discover, most things in life. In addition, the framework provides a structure for identifying how mathematical concepts and understanding are acquired and developed. This framework is called ELPSA and represents five learning…

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

Ling Zou; Hongbin Zhang; Jess Gehin

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

The NASA Auralization Framework and Plugin Architecture

NASA Technical Reports Server (NTRS)

Aumann, Aric R.; Tuttle, Brian C.; Chapin, William L.; Rizzi, Stephen A.

2015-01-01

NASA has a long history of investigating human response to aircraft flyover noise and in recent years has developed a capability to fully auralize the noise of aircraft during their design. This capability is particularly useful for unconventional designs with noise signatures significantly different from the current fleet. To that end, a flexible software architecture has been developed to facilitate rapid integration of new simulation techniques for noise source synthesis and propagation, and to foster collaboration amongst researchers through a common releasable code base. The NASA Auralization Framework (NAF) is a skeletal framework written in C++ with basic functionalities and a plugin architecture that allows users to mix and match NAF capabilities with their own methods through the development and use of dynamically linked libraries. This paper presents the NAF software architecture and discusses several advanced auralization techniques that have been implemented as plugins to the framework.

JCell--a Java-based framework for inferring regulatory networks from time series data.

PubMed

Spieth, C; Supper, J; Streichert, F; Speer, N; Zell, A

2006-08-15

JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

The Future of Electronic Device Design: Device and Process Simulation Find Intelligence on the World Wide Web

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.

1999-01-01

We are on the path to meet the major challenges ahead for TCAD (technology computer aided design). The emerging computational grid will ultimately solve the challenge of limited computational power. The Modular TCAD Framework will solve the TCAD software challenge once TCAD software developers realize that there is no other way to meet industry's needs. The modular TCAD framework (MTF) also provides the ideal platform for solving the TCAD model challenge by rapid implementation of models in a partial differential solver.

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.

Authoring and Hypermedia.

ERIC Educational Resources Information Center

Lieberth, Ann K.; Martin, Doug R.

1995-01-01

Because of the diversity of clients served by speech-language pathologists and audiologists, available commercial software may not meet all needs. Authoring programs allow the clinician to design software that can be customized for individual clients. This article describes an authoring program called HyperCard and its use in preparing hypermedia…

Tele-EnREDando.com: A Multimedia WEB-CALL Software for Mobile Phones.

ERIC Educational Resources Information Center

Garcia, Jose Carlos

2002-01-01

Presents one of the world's first prototypes of language learning software for smart-phones. Tele-EnREDando.com is an Internet based multimedia application designed for 3G mobile phones with audio, video, and interactive exercises for learning Spanish for business. (Author/VWL)

An Open-Source Toolbox for Surrogate Modeling of Joint Contact Mechanics

PubMed Central

Eskinazi, Ilan

2016-01-01

Goal Incorporation of elastic joint contact models into simulations of human movement could facilitate studying the interactions between muscles, ligaments, and bones. Unfortunately, elastic joint contact models are often too expensive computationally to be used within iterative simulation frameworks. This limitation can be overcome by using fast and accurate surrogate contact models that fit or interpolate input-output data sampled from existing elastic contact models. However, construction of surrogate contact models remains an arduous task. The aim of this paper is to introduce an open-source program called Surrogate Contact Modeling Toolbox (SCMT) that facilitates surrogate contact model creation, evaluation, and use. Methods SCMT interacts with the third party software FEBio to perform elastic contact analyses of finite element models and uses Matlab to train neural networks that fit the input-output contact data. SCMT features sample point generation for multiple domains, automated sampling, sample point filtering, and surrogate model training and testing. Results An overview of the software is presented along with two example applications. The first example demonstrates creation of surrogate contact models of artificial tibiofemoral and patellofemoral joints and evaluates their computational speed and accuracy, while the second demonstrates the use of surrogate contact models in a forward dynamic simulation of an open-chain leg extension-flexion motion. Conclusion SCMT facilitates the creation of computationally fast and accurate surrogate contact models. Additionally, it serves as a bridge between FEBio and OpenSim musculoskeletal modeling software. Significance Researchers may now create and deploy surrogate models of elastic joint contact with minimal effort. PMID:26186761

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

PubMed

Döring, Kersten; Grüning, Björn A; Telukunta, Kiran K; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user's system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects.

Knowledge Synthesis with Maps of Neural Connectivity

PubMed Central

Tallis, Marcelo; Thompson, Richard; Russ, Thomas A.; Burns, Gully A. P. C.

2011-01-01

This paper describes software for neuroanatomical knowledge synthesis based on neural connectivity data. This software supports a mature methodology developed since the early 1990s. Over this time, the Swanson laboratory at USC has generated an account of the neural connectivity of the sub-structures of the hypothalamus, amygdala, septum, hippocampus, and bed nucleus of the stria terminalis. This is based on neuroanatomical data maps drawn into a standard brain atlas by experts. In earlier work, we presented an application for visualizing and comparing anatomical macro connections using the Swanson third edition atlas as a framework for accurate registration. Here we describe major improvements to the NeuARt application based on the incorporation of a knowledge representation of experimental design. We also present improvements in the interface and features of the data mapping components within a unified web-application. As a step toward developing an accurate sub-regional account of neural connectivity, we provide navigational access between the data maps and a semantic representation of area-to-area connections that they support. We do so based on an approach called “Knowledge Engineering from Experimental Design” (KEfED) model that is based on experimental variables. We have extended the underlying KEfED representation of tract-tracing experiments by incorporating the definition of a neuronanatomical data map as a measurement variable in the study design. This paper describes the software design of a web-application that allows anatomical data sets to be described within a standard experimental context and thus indexed by non-spatial experimental design features. PMID:22053155

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

PubMed Central

Döring, Kersten; Grüning, Björn A.; Telukunta, Kiran K.; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user’s system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects. PMID:27706202

POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones.

PubMed

Vlachopanos, A; Soupsana, E; Politou, A S; Papamokos, G V

2014-12-01

Mass spectrometry is a widely used technique for protein identification and it has also become the method of choice in order to detect and characterize the post-translational modifications (PTMs) of proteins. Many software tools have been developed to deal with this complication. In this paper we introduce a new, free and user friendly online software tool, named POTAMOS Mass Spectrometry Calculator, which was developed in the open source application framework Ruby on Rails. It can provide calculated mass spectrometry data in a time saving manner, independently of instrumentation. In this web application we have focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation, as suggested by the so called "histone code" hypothesis. The PTMs implemented in this software are: methylations of arginines and lysines, acetylations of lysines and phosphorylations of serines and threonines. The application is able to calculate the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass along with the full set of the unique primary structures produced by the possible distributions along the amino acid sequence. It can also calculate the masses and charges of a fragmented histone variant, which carries predefined modifications already implemented. Additional functionality is provided by the calculation of the masses of fragments produced upon protein cleavage by the proteolytic enzymes that are most widely used in proteomics studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Potential of a suite of robot/computer-assisted motivating systems for personalized, home-based, stroke rehabilitation

PubMed Central

Johnson, Michelle J; Feng, Xin; Johnson, Laura M; Winters, Jack M

2007-01-01

Background There is a need to improve semi-autonomous stroke therapy in home environments often characterized by low supervision of clinical experts and low extrinsic motivation. Our distributed device approach to this problem consists of an integrated suite of low-cost robotic/computer-assistive technologies driven by a novel universal access software framework called UniTherapy. Our design strategy for personalizing the therapy, providing extrinsic motivation and outcome assessment is presented and evaluated. Methods Three studies were conducted to evaluate the potential of the suite. A conventional force-reflecting joystick, a modified joystick therapy platform (TheraJoy), and a steering wheel platform (TheraDrive) were tested separately with the UniTherapy software. Stroke subjects with hemiparesis and able-bodied subjects completed tracking activities with the devices in different positions. We quantify motor performance across subject groups and across device platforms and muscle activation across devices at two positions in the arm workspace. Results Trends in the assessment metrics were consistent across devices with able-bodied and high functioning strokes subjects being significantly more accurate and quicker in their motor performance than low functioning subjects. Muscle activation patterns were different for shoulder and elbow across different devices and locations. Conclusion The Robot/CAMR suite has potential for stroke rehabilitation. By manipulating hardware and software variables, we can create personalized therapy environments that engage patients, address their therapy need, and track their progress. A larger longitudinal study is still needed to evaluate these systems in under-supervised environments such as the home. PMID:17331243

[Computer aided design and rapid manufacturing of removable partial denture frameworks].

PubMed

Han, Jing; Lü, Pei-jun; Wang, Yong

2010-08-01

To introduce a method of digital modeling and fabricating removable partial denture (RPD) frameworks using self-developed software for RPD design and rapid manufacturing system. The three-dimensional data of two partially dentate dental casts were obtained using a three-dimensional crossing section scanner. Self-developed software package for RPD design was used to decide the path of insertion and to design different components of RPD frameworks. The components included occlusal rest, clasp, lingual bar, polymeric retention framework and maxillary major connector. The design procedure for the components was as following: first, determine the outline of the component. Second, build the tissue surface of the component using the scanned data within the outline. Third, preset cross section was used to produce the polished surface. Finally, different RPD components were modeled respectively and connected by minor connectors to form an integrated RPD framework. The finished data were imported into a self-developed selective laser melting (SLM) machine and metal frameworks were fabricated directly. RPD frameworks for the two scanned dental casts were modeled with this self-developed program and metal RPD frameworks were successfully fabricated using SLM method. The finished metal frameworks fit well on the plaster models. The self-developed computer aided design and computer aided manufacture (CAD-CAM) system for RPD design and fabrication has completely independent intellectual property rights. It provides a new method of manufacturing metal RPD frameworks.

STOP-IT: Windows executable software for the stop-signal paradigm.

PubMed

Verbruggen, Frederick; Logan, Gordon D; Stevens, Michaël A

2008-05-01

The stop-signal paradigm is a useful tool for the investigation of response inhibition. In this paradigm, subjects are instructed to respond as fast as possible to a stimulus unless a stop signal is presented after a variable delay. However, programming the stop-signal task is typically considered to be difficult. To overcome this issue, we present software called STOP-IT, for running the stop-signal task, as well as an additional analyzing program called ANALYZE-IT. The main advantage of both programs is that they are a precompiled executable, and for basic use there is no need for additional programming. STOP-IT and ANALYZE-IT are completely based on free software, are distributed under the GNU General Public License, and are available at the personal Web sites of the first two authors or at expsy.ugent.be/tscope/stop.html.

BS-virus-finder: virus integration calling using bisulfite sequencing data.

PubMed

Gao, Shengjie; Hu, Xuesong; Xu, Fengping; Gao, Changduo; Xiong, Kai; Zhao, Xiao; Chen, Haixiao; Zhao, Shancen; Wang, Mengyao; Fu, Dongke; Zhao, Xiaohui; Bai, Jie; Mao, Likai; Li, Bo; Wu, Song; Wang, Jian; Li, Shengbin; Yang, Huangming; Bolund, Lars; Pedersen, Christian N S

2018-01-01

DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data. © The Authors 2017. Published by Oxford University Press.

Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework

PubMed Central

Antonopoulos, Georgios C.; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

2015-01-01

A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available. PMID:26599984

Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework.

PubMed

Antonopoulos, Georgios C; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

2015-01-01

A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available.

Multimedia-modeling integration development environment

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

Pelton, Mitchell A.; Hoopes, Bonnie L.

2002-09-02

There are many framework systems available; however, the purpose of the framework presented here is to capitalize on the successes of the Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) and Multi-media Multi-pathway Multi-receptor Risk Assessment (3MRA) methodology as applied to the Hazardous Waste Identification Rule (HWIR) while focusing on the development of software tools to simplify the module developer?s effort of integrating a module into the framework.

Web Based GIS System For Monitoring the Implementation of County Integrated Development Plan a Case Study of Nandi County, Kenya.

NASA Astrophysics Data System (ADS)

Kurui, P. K.; Mutua, F.

2016-12-01

The paper seek to propose a conceptual framework of a way of monitoring and evaluating the implementation of the projects listed in the county integrated development plan by applying the use of the geospatial technologies with the focus being developing a web based GIS system in which the public can be able to track and monitor the progress of implementation of the projects in various parts of the county , although the guidelines developed by the ministry of devolution provides for the inclusion of the implementation monitoring and evaluation framework specifying projects to be implemented during the plan period and specification of veriable indicators it does not provide mechanisms for public participation during implementation and monitoring stage. This calls for a system that the public can interact with. The web based GIS system has been developed using the free open source softwares. Development projects have been categorized into; ongoing, completed and planned It can also be shown that a web based GIS system can be used as an important tool for monitoring the implementation of the CIDP due to its easy to use nature and supported by the fact that internet is easily accessed by the majority of the public making it a powerful tool for public participation.

A Scalable Cyberinfrastructure for Interactive Visualization of Terascale Microscopy Data

PubMed Central

Venkat, A.; Christensen, C.; Gyulassy, A.; Summa, B.; Federer, F.; Angelucci, A.; Pascucci, V.

2017-01-01

The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits. Researchers require novel software capabilities for compiling, stitching, and visualizing large imagery. In this work, we detail the image acquisition process and a hierarchical streaming platform, ViSUS, that enables interactive visualization of these massive multi-volume datasets using a standard desktop computer. The ViSUS visualization framework has previously been shown to be suitable for 3D combustion simulation, climate simulation and visualization of large scale panoramic images. The platform is organized around a hierarchical cache oblivious data layout, called the IDX file format, which enables interactive visualization and exploration in ViSUS, scaling to the largest 3D images. In this paper we showcase the VISUS framework used in an interactive setting with the microscopy data. PMID:28638896

A Scalable Cyberinfrastructure for Interactive Visualization of Terascale Microscopy Data.

PubMed

Venkat, A; Christensen, C; Gyulassy, A; Summa, B; Federer, F; Angelucci, A; Pascucci, V

2016-08-01

The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits. Researchers require novel software capabilities for compiling, stitching, and visualizing large imagery. In this work, we detail the image acquisition process and a hierarchical streaming platform, ViSUS, that enables interactive visualization of these massive multi-volume datasets using a standard desktop computer. The ViSUS visualization framework has previously been shown to be suitable for 3D combustion simulation, climate simulation and visualization of large scale panoramic images. The platform is organized around a hierarchical cache oblivious data layout, called the IDX file format, which enables interactive visualization and exploration in ViSUS, scaling to the largest 3D images. In this paper we showcase the VISUS framework used in an interactive setting with the microscopy data.

Inference of Ancestral Recombination Graphs through Topological Data Analysis

PubMed Central

Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

2016-01-01

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

Random Testing and Model Checking: Building a Common Framework for Nondeterministic Exploration

NASA Technical Reports Server (NTRS)

Groce, Alex; Joshi, Rajeev

2008-01-01

Two popular forms of dynamic analysis, random testing and explicit-state software model checking, are perhaps best viewed as search strategies for exploring the state spaces introduced by nondeterminism in program inputs. We present an approach that enables this nondeterminism to be expressed in the SPIN model checker's PROMELA language, and then lets users generate either model checkers or random testers from a single harness for a tested C program. Our approach makes it easy to compare model checking and random testing for models with precisely the same input ranges and probabilities and allows us to mix random testing with model checking's exhaustive exploration of non-determinism. The PROMELA language, as intended in its design, serves as a convenient notation for expressing nondeterminism and mixing random choices with nondeterministic choices. We present and discuss a comparison of random testing and model checking. The results derive from using our framework to test a C program with an effectively infinite state space, a module in JPL's next Mars rover mission. More generally, we show how the ability of the SPIN model checker to call C code can be used to extend SPIN's features, and hope to inspire others to use the same methods to implement dynamic analyses that can make use of efficient state storage, matching, and backtracking.

Analyses of requirements for computer control and data processing experiment subsystems: Image data processing system (IDAPS) software description (7094 version), volume 2

NASA Technical Reports Server (NTRS)

1973-01-01

A description of each of the software modules of the Image Data Processing System (IDAPS) is presented. The changes in the software modules are the result of additions to the application software of the system and an upgrade of the IBM 7094 Mod(1) computer to a 1301 disk storage configuration. Necessary information about IDAPS sofware is supplied to the computer programmer who desires to make changes in the software system or who desires to use portions of the software outside of the IDAPS system. Each software module is documented with: module name, purpose, usage, common block(s) description, method (algorithm of subroutine) flow diagram (if needed), subroutines called, and storage requirements.

Road map for implementing the AASHTO pavement ME design software for the Idaho Transportation Department.

DOT National Transportation Integrated Search

2014-04-01

This report provides a Road Map for implementing the AASHTOWare Pavement ME Design software for the Idaho Transportation Department (ITD). The Road Map calls for a series of three stages: Stage 1 - Immediate, Stage 2 - Near Term, and Stage 3 - Future...

Quick Prototyping of Educational Software: An Object-Oriented Approach.

ERIC Educational Resources Information Center

Wong, Simon C-H

1994-01-01

Introduces and demonstrates a quick-prototyping model for educational software development that can be used by teachers developing their own courseware using an object-oriented programming system. Development of a courseware package called "The Match-Maker" is explained as an example that uses HyperCard for quick prototyping. (Contains…

Choosing and Using Text-to-Speech Software

ERIC Educational Resources Information Center

Peters, Tom; Bell, Lori

2007-01-01

This article describes a computer-based technology for generating speech called text-to-speech (TTS). This software is ready for widespread use by libraries, other organizations, and individual users. It offers the affordable ability to turn just about any electronic text that is not image-based into an artificially spoken communication. The…

Software GOLUCA: Knowledge Representation in Mental Calculation

ERIC Educational Resources Information Center

Casas-Garcia, Luis M.; Luengo-Gonzalez, Ricardo; Godinho-Lopes, Vitor

2011-01-01

We present a new software, called Goluca (Godinho, Luengo, and Casas, 2007), based on the technique of Pathfinder Associative Networks (Schvaneveldt, 1989), which produces graphical representations of the cognitive structure of individuals in a given field knowledge. In this case, we studied the strategies used by teachers and its relationship…

Application of Frameworks in the Analysis and (Re)design of Interactive Visual Learning Tools

ERIC Educational Resources Information Center

Liang, Hai-Ning; Sedig, Kamran

2009-01-01

Interactive visual learning tools (IVLTs) are software environments that encode and display information visually and allow learners to interact with the visual information. This article examines the application and utility of frameworks in the analysis and design of IVLTs at the micro level. Frameworks play an important role in any design. They…

The shuttle main engine: A first look

NASA Technical Reports Server (NTRS)

Schreur, Barbara

1996-01-01

Anyone entering the Space Shuttle Main Engine (SSME) team attends a two week course to become familiar with the design and workings of the engine. This course provides intensive coverage of the individual hardware items and their functions. Some individuals, particularly those involved with software maintenance and development, have felt overwhelmed by this volume of material and their lack of a logical framework in which to place it. To provide this logical framework, it was decided that a brief self-taught introduction to the overall operation of the SSME should be designed. To aid the people or new team members with an interest in the software, this new course should also explain the structure and functioning of the controller and its software. This paper presents a description of this presentation.

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.

Self-Regulated Learning: The Continuous-Change Conceptual Framework and a Vision of New Paradigm, Technology System, and Pedagogical Support

ERIC Educational Resources Information Center

Huh, Yeol; Reigeluth, Charles M.

2017-01-01

A modified conceptual framework called the Continuous-Change Framework for self-regulated learning (SRL) is presented. Common elements and limitations among the past frameworks are discussed in relation to the modified conceptual framework. The iterative nature of the goal setting process and overarching presence of self-efficacy and motivational…

The integration of the risk management process with the lifecycle of medical device software.

PubMed

Pecoraro, F; Luzi, D

2014-01-01

The application of software in the Medical Device (MD) domain has become central to the improvement of diagnoses and treatments. The new European regulations that specifically address software as an important component of MD, require complex procedures to make software compliant with safety requirements, introducing thereby new challenges in the qualification and classification of MD software as well as in the performance of risk management activities. Under this perspective, the aim of this paper is to propose an integrated framework that combines the activities to be carried out by the manufacturer to develop safe software within the development lifecycle based on the regulatory requirements reported in US and European regulations as well as in the relevant standards and guidelines. A comparative analysis was carried out to identify the main issues related to the application of the current new regulations. In addition, standards and guidelines recently released to harmonise procedures for the validation of MD software have been used to define the risk management activities to be carried out by the manufacturer during the software development process. This paper highlights the main issues related to the qualification and classification of MD software, providing an analysis of the different regulations applied in Europe and the US. A model that integrates the risk management process within the software development lifecycle has been proposed too. It is based on regulatory requirements and considers software risk analysis as a central input to be managed by the manufacturer already at the initial stages of the software design, in order to prevent MD failures. Relevant changes in the process of MD development have been introduced with the recognition of software being an important component of MDs as stated in regulations and standards. This implies the performance of highly iterative processes that have to integrate the risk management in the framework of software development. It also makes it necessary to involve both medical and software engineering competences to safeguard patient and user safety.

Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales.

PubMed

Miller, Brian S; Calderan, Susannah; Gillespie, Douglas; Weatherup, Graham; Leaper, Russell; Collins, Kym; Double, Michael C

2016-03-01

Directional frequency analysis and recording (DIFAR) sonobuoys can allow real-time acoustic localization of baleen whales for underwater tracking and remote sensing, but limited availability of hardware and software has prevented wider usage. These software limitations were addressed by developing a module in the open-source software PAMGuard. A case study is presented demonstrating that this software provides greater efficiency and accessibility than previous methods for detecting, localizing, and tracking Antarctic blue whales in real time. Additionally, this software can easily be extended to track other low and mid frequency sounds including those from other cetaceans, pinnipeds, icebergs, shipping, and seismic airguns.

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by UAH and provide versions of the software in a Macintosh and Windows compatible format.

A software development and evolution model based on decision-making

NASA Technical Reports Server (NTRS)

Wild, J. Christian; Dong, Jinghuan; Maly, Kurt

1991-01-01

Design is a complex activity whose purpose is to construct an artifact which satisfies a set of constraints and requirements. However the design process is not well understood. The software design and evolution process is the focus of interest, and a three dimensional software development space organized around a decision-making paradigm is presented. An initial instantiation of this model called 3DPM(sub p) which was partly implemented, is presented. Discussion of the use of this model in software reuse and process management is given.

High-energy physics software parallelization using database techniques

NASA Astrophysics Data System (ADS)

Argante, E.; van der Stok, P. D. V.; Willers, I.

1997-02-01

A programming model for software parallelization, called CoCa, is introduced that copes with problems caused by typical features of high-energy physics software. By basing CoCa on the database transaction paradimg, the complexity induced by the parallelization is for a large part transparent to the programmer, resulting in a higher level of abstraction than the native message passing software. CoCa is implemented on a Meiko CS-2 and on a SUN SPARCcenter 2000 parallel computer. On the CS-2, the performance is comparable with the performance of native PVM and MPI.

Software assurance standard

NASA Technical Reports Server (NTRS)

1992-01-01

This standard specifies the software assurance program for the provider of software. It also delineates the assurance activities for the provider and the assurance data that are to be furnished by the provider to the acquirer. In any software development effort, the provider is the entity or individual that actually designs, develops, and implements the software product, while the acquirer is the entity or individual who specifies the requirements and accepts the resulting products. This standard specifies at a high level an overall software assurance program for software developed for and by NASA. Assurance includes the disciplines of quality assurance, quality engineering, verification and validation, nonconformance reporting and corrective action, safety assurance, and security assurance. The application of these disciplines during a software development life cycle is called software assurance. Subsequent lower-level standards will specify the specific processes within these disciplines.

Integrating CCSDS Electronic Data Sheets into Flight Software

NASA Technical Reports Server (NTRS)

Wilmot, Jonathan

2017-01-01

This presentation will describe the new CCSDS Spacecraft Onboard Interfaces Services (SOIS) Electronic Data Sheet (EDS) standards and how they are being applied to data interfaces in software frameworks, tool chains, and ground systems across a range of missions at NASA and other agencies.

Data Centric Development Methodology

ERIC Educational Resources Information Center

Khoury, Fadi E.

2012-01-01

Data centric applications, an important effort of software development in large organizations, have been mostly adopting a software methodology, such as a waterfall or Rational Unified Process, as the framework for its development. These methodologies could work on structural, procedural, or object oriented based applications, but fails to capture…

Integrating a flexible modeling framework (FMF) with the network security assessment instrument to reduce software security risk

NASA Technical Reports Server (NTRS)

Gilliam, D. P.; Powell, J. D.

2002-01-01

This paper presents a portion of an overall research project on the generation of the network security assessment instrument to aid developers in assessing and assuring the security of software in the development and maintenance lifecycles.

PScan 1.0: flexible software framework for polygon based multiphoton microscopy

NASA Astrophysics Data System (ADS)

Li, Yongxiao; Lee, Woei Ming

2016-12-01

Multiphoton laser scanning microscopes exhibit highly localized nonlinear optical excitation and are powerful instruments for in-vivo deep tissue imaging. Customized multiphoton microscopy has a significantly superior performance for in-vivo imaging because of precise control over the scanning and detection system. To date, there have been several flexible software platforms catered to custom built microscopy systems i.e. ScanImage, HelioScan, MicroManager, that perform at imaging speeds of 30-100fps. In this paper, we describe a flexible software framework for high speed imaging systems capable of operating from 5 fps to 1600 fps. The software is based on the MATLAB image processing toolbox. It has the capability to communicate directly with a high performing imaging card (Matrox Solios eA/XA), thus retaining high speed acquisition. The program is also designed to communicate with LabVIEW and Fiji for instrument control and image processing. Pscan 1.0 can handle high imaging rates and contains sufficient flexibility for users to adapt to their high speed imaging systems.

NIRP Core Software Suite v. 1.0

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

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

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

Scout: high-performance heterogeneous computing made simple

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

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

2011-01-26

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

Shifter: Containers for HPC

NASA Astrophysics Data System (ADS)

Gerhardt, Lisa; Bhimji, Wahid; Canon, Shane; Fasel, Markus; Jacobsen, Doug; Mustafa, Mustafa; Porter, Jeff; Tsulaia, Vakho

2017-10-01

Bringing HEP computing to HPC can be difficult. Software stacks are often very complicated with numerous dependencies that are difficult to get installed on an HPC system. To address this issue, NERSC has created Shifter, a framework that delivers Docker-like functionality to HPC. It works by extracting images from native formats and converting them to a common format that is optimally tuned for the HPC environment. We have used Shifter to deliver the CVMFS software stack for ALICE, ATLAS, and STAR on the supercomputers at NERSC. As well as enabling the distribution multi-TB sized CVMFS stacks to HPC, this approach also offers performance advantages. Software startup times are significantly reduced and load times scale with minimal variation to 1000s of nodes. We profile several successful examples of scientists using Shifter to make scientific analysis easily customizable and scalable. We will describe the Shifter framework and several efforts in HEP and NP to use Shifter to deliver their software on the Cori HPC system.

The Regional Hydrologic Extremes Assessment System: A software framework for hydrologic modeling and data assimilation

PubMed Central

Das, Narendra; Stampoulis, Dimitrios; Ines, Amor; Fisher, Joshua B.; Granger, Stephanie; Kawata, Jessie; Han, Eunjin; Behrangi, Ali

2017-01-01

The Regional Hydrologic Extremes Assessment System (RHEAS) is a prototype software framework for hydrologic modeling and data assimilation that automates the deployment of water resources nowcasting and forecasting applications. A spatially-enabled database is a key component of the software that can ingest a suite of satellite and model datasets while facilitating the interfacing with Geographic Information System (GIS) applications. The datasets ingested are obtained from numerous space-borne sensors and represent multiple components of the water cycle. The object-oriented design of the software allows for modularity and extensibility, showcased here with the coupling of the core hydrologic model with a crop growth model. RHEAS can exploit multi-threading to scale with increasing number of processors, while the database allows delivery of data products and associated uncertainty through a variety of GIS platforms. A set of three example implementations of RHEAS in the United States and Kenya are described to demonstrate the different features of the system in real-world applications. PMID:28545077

The Regional Hydrologic Extremes Assessment System: A software framework for hydrologic modeling and data assimilation.

PubMed

Andreadis, Konstantinos M; Das, Narendra; Stampoulis, Dimitrios; Ines, Amor; Fisher, Joshua B; Granger, Stephanie; Kawata, Jessie; Han, Eunjin; Behrangi, Ali

2017-01-01

The Regional Hydrologic Extremes Assessment System (RHEAS) is a prototype software framework for hydrologic modeling and data assimilation that automates the deployment of water resources nowcasting and forecasting applications. A spatially-enabled database is a key component of the software that can ingest a suite of satellite and model datasets while facilitating the interfacing with Geographic Information System (GIS) applications. The datasets ingested are obtained from numerous space-borne sensors and represent multiple components of the water cycle. The object-oriented design of the software allows for modularity and extensibility, showcased here with the coupling of the core hydrologic model with a crop growth model. RHEAS can exploit multi-threading to scale with increasing number of processors, while the database allows delivery of data products and associated uncertainty through a variety of GIS platforms. A set of three example implementations of RHEAS in the United States and Kenya are described to demonstrate the different features of the system in real-world applications.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLABmore » command window.« less

The Transition to a Many-core World

NASA Astrophysics Data System (ADS)

Mattson, T. G.

2012-12-01

The need to increase performance within a fixed energy budget has pushed the computer industry to many core processors. This is grounded in the physics of computing and is not a trend that will just go away. It is hard to overestimate the profound impact of many-core processors on software developers. Virtually every facet of the software development process will need to change to adapt to these new processors. In this talk, we will look at many-core hardware and consider its evolution from a perspective grounded in the CPU. We will show that the number of cores will inevitably increase, but in addition, a quest to maximize performance per watt will push these cores to be heterogeneous. We will show that the inevitable result of these changes is a computing landscape where the distinction between the CPU and the GPU is blurred. We will then consider the much more pressing problem of software in a many core world. Writing software for heterogeneous many core processors is well beyond the ability of current programmers. One solution is to support a software development process where programmer teams are split into two distinct groups: a large group of domain-expert productivity programmers and much smaller team of computer-scientist efficiency programmers. The productivity programmers work in terms of high level frameworks to express the concurrency in their problems while avoiding any details for how that concurrency is exploited. The second group, the efficiency programmers, map applications expressed in terms of these frameworks onto the target many-core system. In other words, we can solve the many-core software problem by creating a software infrastructure that only requires a small subset of programmers to become master parallel programmers. This is different from the discredited dream of automatic parallelism. Note that productivity programmers still need to define the architecture of their software in a way that exposes the concurrency inherent in their problem. We submit that domain-expert programmers understand "what is concurrent". The parallel programming problem emerges from the complexity of "how that concurrency is utilized" on real hardware. The research described in this talk was carried out in collaboration with the ParLab at UC Berkeley. We use a design pattern language to define the high level frameworks exposed to domain-expert, productivity programmers. We then use tools from the SEJITS project (Selective embedded Just In time Specializers) to build the software transformation tool chains thst turn these framework-oriented designs into highly efficient code. The final ingredient is a software platform to serve as a target for these tools. One such platform is the OpenCL industry standard for programming heterogeneous systems. We will briefly describe OpenCL and show how it provides a vendor-neutral software target for current and future many core systems; both CPU-based, GPU-based, and heterogeneous combinations of the two.

The equipment access software for a distributed UNIX-based accelerator control system

NASA Astrophysics Data System (ADS)

Trofimov, Nikolai; Zelepoukine, Serguei; Zharkov, Eugeny; Charrue, Pierre; Gareyte, Claire; Poirier, Hervé

1994-12-01

This paper presents a generic equipment access software package for a distributed control system using computers with UNIX or UNIX-like operating systems. The package consists of three main components, an application Equipment Access Library, Message Handler and Equipment Data Base. An application task, which may run in any computer in the network, sends requests to access equipment through Equipment Library calls. The basic request is in the form Equipment-Action-Data and is routed via a remote procedure call to the computer to which the given equipment is connected. In this computer the request is received by the Message Handler. According to the type of the equipment connection, the Message Handler either passes the request to the specific process software in the same computer or forwards it to a lower level network of equipment controllers using MIL1553B, GPIB, RS232 or BITBUS communication. The answer is then returned to the calling application. Descriptive information required for request routing and processing is stored in the real-time Equipment Data Base. The package has been written to be portable and is currently available on DEC Ultrix, LynxOS, HPUX, XENIX, OS-9 and Apollo domain.

VIEW-Station software and its graphical user interface

NASA Astrophysics Data System (ADS)

Kawai, Tomoaki; Okazaki, Hiroshi; Tanaka, Koichiro; Tamura, Hideyuki

1992-04-01

VIEW-Station is a workstation-based image processing system which merges the state-of-the- art software environment of Unix with the computing power of a fast image processor. VIEW- Station has a hierarchical software architecture, which facilitates device independence when porting across various hardware configurations, and provides extensibility in the development of application systems. The core image computing language is V-Sugar. V-Sugar provides a set of image-processing datatypes and allows image processing algorithms to be simply expressed, using a functional notation. VIEW-Station provides a hardware independent window system extension called VIEW-Windows. In terms of GUI (Graphical User Interface) VIEW-Station has two notable aspects. One is to provide various types of GUI as visual environments for image processing execution. Three types of interpreters called (mu) V- Sugar, VS-Shell and VPL are provided. Users may choose whichever they prefer based on their experience and tasks. The other notable aspect is to provide facilities to create GUI for new applications on the VIEW-Station system. A set of widgets are available for construction of task-oriented GUI. A GUI builder called VIEW-Kid is developed for WYSIWYG interactive interface design.

A Framework for Analyzing and Testing the Performance of Software Services

NASA Astrophysics Data System (ADS)

Bertolino, Antonia; de Angelis, Guglielmo; di Marco, Antinisca; Inverardi, Paola; Sabetta, Antonino; Tivoli, Massimo

Networks "Beyond the 3rd Generation" (B3G) are characterized by mobile and resource-limited devices that communicate through different kinds of network interfaces. Software services deployed in such networks shall adapt themselves according to possible execution contexts and requirement changes. At the same time, software services have to be competitive in terms of the Quality of Service (QoS) provided, or perceived by the end user.

A Recommended Framework for the Network-Centric Acquisition Process

DTIC Science & Technology

2009-09-01

ISO /IEC 12207 , Systems and Software Engineering-Software Life-Cycle Processes  ANSI/EIA 632, Processes for Engineering a System. There are...engineering [46]. Some of the process models presented in the DAG are:  ISO /IEC 15288, Systems and Software Engineering-System Life-Cycle Processes...e.g., ISO , IA, Security, etc.). Vetting developers helps ensure that they are using industry best industry practices and maximize the IA compliance

GNU Radio Sandia Utilities v. 1.0

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

Gilbert, Jacob; Knee, Peter

This software adds a data handling module to the GNU Radio (GR) software defined radio (SDR) framework as well as some general-purpose function blocks (filters, metadata control, etc). This software is useful for processing bursty RF transmissions with GR, and serves as a base for applying SDR signal processing techniques to a whole burst of data at a time, as opposed to streaming data which GR has been primarily focused around.

Survivability as a Tool for Evaluating Open Source Software

DTIC Science & Technology

2015-06-01

the thesis limited the program development, so it is only able to process project issues (bugs or feature requests), which is an important metric for...Ideally, these insights may provide an analytic framework to generate guidance for decision makers that may support the inclusion of OSS to more...refine their efforts to build quality software and to strengthen their software development communities. 1.4 Research Questions This thesis addresses

Test Driven Development of Scientific Models

NASA Technical Reports Server (NTRS)

Clune, Thomas L.

2012-01-01

Test-Driven Development (TDD) is a software development process that promises many advantages for developer productivity and has become widely accepted among professional software engineers. As the name suggests, TDD practitioners alternate between writing short automated tests and producing code that passes those tests. Although this overly simplified description will undoubtedly sound prohibitively burdensome to many uninitiated developers, the advent of powerful unit-testing frameworks greatly reduces the effort required to produce and routinely execute suites of tests. By testimony, many developers find TDD to be addicting after only a few days of exposure, and find it unthinkable to return to previous practices. Of course, scientific/technical software differs from other software categories in a number of important respects, but I nonetheless believe that TDD is quite applicable to the development of such software and has the potential to significantly improve programmer productivity and code quality within the scientific community. After a detailed introduction to TDD, I will present the experience within the Software Systems Support Office (SSSO) in applying the technique to various scientific applications. This discussion will emphasize the various direct and indirect benefits as well as some of the difficulties and limitations of the methodology. I will conclude with a brief description of pFUnit, a unit testing framework I co-developed to support test-driven development of parallel Fortran applications.

Designing Educational Software with Students through Collaborative Design Games: The We!Design&Play Framework

ERIC Educational Resources Information Center

Triantafyllakos, George; Palaigeorgiou, George; Tsoukalas, Ioannis A.

2011-01-01

In this paper, we present a framework for the development of collaborative design games that can be employed in participatory design sessions with students for the design of educational applications. The framework is inspired by idea generation theory and the design games literature, and guides the development of board games which, through the use…

Decision Aids Using Heterogeneous Intelligence Analysis

DTIC Science & Technology

2010-08-20

developing a Geocultural service, a software framework and inferencing engine for the Transparent Urban Structures program. The scope of the effort...has evolved as the program has matured and is including multiple data sources, as well as interfaces out to the ONR architectural framework . Tasks...Interface; Application Program Interface; Application Programmer Interface CAF Common Application Framework EDA Event Driven Architecture a 16. SECURITY