Development of a tool for documenting, tracking, recording, and analyzing improvements to intersection sites and roadway departures in curve locations.

DOT National Transportation Integrated Search

2015-04-01

The principal objectives and scope of this project were to provide a software tracking tool to improve : decision-making for highway safety. A literature search revealed that purchasing and customizing : existing software was not feasible and a new s...

Dependency visualization for complex system understanding

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

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

The Knowledge-Based Software Assistant: Beyond CASE

NASA Technical Reports Server (NTRS)

Carozzoni, Joseph A.

1993-01-01

This paper will outline the similarities and differences between two paradigms of software development. Both support the whole software life cycle and provide automation for most of the software development process, but have different approaches. The CASE approach is based on a set of tools linked by a central data repository. This tool-based approach is data driven and views software development as a series of sequential steps, each resulting in a product. The Knowledge-Based Software Assistant (KBSA) approach, a radical departure from existing software development practices, is knowledge driven and centers around a formalized software development process. KBSA views software development as an incremental, iterative, and evolutionary process with development occurring at the specification level.

Evaluation and Validation (E&V) Team Public Report. Volume 5

DTIC Science & Technology

1990-10-31

aspects, software engineering practices, etc. The E&V requirements which are developed will be used to guide the E&V technical effort. The currently...interoperability of Ada software engineering environment tools and data. The scope of the CAIS-A includes the functionality affecting transportability that is...requirement that they be CAIS conforming tools or data. That is, for example numerous CIVC data exist on special purpose software currently available

An online database for plant image analysis software tools.

PubMed

Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

2013-10-09

Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is best suited for their research. We present an online, manually curated, database referencing more than 90 plant image analysis software solutions. The website, plant-image-analysis.org, presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions. The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.

Managing configuration software of ground software applications with glueware

NASA Technical Reports Server (NTRS)

Larsen, B.; Herrera, R.; Sesplaukis, T.; Cheng, L.; Sarrel, M.

2003-01-01

This paper reports on a simple, low-cost effort to streamline the configuration of the uplink software tools. Even though the existing ground system consisted of JPL and custom Cassini software rather than COTS, we chose a glueware approach--reintegrating with wrappers and bridges and adding minimal new functionality.

Practical Tools for Designing and Weighting Survey Samples

ERIC Educational Resources Information Center

Valliant, Richard; Dever, Jill A.; Kreuter, Frauke

2013-01-01

Survey sampling is fundamentally an applied field. The goal in this book is to put an array of tools at the fingertips of practitioners by explaining approaches long used by survey statisticians, illustrating how existing software can be used to solve survey problems, and developing some specialized software where needed. This book serves at least…

APRON: A Cellular Processor Array Simulation and Hardware Design Tool

NASA Astrophysics Data System (ADS)

Barr, David R. W.; Dudek, Piotr

2009-12-01

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

A software tool to analyze clinical workflows from direct observations.

PubMed

Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

2015-01-01

Observational data of clinical processes need to be managed in a convenient way, so that process information is reliable, valid and viable for further analysis. However, existing tools for allocating observations fail in systematic data collection of specific workflow recordings. We present a software tool which was developed to facilitate the analysis of clinical process observations. The tool was successfully used in the project OntoHealth, to build, store and analyze observations of diabetes routine consultations.

Reverse engineering of integrated circuits

DOEpatents

Chisholm, Gregory H.; Eckmann, Steven T.; Lain, Christopher M.; Veroff, Robert L.

2003-01-01

Software and a method therein to analyze circuits. The software comprises several tools, each of which perform particular functions in the Reverse Engineering process. The analyst, through a standard interface, directs each tool to the portion of the task to which it is most well suited, rendering previously intractable problems solvable. The tools are generally used iteratively to produce a successively more abstract picture of a circuit, about which incomplete a priori knowledge exists.

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

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

PubMed

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

2016-04-01

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

New and revised fire effects tools for fire management

Treesearch

Robert E. Keane; Greg Dillon; Stacy Drury; Robin Innes; Penny Morgan; Duncan Lutes; Susan J. Prichard; Jane Smith; Eva Strand

2014-01-01

Announcing the release of new software packages for application in wildland fire science and management, two fields that are already fully saturated with computer technology, may seem a bit too much to many managers. However, there have been some recent releases of new computer programs and revisions of existing software and information tools that deserve mention...

NREL Improves Building Energy Simulation Programs Through Diagnostic Testing (Fact Sheet)

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

Not Available

2012-01-01

This technical highlight describes NREL research to develop Building Energy Simulation Test for Existing Homes (BESTEST-EX) to increase the quality and accuracy of energy analysis tools for the building retrofit market. Researchers at the National Renewable Energy Laboratory (NREL) have developed a new test procedure to increase the quality and accuracy of energy analysis tools for the building retrofit market. The Building Energy Simulation Test for Existing Homes (BESTEST-EX) is a test procedure that enables software developers to evaluate the performance of their audit tools in modeling energy use and savings in existing homes when utility bills are available formore » model calibration. Similar to NREL's previous energy analysis tests, such as HERS BESTEST and other BESTEST suites included in ANSI/ASHRAE Standard 140, BESTEST-EX compares software simulation findings to reference results generated with state-of-the-art simulation tools such as EnergyPlus, SUNREL, and DOE-2.1E. The BESTEST-EX methodology: (1) Tests software predictions of retrofit energy savings in existing homes; (2) Ensures building physics calculations and utility bill calibration procedures perform to a minimum standard; and (3) Quantifies impacts of uncertainties in input audit data and occupant behavior. BESTEST-EX includes building physics and utility bill calibration test cases. The diagram illustrates the utility bill calibration test cases. Participants are given input ranges and synthetic utility bills. Software tools use the utility bills to calibrate key model inputs and predict energy savings for the retrofit cases. Participant energy savings predictions using calibrated models are compared to NREL predictions using state-of-the-art building energy simulation programs.« less

Software packager user's guide

NASA Technical Reports Server (NTRS)

Callahan, John R.

1995-01-01

Software integration is a growing area of concern for many programmers and software managers because the need to build new programs quickly from existing components is greater than ever. This includes building versions of software products for multiple hardware platforms and operating systems, building programs from components written in different languages, and building systems from components that must execute on different machines in a distributed network. The goal of software integration is to make building new programs from existing components more seamless -- programmers should pay minimal attention to the underlying configuration issues involved. Libraries of reusable components and classes are important tools but only partial solutions to software development problems. Even though software components may have compatible interfaces, there may be other reasons, such as differences between execution environments, why they cannot be integrated. Often, components must be adapted or reimplemented to fit into another application because of implementation differences -- they are implemented in different programming languages, dependent on different operating system resources, or must execute on different physical machines. The software packager is a tool that allows programmers to deal with interfaces between software components and ignore complex integration details. The packager takes modular descriptions of the structure of a software system written in the package specification language and produces an integration program in the form of a makefile. If complex integration tools are needed to integrate a set of components, such as remote procedure call stubs, their use is implied by the packager automatically and stub generation tools are invoked in the corresponding makefile. The programmer deals only with the components themselves and not the details of how to build the system on any given platform.

Open source Modeling and optimization tools for Planning

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

Peles, S.

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward tomore » complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.« less

Computer modeling in the practice of acoustical consulting: An evolving variety of uses from marketing and diagnosis through design to eventually research

NASA Astrophysics Data System (ADS)

Madaras, Gary S.

2002-05-01

The use of computer modeling as a marketing, diagnosis, design, and research tool in the practice of acoustical consulting is discussed. From the time it is obtained, the software can be used as an effective marketing tool. It is not until the software basics are learned and some amount of testing and verification occurs that the software can be used as a tool for diagnosing the acoustics of existing rooms. A greater understanding of the output types and formats as well as experience in interpreting the results is required before the software can be used as an efficient design tool. Lastly, it is only after repetitive use as a design tool that the software can be used as a cost-effective means of conducting research in practice. The discussion is supplemented with specific examples of actual projects provided by various consultants within multiple firms. Focus is placed on the use of CATT-Acoustic software and predicting the room acoustics of large performing arts halls as well as other public assembly spaces.

Process evaluation of software using the international classification of external causes of injuries for collecting burn injury data at burn centers in the United States.

PubMed

Villaveces, Andrés; Peck, Michael; Faraklas, Iris; Hsu-Chang, Naiwei; Joe, Victor; Wibbenmeyer, Lucy

2014-01-01

Detailed information on the cause of burns is necessary to construct effective prevention programs. The International Classification of External Causes of Injury (ICECI) is a data collection tool that allows comprehensive categorization of multiple facets of injury events. The objective of this study was to conduct a process evaluation of software designed to improve the ease of use of the ICECI so as to identify key additional variables useful for understanding the occurrence of burn injuries, and compare this software with existing data-collection practices conducted for burn injuries. The authors completed a process evaluation of the implementation and ease of use of the software in six U.S. burn centers. They also collected preliminary burn injury data and compared them with existing variables reported to the American Burn Association's National Burn Repository (NBR). The authors accomplished their goals of 1) creating a data-collection tool for the ICECI, which can be linked to existing operational programs of the NBR, 2) training registrars in the use of this tool, 3) establishing quality-control mechanisms for ensuring accuracy and reliability, 4) incorporating ICECI data entry into the weekly routine of the burn registrar, and 5) demonstrating the quality differences between data collected using this tool and the NBR. Using this or similar tools with the ICECI structure or key selected variables can improve the quantity and quality of data on burn injuries in the United States and elsewhere and thus can be more useful in informing prevention strategies.

Federal Highway Administration (FHWA) work zone driver model software

DOT National Transportation Integrated Search

2016-11-01

FHWA and the U.S. Department of Transportation (USDOT) Volpe Center are developing a work zone car-following model and simulation software that interfaces with existing microsimulation tools, enabling more accurate simulation of car-following through...

Software engineering techniques and CASE tools in RD13

NASA Astrophysics Data System (ADS)

Buono, S.; Gaponenko, I.; Jones, R.; Khodabandeh, A.; Mapelli, L.; Mornacchi, G.; Prigent, D.; Sanchez-Corral, E.; Skiadelli, M.; Toppers, A.; Duval, P. Y.; Ferrato, D.; Le Van Suu, A.; Qian, Z.; Rondot, C.; Ambrosini, G.; Fumagalli, G.; Polesello, G.; Aguer, M.; Huet, M.

1994-12-01

The RD13 project was approved in April 1991 for the development of a scalable data-taking system suitable for hosting various LHC studies. One of its goals is the exploitation of software engineering techniques, in order to indicate their overall suitability for data acquisition (DAQ), software design and implementation. This paper describes how such techniques have been applied to the development of components of the RD13 DAQ used in test-beam runs at CERN. We describe our experience with the Artifex CASE tool and its associated methodology. The issues raised when code generated by a CASE tool has to be integrated into an existing environment are also discussed.

Evolving software reengineering technology for the emerging innovative-competitive era

NASA Technical Reports Server (NTRS)

Hwang, Phillip Q.; Lock, Evan; Prywes, Noah

1994-01-01

This paper reports on a multi-tool commercial/military environment combining software Domain Analysis techniques with Reusable Software and Reengineering of Legacy Software. It is based on the development of a military version for the Department of Defense (DOD). The integrated tools in the military version are: Software Specification Assistant (SSA) and Software Reengineering Environment (SRE), developed by Computer Command and Control Company (CCCC) for Naval Surface Warfare Center (NSWC) and Joint Logistics Commanders (JLC), and the Advanced Research Project Agency (ARPA) STARS Software Engineering Environment (SEE) developed by Boeing for NAVAIR PMA 205. The paper describes transitioning these integrated tools to commercial use. There is a critical need for the transition for the following reasons: First, to date, 70 percent of programmers' time is applied to software maintenance. The work of these users has not been facilitated by existing tools. The addition of Software Reengineering will also facilitate software maintenance and upgrading. In fact, the integrated tools will support the entire software life cycle. Second, the integrated tools are essential to Business Process Reengineering, which seeks radical process innovations to achieve breakthrough results. Done well, process reengineering delivers extraordinary gains in process speed, productivity and profitability. Most importantly, it discovers new opportunities for products and services in collaboration with other organizations. Legacy computer software must be changed rapidly to support innovative business processes. The integrated tools will provide commercial organizations important competitive advantages. This, in turn, will increase employment by creating new business opportunities. Third, the integrated system will produce much higher quality software than use of the tools separately. The reason for this is that producing or upgrading software requires keen understanding of extremely complex applications which is facilitated by the integrated tools. The radical savings in the time and cost associated with software, due to use of CASE tools that support combined Reuse of Software and Reengineering of Legacy Code, will add an important impetus to improving the automation of enterprises. This will be reflected in continuing operations, as well as in innovating new business processes. The proposed multi-tool software development is based on state of the art technology, which will be further advanced through the use of open systems for adding new tools and experience in their use.

Design Automation in Synthetic Biology.

PubMed

Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

2017-04-03

Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

INTEGRATION OF POLLUTION PREVENTION TOOLS

EPA Science Inventory

A prototype computer-based decision support system was designed to provide small businesses with an integrated pollution prevention methodology. Preliminary research involved compilation of an inventory of existing pollution prevention tools (i.e., methodologies, software, etc.),...

Monitoring software development through dynamic variables

NASA Technical Reports Server (NTRS)

Doerflinger, Carl W.; Basili, Victor R.

1983-01-01

Research conducted by the Software Engineering Laboratory (SEL) on the use of dynamic variables as a tool to monitor software development is described. Project independent measures which may be used in a management tool for monitoring software development are identified. Several FORTRAN projects with similar profiles are examined. The staff was experienced in developing these types of projects. The projects developed serve similar functions. Because these projects are similar some underlying relationships exist that are invariant between projects. These relationships, once well defined, may be used to compare the development of different projects to determine whether they are evolving the same way previous projects in this environment evolved.

Software reengineering

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III

1991-01-01

Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

Software engineering

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III; Hiott, Jim; Golej, Jim; Plumb, Allan

1993-01-01

Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. The Johnson Space Center (JSC) created a significant set of tools to develop and maintain FORTRAN and C code during development of the space shuttle. This tool set forms the basis for an integrated environment to reengineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. The latest release of the environment was in Feb. 1992.

Integrated optomechanical analysis and testing software development at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Stoeckel, Gerhard P.; Doyle, Keith B.

2013-09-01

Advanced analytical software capabilities are being developed to advance the design of prototypical hardware in the Engineering Division at MIT Lincoln Laboratory. The current effort is focused on the integration of analysis tools tailored to the work flow, organizational structure, and current technology demands. These tools are being designed to provide superior insight into the interdisciplinary behavior of optical systems and enable rapid assessment and execution of design trades to optimize the design of optomechanical systems. The custom software architecture is designed to exploit and enhance the functionality of existing industry standard commercial software, provide a framework for centralizing internally developed tools, and deliver greater efficiency, productivity, and accuracy through standardization, automation, and integration. Specific efforts have included the development of a feature-rich software package for Structural-Thermal-Optical Performance (STOP) modeling, advanced Line Of Sight (LOS) jitter simulations, and improved integration of dynamic testing and structural modeling.

NEWFIRM Software--System Integration Using OPC

NASA Astrophysics Data System (ADS)

Daly, P. N.

2004-07-01

The NOAO Extremely Wide-Field Infra-Red Mosaic (NEWFIRM) camera is being built to satisfy the survey science requirements on the KPNO Mayall and CTIO Blanco 4m telescopes in an era of 8m+ aperture telescopes. Rather than re-invent the wheel, the software system to control the instrument has taken existing software packages and re-used what is appropriate. The result is an end-to-end observation control system using technology components from DRAMA, ORAC, observing tools, GWC, existing in-house motor controllers and new developments like the MONSOON pixel server.

Updates to the CMAQ Post Processing and Evaluation Tools for 2016

EPA Science Inventory

In the spring of 2016, the evaluation tools distributed with the CMAQ model code were updated and new tools were added to the existing set of tools. Observation data files, compatible with the AMET software, were also made available on the CMAS website for the first time with the...

Machine learning research 1989-90

NASA Technical Reports Server (NTRS)

Porter, Bruce W.; Souther, Arthur

1990-01-01

Multifunctional knowledge bases offer a significant advance in artificial intelligence because they can support numerous expert tasks within a domain. As a result they amortize the costs of building a knowledge base over multiple expert systems and they reduce the brittleness of each system. Due to the inevitable size and complexity of multifunctional knowledge bases, their construction and maintenance require knowledge engineering and acquisition tools that can automatically identify interactions between new and existing knowledge. Furthermore, their use requires software for accessing those portions of the knowledge base that coherently answer questions. Considerable progress was made in developing software for building and accessing multifunctional knowledge bases. A language was developed for representing knowledge, along with software tools for editing and displaying knowledge, a machine learning program for integrating new information into existing knowledge, and a question answering system for accessing the knowledge base.

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

Trabant, C.; Reyes, C. G.; Clark, A.; Karstens, R.

2012-12-01

SeisCode is a community repository for software used in seismological and related fields. The repository is intended to increase discoverability of such software and to provide a long-term home for software projects. Other places exist where seismological software may be found, but none meet the requirements necessary for an always current, easy to search, well documented, and citable resource for projects. Organizations such as IRIS, ORFEUS, and the USGS have websites with lists of available or contributed seismological software. Since the authors themselves do often not maintain these lists, the documentation often consists of a sentence or paragraph, and the available software may be outdated. Repositories such as GoogleCode and SourceForge, which are directly maintained by the authors, provide version control and issue tracking but do not provide a unified way of locating geophysical software scattered in and among countless unrelated projects. Additionally, projects are hosted at language-specific sites such as Mathworks and PyPI, in FTP directories, and in websites strewn across the Web. Search engines are only partially effective discovery tools, as the desired software is often hidden deep within the results. SeisCode provides software authors a place to present their software, codes, scripts, tutorials, and examples to the seismological community. Authors can choose their own level of involvement. At one end of the spectrum, the author might simply create a web page that points to an existing site. At the other extreme, an author may choose to leverage the many tools provided by SeisCode, such as a source code management tool with integrated issue tracking, forums, news feeds, downloads, wikis, and more. For software development projects with multiple authors, SeisCode can also be used as a central site for collaboration. SeisCode provides the community with an easy way to discover software, while providing authors a way to build a community around their software packages. IRIS invites the seismological community to browse and to submit projects to https://seiscode.iris.washington.edu/

BEopt-CA (Ex): A Tool for Optimal Integration of EE, DR and PV in Existing California Homes

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

Christensen, Craig; Horowitz, Scott; Maguire, Jeff

2014-04-01

This project targeted the development of a software tool, BEopt-CA (Ex) (Building Energy Optimization Tool for California Existing Homes), that aims to facilitate balanced integration of energy efficiency (EE), demand response (DR), and photovoltaics (PV) in the residential retrofit1 market. The intent is to provide utility program managers and contractors in the EE/DR/PV marketplace with a means of balancing the integration of EE, DR, and PV

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualizat...

Tools for Supporting Distributed Agile Project Planning

NASA Astrophysics Data System (ADS)

Wang, Xin; Maurer, Frank; Morgan, Robert; Oliveira, Josyleuda

Agile project planning plays an important part in agile software development. In distributed settings, project planning is severely impacted by the lack of face-to-face communication and the inability to share paper index cards amongst all meeting participants. To address these issues, several distributed agile planning tools were developed. The tools vary in features, functions and running platforms. In this chapter, we first summarize the requirements for distributed agile planning. Then we give an overview on existing agile planning tools. We also evaluate existing tools based on tool requirements. Finally, we present some practical advices for both designers and users of distributed agile planning tools.

ARC-2007-ACD07-0140-001

NASA Image and Video Library

2007-07-31

David L. Iverson of NASA Ames Research center, Moffett Field, California, led development of computer software to monitor the conditions of the gyroscopes that keep the International Space Station (ISS) properly oriented in space as the ISS orbits Earth. The gyroscopes are flywheels that control the station's attitude without the use of propellant fuel. NASA computer scientists designed the new software, the Inductive Monitoring System, to detect warning signs that precede a gyroscope's failure. According to NASA officials, engineers will add the new software tool to a group of existing tools to identify and track problems related to the gyroscopes. If the software detects warning signs, it will quickly warn the space station's mission control center.

Mission Analysis, Operations, and Navigation Toolkit Environment (Monte) Version 040

NASA Technical Reports Server (NTRS)

Sunseri, Richard F.; Wu, Hsi-Cheng; Evans, Scott E.; Evans, James R.; Drain, Theodore R.; Guevara, Michelle M.

2012-01-01

Monte is a software set designed for use in mission design and spacecraft navigation operations. The system can process measurement data, design optimal trajectories and maneuvers, and do orbit determination, all in one application. For the first time, a single software set can be used for mission design and navigation operations. This eliminates problems due to different models and fidelities used in legacy mission design and navigation software. The unique features of Monte 040 include a blowdown thruster model for GRAIL (Gravity Recovery and Interior Laboratory) with associated pressure models, as well as an updated, optimalsearch capability (COSMIC) that facilitated mission design for ARTEMIS. Existing legacy software lacked the capabilities necessary for these two missions. There is also a mean orbital element propagator and an osculating to mean element converter that allows long-term orbital stability analysis for the first time in compiled code. The optimized trajectory search tool COSMIC allows users to place constraints and controls on their searches without any restrictions. Constraints may be user-defined and depend on trajectory information either forward or backwards in time. In addition, a long-term orbit stability analysis tool (morbiter) existed previously as a set of scripts on top of Monte. Monte is becoming the primary tool for navigation operations, a core competency at JPL. The mission design capabilities in Monte are becoming mature enough for use in project proposals as well as post-phase A mission design. Monte has three distinct advantages over existing software. First, it is being developed in a modern paradigm: object- oriented C++ and Python. Second, the software has been developed as a toolkit, which allows users to customize their own applications and allows the development team to implement requirements quickly, efficiently, and with minimal bugs. Finally, the software is managed in accordance with the CMMI (Capability Maturity Model Integration), where it has been ap praised at maturity level 3.

Guidance for the Design and Adoption of Analytic Tools.

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

Bandlow, Alisa

2015-12-01

The goal is to make software developers aware of common issues that can impede the adoption of analytic tools. This paper provides a summary of guidelines, lessons learned and existing research to explain what is currently known about what analysts want and how to better understand what tools they do and don't need.

INDOOR AIR QUALITY AND INHALATION EXPOSURE - SIMULATION TOOL KIT

EPA Science Inventory

A Microsoft Windows-based indoor air quality (IAQ) simulation software package is presented. Named Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure, or IAQX for short, this package complements and supplements existing IAQ simulation programs and is desi...

Software For Computer-Security Audits

NASA Technical Reports Server (NTRS)

Arndt, Kate; Lonsford, Emily

1994-01-01

Information relevant to potential breaches of security gathered efficiently. Automated Auditing Tools for VAX/VMS program includes following automated software tools performing noted tasks: Privileged ID Identification, program identifies users and their privileges to circumvent existing computer security measures; Critical File Protection, critical files not properly protected identified; Inactive ID Identification, identifications of users no longer in use found; Password Lifetime Review, maximum lifetimes of passwords of all identifications determined; and Password Length Review, minimum allowed length of passwords of all identifications determined. Written in DEC VAX DCL language.

Reuse Metrics for Object Oriented Software

NASA Technical Reports Server (NTRS)

Bieman, James M.

1998-01-01

One way to increase the quality of software products and the productivity of software development is to reuse existing software components when building new software systems. In order to monitor improvements in reuse, the level of reuse must be measured. In this NASA supported project we (1) derived a suite of metrics which quantify reuse attributes for object oriented, object based, and procedural software, (2) designed prototype tools to take these measurements in Ada, C++, Java, and C software, (3) evaluated the reuse in available software, (4) analyzed the relationship between coupling, cohesion, inheritance, and reuse, (5) collected object oriented software systems for our empirical analyses, and (6) developed quantitative criteria and methods for restructuring software to improve reusability.

The LINDSAY Virtual Human Project: An immersive Approach to Anatomy and Physiology

ERIC Educational Resources Information Center

Tworek, Janet K.; Jamniczky, Heather A.; Jacob, Christian; Hallgrímsson, Benedikt; Wright, Bruce

2013-01-01

The increasing number of digital anatomy teaching software packages challenges anatomy educators on how to best integrate these tools for teaching and learning. Realistically, there exists a complex interplay of design, implementation, politics, and learning needs in the development and integration of software for education, each of which may be…

Landscape analysis software tools

Treesearch

Don Vandendriesche

2008-01-01

Recently, several new computer programs have been developed to assist in landscape analysis. The “Sequential Processing Routine for Arraying Yields” (SPRAY) program was designed to run a group of stands with particular treatment activities to produce vegetation yield profiles for forest planning. SPRAY uses existing Forest Vegetation Simulator (FVS) software coupled...

Selection of software for mechanical engineering undergraduates

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

Cheah, C. T.; Yin, C. S.; Halim, T.

A major problem with the undergraduate mechanical course is the limited exposure of students to software packages coupled with the long learning curve on the existing software packages. This work proposes the use of appropriate software packages for the entire mechanical engineering curriculum to ensure students get sufficient exposure real life design problems. A variety of software packages are highlighted as being suitable for undergraduate work in mechanical engineering, e.g. simultaneous non-linear equations; uncertainty analysis; 3-D modeling software with the FEA; analysis tools for the solution of problems in thermodynamics, fluid mechanics, mechanical system design, and solid mechanics.

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.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

To forecast the weather situation during aircraft-based atmospheric field campaigns, we employ a tool chain of existing and self-developed open source software tools and open standards. Of particular value are the Python programming language with its extension libraries NumPy, SciPy, PyQt4, Matplotlib and the basemap toolkit, the NetCDF standard with the Climate and Forecast (CF) Metadata conventions, and the Open Geospatial Consortium Web Map Service standard. These open source libraries and open standards helped to implement the "Mission Support System", a Web Map Service based tool to support weather forecasting and flight planning during field campaigns. The tool has been implemented in Python and has also been released as open source (Rautenhaus et al., Geosci. Model Dev., 5, 55-71, 2012). In this presentation we discuss the usage of free and open source software for weather forecasting in the context of research flight planning, and highlight how the field campaign work benefits from using open source tools and open standards.

Quantifying Uncertainties in Navigation and Orbit Propagation Analyses

NASA Technical Reports Server (NTRS)

Krieger, Andrew W.; Welch, Bryan W.

2017-01-01

A tool used to calculate dilution of precision (DOP) was created in order to assist the Space Communications and Navigation (SCaN) program to analyze current and future user missions. The SCaN Center for Engineering, Networks, Integration, and Communication (SCENIC) is developing a new user interface (UI) to augment and replace the capabilities of currently used commercial software, such as Systems Tool Kit (STK). The DOP tool will be integrated in the SCENIC UI and will be used to analyze the accuracy of navigation solutions. This tool was developed using MATLAB and free and open-source tools to save cost and to use already existing orbital software libraries. GPS DOP data was collected and used for validation purposes. The similarities between the DOP tool results and GPS data show that the DOP tool is performing correctly. Additional improvements can be made in the DOP tool to improve its accuracy and performance in analyzing navigation solutions.

Computational science: shifting the focus from tools to models

PubMed Central

Hinsen, Konrad

2014-01-01

Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication of big data sets or complex models. As a consequence, these crucial pieces of information no longer enter the scientific record. Moreover, they have become prisoners of scientific software: many models exist only as software implementations, and the data are often stored in proprietary formats defined by the software. In this article, I argue that this emphasis on software tools over models and data is detrimental to science in the long term, and I propose a means by which this can be reversed. PMID:25309728

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

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...

Techniques for Down-Sampling a Measured Surface Height Map for Model Validation

NASA Technical Reports Server (NTRS)

Sidick, Erkin

2012-01-01

This software allows one to down-sample a measured surface map for model validation, not only without introducing any re-sampling errors, but also eliminating the existing measurement noise and measurement errors. The software tool of the current two new techniques can be used in all optical model validation processes involving large space optical surfaces

Methodology and Software for Gross Defect Detection of Spent Nuclear Fuel at the Atucha-I Reactor [Novel Methodology and Software for Spent Fuel Gross Defect Detection at the Atucha-I Reactor

DOE PAGES

Sitaraman, Shivakumar; Ham, Young S.; Gharibyan, Narek; ...

2017-03-27

Here, fuel assemblies in the spent fuel pool are stored by suspending them in two vertically stacked layers at the Atucha Unit 1 nuclear power plant (Atucha-I). This introduces the unique problem of verifying the presence of fuel in either layer without physically moving the fuel assemblies. Given that the facility uses both natural uranium and slightly enriched uranium at 0.85 wt% 235U and has been in operation since 1974, a wide range of burnups and cooling times can exist in any given pool. A gross defect detection tool, the spent fuel neutron counter (SFNC), has been used at themore » site to verify the presence of fuel up to burnups of 8000 MWd/t. At higher discharge burnups, the existing signal processing software of the tool was found to fail due to nonlinearity of the source term with burnup.« less

An overview of platforms for cloud based development.

PubMed

Fylaktopoulos, G; Goumas, G; Skolarikis, M; Sotiropoulos, A; Maglogiannis, I

2016-01-01

This paper provides an overview of the state of the art technologies for software development in cloud environments. The surveyed systems cover the whole spectrum of cloud-based development including integrated programming environments, code repositories, software modeling, composition and documentation tools, and application management and orchestration. In this work we evaluate the existing cloud development ecosystem based on a wide number of characteristics like applicability (e.g. programming and database technologies supported), productivity enhancement (e.g. editor capabilities, debugging tools), support for collaboration (e.g. repository functionality, version control) and post-development application hosting and we compare the surveyed systems. The conducted survey proves that software engineering in the cloud era has made its initial steps showing potential to provide concrete implementation and execution environments for cloud-based applications. However, a number of important challenges need to be addressed for this approach to be viable. These challenges are discussed in the article, while a conclusion is drawn that although several steps have been made, a compact and reliable solution does not yet exist.

Methodology and Software for Gross Defect Detection of Spent Nuclear Fuel at the Atucha-I Reactor [Novel Methodology and Software for Spent Fuel Gross Defect Detection at the Atucha-I Reactor

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

Sitaraman, Shivakumar; Ham, Young S.; Gharibyan, Narek

Here, fuel assemblies in the spent fuel pool are stored by suspending them in two vertically stacked layers at the Atucha Unit 1 nuclear power plant (Atucha-I). This introduces the unique problem of verifying the presence of fuel in either layer without physically moving the fuel assemblies. Given that the facility uses both natural uranium and slightly enriched uranium at 0.85 wt% 235U and has been in operation since 1974, a wide range of burnups and cooling times can exist in any given pool. A gross defect detection tool, the spent fuel neutron counter (SFNC), has been used at themore » site to verify the presence of fuel up to burnups of 8000 MWd/t. At higher discharge burnups, the existing signal processing software of the tool was found to fail due to nonlinearity of the source term with burnup.« less

Guidance, navigation, and control subsystem equipment selection algorithm using expert system methods

NASA Technical Reports Server (NTRS)

Allen, Cheryl L.

1991-01-01

Enhanced engineering tools can be obtained through the integration of expert system methodologies and existing design software. The application of these methodologies to the spacecraft design and cost model (SDCM) software provides an improved technique for the selection of hardware for unmanned spacecraft subsystem design. The knowledge engineering system (KES) expert system development tool was used to implement a smarter equipment section algorithm than that which is currently achievable through the use of a standard data base system. The guidance, navigation, and control subsystems of the SDCM software was chosen as the initial subsystem for implementation. The portions of the SDCM code which compute the selection criteria and constraints remain intact, and the expert system equipment selection algorithm is embedded within this existing code. The architecture of this new methodology is described and its implementation is reported. The project background and a brief overview of the expert system is described, and once the details of the design are characterized, an example of its implementation is demonstrated.

Implementing an integrated engineering data base system: A developer's experience and the application to IPAD

NASA Technical Reports Server (NTRS)

Bruce, E. A.

1980-01-01

The software developed by the IPAD project, a new and very powerful tool for the implementation of integrated Computer Aided Design (CAD) systems in the aerospace engineering community, is discussed. The IPAD software is a tool and, as such, can be well applied or misapplied in any particular environment. The many benefits of an integrated CAD system are well documented, but there are few such systems in existence, especially in the mechanical engineering disciplines, and therefore little available experience to guide the implementor.

Evaluating geographic information systems technology

USGS Publications Warehouse

Guptill, Stephen C.

1989-01-01

Computerized geographic information systems (GISs) are emerging as the spatial data handling tools of choice for solving complex geographical problems. However, few guidelines exist for assisting potential users in identifying suitable hardware and software. A process to be followed in evaluating the merits of GIS technology is presented. Related standards and guidelines, software functions, hardware components, and benchmarking are discussed. By making users aware of all aspects of adopting GIS technology, they can decide if GIS is an appropriate tool for their application and, if so, which GIS should be used.

Reuse of Software Assets for the NASA Earth Science Decadal Survey Missions

NASA Technical Reports Server (NTRS)

Mattmann, Chris A.; Downs, Robert R.; Marshall, James J.; Most, Neal F.; Samadi, Shahin

2010-01-01

Software assets from existing Earth science missions can be reused for the new decadal survey missions that are being planned by NASA in response to the 2007 Earth Science National Research Council (NRC) Study. The new missions will require the development of software to curate, process, and disseminate the data to science users of interest and to the broader NASA mission community. In this paper, we discuss new tools and a blossoming community that are being developed by the Earth Science Data System (ESDS) Software Reuse Working Group (SRWG) to improve capabilities for reusing NASA software assets.

MK3TOOLS & NetCDF - storing VLBI data in a machine independent array oriented data format

NASA Astrophysics Data System (ADS)

Hobiger, T.; Koyama, Y.; Kondo, T.

2007-07-01

In the beginning of 2002 the International VLBI Service (IVS) has agreed to introduce a Platform-independent VLBI exchange format (PIVEX) which permits the exchange of observational data and stimulates the research across different analysis groups. Unfortunately PIVEX has never been implemented and many analysis software packages are still depending on prior processing (e.g. ambiguity resolution and computation of ionosphere corrections) done by CALC/SOLVE. Thus MK3TOOLS which handles MK3 databases without CALC/SOLVE being installed has been developed. It uses the NetCDF format to store the data and since interfaces exist for a variety of programming languages (FORTRAN, C/C++, JAVA, Perl, Python) it can be easily incorporated in existing and upcoming analysis software packages.

STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications.

PubMed

Spencer, Jean L; Bhatia, Vivek N; Whelan, Stephen A; Costello, Catherine E; McComb, Mark E

2013-12-01

The identification of protein post-translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography-tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi-sample comparison by collating, scoring, and ranking PTMs and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans-Proteomic Pipeline. The easy-to-use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting.

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

Software risk management through independent verification and validation

NASA Technical Reports Server (NTRS)

Callahan, John R.; Zhou, Tong C.; Wood, Ralph

1995-01-01

Software project managers need tools to estimate and track project goals in a continuous fashion before, during, and after development of a system. In addition, they need an ability to compare the current project status with past project profiles to validate management intuition, identify problems, and then direct appropriate resources to the sources of problems. This paper describes a measurement-based approach to calculating the risk inherent in meeting project goals that leverages past project metrics and existing estimation and tracking models. We introduce the IV&V Goal/Questions/Metrics model, explain its use in the software development life cycle, and describe our attempts to validate the model through the reverse engineering of existing projects.

SoftLab: A Soft-Computing Software for Experimental Research with Commercialization Aspects

NASA Technical Reports Server (NTRS)

Akbarzadeh-T, M.-R.; Shaikh, T. S.; Ren, J.; Hubbell, Rob; Kumbla, K. K.; Jamshidi, M

1998-01-01

SoftLab is a software environment for research and development in intelligent modeling/control using soft-computing paradigms such as fuzzy logic, neural networks, genetic algorithms, and genetic programs. SoftLab addresses the inadequacies of the existing soft-computing software by supporting comprehensive multidisciplinary functionalities from management tools to engineering systems. Furthermore, the built-in features help the user process/analyze information more efficiently by a friendly yet powerful interface, and will allow the user to specify user-specific processing modules, hence adding to the standard configuration of the software environment.

Investigation into the development of computer aided design software for space based sensors

NASA Technical Reports Server (NTRS)

Pender, C. W.; Clark, W. L.

1987-01-01

The described effort is phase one of the development of a Computer Aided Design (CAD) software to be used to perform radiometric sensor design. The software package will be referred to as SCAD and is directed toward the preliminary phase of the design of space based sensor system. The approach being followed is to develop a modern, graphic intensive, user friendly software package using existing software as building blocks. The emphasis will be directed toward the development of a shell containing menus, smart defaults, and interfaces, which can accommodate a wide variety of existing application software packages. The shell will offer expected utilities such as graphics, tailored menus, and a variety of drivers for I/O devices. Following the development of the shell, the development of SCAD is planned as chiefly selection and integration of appropriate building blocks. The phase one development activities have included: the selection of hardware which will be used with SCAD; the determination of the scope of SCAD; the preliminary evaluation of a number of software packages for applicability to SCAD; determination of a method for achieving required capabilities where voids exist; and then establishing a strategy for binding the software modules into an easy to use tool kit.

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping.

PubMed

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types.  The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps.  The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon's conclusion, and 2) all software comprising the final pipeline must be open-source or open-use.  Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event.  Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team.

Estimating Software-Development Costs With Greater Accuracy

NASA Technical Reports Server (NTRS)

Baker, Dan; Hihn, Jairus; Lum, Karen

2008-01-01

COCOMOST is a computer program for use in estimating software development costs. The goal in the development of COCOMOST was to increase estimation accuracy in three ways: (1) develop a set of sensitivity software tools that return not only estimates of costs but also the estimation error; (2) using the sensitivity software tools, precisely define the quantities of data needed to adequately tune cost estimation models; and (3) build a repository of software-cost-estimation information that NASA managers can retrieve to improve the estimates of costs of developing software for their project. COCOMOST implements a methodology, called '2cee', in which a unique combination of well-known pre-existing data-mining and software-development- effort-estimation techniques are used to increase the accuracy of estimates. COCOMOST utilizes multiple models to analyze historical data pertaining to software-development projects and performs an exhaustive data-mining search over the space of model parameters to improve the performances of effort-estimation models. Thus, it is possible to both calibrate and generate estimates at the same time. COCOMOST is written in the C language for execution in the UNIX operating system.

LLIMAS: Revolutionizing integrating modeling and analysis at MIT Lincoln Laboratory

NASA Astrophysics Data System (ADS)

Doyle, Keith B.; Stoeckel, Gerhard P.; Rey, Justin J.; Bury, Mark E.

2017-08-01

MIT Lincoln Laboratory's Integrated Modeling and Analysis Software (LLIMAS) enables the development of novel engineering solutions for advanced prototype systems through unique insights into engineering performance and interdisciplinary behavior to meet challenging size, weight, power, environmental, and performance requirements. LLIMAS is a multidisciplinary design optimization tool that wraps numerical optimization algorithms around an integrated framework of structural, thermal, optical, stray light, and computational fluid dynamics analysis capabilities. LLIMAS software is highly extensible and has developed organically across a variety of technologies including laser communications, directed energy, photometric detectors, chemical sensing, laser radar, and imaging systems. The custom software architecture leverages the capabilities of existing industry standard commercial software and supports the incorporation of internally developed tools. Recent advances in LLIMAS's Structural-Thermal-Optical Performance (STOP), aeromechanical, and aero-optical capabilities as applied to Lincoln prototypes are presented.

A Summary of Revisions Applied to a Turbulence Response Analysis Method for Flexible Aircraft Configurations

NASA Technical Reports Server (NTRS)

Funk, Christie J.; Perry, Boyd, III; Silva, Walter A.; Newman, Brett

2014-01-01

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees-of - freedom and allows for the calculation of various airplane responses due to a discrete one-minus- cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and additional output data so as to provide a more useful and precise tool for gust load analysis. In order to improve the original software program to enhance usefulness, a wing control surface and horizontal tail control surface is added, an extended application of the discrete one-minus-cosine gust input is employed, a supplemental continuous turbulence spectrum is implemented, and a capability to animate the total vehicle deformation response to gust inputs is included. These revisions and enhancements are implemented and an analysis of the results is used to validate the modifications.

SAGES: A Suite of Freely-Available Software Tools for Electronic Disease Surveillance in Resource-Limited Settings

PubMed Central

Lewis, Sheri L.; Feighner, Brian H.; Loschen, Wayne A.; Wojcik, Richard A.; Skora, Joseph F.; Coberly, Jacqueline S.; Blazes, David L.

2011-01-01

Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations. PMID:21572957

A software tool for analyzing multichannel cochlear implant signals.

PubMed

Lai, Wai Kong; Bögli, Hans; Dillier, Norbert

2003-10-01

A useful and convenient means to analyze the radio frequency (RF) signals being sent by a speech processor to a cochlear implant would be to actually capture and display them with appropriate software. This is particularly useful for development or diagnostic purposes. sCILab (Swiss Cochlear Implant Laboratory) is such a PC-based software tool intended for the Nucleus family of Multichannel Cochlear Implants. Its graphical user interface provides a convenient and intuitive means for visualizing and analyzing the signals encoding speech information. Both numerical and graphic displays are available for detailed examination of the captured CI signals, as well as an acoustic simulation of these CI signals. sCILab has been used in the design and verification of new speech coding strategies, and has also been applied as an analytical tool in studies of how different parameter settings of existing speech coding strategies affect speech perception. As a diagnostic tool, it is also useful for troubleshooting problems with the external equipment of the cochlear implant systems.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

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.

Pressure distribution under flexible polishing tools. I - Conventional aspheric optics

NASA Astrophysics Data System (ADS)

Mehta, Pravin K.; Hufnagel, Robert E.

1990-10-01

The paper presents a mathematical model, based on Kirchoff's thin flat plate theory, developed to determine polishing pressure distribution for a flexible polishing tool. A two-layered tool in which bending and compressive stiffnesses are equal is developed, which is formulated as a plate on a linearly elastic foundation. An equivalent eigenvalue problem and solution for a free-free plate are created from the plate formulation. For aspheric, anamorphic optical surfaces, the tool misfit is derived; it is defined as the result of movement from the initial perfect fit on the optic to any other position. The Polisher Design (POD) software for circular tools on aspheric optics is introduced. NASTRAN-based finite element analysis results are compared with the POD software, showing high correlation. By employing existing free-free eigenvalues and eigenfunctions, the work may be extended to rectangular polishing tools as well.

The Simple Video Coder: A free tool for efficiently coding social video data.

PubMed

Barto, Daniel; Bird, Clark W; Hamilton, Derek A; Fink, Brandi C

2017-08-01

Videotaping of experimental sessions is a common practice across many disciplines of psychology, ranging from clinical therapy, to developmental science, to animal research. Audio-visual data are a rich source of information that can be easily recorded; however, analysis of the recordings presents a major obstacle to project completion. Coding behavior is time-consuming and often requires ad-hoc training of a student coder. In addition, existing software is either prohibitively expensive or cumbersome, which leaves researchers with inadequate tools to quickly process video data. We offer the Simple Video Coder-free, open-source software for behavior coding that is flexible in accommodating different experimental designs, is intuitive for students to use, and produces outcome measures of event timing, frequency, and duration. Finally, the software also offers extraction tools to splice video into coded segments suitable for training future human coders or for use as input for pattern classification algorithms.

Designing a Humane Multimedia Interface for the Visually Impaired.

ERIC Educational Resources Information Center

Ghaoui, Claude; Mann, M.; Ng, Eng Huat

2001-01-01

Promotes the provision of interfaces that allow users to access most of the functionality of existing graphical user interfaces (GUI) using speech. Uses the design of a speech control tool that incorporates speech recognition and synthesis into existing packaged software such as Teletext, the Internet, or a word processor. (Contains 22…

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Re-Engineering JPL's Mission Planning Ground System Architecture for Cost Efficient Operations in the 21st Century

NASA Technical Reports Server (NTRS)

Fordyce, Jess

1996-01-01

Work carried out to re-engineer the mission analysis segment of JPL's mission planning ground system architecture is reported on. The aim is to transform the existing software tools, originally developed for specific missions on different support environments, into an integrated, general purpose, multi-mission tool set. The issues considered are: the development of a partnership between software developers and users; the definition of key mission analysis functions; the development of a consensus based architecture; the move towards evolutionary change instead of revolutionary replacement; software reusability, and the minimization of future maintenance costs. The current status and aims of new developments are discussed and specific examples of cost savings and improved productivity are presented.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

PubMed

Crowell, Kevin L; Slysz, Gordon W; Baker, Erin S; LaMarche, Brian L; Monroe, Matthew E; Ibrahim, Yehia M; Payne, Samuel H; Anderson, Gordon A; Smith, Richard D

2013-11-01

The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension. LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README). rds@pnnl.gov. Supplementary data are available at Bioinformatics online.

A Project Management Approach to Using Simulation for Cost Estimation on Large, Complex Software Development Projects

NASA Technical Reports Server (NTRS)

Mizell, Carolyn; Malone, Linda

2007-01-01

It is very difficult for project managers to develop accurate cost and schedule estimates for large, complex software development projects. None of the approaches or tools available today can estimate the true cost of software with any high degree of accuracy early in a project. This paper provides an approach that utilizes a software development process simulation model that considers and conveys the level of uncertainty that exists when developing an initial estimate. A NASA project will be analyzed using simulation and data from the Software Engineering Laboratory to show the benefits of such an approach.

Megasite Management Tool (mmt): a Decision Support System Built Using Mapwindow Activex Control

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Megasite Management Tool (MMT) is planning and evaluation software for contaminated sites. Using different statistical modules, MMT produces maps which help decision makers in rehabilitating contaminated sites. The input data used by MMT is of geographic nature and exists as shapefile and raster format. As MMT is built using simple windows forms application, the objective of the study was to find a way to visualize geographic data and to allow the user to edit its attribute information. Therefore, the application requirement was to find GIS libraries which offer capabilities such as (1) map viewer with navigation tools (2) library to read/write geographic data and (3) software which allows free distribution of the developed components. A research on these requirements led to the discovery of MapWindow ActiveX components which not only offered these capabilities but also provided free and open source licensing options for redistribution. Although considerable amount of reports and publications exist on MMT, the major contribution provided by MapWindow libraries have been under played. The current study emphasises upon the contribution and advantages MapWindow ActiveX provides for incorporating GIS functionality to an already existing application. Similar components for other languages have also been reviewed.

CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

PubMed

Bumm, Klaus; Zheng, Mingzhong; Bailey, Clyde; Zhan, Fenghuang; Chiriva-Internati, M; Eddlemon, Paul; Terry, Julian; Barlogie, Bart; Shaughnessy, John D

2002-02-01

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.

A thermal sensation prediction tool for use by the profession

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

Fountain, M.E.; Huizenga, C.

1997-12-31

As part of a recent ASHRAE research project (781-RP), a thermal sensation prediction tool has been developed. This paper introduces the tool, describes the component thermal sensation models, and presents examples of how the tool can be used in practice. Since the main end product of the HVAC industry is the comfort of occupants indoors, tools for predicting occupant thermal response can be an important asset to designers of indoor climate control systems. The software tool presented in this paper incorporates several existing models for predicting occupant comfort.

Social Software and Academic Practice: Postgraduate Students as Co-Designers of Web 2.0 Tools

ERIC Educational Resources Information Center

Carmichael, Patrick; Burchmore, Helen

2010-01-01

In order to develop potentially transformative Web 2.0 tools in higher education, the complexity of existing academic practices, including current patterns of technology use, must be recognised. This paper describes how a series of participatory design activities allowed postgraduate students in education, social sciences and computer sciences to…

Development of a Competency Mapping Tool for Undergraduate Professional Degree Programmes, Using Mechanical Engineering as a Case Study

ERIC Educational Resources Information Center

Holmes, David W.; Sheehan, Madoc; Birks, Melanie; Smithson, John

2018-01-01

Mapping the curriculum of a professional degree to the associated competency standard ensures graduates have the competence to perform as professionals. Existing approaches to competence mapping vary greatly in depth, complexity, and effectiveness, and a standardised approach remains elusive. This paper describes a new mapping software tool that…

The Dairy Greenhouse Gas Model: A Tool for estimating greenhouse gas emissions and the carbon footprint of dairy production systems

USDA-ARS?s Scientific Manuscript database

Greenhouse gas (GHG) emissions and their potential impact on the environment has become an important national and international concern. Animal agriculture is a recognized source of GHG emissions, but good information does not exist on the net emissions from our farms. A software tool called the Dai...

Graphical Requirements for Force Level Planning. Volume 2

DTIC Science & Technology

1991-09-01

technology review includes graphics algorithms, computer hardware, computer software, and design methodologies. The technology can either exist today or...level graphics language. 7.4 User Interface Design Tools As user interfaces have become more sophisticated, they have become harder to develop. Xl...Setphen M. Pizer, editors. Proceedings 1986 Workshop on Interactive 31) Graphics , October 1986. 18 J. S. Dumas. Designing User Interface Software. Prentice

DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

PubMed Central

Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng

2015-01-01

Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three ‘tier’ design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and ‘debugging’ the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems. PMID:26423437

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

PubMed Central

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types.  The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps.  The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon’s conclusion, and 2) all software comprising the final pipeline must be open-source or open-use.  Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event.  Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team. PMID:27134733

Analysis of a mammography teaching program based on an affordance design model.

PubMed

Luo, Ping; Eikman, Edward A; Kealy, William; Qian, Wei

2006-12-01

The wide use of computer technology in education, particularly in mammogram reading, asks for e-learning evaluation. The existing media comparative studies, learner attitude evaluations, and performance tests are problematic. Based on an affordance design model, this study examined an existing e-learning program on mammogram reading. The selection criteria include content relatedness, representativeness, e-learning orientation, image quality, program completeness, and accessibility. A case study was conducted to examine the affordance features, functions, and presentations of the selected software. Data collection and analysis methods include interviews, protocol-based document analysis, and usability tests and inspection. Also some statistics were calculated. The examination of PBE identified that this educational software designed and programmed some tools. The learner can use these tools in the process of optimizing displays, scanning images, comparing different projections, marking the region of interests, constructing a descriptive report, assessing one's learning outcomes, and comparing one's decisions with the experts' decisions. Further, PBE provides some resources for the learner to construct one's knowledge and skills, including a categorized image library, a term-searching function, and some teaching links. Besides, users found it easy to navigate and carry out tasks. The users also reacted positively toward PBE's navigation system, instructional aids, layout, pace and flow of information, graphics, and other presentation design. The software provides learners with some cognitive tools, supporting their perceptual problem-solving processes and extending their capabilities. Learners can internalize the mental models in mammogram reading through multiple perceptual triangulations, sensitization of related features, semantic description of mammogram findings, and expert-guided semantic report construction. The design of these cognitive tools and the software interface matches the findings and principles in human learning and instructional design. Working with PBE's case-based simulations and categorized gallery, learners can enrich and transfer their experience to their jobs.

Multidisciplinary Optimization for Aerospace Using Genetic Optimization

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Hahn, Edward E.; Herrera, Claudia Y.

2007-01-01

In support of the ARMD guidelines NASA's Dryden Flight Research Center is developing a multidisciplinary design and optimization tool This tool will leverage existing tools and practices, and allow the easy integration and adoption of new state-of-the-art software. Optimization has made its way into many mainstream applications. For example NASTRAN(TradeMark) has its solution sequence 200 for Design Optimization, and MATLAB(TradeMark) has an Optimization Tool box. Other packages, such as ZAERO(TradeMark) aeroelastic panel code and the CFL3D(TradeMark) Navier-Stokes solver have no built in optimizer. The goal of the tool development is to generate a central executive capable of using disparate software packages ina cross platform network environment so as to quickly perform optimization and design tasks in a cohesive streamlined manner. A provided figure (Figure 1) shows a typical set of tools and their relation to the central executive. Optimization can take place within each individual too, or in a loop between the executive and the tool, or both.

ORAC: 21st Century Observing at UKIRT

NASA Astrophysics Data System (ADS)

Bridger, A.; Wright, G. S.; Tan, M.; Pickup, D. A.; Economou, F.; Currie, M. J.; Adamson, A. J.; Rees, N. P.; Purves, M. H.

The Observatory Reduction and Acquisition Control system replaces all of the existing software which interacts with the observers at UKIRT. The aim is to improve observing efficiency with a set of integrated tools that take the user from pre-observing preparation, through the acquisition of observations to the reduction using a data-driven pipeline. ORAC is designed to be flexible and extensible, and is intended for use with all future UKIRT instruments, as well as existing telescope hardware and ``legacy'' instruments. It is also designed to allow integration with phase-1 and queue-scheduled observing tools in anticipation of possible future requirements. A brief overview of the project and its relationship to other systems is given. ORAC also re-uses much code from other systems and we discuss issues relating to the trade-off between reuse and the generation of new software specific to our requirements.

Tailoring a software production environment for a large project

NASA Technical Reports Server (NTRS)

Levine, D. R.

1984-01-01

A software production environment was constructed to meet the specific goals of a particular large programming project. These goals, the specific solutions as implemented, and the experiences on a project of over 100,000 lines of source code are discussed. The base development environment for this project was an ordinary PWB Unix (tm) system. Several important aspects of the development process required support not available in the existing tool set.

An Overview of Modifications Applied to a Turbulence Response Analysis Method for Flexible Aircraft Configurations

NASA Technical Reports Server (NTRS)

Funk, Christie J.

2013-01-01

A software program and associated methodology to study gust loading on aircraft exists for a classification of geometrically simplified flexible configurations. This program consists of a simple aircraft response model with two rigid and three flexible symmetric degrees of freedom and allows for the calculation of various airplane responses due to a discrete one-minus-cosine gust as well as continuous turbulence. Simplifications, assumptions, and opportunities for potential improvements pertaining to the existing software program are first identified, then a revised version of the original software tool is developed with improved methodology to include more complex geometries, additional excitation cases, and output data so as to provide a more useful and accurate tool for gust load analysis. Revisions are made in the categories of aircraft geometry, computation of aerodynamic forces and moments, and implementation of horizontal tail mode shapes. In order to improve the original software program to enhance usefulness, a wing control surface and horizontal tail control surface is added, an extended application of the discrete one-minus-cosine gust input is employed, a supplemental continuous turbulence spectrum is implemented, and a capability to animate the total vehicle deformation response to gust inputs in included. These revisions and enhancements are implemented and an analysis of the results is used to validate the modifications.

Teaching the Teacher: Tutoring SimStudent Leads to More Effective Cognitive Tutor Authoring

ERIC Educational Resources Information Center

Matsuda, Noboru; Cohen, William W.; Koedinger, Kenneth R.

2015-01-01

SimStudent is a machine-learning agent initially developed to help novice authors to create cognitive tutors without heavy programming. Integrated into an existing suite of software tools called Cognitive Tutor Authoring Tools (CTAT), SimStudent helps authors to create an expert model for a cognitive tutor by tutoring SimStudent on how to solve…

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

An expert system based software sizing tool, phase 2

NASA Technical Reports Server (NTRS)

Friedlander, David

1990-01-01

A software tool was developed for predicting the size of a future computer program at an early stage in its development. The system is intended to enable a user who is not expert in Software Engineering to estimate software size in lines of source code with an accuracy similar to that of an expert, based on the program's functional specifications. The project was planned as a knowledge based system with a field prototype as the goal of Phase 2 and a commercial system planned for Phase 3. The researchers used techniques from Artificial Intelligence and knowledge from human experts and existing software from NASA's COSMIC database. They devised a classification scheme for the software specifications, and a small set of generic software components that represent complexity and apply to large classes of programs. The specifications are converted to generic components by a set of rules and the generic components are input to a nonlinear sizing function which makes the final prediction. The system developed for this project predicted code sizes from the database with a bias factor of 1.06 and a fluctuation factor of 1.77, an accuracy similar to that of human experts but without their significant optimistic bias.

A new scoring function for top-down spectral deconvolution

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

Kou, Qiang; Wu, Si; Liu, Xiaowen

2014-12-18

Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showedmore » that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.« less

Systems biology driven software design for the research enterprise.

PubMed

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-06-25

In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.

Performance profiling for brachytherapy applications

NASA Astrophysics Data System (ADS)

Choi, Wonqook; Cho, Kihyeon; Yeo, Insung

2018-05-01

In many physics applications, a significant amount of software (e.g. R, ROOT and Geant4) is developed on novel computing architectures, and much effort is expended to ensure the software is efficient in terms of central processing unit (CPU) time and memory usage. Profiling tools are used during the evaluation process to evaluate the efficiency; however, few such tools are able to accommodate low-energy physics regions. To address this limitation, we developed a low-energy physics profiling system in Geant4 to profile the CPU time and memory of software applications in brachytherapy applications. This paper describes and evaluates specific models that are applied to brachytherapy applications in Geant4, such as QGSP_BIC_LIV, QGSP_BIC_EMZ, and QGSP_BIC_EMY. The physics range in this tool allows it to be used to generate low energy profiles in brachytherapy applications. This was a limitation in previous studies, which caused us to develop a new profiling tool that supports profiling in the MeV range, in contrast to the TeV range that is supported by existing high-energy profiling tools. In order to easily compare the profiling results between low-energy and high-energy modes, we employed the same software architecture as that in the SimpliCarlo tool developed at the Fermilab National Accelerator Laboratory (FNAL) for the Large Hadron Collider (LHC). The results show that the newly developed profiling system for low-energy physics (less than MeV) complements the current profiling system used for high-energy physics (greater than TeV) applications.

Reusable science tools for analog exploration missions: xGDS Web Tools, VERVE, and Gigapan Voyage

NASA Astrophysics Data System (ADS)

Lee, Susan Y.; Lees, David; Cohen, Tamar; Allan, Mark; Deans, Matthew; Morse, Theodore; Park, Eric; Smith, Trey

2013-10-01

The Exploration Ground Data Systems (xGDS) project led by the Intelligent Robotics Group (IRG) at NASA Ames Research Center creates software tools to support multiple NASA-led planetary analog field experiments. The two primary tools that fall under the xGDS umbrella are the xGDS Web Tools (xGDS-WT) and Visual Environment for Remote Virtual Exploration (VERVE). IRG has also developed a hardware and software system that is closely integrated with our xGDS tools and is used in multiple field experiments called Gigapan Voyage. xGDS-WT, VERVE, and Gigapan Voyage are examples of IRG projects that improve the ratio of science return versus development effort by creating generic and reusable tools that leverage existing technologies in both hardware and software. xGDS Web Tools provides software for gathering and organizing mission data for science and engineering operations, including tools for planning traverses, monitoring autonomous or piloted vehicles, visualization, documentation, analysis, and search. VERVE provides high performance three dimensional (3D) user interfaces used by scientists, robot operators, and mission planners to visualize robot data in real time. Gigapan Voyage is a gigapixel image capturing and processing tool that improves situational awareness and scientific exploration in human and robotic analog missions. All of these technologies emphasize software reuse and leverage open source and/or commercial-off-the-shelf tools to greatly improve the utility and reduce the development and operational cost of future similar technologies. Over the past several years these technologies have been used in many NASA-led robotic field campaigns including the Desert Research and Technology Studies (DRATS), the Pavilion Lake Research Project (PLRP), the K10 Robotic Follow-Up tests, and most recently we have become involved in the NASA Extreme Environment Mission Operations (NEEMO) field experiments. A major objective of these joint robot and crew experiments is to improve NASAs understanding of how to most effectively execute and increase science return from exploration missions. This paper focuses on an integrated suite of xGDS software and compatible hardware tools: xGDS Web Tools, VERVE, and Gigapan Voyage, how they are used, and the design decisions that were made to allow them to be easily developed, integrated, tested, and reused by multiple NASA field experiments and robotic platforms.

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

NASA Astrophysics Data System (ADS)

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

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

MEMS product engineering: methodology and tools

NASA Astrophysics Data System (ADS)

Ortloff, Dirk; Popp, Jens; Schmidt, Thilo; Hahn, Kai; Mielke, Matthias; Brück, Rainer

2011-03-01

The development of MEMS comprises the structural design as well as the definition of an appropriate manufacturing process. Technology constraints have a considerable impact on the device design and vice-versa. Product design and technology development are therefore concurrent tasks. Based on a comprehensive methodology the authors introduce a software environment that links commercial design tools from both area into a common design flow. In this paper emphasis is put on automatic low threshold data acquisition. The intention is to collect and categorize development data for further developments with minimum overhead and minimum disturbance of established business processes. As a first step software tools that automatically extract data from spreadsheets or file-systems and put them in context with existing information are presented. The developments are currently carried out in a European research project.

Compact Graphical Representation of Phylogenetic Data and Metadata with GraPh1An

DTIC Science & Technology

2016-09-12

pipelines . This allows for a higher degree of analysis reproducibility, but the software must correspondingly be available for local installation and callable...these operations are available in the GraPhlAn software repository). Reproducible integration with existing analysis tools and pipelines Graphical...from different analysis pipelines , generating the necessary input files for GraPhlAn. Export2graphlan directly supports MetaPhlAn2, LEfSe, and HUMAnN

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

NASA Technical Reports Server (NTRS)

Schumann, Johann; Denney, Ewen

2006-01-01

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

The center for causal discovery of biomedical knowledge from big data

PubMed Central

Bahar, Ivet; Becich, Michael J; Benos, Panayiotis V; Berg, Jeremy; Espino, Jeremy U; Glymour, Clark; Jacobson, Rebecca Crowley; Kienholz, Michelle; Lee, Adrian V; Lu, Xinghua; Scheines, Richard

2015-01-01

The Big Data to Knowledge (BD2K) Center for Causal Discovery is developing and disseminating an integrated set of open source tools that support causal modeling and discovery of biomedical knowledge from large and complex biomedical datasets. The Center integrates teams of biomedical and data scientists focused on the refinement of existing and the development of new constraint-based and Bayesian algorithms based on causal Bayesian networks, the optimization of software for efficient operation in a supercomputing environment, and the testing of algorithms and software developed using real data from 3 representative driving biomedical projects: cancer driver mutations, lung disease, and the functional connectome of the human brain. Associated training activities provide both biomedical and data scientists with the knowledge and skills needed to apply and extend these tools. Collaborative activities with the BD2K Consortium further advance causal discovery tools and integrate tools and resources developed by other centers. PMID:26138794

A survey of tools for the analysis of quantitative PCR (qPCR) data.

PubMed

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

Needs challenge software

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

NONE

1997-07-01

New hardware and software tools build on existing platforms and add performance and ease-of-use benefits as the struggle to find and produce hydrocarbons at the lowest cost becomes more and more competitive. Software tools now provide geoscientists and petroleum engineers with a better understanding of reservoirs from the shape and makeup of formation to behavior projections as hydrocarbons are extracted. Petroleum software tools allow scientists to simulate oil flow, predict the life expectancy of a reservoir, and even help determine how to extend the life and economic viability of the reservoir. The requirement of the petroleum industry to find andmore » extract petroleum more efficiently drives the solutions provided by software and service companies. To one extent or another, most of the petroleum software products available today have achieved an acceptable level of competency. Innovative, high-impact products from small, focussed companies often were bought out by larger companies with deeper pockets if their developers couldn`t fund their expansion. Other products disappeared from the scene, because they were unable to evolve fast enough to compete. There are still enough small companies around producing excellent products to prevent the marketplace from feeling too narrow and lacking in choice. Oil companies requiring specific solutions to their problems have helped fund product development within the commercial sector. As the industry has matured, strategic alliances between vendors, both hardware and software, have provided market advantages, often combining strengths to enter new and undeveloped areas for technology. The pace of technological development has been fast and constant.« less

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

McCaskey, Alexander J.

There is a lack of state-of-the-art HPC simulation tools for simulating general quantum computing. Furthermore, there are no real software tools that integrate current quantum computers into existing classical HPC workflows. This product, the Quantum Virtual Machine (QVM), solves this problem by providing an extensible framework for pluggable virtual, or physical, quantum processing units (QPUs). It enables the execution of low level quantum assembly codes and returns the results of such executions.

hydropower biological evaluation tools

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

This software is a set of analytical tools to evaluate the physical and biological performance of existing, refurbished, or newly installed conventional hydro-turbines nationwide where fish passage is a regulatory concern. The current version is based on information collected by the Sensor Fish. Future version will include other technologies. The tool set includes data acquisition, data processing, and biological response tools with applications to various turbine designs and other passage alternatives. The associated database is centralized, and can be accessed remotely. We have demonstrated its use for various applications including both turbines and spillways

Analyzing Saturn's Magnetospheric Data After Cassini - Improving and Future-Proofing Cassini / MAPS Tools and Data

NASA Astrophysics Data System (ADS)

Brown, L. E.; Faden, J.; Vandegriff, J. D.; Kurth, W. S.; Mitchell, D. G.

2017-12-01

We present a plan to provide enhanced longevity to analysis software and science data used throughout the Cassini mission for viewing Magnetosphere and Plasma Science (MAPS) data. While a final archive is being prepared for Cassini, the tools that read from this archive will eventually become moribund as real world hardware and software systems evolve. We will add an access layer over existing and planned Cassini data products that will allow multiple tools to access many public MAPS datasets. The access layer is called the Heliophysics Application Programmer's Interface (HAPI), and this is a mechanism being adopted at many data centers across Heliophysics and planetary science for the serving of time series data. Two existing tools are also being enhanced to read from HAPI servers, namely Autoplot from the University of Iowa and MIDL (Mission Independent Data Layer) from The Johns Hopkins Applied Physics Lab. Thus both tools will be able to access data from RPWS, MAG, CAPS, and MIMI. In addition to being able to access data from each other's institutions, these tools will be able to read from all the new datasets expected to come online using the HAPI standard in the near future. The PDS also plans to use HAPI for all the holdings at the Planetary and Plasma Interactions (PPI) node. A basic presentation of the new HAPI data server mechanism is presented, as is an early demonstration of the modified tools.

Impacts of software and its engineering on the carbon footprint of ICT

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

Kern, Eva, E-mail: e.kern@umwelt-campus.de; Dick, Markus, E-mail: sustainablesoftwareblog@gmail.com; Naumann, Stefan, E-mail: s.naumann@umwelt-campus.de

2015-04-15

The energy consumption of information and communication technology (ICT) is still increasing. Even though several solutions regarding the hardware side of Green IT exist, the software contribution to Green IT is not well investigated. The carbon footprint is one way to rate the environmental impacts of ICT. In order to get an impression of the induced CO{sub 2} emissions of software, we will present a calculation method for the carbon footprint of a software product over its life cycle. We also offer an approach on how to integrate some aspects of carbon footprint calculation into software development processes and discussmore » impacts and tools regarding this calculation method. We thus show the relevance of energy measurements and the attention to impacts on the carbon footprint by software within Green Software Engineering.« less

Remote Sensing: A valuable tool in the Forest Service decision making process. [in Utah

NASA Technical Reports Server (NTRS)

Stanton, F. L.

1975-01-01

Forest Service studies for integrating remotely sensed data into existing information systems highlight a need to: (1) re-examine present methods of collecting and organizing data, (2) develop an integrated information system for rapidly processing and interpreting data, (3) apply existing technological tools in new ways, and (4) provide accurate and timely information for making right management decisions. The Forest Service developed an integrated information system using remote sensors, microdensitometers, computer hardware and software, and interactive accessories. Their efforts substantially reduce the time it takes for collecting and processing data.

TeamWATCH: Visualizing development activities using a 3-D city metaphor to improve conflict detection and team awareness

PubMed Central

Ye, Xin

2018-01-01

The awareness of others’ activities has been widely recognized as essential in facilitating coordination in a team among Computer-Supported Cooperative Work communities. Several field studies of software developers in large software companies such as Microsoft have shown that coworker and artifact awareness are the most common information needs for software developers; however, they are also two of the seven most frequently unsatisfied information needs. To address this problem, we built a workspace awareness tool named TeamWATCH to visualize developer activities using a 3-D city metaphor. In this paper, we discuss the importance of awareness in software development, review existing workspace awareness tools, present the design and implementation of TeamWATCH, and evaluate how it could help detect and resolve conflicts earlier and better maintain group awareness via a controlled experiment. The experimental results showed that the subjects using TeamWATCH performed significantly better with respect to early conflict detection and resolution. PMID:29558519

Verification and Validation in a Rapid Software Development Process

NASA Technical Reports Server (NTRS)

Callahan, John R.; Easterbrook, Steve M.

1997-01-01

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

metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

PubMed

Lommen, Arjen; van der Kamp, Henk J; Kools, Harrie J; van der Lee, Martijn K; van der Weg, Guido; Mol, Hans G J

2012-11-09

A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has been developed for and tested on LECO data. The software is developed to run multi-threaded (one thread per processor core) on a standard PC (personal computer) under different operating systems and is as such capable of processing multiple data sets simultaneously. Raw data files are converted into netCDF (network Common Data Form) format using a fast conversion tool. They are then preprocessed using previously developed algorithms originating from metAlign software. Next, the resulting reduced data files are searched against a user-composed library (derived from user or commercial NIST-compatible libraries) (NIST=National Institute of Standards and Technology) and the identified compounds, including an indicative concentration, are reported in Excel format. Data can be processed batch wise. The overall time needed for conversion together with processing and searching of 30 raw data sets for 560 compounds is routinely within an hour. The screening performance is evaluated for detection of pesticides and contaminants in raw data obtained after analysis of soil and plant samples. Results are compared to the existing data-handling routine based on proprietary software (LECO, ChromaTOF). The developed software tool set, which is freely downloadable at www.metalign.nl, greatly accelerates data-analysis and offers more options for fine-tuning automated identification toward specific application needs. The quality of the results obtained is slightly better than the standard processing and also adds a quantitative estimate. The software tool set in combination with two-dimensional gas chromatography coupled to time-of-flight mass spectrometry shows great potential as a highly-automated and fast multi-residue instrumental screening method. Copyright © 2012 Elsevier B.V. All rights reserved.

Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing.

PubMed

Sorbello, Alfred; Ripple, Anna; Tonning, Joseph; Munoz, Monica; Hasan, Rashedul; Ly, Thomas; Francis, Henry; Bodenreider, Olivier

2017-03-22

We seek to develop a prototype software analytical tool to augment FDA regulatory reviewers' capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool. A prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use. All usability test participants cited the tool's ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool's automated literature search relative to a manual 'all fields' PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools. Usability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction.

Modeling Tools Predict Flow in Fluid Dynamics

NASA Technical Reports Server (NTRS)

2010-01-01

"Because rocket engines operate under extreme temperature and pressure, they present a unique challenge to designers who must test and simulate the technology. To this end, CRAFT Tech Inc., of Pipersville, Pennsylvania, won Small Business Innovation Research (SBIR) contracts from Marshall Space Flight Center to develop software to simulate cryogenic fluid flows and related phenomena. CRAFT Tech enhanced its CRUNCH CFD (computational fluid dynamics) software to simulate phenomena in various liquid propulsion components and systems. Today, both government and industry clients in the aerospace, utilities, and petrochemical industries use the software for analyzing existing systems as well as designing new ones."

Desiderata for a Computer-Assisted Audit Tool for Clinical Data Source Verification Audits

PubMed Central

Duda, Stephany N.; Wehbe, Firas H.; Gadd, Cynthia S.

2013-01-01

Clinical data auditing often requires validating the contents of clinical research databases against source documents available in health care settings. Currently available data audit software, however, does not provide features necessary to compare the contents of such databases to source data in paper medical records. This work enumerates the primary weaknesses of using paper forms for clinical data audits and identifies the shortcomings of existing data audit software, as informed by the experiences of an audit team evaluating data quality for an international research consortium. The authors propose a set of attributes to guide the development of a computer-assisted clinical data audit tool to simplify and standardize the audit process. PMID:20841814

Integrating information technologies as tools for surgical research.

PubMed

Schell, Scott R

2005-10-01

Surgical research is dependent upon information technologies. Selection of the computer, operating system, and software tool that best support the surgical investigator's needs requires careful planning before research commences. This manuscript presents a brief tutorial on how surgical investigators can best select these information technologies, with comparisons and recommendations between existing systems, software, and solutions. Privacy concerns, based upon HIPAA and other regulations, now require careful proactive attention to avoid legal penalties, civil litigation, and financial loss. Security issues are included as part of the discussions related to selection and application of information technology. This material was derived from a segment of the Association for Academic Surgery's Fundamentals of Surgical Research course.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

LEGOS: Object-based software components for mission-critical systems. Final report, June 1, 1995--December 31, 1997

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

NONE

1998-08-01

An estimated 85% of the installed base of software is a custom application with a production quantity of one. In practice, almost 100% of military software systems are custom software. Paradoxically, the marginal costs of producing additional units are near zero. So why hasn`t the software market, a market with high design costs and low productions costs evolved like other similar custom widget industries, such as automobiles and hardware chips? The military software industry seems immune to market pressures that have motivated a multilevel supply chain structure in other widget industries: design cost recovery, improve quality through specialization, and enablemore » rapid assembly from purchased components. The primary goal of the ComponentWare Consortium (CWC) technology plan was to overcome barriers to building and deploying mission-critical information systems by using verified, reusable software components (Component Ware). The adoption of the ComponentWare infrastructure is predicated upon a critical mass of the leading platform vendors` inevitable adoption of adopting emerging, object-based, distributed computing frameworks--initially CORBA and COM/OLE. The long-range goal of this work is to build and deploy military systems from verified reusable architectures. The promise of component-based applications is to enable developers to snap together new applications by mixing and matching prefabricated software components. A key result of this effort is the concept of reusable software architectures. A second important contribution is the notion that a software architecture is something that can be captured in a formal language and reused across multiple applications. The formalization and reuse of software architectures provide major cost and schedule improvements. The Unified Modeling Language (UML) is fast becoming the industry standard for object-oriented analysis and design notation for object-based systems. However, the lack of a standard real-time distributed object operating system, lack of a standard Computer-Aided Software Environment (CASE) tool notation and lack of a standard CASE tool repository has limited the realization of component software. The approach to fulfilling this need is the software component factory innovation. The factory approach takes advantage of emerging standards such as UML, CORBA, Java and the Internet. The key technical innovation of the software component factory is the ability to assemble and test new system configurations as well as assemble new tools on demand from existing tools and architecture design repositories.« less

RDMO - Research Data Management Organiser

NASA Astrophysics Data System (ADS)

Klar, Jochen; Engelhardt, Claudia; Neuroth, Heike; Enke, Harry; Ludwig, Jens

2017-04-01

The Research Data Management Organiser (RDMO) is a new tool to support the structured planning and implementation of the research data management in a scientific project and, in addition, provide the scientist with a textual Data Management Plan (DMP). While DMP are in principle a great tool to optimise the data management during all stages of a research project and to serve as a roadmap for the various data management tasks, their current usage is strongly focused on the requirements of funding agencies. Existing software tools for DMP creation and editing are useful in that respect, but do not sufficiently support the full data life cycle of a project. The RDMO is meant to be a companion for data management issues during and after the whole project. Starting from a structured interview about the project and the data involved, it organizes the data management along tasks and comprises all relevant stakeholders, i.e. researchers, PIs, institutional data managers, IT departments. Adaptations to discipline-specific or institutional needs are supported. The installation of the tool into local environments and its integration into existing administrative IT infrastructure and work flows is given special consideration. The tool is multilingual (at first German and English). In my talk, I will present the different features of the software, show its current stage of development, and how RDMO can be deployed for your institution.

Planform: an application and database of graph-encoded planarian regenerative experiments.

PubMed

Lobo, Daniel; Malone, Taylor J; Levin, Michael

2013-04-15

Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype-phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset. The database and software tool are freely available at http://planform.daniel-lobo.com.

The enhanced Software Life Cyle Support Environment (ProSLCSE): Automation for enterprise and process modeling

NASA Technical Reports Server (NTRS)

Milligan, James R.; Dutton, James E.

1993-01-01

In this paper, we have introduced a comprehensive method for enterprise modeling that addresses the three important aspects of how an organization goes about its business. FirstEP includes infrastructure modeling, information modeling, and process modeling notations that are intended to be easy to learn and use. The notations stress the use of straightforward visual languages that are intuitive, syntactically simple, and semantically rich. ProSLCSE will be developed with automated tools and services to facilitate enterprise modeling and process enactment. In the spirit of FirstEP, ProSLCSE tools will also be seductively easy to use. Achieving fully managed, optimized software development and support processes will be long and arduous for most software organizations, and many serious problems will have to be solved along the way. ProSLCSE will provide the ability to document, communicate, and modify existing processes, which is the necessary first step.

Systems biology driven software design for the research enterprise

PubMed Central

Boyle, John; Cavnor, Christopher; Killcoyne, Sarah; Shmulevich, Ilya

2008-01-01

Background In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. Results We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. Conclusion By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data. PMID:18578887

CytoBayesJ: software tools for Bayesian analysis of cytogenetic radiation dosimetry data.

PubMed

Ainsbury, Elizabeth A; Vinnikov, Volodymyr; Puig, Pedro; Maznyk, Nataliya; Rothkamm, Kai; Lloyd, David C

2013-08-30

A number of authors have suggested that a Bayesian approach may be most appropriate for analysis of cytogenetic radiation dosimetry data. In the Bayesian framework, probability of an event is described in terms of previous expectations and uncertainty. Previously existing, or prior, information is used in combination with experimental results to infer probabilities or the likelihood that a hypothesis is true. It has been shown that the Bayesian approach increases both the accuracy and quality assurance of radiation dose estimates. New software entitled CytoBayesJ has been developed with the aim of bringing Bayesian analysis to cytogenetic biodosimetry laboratory practice. CytoBayesJ takes a number of Bayesian or 'Bayesian like' methods that have been proposed in the literature and presents them to the user in the form of simple user-friendly tools, including testing for the most appropriate model for distribution of chromosome aberrations and calculations of posterior probability distributions. The individual tools are described in detail and relevant examples of the use of the methods and the corresponding CytoBayesJ software tools are given. In this way, the suitability of the Bayesian approach to biological radiation dosimetry is highlighted and its wider application encouraged by providing a user-friendly software interface and manual in English and Russian. Copyright © 2013 Elsevier B.V. All rights reserved.

Software Safety Risk in Legacy Safety-Critical Computer Systems

NASA Technical Reports Server (NTRS)

Hill, Janice; Baggs, Rhoda

2007-01-01

Safety-critical computer systems must be engineered to meet system and software safety requirements. For legacy safety-critical computer systems, software safety requirements may not have been formally specified during development. When process-oriented software safety requirements are levied on a legacy system after the fact, where software development artifacts don't exist or are incomplete, the question becomes 'how can this be done?' The risks associated with only meeting certain software safety requirements in a legacy safety-critical computer system must be addressed should such systems be selected as candidates for reuse. This paper proposes a method for ascertaining formally, a software safety risk assessment, that provides measurements for software safety for legacy systems which may or may not have a suite of software engineering documentation that is now normally required. It relies upon the NASA Software Safety Standard, risk assessment methods based upon the Taxonomy-Based Questionnaire, and the application of reverse engineering CASE tools to produce original design documents for legacy systems.

Path generation algorithm for UML graphic modeling of aerospace test software

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Chen, Chao

2018-03-01

Aerospace traditional software testing engineers are based on their own work experience and communication with software development personnel to complete the description of the test software, manual writing test cases, time-consuming, inefficient, loopholes and more. Using the high reliability MBT tools developed by our company, the one-time modeling can automatically generate test case documents, which is efficient and accurate. UML model to describe the process accurately express the need to rely on the path is reached, the existing path generation algorithm are too simple, cannot be combined into a path and branch path with loop, or too cumbersome, too complicated arrangement generates a path is meaningless, for aerospace software testing is superfluous, I rely on our experience of ten load space, tailor developed a description of aerospace software UML graphics path generation algorithm.

Virtual Observatory Science Applications

NASA Technical Reports Server (NTRS)

McGlynn, Tom

2005-01-01

Many Virtual-Observatory-based applications are now available to astronomers for use in their research. These span data discovery, access, visualization and analysis. Tools can quickly gather and organize information from sites around the world to help in planning a response to a gamma-ray burst, help users pick filters to isolate a desired feature, make an average template for z=2 AGN, select sources based upon information in many catalogs, or correlate massive distributed databases. Using VO protocols, the reach of existing software tools and packages can be greatly extended, allowing users to find and access remote information almost as conveniently as local data. The talk highlights just a few of the tools available to scientists, describes how both large and small scale projects can use existing tools, and previews some of the new capabilities that will be available in the next few years.

Global review of open access risk assessment software packages valid for global or continental scale analysis

NASA Astrophysics Data System (ADS)

Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

2015-04-01

Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user-defined exposure and vulnerability. Without this function, many tools can only be used regionally and not at global or continental scale. It is becoming increasingly easy to use multiple packages for a single region and/or hazard to characterize the uncertainty in the risk, or use as checks for the sensitivities in the analysis. There is a potential for valuable synergy between existing software. A number of open source software packages could be combined to generate a multi-risk model with multiple views of a hazard. This extensive review has simply attempted to provide a platform for dialogue between all open source and open access software packages and to hopefully inspire collaboration between developers, given the great work done by all open access and open source developers.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

Flexible control techniques for a lunar base

NASA Technical Reports Server (NTRS)

Kraus, Thomas W.

1992-01-01

The fundamental elements found in every terrestrial control system can be employed in all lunar applications. These elements include sensors which measure physical properties, controllers which acquire sensor data and calculate a control response, and actuators which apply the control output to the process. The unique characteristics of the lunar environment will certainly require the development of new control system technology. However, weightlessness, harsh atmospheric conditions, temperature extremes, and radiation hazards will most significantly impact the design of sensors and actuators. The controller and associated control algorithms, which are the most complex element of any control system, can be derived in their entirety from existing technology. Lunar process control applications -- ranging from small-scale research projects to full-scale processing plants -- will benefit greatly from the controller advances being developed today. In particular, new software technology aimed at commercial process monitoring and control applications will almost completely eliminate the need for custom programs and the lengthy development and testing cycle they require. The applicability of existing industrial software to lunar applications has other significant advantages in addition to cost and quality. This software is designed to run on standard hardware platforms and takes advantage of existing LAN and telecommunications technology. Further, in order to exploit the existing commercial market, the software is being designed to be implemented by users of all skill levels -- typically users who are familiar with their process, but not necessarily with software or control theory. This means that specialized technical support personnel will not need to be on-hand, and the associated costs are eliminated. Finally, the latest industrial software designed for the commercial market is extremely flexible, in order to fit the requirements of many types of processing applications with little or no customization. This means that lunar process control projects will not be delayed by unforeseen problems or last minute process modifications. The software will include all of the tools needed to adapt to virtually any changes. In contrast to other space programs which required the development of tremendous amounts of custom software, lunar-based processing facilities will benefit from the use of existing software technology which is being proven in commercial applications on Earth.

A toolbox and a record for scientific model development

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Scientific computation can benefit from software tools that facilitate construction of computational models, control the application of models, and aid in revising models to handle new situations. Existing environments for scientific programming provide only limited means of handling these tasks. This paper describes a two pronged approach for handling these tasks: (1) designing a 'Model Development Toolbox' that includes a basic set of model constructing operations; and (2) designing a 'Model Development Record' that is automatically generated during model construction. The record is subsequently exploited by tools that control the application of scientific models and revise models to handle new situations. Our two pronged approach is motivated by our belief that the model development toolbox and record should be highly interdependent. In particular, a suitable model development record can be constructed only when models are developed using a well defined set of operations. We expect this research to facilitate rapid development of new scientific computational models, to help ensure appropriate use of such models and to facilitate sharing of such models among working computational scientists. We are testing this approach by extending SIGMA, and existing knowledge-based scientific software design tool.

Integrating existing software toolkits into VO system

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Zhao, Yong-Heng; Wang, Xiaoqian; Sang, Jian; Luo, Ze

2004-09-01

Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and "Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.

IDEAL: Images Across Domains, Experiments, Algorithms and Learning

NASA Astrophysics Data System (ADS)

Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

2016-11-01

Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

CMS-2 Reverse Engineering and ENCORE/MODEL Integration

DTIC Science & Technology

1992-05-01

Automated extraction of design information from an existing software system written in CMS-2 can be used to document that system as-built, and that I The...extracted information is provided by a commer- dally available CASE tool. * Information describing software system design is automatically extracted...the displays in Figures 1, 2, and 3. T achiev ths GE 11 b iuo w as rjcs CM-2t Aa nsltr(M2da 1 n Joia Reverse EwngiernTcnlg 5RT [2GRE] . Two xampe fD

Data Center IT Equipment Energy Assessment Tools: Current State of Commercial Tools, Proposal for a Future Set of Assessment Tools

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

Radhakrishnan, Ben D.

2012-06-30

This research project, which was conducted during the Summer and Fall of 2011, investigated some commercially available assessment tools with a focus on IT equipment to see if such tools could round out the DC Pro tool suite. In this research, the assessment capabilities of the various tools were compiled to help make “non-biased” information available to the public. This research should not be considered to be exhaustive on all existing vendor tools although a number of vendors were contacted. Large IT equipment OEM’s like IBM and Dell provide their proprietary internal automated software which does not work on anymore » other IT equipment. However, found two companies with products that showed promise in performing automated assessments for IT equipment from different OEM vendors. This report documents the research and provides a list of software products reviewed, contacts and websites, product details, discussions with specific companies, a set of recommendations, and next steps. As a result of this research, a simple 3-level approach to an IT assessment tool is proposed along with an example of an assessment using a simple IT equipment data collection tool (Level 1, spreadsheet). The tool has been reviewed with the Green Grid and LBNL staff. The initial feedback has been positive although further refinement to the tool will be necessary. Proposed next steps include a field trial of at least two vendors’ software in two different data centers with an objective to prove the concept, ascertain the extent of energy and computational assessment, ease of installation and opportunities for continuous improvement. Based on the discussions, field trials (or case studies) are proposed with two vendors – JouleX (expected to be completed in 2012) and Sentilla.« less

MAPPER: A personal computer map projection tool

NASA Technical Reports Server (NTRS)

Bailey, Steven A.

1993-01-01

MAPPER is a set of software tools designed to let users create and manipulate map projections on a personal computer (PC). The capability exists to generate five popular map projections. These include azimuthal, cylindrical, mercator, lambert, and sinusoidal projections. Data for projections are contained in five coordinate databases at various resolutions. MAPPER is managed by a system of pull-down windows. This interface allows the user to intuitively create, view and export maps to other platforms.

The Design of a Multi-Agent NDE Inspection Qualification System

NASA Astrophysics Data System (ADS)

McLean, N.; McKenna, J. P.; Gachagan, A.; McArthur, S.; Hayward, G.

2007-03-01

A novel Multi-Agent system (MAS) for NDE inspection qualification is being developed to facilitate a scalable environment allowing integration and automation of new and existing inspection qualification tools. This paper discusses the advantages of using a MAS approach to integrate the large number of disparate NDE software tools. The design and implementation of the system architecture is described, including the development of an ontology to describe the NDE domain.

Availability of Ada and C++ Compilers, Tools, Education and Training

DTIC Science & Technology

1991-07-01

executable mini-specs, to support import of existing code. Automated database population/change propagation. 9. Documentation generation: via FrameMaker . 10...formats. 12. Links to other tools: i. Atherton’s Software Backplane. ii. 4GLS iii. Interleaf and FrameMaker publishing. 13. Output formats: PostScript...by end 󈨟. 11. Output formats: ASCII, PostScript, Interleaf, HPGL, Troff, nroff, FrameMaker , WordPerfect. 12. User interface: Menu and mouse

The OME Framework for genome-scale systems biology

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

Palsson, Bernhard O.; Ebrahim, Ali; Federowicz, Steve

The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed [1-3]. However, few of these tools have been forced to deal with the full complexity ofmore » genome-scale models along with high throughput genome- scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind [4]. It is also evident that, given the plethora of databases and software efforts [5-12], it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models [13-15]. We work at the forefront of model creation and systems scale data generation [16-18]. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities [13, 19-24] towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome-scale metabolic models or for genome-scale data analysis, no implementations exist that explicitly handle data and models concurrently. The OME Framework structures data in a connected loop with models and the components those models are composed of. This results in the first full, practical implementation of a framework that can enable genome-scale design-build-test. Over the coming years many more software packages will be developed and tools will necessarily change. However, we hope that the underlying designs shared here can help to inform the design of future software.« less

Playbook Data Analysis Tool: Collecting Interaction Data from Extremely Remote Users

NASA Technical Reports Server (NTRS)

Kanefsky, Bob; Zheng, Jimin; Deliz, Ivonne; Marquez, Jessica J.; Hillenius, Steven

2017-01-01

Typically, user tests for software tools are conducted in person. At NASA, the users may be located at the bottom of the ocean in a pressurized habitat, above the atmosphere in the International Space Station, or in an isolated capsule on a simulated asteroid mission. The Playbook Data Analysis Tool (P-DAT) is a human-computer interaction (HCI) evaluation tool that the NASA Ames HCI Group has developed to record user interactions with Playbook, the group's existing planning-and-execution software application. Once the remotely collected user interaction data makes its way back to Earth, researchers can use P-DAT for in-depth analysis. Since a critical component of the Playbook project is to understand how to develop more intuitive software tools for astronauts to plan in space, P-DAT helps guide us in the development of additional easy-to-use features for Playbook, informing the design of future crew autonomy tools.P-DAT has demonstrated the capability of discreetly capturing usability data in amanner that is transparent to Playbook’s end-users. In our experience, P-DAT data hasalready shown its utility, revealing potential usability patterns, helping diagnose softwarebugs, and identifying metrics and events that are pertinent to Playbook usage aswell as spaceflight operations. As we continue to develop this analysis tool, P-DATmay yet provide a method for long-duration, unobtrusive human performance collectionand evaluation for mission controllers back on Earth and researchers investigatingthe effects and mitigations related to future human spaceflight performance.

pyLIMA : an open source microlensing software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne

2017-01-01

Planetary microlensing is a unique tool to detect cold planets around low-mass stars which is approaching a watershed in discoveries as near-future missions incorporate dedicated surveys. NASA and ESA have decided to complement WFIRST-AFTA and Euclid with microlensing programs to enrich our statistics about this planetary population. Of the nany challenges in- herent in these missions, the data analysis is of primary importance, yet is often perceived as time consuming, complex and daunting barrier to participation in the field. We present the first open source modeling software to conduct a microlensing analysis. This software is written in Python and use as much as possible existing packages.

ESSAA: Embedded system safety analysis assistant

NASA Technical Reports Server (NTRS)

Wallace, Peter; Holzer, Joseph; Guarro, Sergio; Hyatt, Larry

1987-01-01

The Embedded System Safety Analysis Assistant (ESSAA) is a knowledge-based tool that can assist in identifying disaster scenarios. Imbedded software issues hazardous control commands to the surrounding hardware. ESSAA is intended to work from outputs to inputs, as a complement to simulation and verification methods. Rather than treating the software in isolation, it examines the context in which the software is to be deployed. Given a specified disasterous outcome, ESSAA works from a qualitative, abstract model of the complete system to infer sets of environmental conditions and/or failures that could cause a disasterous outcome. The scenarios can then be examined in depth for plausibility using existing techniques.

Web Time-Management Tool

NASA Technical Reports Server (NTRS)

2000-01-01

Oak Grove Reactor, developed by Oak Grove Systems, is a new software program that allows users to integrate workflow processes. It can be used with portable communication devices. The software can join e-mail, calendar/scheduling and legacy applications into one interactive system via the web. Priority tasks and due dates are organized and highlighted to keep the user up to date with developments. Reactor works with existing software and few new skills are needed to use it. Using a web browser, a user can can work on something while other users can work on the same procedure or view its status while it is being worked on at another site. The software was developed by the Jet Propulsion Lab and originally put to use at Johnson Space Center.

3-d finite element model development for biomechanics: a software demonstration

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

Hollerbach, K.; Hollister, A.M.; Ashby, E.

1997-03-01

Finite element analysis is becoming an increasingly important part of biomechanics and orthopedic research, as computational resources become more powerful, and data handling algorithms become more sophisticated. Until recently, tools with sufficient power did not exist or were not accessible to adequately model complicated, three-dimensional, nonlinear biomechanical systems. In the past, finite element analyses in biomechanics have often been limited to two-dimensional approaches, linear analyses, or simulations of single tissue types. Today, we have the resources to model fully three-dimensional, nonlinear, multi-tissue, and even multi-joint systems. The authors will present the process of developing these kinds of finite element models,more » using human hand and knee examples, and will demonstrate their software tools.« less

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

Prasser, Fabian; Kohlmayer, Florian; Lautenschläger, Ronald; Kuhn, Klaus A.

2014-01-01

Collaboration and data sharing have become core elements of biomedical research. Especially when sensitive data from distributed sources are linked, privacy threats have to be considered. Statistical disclosure control allows the protection of sensitive data by introducing fuzziness. Reduction of data quality, however, needs to be balanced against gains in protection. Therefore, tools are needed which provide a good overview of the anonymization process to those responsible for data sharing. These tools require graphical interfaces and the use of intuitive and replicable methods. In addition, extensive testing, documentation and openness to reviews by the community are important. Existing publicly available software is limited in functionality, and often active support is lacking. We present ARX, an anonymization tool that i) implements a wide variety of privacy methods in a highly efficient manner, ii) provides an intuitive cross-platform graphical interface, iii) offers a programming interface for integration into other software systems, and iv) is well documented and actively supported. PMID:25954407

Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling.

PubMed

Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver

2015-08-01

Reliable detection of peptides in LC-MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low-intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An overview of suite for automated global electronic biosurveillance (SAGES)

NASA Astrophysics Data System (ADS)

Lewis, Sheri L.; Feighner, Brian H.; Loschen, Wayne A.; Wojcik, Richard A.; Skora, Joseph F.; Coberly, Jacqueline S.; Blazes, David L.

2012-06-01

Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations.

Teaching IP Networking Fundamentals in Resource Constrained Educational Environments

ERIC Educational Resources Information Center

Armitage, Grenville; Harrop, Warren

2005-01-01

Many educational institutions suffer from a lack of funding to keep telecommunications laboratory classes up to date and flexible. This paper describes our Remote Unix Lab Environment (RULE), a solution for exposing students to the latest Internet based telecommunications software tools in a Unix like environment. RULE leverages existing PC…

Introduction to the Graduation Tracking System (GTS)

ERIC Educational Resources Information Center

Alabama Department of Education, 2011

2011-01-01

This guide is a training and supportive tool for use by local education agencies (LEAs) in the state of Alabama that are utilizing the Science, Technology and Innovation (STI) Information-INow-INFocus information system software. The Graduation Tracking System (GTS) utilizes existing STI technology to capture student information pertaining to…

Getting Started in Multimedia Training: Cutting or Bleeding Edge?

ERIC Educational Resources Information Center

Anderson, Vicki; Sleezer, Catherine M.

1995-01-01

Defines multimedia, explores uses of multimedia training, and discusses the effects and challenges of adding multimedia such as graphics, photographs, full motion video, sound effects, or CD-ROMs to existing training methods. Offers planning tips, and suggests software and hardware tools to help set up multimedia training programs. (JMV)

Analytical Design Package (ADP2): A computer aided engineering tool for aircraft transparency design

NASA Technical Reports Server (NTRS)

Wuerer, J. E.; Gran, M.; Held, T. W.

1994-01-01

The Analytical Design Package (ADP2) is being developed as a part of the Air Force Frameless Transparency Program (FTP). ADP2 is an integrated design tool consisting of existing analysis codes and Computer Aided Engineering (CAE) software. The objective of the ADP2 is to develop and confirm an integrated design methodology for frameless transparencies, related aircraft interfaces, and their corresponding tooling. The application of this methodology will generate high confidence for achieving a qualified part prior to mold fabrication. ADP2 is a customized integration of analysis codes, CAE software, and material databases. The primary CAE integration tool for the ADP2 is P3/PATRAN, a commercial-off-the-shelf (COTS) software tool. The open architecture of P3/PATRAN allows customized installations with different applications modules for specific site requirements. Integration of material databases allows the engineer to select a material, and those material properties are automatically called into the relevant analysis code. The ADP2 materials database will be composed of four independent schemas: CAE Design, Processing, Testing, and Logistics Support. The design of ADP2 places major emphasis on the seamless integration of CAE and analysis modules with a single intuitive graphical interface. This tool is being designed to serve and be used by an entire project team, i.e., analysts, designers, materials experts, and managers. The final version of the software will be delivered to the Air Force in Jan. 1994. The Analytical Design Package (ADP2) will then be ready for transfer to industry. The package will be capable of a wide range of design and manufacturing applications.

Adaptive System Modeling for Spacecraft Simulation

NASA Technical Reports Server (NTRS)

Thomas, Justin

2011-01-01

This invention introduces a methodology and associated software tools for automatically learning spacecraft system models without any assumptions regarding system behavior. Data stream mining techniques were used to learn models for critical portions of the International Space Station (ISS) Electrical Power System (EPS). Evaluation on historical ISS telemetry data shows that adaptive system modeling reduces simulation error anywhere from 50 to 90 percent over existing approaches. The purpose of the methodology is to outline how someone can create accurate system models from sensor (telemetry) data. The purpose of the software is to support the methodology. The software provides analysis tools to design the adaptive models. The software also provides the algorithms to initially build system models and continuously update them from the latest streaming sensor data. The main strengths are as follows: Creates accurate spacecraft system models without in-depth system knowledge or any assumptions about system behavior. Automatically updates/calibrates system models using the latest streaming sensor data. Creates device specific models that capture the exact behavior of devices of the same type. Adapts to evolving systems. Can reduce computational complexity (faster simulations).

Assessing ergonomic risks of software: Development of the SEAT.

PubMed

Peres, S Camille; Mehta, Ranjana K; Ritchey, Paul

2017-03-01

Software utilizing interaction designs that require extensive dragging or clicking of icons may increase users' risks for upper extremity cumulative trauma disorders. The purpose of this research is to develop a Self-report Ergonomic Assessment Tool (SEAT) for assessing the risks of software interaction designs and facilitate mitigation of those risks. A 28-item self-report measure was developed by combining and modifying items from existing industrial ergonomic tools. Data were collected from 166 participants after they completed four different tasks that varied by method of input (touch or keyboard and mouse) and type of task (selecting or typing). Principal component analysis found distinct factors associated with stress (i.e., demands) and strain (i.e., response). Repeated measures analyses of variance showed that participants could discriminate the different strain induced by the input methods and tasks. However, participants' ability to discriminate between the stressors associated with that strain was mixed. Further validation of the SEAT is necessary but these results indicate that the SEAT may be a viable method of assessing ergonomics risks presented by software design. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards easing the configuration and new team member accommodation for open source software based portals

NASA Astrophysics Data System (ADS)

Fu, L.; West, P.; Zednik, S.; Fox, P. A.

2013-12-01

For simple portals such as vocabulary based services, which contain small amounts of data and require only hyper-textual representation, it is often an overkill to adopt the whole software stack of database, middleware and front end, or to use a general Web development framework as the starting point of development. Directly combining open source software is a much more favorable approach. However, our experience with the Coastal and Marine Spatial Planning Vocabulary (CMSPV) service portal shows that there are still issues such as system configuration and accommodating a new team member that need to be handled carefully. In this contribution, we share our experience in the context of the CMSPV portal, and focus on the tools and mechanisms we've developed to ease the configuration job and the incorporation process of new project members. We discuss the configuration issues that arise when we don't have complete control over how the software in use is configured and need to follow existing configuration styles that may not be well documented, especially when multiple pieces of such software need to work together as a combined system. As for the CMSPV portal, it is built on two pieces of open source software that are still under rapid development: a Fuseki data server and Epimorphics Linked Data API (ELDA) front end. Both lack mature documentation and tutorials. We developed comparison and labeling tools to ease the problem of system configuration. Another problem that slowed down the project is that project members came and went during the development process, so new members needed to start with a partially configured system and incomplete documentation left by old members. We developed documentation/tutorial maintenance mechanisms based on our comparison and labeling tools to make it easier for the new members to be incorporated into the project. These tools and mechanisms also provided benefit to other projects that reused the software components from the CMSPV system.

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.

PubMed

Kartasalo, Kimmo; Pölönen, Risto-Pekka; Ojala, Marisa; Rasku, Jyrki; Lekkala, Jukka; Aalto-Setälä, Katriina; Kallio, Pasi

2015-10-26

Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation. We developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching. CytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

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

Conjunctive programming: An interactive approach to software system synthesis

NASA Technical Reports Server (NTRS)

Tausworthe, Robert C.

1992-01-01

This report introduces a technique of software documentation called conjunctive programming and discusses its role in the development and maintenance of software systems. The report also describes the conjoin tool, an adjunct to assist practitioners. Aimed at supporting software reuse while conforming with conventional development practices, conjunctive programming is defined as the extraction, integration, and embellishment of pertinent information obtained directly from an existing database of software artifacts, such as specifications, source code, configuration data, link-edit scripts, utility files, and other relevant information, into a product that achieves desired levels of detail, content, and production quality. Conjunctive programs typically include automatically generated tables of contents, indexes, cross references, bibliographic citations, tables, and figures (including graphics and illustrations). This report presents an example of conjunctive programming by documenting the use and implementation of the conjoin program.

Introducing a New Software for Geodetic Analysis

NASA Astrophysics Data System (ADS)

Hjelle, G. A.; Dähnn, M.; Fausk, I.; Kirkvik, A. S.; Mysen, E.

2016-12-01

At the Norwegian Mapping Authority, we are currently developing Where, a newsoftware for geodetic analysis. Where is built on our experiences with theGeosat software, and will be able to analyse and combine data from VLBI, SLR,GNSS and DORIS. The software is mainly written in Python which has proved veryfruitful. The code is quick to write and the architecture is easily extendableand maintainable. The Python community provides a rich eco-system of tools fordoing data-analysis, including effective data storage and powerfulvisualization. Python interfaces well with other languages so that we can easilyreuse existing, well-tested code like the SOFA and IERS libraries. This presentation will show some of the current capabilities of Where,including benchmarks against other software packages. In addition we will reporton some simple investigations we have done using the software, and outline ourplans for further progress.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.

PubMed

Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon; Hurwitz, Bonnie L; Sullivan, Matthew B

2017-01-01

Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as 'Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

PubMed Central

Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon; Hurwitz, Bonnie L; Sullivan, Matthew B

2017-01-01

Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature. PMID:27420028

Bringing the Unidata IDV to the Cloud

NASA Astrophysics Data System (ADS)

Fisher, W. I.; Oxelson Ganter, J.

2015-12-01

Maintaining software compatibility across new computing environments and the associated underlying hardware is a common problem for software engineers and scientific programmers. While traditional software engineering provides a suite of tools and methodologies which may mitigate this issue, they are typically ignored by developers lacking a background in software engineering. Causing further problems, these methodologies are best applied at the start of project; trying to apply them to an existing, mature project can require an immense effort. Visualization software is particularly vulnerable to this problem, given the inherent dependency on particular graphics hardware and software API's. As a result of these issues, there exists a large body of software which is simultaneously critical to the scientists who are dependent upon it, and yet increasingly difficult to maintain.The solution to this problem was partially provided with the advent of Cloud Computing; Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations, with little-to-no re-engineering required. When coupled with containerization technology such as Docker, we are able to easily bring the same visualization software to a desktop, a netbook, a smartphone, and the next generation of hardware, whatever it may be.Unidata has been able to harness Application Streaming to provide a tablet-compatible version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

A software system for the simulation of chest lesions

NASA Astrophysics Data System (ADS)

Ryan, John T.; McEntee, Mark; Barrett, Saoirse; Evanoff, Michael; Manning, David; Brennan, Patrick

2007-03-01

We report on the development of a novel software tool for the simulation of chest lesions. This software tool was developed for use in our study to attain optimal ambient lighting conditions for chest radiology. This study involved 61 consultant radiologists from the American Board of Radiology. Because of its success, we intend to use the same tool for future studies. The software has two main functions: the simulation of lesions and retrieval of information for ROC (Receiver Operating Characteristic) and JAFROC (Jack-Knife Free Response ROC) analysis. The simulation layer operates by randomly selecting an image from a bank of reportedly normal chest x-rays. A random location is then generated for each lesion, which is checked against a reference lung-map. If the location is within the lung fields, as derived from the lung-map, a lesion is superimposed. Lesions are also randomly selected from a bank of manually created chest lesion images. A blending algorithm determines which are the best intensity levels for the lesion to sit naturally within the chest x-ray. The same software was used to run a study for all 61 radiologists. A sequence of images is displayed in random order. Half of these images had simulated lesions, ranging from subtle to obvious, and half of the images were normal. The operator then selects locations where he/she thinks lesions exist and grades the lesion accordingly. We have found that this software was very effective in this study and intend to use the same principles for future studies.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.

PubMed

Brown, Jason L; Bennett, Joseph R; French, Connor M

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model's discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have 'universal' analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates-to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

Microscopic transport model animation visualisation on KML base

NASA Astrophysics Data System (ADS)

Yatskiv, I.; Savrasovs, M.

2012-10-01

By reading classical literature devoted to the simulation theory it could be found that one of the greatest possibilities of simulation is the ability to present processes inside the system by animation. This gives to the simulation model additional value during presentation of simulation results for the public and authorities who are not familiar enough with simulation. That is why most of universal and specialised simulation tools have the ability to construct 2D and 3D representation of the model. Usually the development of such representation could take much time and there must be put a lot forces into creating an adequate 3D representation of the model. For long years such well-known microscopic traffic flow simulation software tools as VISSIM, AIMSUN and PARAMICS have had a possibility to produce 2D and 3D animation. But creation of realistic 3D model of the place where traffic flows are simulated, even in these professional software tools it is a hard and time consuming action. The goal of this paper is to describe the concepts of use the existing on-line geographical information systems for visualisation of animation produced by simulation software. For demonstration purposes the following technologies and tools have been used: PTV VISION VISSIM, KML and Google Earth.

Building Energy Simulation Test for Existing Homes (BESTEST-EX) (Presentation)

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

Judkoff, R.; Neymark, J.; Polly, B.

2011-12-01

This presentation discusses the goals of NREL Analysis Accuracy R&D; BESTEST-EX goals; what BESTEST-EX is; how it works; 'Building Physics' cases; 'Building Physics' reference results; 'utility bill calibration' cases; limitations and potential future work. Goals of NREL Analysis Accuracy R&D are: (1) Provide industry with the tools and technical information needed to improve the accuracy and consistency of analysis methods; (2) Reduce the risks associated with purchasing, financing, and selling energy efficiency upgrades; and (3) Enhance software and input collection methods considering impacts on accuracy, cost, and time of energy assessments. BESTEST-EX Goals are: (1) Test software predictions of retrofitmore » energy savings in existing homes; (2) Ensure building physics calculations and utility bill calibration procedures perform up to a minimum standard; and (3) Quantify impact of uncertainties in input audit data and occupant behavior. BESTEST-EX is a repeatable procedure that tests how well audit software predictions compare to the current state of the art in building energy simulation. There is no direct truth standard. However, reference software have been subjected to validation testing, including comparisons with empirical data.« less

Thermography based prescreening software tool for veterinary clinics

NASA Astrophysics Data System (ADS)

Dahal, Rohini; Umbaugh, Scott E.; Mishra, Deependra; Lama, Norsang; Alvandipour, Mehrdad; Umbaugh, David; Marino, Dominic J.; Sackman, Joseph

2017-05-01

Under development is a clinical software tool which can be used in the veterinary clinics as a prescreening tool for these pathologies: anterior cruciate ligament (ACL) disease, bone cancer and feline hyperthyroidism. Currently, veterinary clinical practice uses several imaging techniques including radiology, computed tomography (CT), and magnetic resonance imaging (MRI). But, harmful radiation involved during imaging, expensive equipment setup, excessive time consumption and the need for a cooperative patient during imaging, are major drawbacks of these techniques. In veterinary procedures, it is very difficult for animals to remain still for the time periods necessary for standard imaging without resorting to sedation - which creates another set of complexities. Therefore, clinical application software integrated with a thermal imaging system and the algorithms with high sensitivity and specificity for these pathologies, can address the major drawbacks of the existing imaging techniques. A graphical user interface (GUI) has been created to allow ease of use for the clinical technician. The technician inputs an image, enters patient information, and selects the camera view associated with the image and the pathology to be diagnosed. The software will classify the image using an optimized classification algorithm that has been developed through thousands of experiments. Optimal image features are extracted and the feature vector is then used in conjunction with the stored image database for classification. Classification success rates as high as 88% for bone cancer, 75% for ACL and 90% for feline hyperthyroidism have been achieved. The software is currently undergoing preliminary clinical testing.

Visualising biological data: a semantic approach to tool and database integration

PubMed Central

Pettifer, Steve; Thorne, David; McDermott, Philip; Marsh, James; Villéger, Alice; Kell, Douglas B; Attwood, Teresa K

2009-01-01

Motivation In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. Methods To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. Results The toolkit, named Utopia, is freely available from . PMID:19534744

Visualising biological data: a semantic approach to tool and database integration.

PubMed

Pettifer, Steve; Thorne, David; McDermott, Philip; Marsh, James; Villéger, Alice; Kell, Douglas B; Attwood, Teresa K

2009-06-16

In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customized for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research. To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks. The toolkit, named Utopia, is freely available from http://utopia.cs.man.ac.uk/.

Full Life-Cycle Defect Management Assessment: Initial Inspection Data Collection Results and Research Questions for Further Study

NASA Technical Reports Server (NTRS)

Shull, Forrest; Feldmann, Raimund; Haingaertner, Ralf; Regardie, Myrna; Seaman, Carolyn

2007-01-01

It is often the case in software projects that when schedule and budget resources are limited, the Verification and Validation (V&V) activities suffer. Fewer V&V activities can be afforded and moreover, short-term challenges can result in V&V activities being scaled back or dropped altogether. As a result, too often the default solution is to save activities for improving software quality until too late in the life-cycle, relying on late-term code inspections followed by thorough testing activities to reduce defect counts to acceptable levels. As many project managers realize, however, this is a resource-intensive way of achieving the required quality for software. The Full Life-cycle Defect Management Assessment Initiative, funded by NASA s Office of Safety and Mission Assurance under the Software Assurance Research Program, aims to address these problems by: Improving the effectiveness of early life-cycle V&V activities to make their benefits more attractive to team leads. Specifically, we focus on software inspection, a proven method that can be applied to any software work product, long before executable code has been developed; Better communicating this effectiveness to software development teams, along with suggestions for parameters to improve in the future to increase effectiveness; Analyzing the impact of early life-cycle V&V on the effectiveness and cost required for late life-cycle V&V activities, such as testing, in order to make the tradeoffs more apparent. This white paper reports on an initial milestone in this work, the development of a preliminary model of inspection effectiveness across multiple NASA Centers. This model contributes toward reaching our project goals by: Allowing an examination of inspection parameters, across different types of projects and different work products, for an analysis of factors that impact defect detection effectiveness. Allowing a comparison of this NASA-specific model to existing recommendations in the literature regarding how to plan effective inspections. Forming a baseline model which can be extended to incorporate factors describing: the numbers and types of defects that are missed by inspections; how such defects flow downstream through software development phases; how effectively they can be caught by testing activities in the late stages of development. The model has been implemented in a prototype web-enabled decision-support tool which allows developers to enter their inspection data and receive feedback based on a comparison against the model. The tool also allows users to access reusable materials (such as checklists) from projects included in the baseline. Both the tool itself and the model underlying it will continue to be extended throughout the remainder of this initiative. As results of analyzing inspection effectiveness for defect containment are determined, they can be shared via the tool and also via updates to existing training courses on metrics and software inspections. Moreover, the tool will help satisfy key CMMI requirements for the NASA Centers, as it will enable NASA to take a global view across peer review results for various types of projects to identify systemic problems. This analysis can result in continuous improvements to the approach to verification.

Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

NASA Technical Reports Server (NTRS)

Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

2006-01-01

Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

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.

BGFit: management and automated fitting of biological growth curves.

PubMed

Veríssimo, André; Paixão, Laura; Neves, Ana Rute; Vinga, Susana

2013-09-25

Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easily organize experimental data and simultaneously extract relevant parameters in an efficient way is crucial. BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way. The data managing system allows to organize projects, experiments and measurements data and also to define teams with different editing and viewing permission. Several dynamic and algebraic models are already implemented, such as polynomial regression, Gompertz, Baranyi, Logistic and Live Cell Fraction models and the user can add easily new models thus expanding current ones. BGFit allows users to easily manage their data and models in an integrated way, even if they are not familiar with databases or existing computational tools for parameter estimation. BGFit is designed with a flexible architecture that focus on extensibility and leverages free software with existing tools and methods, allowing to compare and evaluate different data modeling techniques. The application is described in the context of bacterial and tumor cells growth data fitting, but it is also applicable to any type of two-dimensional data, e.g. physical chemistry and macroeconomic time series, being fully scalable to high number of projects, data and model complexity.

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Functional specifications for AI software tools for electric power applications. Final report

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

Faught, W.S.

1985-08-01

The principle barrier to the introduction of artificial intelligence (AI) technology to the electric power industry has not been a lack of interest or appropriate problems, for the industry abounds in both. Like most others, however, the electric power industry lacks the personnel - knowledge engineers - with the special combination of training and skills AI programming demands. Conversely, very few AI specialists are conversant with electric power industry problems and applications. The recent availability of sophisticated AI programming environments is doing much to alleviate this shortage. These products provide a set of powerful and usable software tools that enablemore » even non-AI scientists to rapidly develop AI applications. The purpose of this project was to develop functional specifications for programming tools that, when integrated with existing general-purpose knowledge engineering tools, would expedite the production of AI applications for the electric power industry. Twelve potential applications, representative of major problem domains within the nuclear power industry, were analyzed in order to identify those tools that would be of greatest value in application development. Eight tools were specified, including facilities for power plant modeling, data base inquiry, simulation and machine-machine interface.« less

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.

PsychoPy--Psychophysics software in Python.

PubMed

Peirce, Jonathan W

2007-05-15

The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits.

SmaggIce 2D Version 1.8: Software Toolkit Developed for Aerodynamic Simulation Over Iced Airfoils

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Vickerman, Mary B.

2005-01-01

SmaggIce 2D version 1.8 is a software toolkit developed at the NASA Glenn Research Center that consists of tools for modeling the geometry of and generating the grids for clean and iced airfoils. Plans call for the completed SmaggIce 2D version 2.0 to streamline the entire aerodynamic simulation process--the characterization and modeling of ice shapes, grid generation, and flow simulation--and to be closely coupled with the public-domain application flow solver, WIND. Grid generated using version 1.8, however, can be used by other flow solvers. SmaggIce 2D will help researchers and engineers study the effects of ice accretion on airfoil performance, which is difficult to do with existing software tools because of complex ice shapes. Using SmaggIce 2D, when fully developed, to simulate flow over an iced airfoil will help to reduce the cost of performing flight and wind-tunnel tests for certifying aircraft in natural and simulated icing conditions.

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data

PubMed Central

Vernick, Kenneth D.

2017-01-01

Metavisitor is a software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets. The package is composed of a set of modular bioinformatic tools and workflows that are implemented in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions. PMID:28045932

PsychoPy—Psychophysics software in Python

PubMed Central

Peirce, Jonathan W.

2007-01-01

The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits. PMID:17254636

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

PubMed Central

Kumar, Shailesh; Vo, Angie Duy; Qin, Fujun; Li, Hui

2016-01-01

RNA-Seq made possible the global identification of fusion transcripts, i.e. “chimeric RNAs”. Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users, and developers to have an unbiased assessment of the performance of existing fusion detection tools. Toward this goal, we compared the performance of 12 well-known fusion detection software packages. We evaluated the sensitivity, false discovery rate, computing time, and memory usage of these tools in four different datasets (positive, negative, mixed, and test). We conclude that some tools are better than others in terms of sensitivity, positive prediction value, time consumption and memory usage. We also observed small overlaps of the fusions detected by different tools in the real dataset (test dataset). This could be due to false discoveries by various tools, but could also be due to the reason that none of the tools are inclusive. We have found that the performance of the tools depends on the quality, read length, and number of reads of the RNA-Seq data. We recommend that users choose the proper tools for their purpose based on the properties of their RNA-Seq data. PMID:26862001

The COLA Collision Avoidance Method

NASA Astrophysics Data System (ADS)

Assmann, K.; Berger, J.; Grothkopp, S.

2009-03-01

In the following we present a collision avoidance method named COLA. The method has been designed to predict collisions for Earth orbiting spacecraft on any orbits, including orbit changes, with other space-born objects. The point in time of a collision and the collision probability are determined. To guarantee effective processing the COLA method uses a modular design and is composed of several components which are either developed within this work or deduced from existing algorithms: A filtering module, the close approach determination, the collision detection and the collision probability calculation. A software tool which implements the COLA method has been verified using various test cases built from sample missions. This software has been implemented in the C++ programming language and serves as a universal collision detection tool at LSE Space Engineering & Operations AG.

What Is An Expert System? ERIC Digest.

ERIC Educational Resources Information Center

Boss, Richard W.

This digest describes and defines the various components of an expert system, e.g., a computerized tool designed to enhance the quality and availability of knowledge required by decision makers. It is noted that expert systems differ from conventional applications software in the following areas: (1) the existence of the expert systems shell, or…

A Dynamic Social Feedback System to Support Learning and Social Interaction in Higher Education

ERIC Educational Resources Information Center

Thoms, Brian

2011-01-01

In this research, we examine the design, construction, and implementation of a dynamic, easy to use, feedback mechanism for social software. The tool was integrated into an existing university's online learning community (OLC). In line with constructivist learning models and practical information systems (IS) design, the feedback system provides…

Generalized Data Management Systems--Some Perspectives.

ERIC Educational Resources Information Center

Minker, Jack

A Generalized Data Management System (GDMS) is a software environment provided as a tool for analysts, administrators, and programmers who are responsible for the maintenance, query and analysis of a data base to permit the manipulation of newly defined files and data with the existing programs and system. Because the GDMS technology is believed…

The Learning and Productivity Benefits to Student Programmers from Real-World Development Environments

ERIC Educational Resources Information Center

Debuse, Justin C. W.; Lawley, Meredith

2012-01-01

Existing research and practice in software development environments shows no clear consensus on the most appropriate development tools to use; these may range from simple text editors through teaching-oriented examples to full commercial integrated development environments (IDEs). This study addresses this gap by examining student perceptions of…

An Advanced, Interactive, High-Performance Liquid Chromatography Simulator and Instructor Resources

ERIC Educational Resources Information Center

Boswell, Paul G.; Stoll, Dwight R.; Carr, Peter W.; Nagel, Megan L.; Vitha, Mark F.; Mabbott, Gary A.

2013-01-01

High-performance liquid chromatography (HPLC) simulation software has long been recognized as an effective educational tool, yet many of the existing HPLC simulators are either too expensive, outdated, or lack many important features necessary to make them widely useful for educational purposes. Here, a free, open-source HPLC simulator is…

Interactive visual analysis promotes exploration of long-term ecological data

Treesearch

T.N. Pham; J.A. Jones; R. Metoyer; F.J. Swanson; R.J. Pabst

2013-01-01

Long-term ecological data are crucial in helping ecologists understand ecosystem function and environmental change. Nevertheless, these kinds of data sets are difficult to analyze because they are usually large, multivariate, and spatiotemporal. Although existing analysis tools such as statistical methods and spreadsheet software permit rigorous tests of pre-conceived...

Music Teacher Perceptions of a Model of Technology Training and Support in Virginia

ERIC Educational Resources Information Center

Welch, Lee Arthur

2013-01-01

A plethora of technology resources currently exists for the music classroom of the twenty-first century, including digital audio and video, music software, electronic instruments, Web 2.0 tools and more. Research shows a strong need for professional development for teachers to properly implement and integrate instructional technology resources…

A Multi-Language System for Knowledge Extraction in E-Learning Videos

ERIC Educational Resources Information Center

Sood, Aparesh; Mittal, Ankush; Sarthi, Divya

2006-01-01

The existing multimedia software in E-Learning does not provide par excellence multimedia data service to the common user, hence E-Learning services are still short of intelligence and sophisticated end user tools for visualization and retrieval. An efficient approach to achieve the tasks such as, regional language narration, regional language…

Synchronous Chat and Electronic Ink for Distance Support in Mathematics

ERIC Educational Resources Information Center

Loch, Birgit; McDonald, Christine

2007-01-01

For online mathematics instructors, synchronous communication can be a challenge due to the need for specialized symbols, graphics, or notations to explain key concepts. While software tools exist to support such communication, they can often be cumbersome and time-consuming for users to adopt in online exchanges. As one way of addressing this…

Mining Marketing Data

NASA Technical Reports Server (NTRS)

2002-01-01

MarketMiner(R) Products, a line of automated marketing analysis tools manufactured by MarketMiner, Inc., can benefit organizations that perform significant amounts of direct marketing. MarketMiner received a Small Business Innovation Research (SBIR) contract from NASA's Johnson Space Center to develop the software as a data modeling tool for space mission applications. The technology was then built into the company current products to provide decision support for business and marketing applications. With the tool, users gain valuable information about customers and prospects from existing data in order to increase sales and profitability. MarketMiner(R) is a registered trademark of MarketMiner, Inc.

Teaching NMR spectra analysis with nmr.cheminfo.org.

PubMed

Patiny, Luc; Bolaños, Alejandro; Castillo, Andrés M; Bernal, Andrés; Wist, Julien

2018-06-01

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

A parallel and sensitive software tool for methylation analysis on multicore platforms.

PubMed

Tárraga, Joaquín; Pérez, Mariano; Orduña, Juan M; Duato, José; Medina, Ignacio; Dopazo, Joaquín

2015-10-01

DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads. Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password 'anonymous'). juan.orduna@uv.es or jdopazo@cipf.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

S-Cube: Enabling the Next Generation of Software Services

NASA Astrophysics Data System (ADS)

Metzger, Andreas; Pohl, Klaus

The Service Oriented Architecture (SOA) paradigm is increasingly adopted by industry for building distributed software systems. However, when designing, developing and operating innovative software services and servicebased systems, several challenges exist. Those challenges include how to manage the complexity of those systems, how to establish, monitor and enforce Quality of Service (QoS) and Service Level Agreements (SLAs), as well as how to build those systems such that they can proactively adapt to dynamically changing requirements and context conditions. Developing foundational solutions for those challenges requires joint efforts of different research communities such as Business Process Management, Grid Computing, Service Oriented Computing and Software Engineering. This paper provides an overview of S-Cube, the European Network of Excellence on Software Services and Systems. S-Cube brings together researchers from leading research institutions across Europe, who join their competences to develop foundations, theories as well as methods and tools for future service-based systems.

Real-time animation software for customized training to use motor prosthetic systems.

PubMed

Davoodi, Rahman; Loeb, Gerald E

2012-03-01

Research on control of human movement and development of tools for restoration and rehabilitation of movement after spinal cord injury and amputation can benefit greatly from software tools for creating precisely timed animation sequences of human movement. Despite their ability to create sophisticated animation and high quality rendering, existing animation software are not adapted for application to neural prostheses and rehabilitation of human movement. We have developed a software tool known as MSMS (MusculoSkeletal Modeling Software) that can be used to develop models of human or prosthetic limbs and the objects with which they interact and to animate their movement using motion data from a variety of offline and online sources. The motion data can be read from a motion file containing synthesized motion data or recordings from a motion capture system. Alternatively, motion data can be streamed online from a real-time motion capture system, a physics-based simulation program, or any program that can produce real-time motion data. Further, animation sequences of daily life activities can be constructed using the intuitive user interface of Microsoft's PowerPoint software. The latter allows expert and nonexpert users alike to assemble primitive movements into a complex motion sequence with precise timing by simply arranging the order of the slides and editing their properties in PowerPoint. The resulting motion sequence can be played back in an open-loop manner for demonstration and training or in closed-loop virtual reality environments where the timing and speed of animation depends on user inputs. These versatile animation utilities can be used in any application that requires precisely timed animations but they are particularly suited for research and rehabilitation of movement disorders. MSMS's modeling and animation tools are routinely used in a number of research laboratories around the country to study the control of movement and to develop and test neural prostheses for patients with paralysis or amputations.

The integration of a LANDSAT analysis capability with a geographic information system

NASA Technical Reports Server (NTRS)

Nordstrand, E. A.

1981-01-01

The integration of LANDSAT data was achieved through the development of a flexible, compatible analysis tool and using an existing data base to select the usable data from a LANDSAT analysis. The software package allows manipulation of grid cell data plus the flexibility to allow the user to include FORTRAN statements for special functions. Using this combination of capabilities the user can classify a LANDSAT image and then selectivity merge the results with other data that may exist for the study area.

Omics Metadata Management Software (OMMS).

PubMed

Perez-Arriaga, Martha O; Wilson, Susan; Williams, Kelly P; Schoeniger, Joseph; Waymire, Russel L; Powell, Amy Jo

2015-01-01

Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for webbased deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed. The OMMS can be obtained at http://omms.sandia.gov. The OMMS can be obtained at http://omms.sandia.gov.

Omics Metadata Management Software (OMMS)

PubMed Central

Perez-Arriaga, Martha O; Wilson, Susan; Williams, Kelly P; Schoeniger, Joseph; Waymire, Russel L; Powell, Amy Jo

2015-01-01

Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for webbased deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed. The OMMS can be obtained at http://omms.sandia.gov. Availability The OMMS can be obtained at http://omms.sandia.gov PMID:26124554

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 formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

PubMed Central

2011-01-01

Background The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim. PMID:21586134

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

PubMed

Luna, Augustin; Karac, Evrim I; Sunshine, Margot; Chang, Lucas; Nussinov, Ruth; Aladjem, Mirit I; Kohn, Kurt W

2011-05-17

The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

PubMed Central

Bennett, Joseph R.; French, Connor M.

2017-01-01

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user. PMID:29230356

The ALMA common software: dispatch from the trenches

NASA Astrophysics Data System (ADS)

Schwarz, J.; Sommer, H.; Jeram, B.; Sekoranja, M.; Chiozzi, G.; Grimstrup, A.; Caproni, A.; Paredes, C.; Allaert, E.; Harrington, S.; Turolla, S.; Cirami, R.

2008-07-01

The ALMA Common Software (ACS) provides both an application framework and CORBA-based middleware for the distributed software system of the Atacama Large Millimeter Array. Building upon open-source tools such as the JacORB, TAO and OmniORB ORBs, ACS supports the development of component-based software in any of three languages: Java, C++ and Python. Now in its seventh major release, ACS has matured, both in its feature set as well as in its reliability and performance. However, it is only recently that the ALMA observatory's hardware and application software has reached a level at which it can exploit and challenge the infrastructure that ACS provides. In particular, the availability of an Antenna Test Facility(ATF) at the site of the Very Large Array in New Mexico has enabled us to exercise and test the still evolving end-to-end ALMA software under realistic conditions. The major focus of ACS, consequently, has shifted from the development of new features to consideration of how best to use those that already exist. Configuration details which could be neglected for the purpose of running unit tests or skeletal end-to-end simulations have turned out to be sensitive levers for achieving satisfactory performance in a real-world environment. Surprising behavior in some open-source tools has required us to choose between patching code that we did not write or addressing its deficiencies by implementing workarounds in our own software. We will discuss these and other aspects of our recent experience at the ATF and in simulation.

The center for causal discovery of biomedical knowledge from big data.

PubMed

Cooper, Gregory F; Bahar, Ivet; Becich, Michael J; Benos, Panayiotis V; Berg, Jeremy; Espino, Jeremy U; Glymour, Clark; Jacobson, Rebecca Crowley; Kienholz, Michelle; Lee, Adrian V; Lu, Xinghua; Scheines, Richard

2015-11-01

The Big Data to Knowledge (BD2K) Center for Causal Discovery is developing and disseminating an integrated set of open source tools that support causal modeling and discovery of biomedical knowledge from large and complex biomedical datasets. The Center integrates teams of biomedical and data scientists focused on the refinement of existing and the development of new constraint-based and Bayesian algorithms based on causal Bayesian networks, the optimization of software for efficient operation in a supercomputing environment, and the testing of algorithms and software developed using real data from 3 representative driving biomedical projects: cancer driver mutations, lung disease, and the functional connectome of the human brain. Associated training activities provide both biomedical and data scientists with the knowledge and skills needed to apply and extend these tools. Collaborative activities with the BD2K Consortium further advance causal discovery tools and integrate tools and resources developed by other centers. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.All rights reserved. For Permissions, please email: journals.permissions@oup.com.

ExAtlas: An interactive online tool for meta-analysis of gene expression data.

PubMed

Sharov, Alexei A; Schlessinger, David; Ko, Minoru S H

2015-12-01

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data sets (e.g. GNF/BioGPS, Gene Ontology, KEGG, GAD phenotypes, BrainScan, ENCODE ChIP-seq, and protein-protein interaction) are pre-loaded and can be used for functional annotations.

OpenComet: An automated tool for comet assay image analysis

PubMed Central

Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

OpenComet: an automated tool for comet assay image analysis.

PubMed

Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

Systems analysis of a planetary entry (SAPE), descent, and landing (EDL) is a multidisciplinary activity in nature. SAPE improves the performance of the systems analysis team by automating and streamlining the process, and this improvement can reduce the errors that stem from manual data transfer among discipline experts. SAPE is a multidisciplinary tool for systems analysis of planetary EDL for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. It performs EDL systems analysis for any planet, operates cross-platform (i.e., Windows, Mac, and Linux operating systems), uses existing software components and open-source software to avoid software licensing issues, performs low-fidelity systems analysis in one hour on a computer that is comparable to an average laptop, and keeps discipline experts in the analysis loop. SAPE uses Python, a platform-independent, open-source language, for integration and for the user interface. Development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE currently includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and interface for structural sizing.

Software Testing and Verification in Climate Model Development

NASA Technical Reports Server (NTRS)

Clune, Thomas L.; Rood, RIchard B.

2011-01-01

Over the past 30 years most climate models have grown from relatively simple representations of a few atmospheric processes to a complex multi-disciplinary system. Computer infrastructure over that period has gone from punch card mainframes to modem parallel clusters. Model implementations have become complex, brittle, and increasingly difficult to extend and maintain. Existing verification processes for model implementations rely almost exclusively upon some combination of detailed analysis of output from full climate simulations and system-level regression tests. In additional to being quite costly in terms of developer time and computing resources, these testing methodologies are limited in terms of the types of defects that can be detected, isolated and diagnosed. Mitigating these weaknesses of coarse-grained testing with finer-grained "unit" tests has been perceived as cumbersome and counter-productive. In the commercial software sector, recent advances in tools and methodology have led to a renaissance for systematic fine-grained testing. We discuss the availability of analogous tools for scientific software and examine benefits that similar testing methodologies could bring to climate modeling software. We describe the unique challenges faced when testing complex numerical algorithms and suggest techniques to minimize and/or eliminate the difficulties.

MIA - A free and open source software for gray scale medical image analysis

PubMed Central

2013-01-01

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed. PMID:24119305

MIA - A free and open source software for gray scale medical image analysis.

PubMed

Wollny, Gert; Kellman, Peter; Ledesma-Carbayo, María-Jesus; Skinner, Matthew M; Hublin, Jean-Jaques; Hierl, Thomas

2013-10-11

Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large.Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers.One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development.Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don't provide an clear approach when one wants to shape a new command line tool from a prototype shell script. The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Software Tools for Development on the Peregrine System | High-Performance

Science.gov Websites

Computing | NREL Software Tools for Development on the Peregrine System Software Tools for and manage software at the source code level. Cross-Platform Make and SCons The "Cross-Platform Make" (CMake) package is from Kitware, and SCons is a modern software build tool based on Python

a Standardized Approach to Topographic Data Processing and Workflow Management

NASA Astrophysics Data System (ADS)

Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

2013-12-01

An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and sharing effective topographic processing workflows.

Scientific Platform as a Service - Tools and solutions for efficient access to and analysis of oceanographic data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hansen, Morten W.; Korosov, Anton

2017-04-01

Existing infrastructure international and Norwegian projects, e.g., NorDataNet, NMDC and NORMAP, provide open data access through the OPeNDAP protocol following the conventions for CF (Climate and Forecast) metadata, designed to promote the processing and sharing of files created with the NetCDF application programming interface (API). This approach is now also being implemented in the Norwegian Sentinel Data Hub (satellittdata.no) to provide satellite EO data to the user community. Simultaneously with providing simplified and unified data access, these projects also seek to use and establish common standards for use and discovery metadata. This then allows development of standardized tools for data search and (subset) streaming over the internet to perform actual scientific analysis. A combinnation of software tools, which we call a Scientific Platform as a Service (SPaaS), will take advantage of these opportunities to harmonize and streamline the search, retrieval and analysis of integrated satellite and auxiliary observations of the oceans in a seamless system. The SPaaS is a cloud solution for integration of analysis tools with scientific datasets via an API. The core part of the SPaaS is a distributed metadata catalog to store granular metadata describing the structure, location and content of available satellite, model, and in situ datasets. The analysis tools include software for visualization (also online), interactive in-depth analysis, and server-based processing chains. The API conveys search requests between system nodes (i.e., interactive and server tools) and provides easy access to the metadata catalog, data repositories, and the tools. The SPaaS components are integrated in virtual machines, of which provisioning and deployment are automatized using existing state-of-the-art open-source tools (e.g., Vagrant, Ansible, Docker). The open-source code for scientific tools and virtual machine configurations is under version control at https://github.com/nansencenter/, and is coupled to an online continuous integration system (e.g., Travis CI).

Extracting patterns of database and software usage from the bioinformatics literature

PubMed Central

Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L.; Stevens, Robert

2014-01-01

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/ Contact: robert.stevens@manchester.ac.uk PMID:25161253

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

PubMed

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

2013-06-01

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

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

NASA Technical Reports Server (NTRS)

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

An Assessment of IMPAC - Integrated Methodology for Propulsion and Airframe Controls

NASA Technical Reports Server (NTRS)

Walker, G. P.; Wagner, E. A.; Bodden, D. S.

1996-01-01

This report documents the work done under a NASA sponsored contract to transition to industry technologies developed under the NASA Lewis Research Center IMPAC (Integrated Methodology for Propulsion and Airframe Control) program. The critical steps in IMPAC are exercised on an example integrated flight/propulsion control design for linear airframe/engine models of a conceptual STOVL (Short Take-Off and Vertical Landing) aircraft, and MATRIXX (TM) executive files to implement each step are developed. The results from the example study are analyzed and lessons learned are listed along with recommendations that will improve the application of each design step. The end product of this research is a set of software requirements for developing a user-friendly control design tool which will automate the steps in the IMPAC methodology. Prototypes for a graphical user interface (GUI) are sketched to specify how the tool will interact with the user, and it is recommended to build the tool around existing computer aided control design software packages.

Automatic Generation of Overlays and Offset Values Based on Visiting Vehicle Telemetry and RWS Visuals

NASA Technical Reports Server (NTRS)

Dunne, Matthew J.

2011-01-01

The development of computer software as a tool to generate visual displays has led to an overall expansion of automated computer generated images in the aerospace industry. These visual overlays are generated by combining raw data with pre-existing data on the object or objects being analyzed on the screen. The National Aeronautics and Space Administration (NASA) uses this computer software to generate on-screen overlays when a Visiting Vehicle (VV) is berthing with the International Space Station (ISS). In order for Mission Control Center personnel to be a contributing factor in the VV berthing process, computer software similar to that on the ISS must be readily available on the ground to be used for analysis. In addition, this software must perform engineering calculations and save data for further analysis.

Using a Modular Construction Kit for the Realization of an Interactive Computer Graphics Course.

ERIC Educational Resources Information Center

Klein, Reinhard; Hanisch, Frank

Recently, platform independent software components, like JavaBeans, have appeared that allow writing reusable components and composing them in a visual builder tool into new applications. This paper describes the use of such models to transform an existing course into a modular construction kit consisting of components of teaching text and program…

Marrying Two Existing Software Packages into an Efficient Online Tutoring Tool

ERIC Educational Resources Information Center

Byrne, Timothy

2007-01-01

Many teachers today use Learning Management Systems (LMS), several of which are open-source. Specific examples are Claroline and Moodle. However, they are not specifically designed for language learning, and hence not entirely suitable. In this article, I will compare two uses of the Claroline LMS available at Louvain-la-Neuve within the framework…

Three Applications of Automated Test Assembly within a User-Friendly Modeling Environment

ERIC Educational Resources Information Center

Cor, Ken; Alves, Cecilia; Gierl, Mark

2009-01-01

While linear programming is a common tool in business and industry, there have not been many applications in educational assessment and only a handful of individuals have been actively involved in conducting psychometric research in this area. Perhaps this is due, at least in part, to the complexity of existing software packages. This article…

EPCAL: ETS Platform for Collaborative Assessment and Learning. Research Report. ETS RR-17-49

ERIC Educational Resources Information Center

Hao, Jiangang; Liu, Lei; von Davier, Alina A.; Lederer, Nathan; Zapata-Rivera, Diego; Jaki, Peter; Bakkenson, Michael

2017-01-01

Most existing software tools for online collaboration are designed to support the collaboration itself instead of the study of collaboration with a systematic team and task management system. In this report, we identify six important features for a platform to facilitate the study of online collaboration. We then introduce the Educational Testing…

Myokit: A simple interface to cardiac cellular electrophysiology.

PubMed

Clerx, Michael; Collins, Pieter; de Lange, Enno; Volders, Paul G A

2016-01-01

Myokit is a new powerful and versatile software tool for modeling and simulation of cardiac cellular electrophysiology. Myokit consists of an easy-to-read modeling language, a graphical user interface, single and multi-cell simulation engines and a library of advanced analysis tools accessible through a Python interface. Models can be loaded from Myokit's native file format or imported from CellML. Model export is provided to C, MATLAB, CellML, CUDA and OpenCL. Patch-clamp data can be imported and used to estimate model parameters. In this paper, we review existing tools to simulate the cardiac cellular action potential to find that current tools do not cater specifically to model development and that there is a gap between easy-to-use but limited software and powerful tools that require strong programming skills from their users. We then describe Myokit's capabilities, focusing on its model description language, simulation engines and import/export facilities in detail. Using three examples, we show how Myokit can be used for clinically relevant investigations, multi-model testing and parameter estimation in Markov models, all with minimal programming effort from the user. This way, Myokit bridges a gap between performance, versatility and user-friendliness. Copyright © 2015 Elsevier Ltd. All rights reserved.

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

PubMed

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

Water Quality Analysis Tool (WQAT) | Science Inventory | US ...

EPA Pesticide Factsheets

The purpose of the Water Quality Analysis Tool (WQAT) software is to provide a means for analyzing and producing useful remotely sensed data products for an entire estuary, a particular point or area of interest (AOI or POI) in estuaries, or water bodies of interest where pre-processed and geographically gridded remotely sensed images are available. A graphical user interface (GUI), was created to enable the user to select and display imagery from a variety of remote sensing data sources. The user can select a date (or date range) and location to extract pixels from the remotely sensed imagery. The GUI is used to obtain all available pixel values (i.e. pixel from all available bands of all available satellites) for a given location on a given date and time. The resultant data set can be analyzed or saved to a file for future use. The WQAT software provides users with a way to establish algorithms between remote sensing reflectance (Rrs) and any available in situ parameters, as well as statistical and regression analysis. The combined data sets can be used to improve water quality research and studies. Satellites provide spatially synoptic data at high frequency (daily to weekly). These characteristics are desirable for supplementing existing water quality observations and for providing information for large aquatic ecosystems that are historically under-sampled by field programs. Thus, the Water Quality Assessment Tool (WQAT) software tool was developed to suppo

Sighten Final Technical Report DEEE0006690 Deploying an integrated and comprehensive solar financing software platform

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

O'Leary, Conlan

Over the project, Sighten built a comprehensive software-as-a-service (Saas) platform to automate and streamline the residential solar financing workflow. Before the project period, significant time and money was spent by companies on front-end tools related to system design and proposal creation, but comparatively few resources were available to support the many back-end calculations and data management processes that underpin third party financing. Without a tool like Sighten, the solar financing processes involved passing information from the homeowner prospect into separate tools for system design, financing, and then later to reporting tools including Microsoft Excel, CRM software, in-house software, outside software,more » and offline, manual processes. Passing data between tools and attempting to connect disparate systems results in inefficiency and inaccuracy for the industry. Sighten was built to consolidate all financial and solar-related calculations in a single software platform. It significantly improves upon the accuracy of these calculations and exposes sophisticated new analysis tools resulting in a rigorous, efficient and cost-effective toolset for scaling residential solar. Widely deploying a platform like Sighten’s significantly and immediately impacts the residential solar space in several important ways: 1) standardizing and improving the quality of all quantitative calculations involved in the residential financing process, most notably project finance, system production and reporting calculations; 2) representing a true step change in terms of reporting and analysis capabilities by maintaining more accurate data and exposing sophisticated tools around simulation, tranching, and financial reporting, among others, to all stakeholders in the space; 3) allowing a broader group of developers/installers/finance companies to access the capital markets by providing an out-of-the-box toolset that handles the execution of running investor capital through a rooftop solar financing program. Standardizing and improving all calculations, improving data quality, and exposing new analysis tools previously unavailable affects investment in the residential space in several important ways: 1) lowering the cost of capital for existing capital providers by mitigating uncertainty and de-risking the solar asset class; 2) attracting new, lower cost investors to the solar asset class as reporting and data quality resemble standards of more mature asset classes; 3) increasing the prevalence of liquidity options for investors through back leverage, securitization, or secondary sale by providing the tools necessary for lenders, ratings agencies, etc. to properly understand a portfolio of residential solar assets. During the project period, Sighten successfully built and scaled a commercially ready tool for the residential solar market. The software solution built by Sighten has been deployed with key target customer segments identified in the award deliverables: solar installers, solar developers/channel managers, and solar financiers, including lenders. Each of these segments greatly benefits from the availability of the Sighten toolset.« less

Extension of an Object-Oriented Optimization Tool: User's Reference Manual

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Truong, Samson S.

2015-01-01

The National Aeronautics and Space Administration Armstrong Flight Research Center has developed a cost-effective and flexible object-oriented optimization (O (sup 3)) tool that leverages existing tools and practices and allows easy integration and adoption of new state-of-the-art software. This object-oriented framework can integrate the analysis codes for multiple disciplines, as opposed to relying on one code to perform analysis for all disciplines. Optimization can thus take place within each discipline module, or in a loop between the O (sup 3) tool and the discipline modules, or both. Six different sample mathematical problems are presented to demonstrate the performance of the O (sup 3) tool. Instructions for preparing input data for the O (sup 3) tool are detailed in this user's manual.

A pluggable framework for parallel pairwise sequence search.

PubMed

Archuleta, Jeremy; Feng, Wu-chun; Tilevich, Eli

2007-01-01

The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.

LHCb migration from Subversion to Git

NASA Astrophysics Data System (ADS)

Clemencic, M.; Couturier, B.; Closier, J.; Cattaneo, M.

2017-10-01

Due to user demand and to support new development workflows based on code review and multiple development streams, LHCb decided to port the source code management from Subversion to Git, using the CERN GitLab hosting service. Although tools exist for this kind of migration, LHCb specificities and development models required careful planning of the migration, development of migration tools, changes to the development model, and redefinition of the release procedures. Moreover we had to support a hybrid situation with some software projects hosted in Git and others still in Subversion, or even branches of one projects hosted in different systems. We present the way we addressed the special LHCb requirements, the technical details of migrating large non standard Subversion repositories, and how we managed to smoothly migrate the software projects following the schedule of each project manager.

Microscopy image segmentation tool: Robust image data analysis

NASA Astrophysics Data System (ADS)

Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

2014-03-01

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

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

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Beckman, Carol S.; Benzinger, Leonora; Beshers, George; Hammerslag, David; Kimball, John; Kirslis, Peter A.; Render, Hal; Richards, Paul; Terwilliger, Robert

1985-01-01

The SAGA system is a software environment that is designed to support most of the software development activities that occur in a software lifecycle. The system can be configured to support specific software development applications using given programming languages, tools, and methodologies. Meta-tools are provided to ease configuration. The SAGA system consists of a small number of software components that are adapted by the meta-tools into specific tools for use in the software development application. The modules are design so that the meta-tools can construct an environment which is both integrated and flexible. The SAGA project is documented in several papers which are presented.

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

High-Performance Computing | NREL Debugging and Performance Analysis Software Tools for Peregrine System Debugging and Performance Analysis Software Tools for Peregrine System Learn about debugging and performance analysis software tools available to use with the Peregrine system. Allinea

Computer Aided Instruction (CAI) for the Shipboard Nontactical ADP Program (SNAP). Interim report

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

Duncan, L.D.; Hammons, C.E.; Hume, R.

Oak Ridge National Laboratory is developing a prototype computer aided instruction package for the Navy Management Systems Support Office. This report discusses the background of the project and the progress to date including a description of the software design, problems encountered, solutions found, and recommendations. The objective of this project is to provide a prototype that will enhance training and can be used as a shipboard refresher and retraining tool. The prototype system will be installed onboard ships where Navy personnel will have ready access to the training. The subsequent testing and evaluation of the prototype could provide the basismore » for a Navy-wide effort to implement computer aided instruction. The work to date has followed a rigorous structured analysis methodology based on the Yourdon/DeMarco techniques. A set of data flow diagrams and a data dictionary are included in the appendices. The problems encountered revolve around requirements to use existing hardware, software, and programmer capabilities for development, implementation, and maintenance of the instructional software. Solutions have been developed which will allow the software to exist in the given environment and still provide advanced features not available in commercial courses.« less

Software Tools to Support the Assessment of System Health

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

2013-01-01

This presentation provides an overview of three software tools that were developed by the NASA Glenn Research Center to support the assessment of system health: the Propulsion Diagnostic Method Evaluation Strategy (ProDIMES), the Systematic Sensor Selection Strategy (S4), and the Extended Testability Analysis (ETA) tool. Originally developed to support specific NASA projects in aeronautics and space, these software tools are currently available to U.S. citizens through the NASA Glenn Software Catalog. The ProDiMES software tool was developed to support a uniform comparison of propulsion gas path diagnostic methods. Methods published in the open literature are typically applied to dissimilar platforms with different levels of complexity. They often address different diagnostic problems and use inconsistent metrics for evaluating performance. As a result, it is difficult to perform a one ]to ]one comparison of the various diagnostic methods. ProDIMES solves this problem by serving as a theme problem to aid in propulsion gas path diagnostic technology development and evaluation. The overall goal is to provide a tool that will serve as an industry standard, and will truly facilitate the development and evaluation of significant Engine Health Management (EHM) capabilities. ProDiMES has been developed under a collaborative project of The Technical Cooperation Program (TTCP) based on feedback provided by individuals within the aircraft engine health management community. The S4 software tool provides a framework that supports the optimal selection of sensors for health management assessments. S4 is structured to accommodate user ]defined applications, diagnostic systems, search techniques, and system requirements/constraints. One or more sensor suites that maximize this performance while meeting other user ]defined system requirements that are presumed to exist. S4 provides a systematic approach for evaluating combinations of sensors to determine the set or sets of sensors that optimally meet the performance goals and the constraints. It identifies optimal sensor suite solutions by utilizing a merit (i.e., cost) function with one of several available optimization approaches. As part of its analysis, S4 can expose fault conditions that are difficult to diagnose due to an incomplete diagnostic philosophy and/or a lack of sensors. S4 was originally developed and applied to liquid rocket engines. It was subsequently used to study the optimized selection of sensors for a simulation ]based aircraft engine diagnostic system. The ETA Tool is a software ]based analysis tool that augments the testability analysis and reporting capabilities of a commercial ]off ]the ]shelf (COTS) package. An initial diagnostic assessment is performed by the COTS software using a user ]developed, qualitative, directed ]graph model of the system being analyzed. The ETA Tool accesses system design information captured within the model and the associated testability analysis output to create a series of six reports for various system engineering needs. These reports are highlighted in the presentation. The ETA Tool was developed by NASA to support the verification of fault management requirements early in the Launch Vehicle process. Due to their early development during the design process, the TEAMS ]based diagnostic model and the ETA Tool were able to positively influence the system design by highlighting gaps in failure detection, fault isolation, and failure recovery.

Clinical code set engineering for reusing EHR data for research: A review.

PubMed

Williams, Richard; Kontopantelis, Evangelos; Buchan, Iain; Peek, Niels

2017-06-01

The construction of reliable, reusable clinical code sets is essential when re-using Electronic Health Record (EHR) data for research. Yet code set definitions are rarely transparent and their sharing is almost non-existent. There is a lack of methodological standards for the management (construction, sharing, revision and reuse) of clinical code sets which needs to be addressed to ensure the reliability and credibility of studies which use code sets. To review methodological literature on the management of sets of clinical codes used in research on clinical databases and to provide a list of best practice recommendations for future studies and software tools. We performed an exhaustive search for methodological papers about clinical code set engineering for re-using EHR data in research. This was supplemented with papers identified by snowball sampling. In addition, a list of e-phenotyping systems was constructed by merging references from several systematic reviews on this topic, and the processes adopted by those systems for code set management was reviewed. Thirty methodological papers were reviewed. Common approaches included: creating an initial list of synonyms for the condition of interest (n=20); making use of the hierarchical nature of coding terminologies during searching (n=23); reviewing sets with clinician input (n=20); and reusing and updating an existing code set (n=20). Several open source software tools (n=3) were discovered. There is a need for software tools that enable users to easily and quickly create, revise, extend, review and share code sets and we provide a list of recommendations for their design and implementation. Research re-using EHR data could be improved through the further development, more widespread use and routine reporting of the methods by which clinical codes were selected. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Development of a comprehensive software engineering environment

NASA Technical Reports Server (NTRS)

Hartrum, Thomas C.; Lamont, Gary B.

1987-01-01

The generation of a set of tools for software lifecycle is a recurring theme in the software engineering literature. The development of such tools and their integration into a software development environment is a difficult task because of the magnitude (number of variables) and the complexity (combinatorics) of the software lifecycle process. An initial development of a global approach was initiated in 1982 as the Software Development Workbench (SDW). Continuing efforts focus on tool development, tool integration, human interfacing, data dictionaries, and testing algorithms. Current efforts are emphasizing natural language interfaces, expert system software development associates and distributed environments with Ada as the target language. The current implementation of the SDW is on a VAX-11/780. Other software development tools are being networked through engineering workstations.

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

A Standalone Vision Impairments Simulator for Java Swing Applications

NASA Astrophysics Data System (ADS)

Oikonomou, Theofanis; Votis, Konstantinos; Korn, Peter; Tzovaras, Dimitrios; Likothanasis, Spriridon

A lot of work has been done lately in an attempt to assess accessibility. For the case of web rich-client applications several tools exist that simulate how a vision impaired or colour-blind person would perceive this content. In this work we propose a simulation tool for non-web JavaTM Swing applications. Developers and designers face a real challenge when creating software that has to cope with a lot of interaction situations, as well as specific directives for ensuring an accessible interaction. The proposed standalone tool will assist them to explore user-centered design and important accessibility issues for their JavaTM Swing implementations.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

PubMed Central

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community. PMID:26913191

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

PubMed

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering

PubMed Central

Sun, Peng; Speicher, Nora K.; Röttger, Richard; Guo, Jiong; Baumbach, Jan

2014-01-01

Abstract The explosion of the biological data has dramatically reformed today's biological research. The need to integrate and analyze high-dimensional biological data on a large scale is driving the development of novel bioinformatics approaches. Biclustering, also known as ‘simultaneous clustering’ or ‘co-clustering’, has been successfully utilized to discover local patterns in gene expression data and similar biomedical data types. Here, we contribute a new heuristic: ‘Bi-Force’. It is based on the weighted bicluster editing model, to perform biclustering on arbitrary sets of biological entities, given any kind of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A comparative analysis of biclustering algorithms for gene expressiondata. Brief. Bioinform., 14:279–292.) and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, BiMax, Spectral, xMOTIFs and ISA. To this end, a suite of synthetic datasets as well as nine large gene expression datasets from Gene Expression Omnibus were analyzed. All resulting biclusters were subsequently investigated by Gene Ontology enrichment analysis to evaluate their biological relevance. The distinct theoretical foundation of Bi-Force (bicluster editing) is more powerful than strict biclustering. We thus outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used datasets are publicly available at http://biclue.mpi-inf.mpg.de. PMID:24682815

Status of the AIAA Modeling and Simulation Format Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Hildreth, Bruce L.

2008-01-01

The current draft AIAA Standard for flight simulation models represents an on-going effort to improve the productivity of practitioners of the art of digital flight simulation (one of the original digital computer applications). This initial release provides the capability for the efficient representation and exchange of an aerodynamic model in full fidelity; the DAVE-ML format can be easily imported (with development of site-specific import tools) in an unambiguous way with automatic verification. An attractive feature of the standard is the ability to coexist with existing legacy software or tools. The draft Standard is currently limited in scope to static elements of dynamic flight simulations; however, these static elements represent the bulk of typical flight simulation mathematical models. It is already seeing application within U.S. and Australian government agencies in an effort to improve productivity and reduce model rehosting overhead. An existing tool allows import of DAVE-ML models into a popular simulation modeling and analysis tool, and other community-contributed tools and libraries can simplify the use of DAVE-ML compliant models at compile- or run-time of high-fidelity flight simulation.

Challenges and Demands on Automated Software Revision

NASA Technical Reports Server (NTRS)

Bonakdarpour, Borzoo; Kulkarni, Sandeep S.

2008-01-01

In the past three decades, automated program verification has undoubtedly been one of the most successful contributions of formal methods to software development. However, when verification of a program against a logical specification discovers bugs in the program, manual manipulation of the program is needed in order to repair it. Thus, in the face of existence of numerous unverified and un- certified legacy software in virtually any organization, tools that enable engineers to automatically verify and subsequently fix existing programs are highly desirable. In addition, since requirements of software systems often evolve during the software life cycle, the issue of incomplete specification has become a customary fact in many design and development teams. Thus, automated techniques that revise existing programs according to new specifications are of great assistance to designers, developers, and maintenance engineers. As a result, incorporating program synthesis techniques where an algorithm generates a program, that is correct-by-construction, seems to be a necessity. The notion of manual program repair described above turns out to be even more complex when programs are integrated with large collections of sensors and actuators in hostile physical environments in the so-called cyber-physical systems. When such systems are safety/mission- critical (e.g., in avionics systems), it is essential that the system reacts to physical events such as faults, delays, signals, attacks, etc, so that the system specification is not violated. In fact, since it is impossible to anticipate all possible such physical events at design time, it is highly desirable to have automated techniques that revise programs with respect to newly identified physical events according to the system specification.

Ensemble Eclipse: A Process for Prefab Development Environment for the Ensemble Project

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Mittman, David S.; Shams, Khawaja, S.; Bachmann, Andrew G.; Ludowise, Melissa

2013-01-01

This software simplifies the process of having to set up an Eclipse IDE programming environment for the members of the cross-NASA center project, Ensemble. It achieves this by assembling all the necessary add-ons and custom tools/preferences. This software is unique in that it allows developers in the Ensemble Project (approximately 20 to 40 at any time) across multiple NASA centers to set up a development environment almost instantly and work on Ensemble software. The software automatically has the source code repositories and other vital information and settings included. The Eclipse IDE is an open-source development framework. The NASA (Ensemble-specific) version of the software includes Ensemble-specific plug-ins as well as settings for the Ensemble project. This software saves developers the time and hassle of setting up a programming environment, making sure that everything is set up in the correct manner for Ensemble development. Existing software (i.e., standard Eclipse) requires an intensive setup process that is both time-consuming and error prone. This software is built once by a single user and tested, allowing other developers to simply download and use the software

Free and Open Source Software for Geospatial in the field of planetary science

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

Information technology applied to geospatial analyses has spread quickly in the last ten years. The availability of OpenData and data from collaborative mapping projects increased the interest on tools, procedures and methods to handle spatially-related information. Free Open Source Software projects devoted to geospatial data handling are gaining a good success as the use of interoperable formats and protocols allow the user to choose what pipeline of tools and libraries is needed to solve a particular task, adapting the software scene to his specific problem. In particular, the Free Open Source model of development mimics the scientific method very well, and researchers should be naturally encouraged to take part to the development process of these software projects, as this represent a very agile way to interact among several institutions. When it comes to planetary sciences, geospatial Free Open Source Software is gaining a key role in projects that commonly involve different subjects in an international scenario. Very popular software suites for processing scientific mission data (for example, ISIS) and for navigation/planning (SPICE) are being distributed along with the source code and the interaction between user and developer is often very strict, creating a continuum between these two figures. A very widely spread library for handling geospatial data (GDAL) has started to support planetary data from the Planetary Data System, and recent contributions enabled the support to other popular data formats used in planetary science, as the Vicar one. The use of Geographic Information System in planetary science is now diffused, and Free Open Source GIS, open GIS formats and network protocols allow to extend existing tools and methods developed to solve Earth based problems, also to the case of the study of solar system bodies. A day in the working life of a researcher using Free Open Source Software for geospatial will be presented, as well as benefits and solutions to possible detriments coming from the effort required by using, supporting and contributing.

Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.

PubMed

Taylor, Louis J; Strebel, Klaus

2017-01-07

Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts. Pyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes. Pyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface ( http://louiejtaylor.github.io/pyViKO/ ), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.

NSTX-U Advances in Real-Time C++11 on Linux

NASA Astrophysics Data System (ADS)

Erickson, Keith G.

2015-08-01

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11 standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.

Summary of the Ratfor language, an extended portable dialect called REP, its style and flavor, and details of its implementation on the PDP-10

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

Figen, J.

1981-09-10

Ratfor (RATional FORtran) is a dialect of Fortran that allows structured programming and the use of simple macros. It is the language of the Software Tools package, and is documented in the book Software Tools. It has proved significantly easier than Fortran to read, write, and understand. Although debugging is slightly harder in Ratfor than in Fortran, there is usually less of it to do, since Ratfor lends itself to better program design. Ratfor operates as a preprocessor to any existing Fortran system. It is relatively easy, using Ratfor, to write programs that are portable with little or no changemore » to any environment that supports standard Fortran. REP (Ratfor Extended and Portable) is an extended version of Ratfor. It is fully upward compatible with the Addison-Wesley translator, though there are a few divergences from certain Unix and Software Tools User Group dialects. The principal feature of REP is its fully developed macro facility, a language within a language, capable of doing such things as creating new data types, data structuring, recursive procedures, and much more, portably, and in the spirit of Ratfor, but there are many other lesser though nevertheless important extensions.« less

SU-F-P-04: Implementation of Dose Monitoring Software: Successes and Pitfalls

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

Och, J

2016-06-15

Purpose: to successfully install a dose monitoring software (DMS) application to assist in CT protocol and dose management. Methods: Upon selecting the DMS, we began our implementation of the application. A working group composed of Medical Physics, Radiology Administration, Information Technology, and CT technologists was formed. On-site training in the application was supplied by the vendor. The decision was made to apply the process for all the CT protocols on all platforms at all facilities. Protocols were painstakingly mapped to the correct masters, and the system went ‘live’. Results: We are routinely using DMS as a tool in our Clinicalmore » Performance CT QA program. It is useful in determining the effectiveness of revisions to existing protocols, and establishing performance baselines for new units. However, the implementation was not without difficulty. We identified several pitfalls and obstacles which frustrated progress. Including: Training deficiencies, Nomenclature problems, Communication, DICOM variability. Conclusion: Dose monitoring software can be a potent tool for QA. However, implementation of the program can be problematic and requires planning, organization and commitment.« less

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Identifying impact of software dependencies on replicability of biomedical workflows.

PubMed

Miksa, Tomasz; Rauber, Andreas; Mina, Eleni

2016-12-01

Complex data driven experiments form the basis of biomedical research. Recent findings warn that the context in which the software is run, that is the infrastructure and the third party dependencies, can have a crucial impact on the final results delivered by a computational experiment. This implies that in order to replicate the same result, not only the same data must be used, but also it must be run on an equivalent software stack. In this paper we present the VFramework that enables assessing replicability of workflows. It identifies whether any differences in software dependencies among two executions of the same workflow exist and whether they have impact on the produced results. We also conduct a case study in which we investigate the impact of software dependencies on replicability of Taverna workflows used in biomedical research of Huntington's disease. We re-execute analysed workflows in environments differing in operating system distribution and configuration. The results show that the VFramework can be used to identify the impact of software dependencies on the replicability of biomedical workflows. Furthermore, we observe that despite the fact that the workflows are executed in a controlled environment, they still depend on specific tools installed in the environment. The context model used by the VFramework improves the deficiencies of provenance traces and documents also such tools. Based on our findings we define guidelines for workflow owners that enable them to improve replicability of their workflows. Copyright © 2016 Elsevier Inc. All rights reserved.

Vids: Version 2.0 Alpha Visualization Engine

DTIC Science & Technology

2018-04-25

fidelity than existing efforts. Vids is a project aimed at producing more dynamic and interactive visualization tools using modern computer game ...move through and interact with the data to improve informational understanding. The Vids software leverages off-the-shelf modern game development...analysis and correlations. Recently, an ARL-pioneered project named Virtual Reality Data Analysis Environment (VRDAE) used VR and a modern game engine

Impact of Machine-Translated Text on Entity and Relationship Extraction

DTIC Science & Technology

2014-12-01

20 1 1. Introduction Using social network analysis tools is an important asset in...semantic modeling software to automatically build detailed network models from unstructured text. Contour imports unstructured text and then maps the text...onto an existing ontology of frames at the sentence level, using FrameNet, a structured language model, and through Semantic Role Labeling ( SRL

NetCDF-CF: Supporting Earth System Science with Data Access, Analysis, and Visualization

NASA Astrophysics Data System (ADS)

Davis, E.; Zender, C. S.; Arctur, D. K.; O'Brien, K.; Jelenak, A.; Santek, D.; Dixon, M. J.; Whiteaker, T. L.; Yang, K.

2017-12-01

NetCDF-CF is a community-developed convention for storing and describing earth system science data in the netCDF binary data format. It is an OGC recognized standard with numerous existing FOSS (Free and Open Source Software) and commercial software tools can explore, analyze, and visualize data that is stored and described as netCDF-CF data. To better support a larger segment of the earth system science community, a number of efforts are underway to extend the netCDF-CF convention with the goal of increasing the types of data that can be represented as netCDF-CF data. This presentation will provide an overview and update of work to extend the existing netCDF-CF convention. It will detail the types of earth system science data currently supported by netCDF-CF and the types of data targeted for support by current netCDF-CF convention development efforts. It will also describe some of the tools that support the use of netCDF-CF compliant datasets, the types of data they support, and efforts to extend them to handle the new data types that netCDF-CF will support.

Code Parallelization with CAPO: A User Manual

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2001-01-01

A software tool has been developed to assist the parallelization of scientific codes. This tool, CAPO, extends an existing parallelization toolkit, CAPTools developed at the University of Greenwich, to generate OpenMP parallel codes for shared memory architectures. This is an interactive toolkit to transform a serial Fortran application code to an equivalent parallel version of the software - in a small fraction of the time normally required for a manual parallelization. We first discuss the way in which loop types are categorized and how efficient OpenMP directives can be defined and inserted into the existing code using the in-depth interprocedural analysis. The use of the toolkit on a number of application codes ranging from benchmark to real-world application codes is presented. This will demonstrate the great potential of using the toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of processors. The second part of the document gives references to the parameters and the graphic user interface implemented in the toolkit. Finally a set of tutorials is included for hands-on experiences with this toolkit.

A multiphysics and multiscale software environment for modeling astrophysical systems

NASA Astrophysics Data System (ADS)

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

2009-05-01

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a "Noah's Ark" milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

Capricorn-A Web-Based Automatic Case Log and Volume Analytics for Diagnostic Radiology Residents.

PubMed

Chen, Po-Hao; Chen, Yin Jie; Cook, Tessa S

2015-10-01

On-service clinical learning is a mainstay of radiology education. However, an accurate and timely case log is difficult to keep, especially in the absence of software tools tailored to resident education. Furthermore, volume-related feedback from the residency program sometimes occurs months after a rotation ends, limiting the opportunity for meaningful intervention. We surveyed the residents of a single academic institution to evaluate the current state of and the existing need for tracking interpretation volume. Using the results of the survey, we created an open-source automated case log software. Finally, we evaluated the effect of the software tool on the residency in a 1-month, postimplementation survey. Before implementation of the system, 89% of respondents stated that volume is an important component of training, but 71% stated that volume data was inconvenient to obtain. Although the residency program provides semiannual reviews, 90% preferred reviewing interpretation volumes at least once monthly. After implementation, 95% of the respondents stated that the software is convenient to access, 75% found it useful, and 88% stated they would use the software at least once a month. The included analytics module, which benchmarks the user using historical aggregate average volumes, is the most often used feature of the software. Server log demonstrates that, on average, residents use the system approximately twice a week. An automated case log software system may fulfill a previously unmet need in diagnostic radiology training, making accurate and timely review of volume-related performance analytics a convenient process. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

A first-generation software product line for data acquisition systems in astronomy

NASA Astrophysics Data System (ADS)

López-Ruiz, J. C.; Heradio, Rubén; Cerrada Somolinos, José Antonio; Coz Fernandez, José Ramón; López Ramos, Pablo

2008-07-01

This article presents a case study on developing a software product line for data acquisition systems in astronomy based on the Exemplar Driven Development methodology and the Exemplar Flexibilization Language tool. The main strategies to build the software product line are based on the domain commonality and variability, the incremental scope and the use of existing artifacts. It consists on a lean methodology with little impact on the organization, suitable for small projects, which reduces product line start-up time. Software Product Lines focuses on creating a family of products instead of individual products. This approach has spectacular benefits on reducing the time to market, maintaining the know-how, reducing the development costs and increasing the quality of new products. The maintenance of the products is also enhanced since all the data acquisition systems share the same product line architecture.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Moore, Michael S.; Price, Jeremy C.; Reinhart, Richard; Liebetreu, John; Kacpura, Tom J.

2005-01-01

This paper presents the tool chain, methodology, and results of an on-going study being performed jointly by Space Communication Experts at NASA Glenn Research Center (GRC), General Dynamics C4 Systems (GD), and Southwest Research Institute (SwRI). The team is evaluating the applicability and tradeoffs concerning the use of Software Defined Radio (SDR) technologies for Space missions. The Space Telecommunications Radio Systems (STRS) project is developing an approach toward building SDR-based transceivers for space communications applications based on an accompanying software architecture that can be used to implement transceivers for NASA space missions. The study is assessing the overall cost and benefit of employing SDR technologies in general, and of developing a software architecture standard for its space SDR transceivers. The study is considering the cost and benefit of existing architectures, such as the Joint Tactical Radio Systems (JTRS) Software Communications Architecture (SCA), as well as potential new space-specific architectures.

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

Hiatt, S. H.; Hashimoto, H.; Melton, F. S.; Michaelis, A. R.; Milesi, C.; Nemani, R. R.; Wang, W.

2008-12-01

The Terrestrial Observation and Prediction System (TOPS) at NASA Ames Research Center is a modeling system that generates a suite of gridded data products in near real-time that are designed to enhance management decisions related to floods, droughts, forest fires, human health, as well as crop, range, and forest production. While these data products introduce great possibilities for assisting management decisions and informing further research, realization of their full potential is complicated by their shear volume and by the need for a necessary infrastructure for remotely browsing, visualizing, and analyzing the data. In order to address these difficulties we have built an OGC-compliant WMS and WCS server based on an open source software stack that provides standardized access to our archive of data. This server is built using the open source Java library GeoTools which achieves efficient I/O and image rendering through Java Advanced Imaging. We developed spatio-temporal raster management capabilities using the PostGrid raster indexation engine. We provide visualization and browsing capabilities through a customized Ajax web interface derived from the kaMap project. This interface allows resource managers to quickly assess ecosystem conditions and identify significant trends and anomalies from within their web browser without the need to download source data or install special software. Our standardized web services also expose TOPS data to a range of potential clients, from web mapping applications to virtual globes and desktop GIS packages. However, support for managing the temporal dimension of our data is currently limited in existing software systems. Future work will attempt to overcome this shortcoming by building time-series visualization and analysis tools that can be integrated with existing geospatial software.

Adapting a standardised international 24 h dietary recall methodology (GloboDiet software) for research and dietary surveillance in Korea.

PubMed

Park, Min Kyung; Park, Jin Young; Nicolas, Geneviève; Paik, Hee Young; Kim, Jeongseon; Slimani, Nadia

2015-06-14

During the past decades, a rapid nutritional transition has been observed along with economic growth in the Republic of Korea. Since this dramatic change in diet has been frequently associated with cancer and other non-communicable diseases, dietary monitoring is essential to understand the association. Benefiting from pre-existing standardised dietary methodologies, the present study aimed to evaluate the feasibility and describe the development of a Korean version of the international computerised 24 h dietary recall method (GloboDiet software) and its complementary tools, developed at the International Agency for Research on Cancer (IARC), WHO. Following established international Standard Operating Procedures and guidelines, about seventy common and country-specific databases on foods, recipes, dietary supplements, quantification methods and coefficients were customised and translated. The main results of the present study highlight the specific adaptations made to adapt the GloboDiet software for research and dietary surveillance in Korea. New (sub-) subgroups were added into the existing common food classification, and new descriptors were added to the facets to classify and describe specific Korean foods. Quantification methods were critically evaluated and adapted considering the foods and food packages available in the Korean market. Furthermore, a picture book of foods/dishes was prepared including new pictures and food portion sizes relevant to Korean diet. The development of the Korean version of GloboDiet demonstrated that it was possible to adapt the IARC-WHO international dietary tool to an Asian context without compromising its concept of standardisation and software structure. It, thus, confirms that this international dietary methodology, used so far only in Europe, is flexible and robust enough to be customised for other regions worldwide.

Distributed Engine Control Empirical/Analytical Verification Tools

NASA Technical Reports Server (NTRS)

DeCastro, Jonathan; Hettler, Eric; Yedavalli, Rama; Mitra, Sayan

2013-01-01

NASA's vision for an intelligent engine will be realized with the development of a truly distributed control system featuring highly reliable, modular, and dependable components capable of both surviving the harsh engine operating environment and decentralized functionality. A set of control system verification tools was developed and applied to a C-MAPSS40K engine model, and metrics were established to assess the stability and performance of these control systems on the same platform. A software tool was developed that allows designers to assemble easily a distributed control system in software and immediately assess the overall impacts of the system on the target (simulated) platform, allowing control system designers to converge rapidly on acceptable architectures with consideration to all required hardware elements. The software developed in this program will be installed on a distributed hardware-in-the-loop (DHIL) simulation tool to assist NASA and the Distributed Engine Control Working Group (DECWG) in integrating DCS (distributed engine control systems) components onto existing and next-generation engines.The distributed engine control simulator blockset for MATLAB/Simulink and hardware simulator provides the capability to simulate virtual subcomponents, as well as swap actual subcomponents for hardware-in-the-loop (HIL) analysis. Subcomponents can be the communication network, smart sensor or actuator nodes, or a centralized control system. The distributed engine control blockset for MATLAB/Simulink is a software development tool. The software includes an engine simulation, a communication network simulation, control algorithms, and analysis algorithms set up in a modular environment for rapid simulation of different network architectures; the hardware consists of an embedded device running parts of the CMAPSS engine simulator and controlled through Simulink. The distributed engine control simulation, evaluation, and analysis technology provides unique capabilities to study the effects of a given change to the control system in the context of the distributed paradigm. The simulation tool can support treatment of all components within the control system, both virtual and real; these include communication data network, smart sensor and actuator nodes, centralized control system (FADEC full authority digital engine control), and the aircraft engine itself. The DECsim tool can allow simulation-based prototyping of control laws, control architectures, and decentralization strategies before hardware is integrated into the system. With the configuration specified, the simulator allows a variety of key factors to be systematically assessed. Such factors include control system performance, reliability, weight, and bandwidth utilization.

Manpower and project planning

NASA Technical Reports Server (NTRS)

Johnson, David W.

1991-01-01

The purpose was to study how manpower and projects are planned at the Facilities Engineering Division (FENGD) within the Systems Engineering and Operations Directorate of the LaRC and to make recommendations for improving the effectiveness and productivity ot the tools that are used. The existing manpower and project planning processes (including the management plan for the FENGD, existing manpower planning reports, project reporting to LaRC and NASA Headquarters, employee time reporting, financial reporting, and coordination/tracking reports for procurement) were discussed with several people, and project planning software was evaluated.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales.

PubMed

Rueckl, Martin; Lenzi, Stephen C; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca 2+ -imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca 2+ imaging datasets, particularly when these have been acquired at different spatial scales.

pySPACE—a signal processing and classification environment in Python

PubMed Central

Krell, Mario M.; Straube, Sirko; Seeland, Anett; Wöhrle, Hendrik; Teiwes, Johannes; Metzen, Jan H.; Kirchner, Elsa A.; Kirchner, Frank

2013-01-01

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries. PMID:24399965

pySPACE-a signal processing and classification environment in Python.

PubMed

Krell, Mario M; Straube, Sirko; Seeland, Anett; Wöhrle, Hendrik; Teiwes, Johannes; Metzen, Jan H; Kirchner, Elsa A; Kirchner, Frank

2013-01-01

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries.

Case Study: Test Results of a Tool and Method for In-Flight, Adaptive Control System Verification on a NASA F-15 Flight Research Aircraft

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.; Schumann, Johann; Guenther, Kurt; Bosworth, John

2006-01-01

Adaptive control technologies that incorporate learning algorithms have been proposed to enable autonomous flight control and to maintain vehicle performance in the face of unknown, changing, or poorly defined operating environments [1-2]. At the present time, however, it is unknown how adaptive algorithms can be routinely verified, validated, and certified for use in safety-critical applications. Rigorous methods for adaptive software verification end validation must be developed to ensure that. the control software functions as required and is highly safe and reliable. A large gap appears to exist between the point at which control system designers feel the verification process is complete, and when FAA certification officials agree it is complete. Certification of adaptive flight control software verification is complicated by the use of learning algorithms (e.g., neural networks) and degrees of system non-determinism. Of course, analytical efforts must be made in the verification process to place guarantees on learning algorithm stability, rate of convergence, and convergence accuracy. However, to satisfy FAA certification requirements, it must be demonstrated that the adaptive flight control system is also able to fail and still allow the aircraft to be flown safely or to land, while at the same time providing a means of crew notification of the (impending) failure. It was for this purpose that the NASA Ames Confidence Tool was developed [3]. This paper presents the Confidence Tool as a means of providing in-flight software assurance monitoring of an adaptive flight control system. The paper will present the data obtained from flight testing the tool on a specially modified F-15 aircraft designed to simulate loss of flight control faces.

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales

PubMed Central

Rueckl, Martin; Lenzi, Stephen C.; Moreno-Velasquez, Laura; Parthier, Daniel; Schmitz, Dietmar; Ruediger, Sten; Johenning, Friedrich W.

2017-01-01

The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. PMID:28706482

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Pipe dream? Envisioning a grassroots Python ecosystem of open, common software tools and data access in support of river and coastal biogeochemical research (Invited)

NASA Astrophysics Data System (ADS)

Mayorga, E.

2013-12-01

Practical, problem oriented software developed by scientists and graduate students in domains lacking a strong software development tradition is often balkanized into the scripting environments provided by dominant, typically proprietary tools. In environmental fields, these tools include ArcGIS, Matlab, SAS, Excel and others, and are often constrained to specific operating systems. While this situation is the outcome of rational choices, it limits the dissemination of useful tools and their integration into loosely coupled frameworks that can meet wider needs and be developed organically by groups addressing their own needs. Open-source dynamic languages offer the advantages of an accessible programming syntax, a wealth of pre-existing libraries, multi-platform access, linkage to community libraries developed in lower level languages such as C or FORTRAN, and access to web service infrastructure. Python in particular has seen a large and increasing uptake in scientific communities, as evidenced by the continued growth of the annual SciPy conference. Ecosystems with distinctive physical structures and organization, and mechanistic processes that are well characterized, are both factors that have often led to the grass-roots development of useful code meeting the needs of a range of communities. In aquatic applications, examples include river and watershed analysis tools (River Tools, Taudem, etc), and geochemical modules such as CO2SYS, PHREEQ and LOADEST. I will review the state of affairs and explore the potential offered by a Python tool ecosystem in supporting aquatic biogeochemistry and water quality research. This potential is multi-faceted and broadly involves accessibility to lone grad students, access to a wide community of programmers and problem solvers via online resources such as StackExchange, and opportunities to leverage broader cyberinfrastructure efforts and tools, including those from widely different domains. Collaborative development of such tools can provide the additional advantage of enhancing cohesion and communication across specific research areas, and reducing research obstacles in a range of disciplines.

ScanImage: flexible software for operating laser scanning microscopes.

PubMed

Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel

2003-05-17

Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality. We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

Designing Real-time Decision Support for Trauma Resuscitations

PubMed Central

Yadav, Kabir; Chamberlain, James M.; Lewis, Vicki R.; Abts, Natalie; Chawla, Shawn; Hernandez, Angie; Johnson, Justin; Tuveson, Genevieve; Burd, Randall S.

2016-01-01

Background Use of electronic clinical decision support (eCDS) has been recommended to improve implementation of clinical decision rules. Many eCDS tools, however, are designed and implemented without taking into account the context in which clinical work is performed. Implementation of the pediatric traumatic brain injury (TBI) clinical decision rule at one Level I pediatric emergency department includes an electronic questionnaire triggered when ordering a head computed tomography using computerized physician order entry (CPOE). Providers use this CPOE tool in less than 20% of trauma resuscitation cases. A human factors engineering approach could identify the implementation barriers that are limiting the use of this tool. Objectives The objective was to design a pediatric TBI eCDS tool for trauma resuscitation using a human factors approach. The hypothesis was that clinical experts will rate a usability-enhanced eCDS tool better than the existing CPOE tool for user interface design and suitability for clinical use. Methods This mixed-methods study followed usability evaluation principles. Pediatric emergency physicians were surveyed to identify barriers to using the existing eCDS tool. Using standard trauma resuscitation protocols, a hierarchical task analysis of pediatric TBI evaluation was developed. Five clinical experts, all board-certified pediatric emergency medicine faculty members, then iteratively modified the hierarchical task analysis until reaching consensus. The software team developed a prototype eCDS display using the hierarchical task analysis. Three human factors engineers provided feedback on the prototype through a heuristic evaluation, and the software team refined the eCDS tool using a rapid prototyping process. The eCDS tool then underwent iterative usability evaluations by the five clinical experts using video review of 50 trauma resuscitation cases. A final eCDS tool was created based on their feedback, with content analysis of the evaluations performed to ensure all concerns were identified and addressed. Results Among 26 EPs (76% response rate), the main barriers to using the existing tool were that the information displayed is redundant and does not fit clinical workflow. After the prototype eCDS tool was developed based on the trauma resuscitation hierarchical task analysis, the human factors engineers rated it to be better than the CPOE tool for nine of 10 standard user interface design heuristics on a three-point scale. The eCDS tool was also rated better for clinical use on the same scale, in 84% of 50 expert–video pairs, and was rated equivalent in the remainder. Clinical experts also rated barriers to use of the eCDS tool as being low. Conclusions An eCDS tool for diagnostic imaging designed using human factors engineering methods has improved perceived usability among pediatric emergency physicians. PMID:26300010

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

DOE PAGES

Kang, Dongwan D.; Froula, Jeff; Egan, Rob; ...

2015-01-01

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically formsmore » hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.« less

Improving Earth Science Metadata: Modernizing ncISO

NASA Astrophysics Data System (ADS)

O'Brien, K.; Schweitzer, R.; Neufeld, D.; Burger, E. F.; Signell, R. P.; Arms, S. C.; Wilcox, K.

2016-12-01

ncISO is a package of tools developed at NOAA's National Center for Environmental Information (NCEI) that facilitates the generation of ISO 19115-2 metadata from NetCDF data sources. The tool currently exists in two iterations: a command line utility and a web-accessible service within the THREDDS Data Server (TDS). Several projects, including NOAA's Unified Access Framework (UAF), depend upon ncISO to generate the ISO-compliant metadata from their data holdings and use the resulting information to populate discovery tools such as NCEI's ESRI Geoportal and NOAA's data.noaa.gov CKAN system. In addition to generating ISO 19115-2 metadata, the tool calculates a rubric score based on how well the dataset follows the Attribute Conventions for Dataset Discovery (ACDD). The result of this rubric calculation, along with information about what has been included and what is missing is displayed in an HTML document generated by the ncISO software package. Recently ncISO has fallen behind in terms of supporting updates to conventions such updates to the ACDD. With the blessing of the original programmer, NOAA's UAF has been working to modernize the ncISO software base. In addition to upgrading ncISO to utilize version1.3 of the ACDD, we have been working with partners at Unidata and IOOS to unify the tool's code base. In essence, we are merging the command line capabilities into the same software that will now be used by the TDS service, allowing easier updates when conventions such as ACDD are updated in the future. In this presentation, we will discuss the work the UAF project has done to support updated conventions within ncISO, as well as describe how the updated tool is helping to improve metadata throughout the earth and ocean sciences.

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing.

PubMed

Rastogi, Achal; Murik, Omer; Bowler, Chris; Tirichine, Leila

2016-07-01

With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an efficient and accurate reverse genetic tool for genome editing. Several computational tools have been published allowing researchers to find candidate target sequences for the engineering of the CRISPR vectors, while searching possible off-targets for the predicted candidates. These tools provide built-in genome databases of common model organisms that are used for CRISPR target prediction. Although their predictions are highly sensitive, the applicability to non-model genomes, most notably protists, makes their design inadequate. This motivated us to design a new CRISPR target finding tool, PhytoCRISP-Ex. Our software offers CRIPSR target predictions using an extended list of phytoplankton genomes and also delivers a user-friendly standalone application that can be used for any genome. The software attempts to integrate, for the first time, most available phytoplankton genomes information and provide a web-based platform for Cas9 target prediction within them with high sensitivity. By offering a standalone version, PhytoCRISP-Ex maintains an independence to be used with any organism and widens its applicability in high throughput pipelines. PhytoCRISP-Ex out pars all the existing tools by computing the availability of restriction sites over the most probable Cas9 cleavage sites, which can be ideal for mutant screens. PhytoCRISP-Ex is a simple, fast and accurate web interface with 13 pre-indexed and presently updating phytoplankton genomes. The software was also designed as a UNIX-based standalone application that allows the user to search for target sequences in the genomes of a variety of other species.

Meta-analyzing dependent correlations: an SPSS macro and an R script.

PubMed

Cheung, Shu Fai; Chan, Darius K-S

2014-06-01

The presence of dependent correlation is a common problem in meta-analysis. Cheung and Chan (2004, 2008) have shown that samplewise-adjusted procedures perform better than the more commonly adopted simple within-sample mean procedures. However, samplewise-adjusted procedures have rarely been applied in meta-analytic reviews, probably due to the lack of suitable ready-to-use programs. In this article, we compare the samplewise-adjusted procedures with existing procedures to handle dependent effect sizes, and present the samplewise-adjusted procedures in a way that will make them more accessible to researchers conducting meta-analysis. We also introduce two tools, an SPSS macro and an R script, that researchers can apply to their meta-analyses; these tools are compatible with existing meta-analysis software packages.

Easy Web Interfaces to IDL Code for NSTX Data Analysis

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

W.M. Davis

Reusing code is a well-known Software Engineering practice to substantially increase the efficiency of code production, as well as to reduce errors and debugging time. A variety of "Web Tools" for the analysis and display of raw and analyzed physics data are in use on NSTX [1], and new ones can be produced quickly from existing IDL [2] code. A Web Tool with only a few inputs, and which calls an IDL routine written in the proper style, can be created in less than an hour; more typical Web Tools with dozens of inputs, and the need for some adaptationmore » of existing IDL code, can be working in a day or so. Efficiency is also increased for users of Web Tools because o f the familiar interface of the web browser, and not needing X-windows, accounts, passwords, etc. Web Tools were adapted for use by PPPL physicists accessing EAST data stored in MDSplus with only a few man-weeks of effort; adapting to additional sites should now be even easier. An overview of Web Tools in use on NSTX, and a list of the most useful features, is also presented.« less

JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Grey, Melissa

2017-08-01

Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-30

information that are returned from the tools to the human user, and the forms in which these outputs are presented. Page 2 of 4 STAGE OF DEVELOPMENT: What... AUTOMIATED SOFTWARE TOOL MONITORING SYSTEM APPENDIX 2 2-1 INTRODUCTION This document and Automated Software Tool Monitoring Program (Appendix 1) are...t Output Output features provide links from the tool to both the human user and the target machine (where applicable). They describe the types

A graphic user interface for efficient 3D photo-reconstruction based on free software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael; Gómez, Jose A.

2015-04-01

Recently, different studies have stressed the applicability of 3D photo-reconstruction based on Structure from Motion algorithms in a wide range of geoscience applications. For the purpose of image photo-reconstruction, a number of commercial and freely available software packages have been developed (e.g. Agisoft Photoscan, VisualSFM). The workflow involves typically different stages such as image matching, sparse and dense photo-reconstruction, point cloud filtering and georeferencing. For approaches using open and free software, each of these stages usually require different applications. In this communication, we present an easy-to-use graphic user interface (GUI) developed in Matlab® code as a tool for efficient 3D photo-reconstruction making use of powerful existing software: VisualSFM (Wu, 2015) for photo-reconstruction and CloudCompare (Girardeau-Montaut, 2015) for point cloud processing. The GUI performs as a manager of configurations and algorithms, taking advantage of the command line modes of existing software, which allows an intuitive and automated processing workflow for the geoscience user. The GUI includes several additional features: a) a routine for significantly reducing the duration of the image matching operation, normally the most time consuming stage; b) graphical outputs for understanding the overall performance of the algorithm (e.g. camera connectivity, point cloud density); c) a number of useful options typically performed before and after the photo-reconstruction stage (e.g. removal of blurry images, image renaming, vegetation filtering); d) a manager of batch processing for the automated reconstruction of different image datasets. In this study we explore the advantages of this new tool by testing its performance using imagery collected in several soil erosion applications. References Girardeau-Montaut, D. 2015. CloudCompare documentation accessed at http://cloudcompare.org/ Wu, C. 2015. VisualSFM documentation access at http://ccwu.me/vsfm/doc.html#.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

FAST: A multi-processed environment for visualization of computational fluid dynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Merritt, Fergus J.; Plessel, Todd C.; Kelaita, Paul G.; Mccabe, R. Kevin

1991-01-01

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Software Engineering Laboratory (SEL) compendium of tools, revision 1

NASA Technical Reports Server (NTRS)

1982-01-01

A set of programs used to aid software product development is listed. Known as software tools, such programs include requirements analyzers, design languages, precompilers, code auditors, code analyzers, and software librarians. Abstracts, resource requirements, documentation, processing summaries, and availability are indicated for most tools.

Integrating interactive computational modeling in biology curricula.

PubMed

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

A quality-refinement process for medical imaging applications.

PubMed

Neuhaus, J; Maleike, D; Nolden, M; Kenngott, H-G; Meinzer, H-P; Wolf, I

2009-01-01

To introduce and evaluate a process for refinement of software quality that is suitable to research groups. In order to avoid constraining researchers too much, the quality improvement process has to be designed carefully. The scope of this paper is to present and evaluate a process to advance quality aspects of existing research prototypes in order to make them ready for initial clinical studies. The proposed process is tailored for research environments and therefore more lightweight than traditional quality management processes. Focus on quality criteria that are important at the given stage of the software life cycle. Usage of tools that automate aspects of the process is emphasized. To evaluate the additional effort that comes along with the process, it was exemplarily applied for eight prototypical software modules for medical image processing. The introduced process has been applied to improve the quality of all prototypes so that they could be successfully used in clinical studies. The quality refinement yielded an average of 13 person days of additional effort per project. Overall, 107 bugs were found and resolved by applying the process. Careful selection of quality criteria and the usage of automated process tools lead to a lightweight quality refinement process suitable for scientific research groups that can be applied to ensure a successful transfer of technical software prototypes into clinical research workflows.

Northwestern University Schizophrenia Data and Software Tool (NUSDAST)

PubMed Central

Wang, Lei; Kogan, Alex; Cobia, Derin; Alpert, Kathryn; Kolasny, Anthony; Miller, Michael I.; Marcus, Daniel

2013-01-01

The schizophrenia research community has invested substantial resources on collecting, managing and sharing large neuroimaging datasets. As part of this effort, our group has collected high resolution magnetic resonance (MR) datasets from individuals with schizophrenia, their non-psychotic siblings, healthy controls and their siblings. This effort has resulted in a growing resource, the Northwestern University Schizophrenia Data and Software Tool (NUSDAST), an NIH-funded data sharing project to stimulate new research. This resource resides on XNAT Central, and it contains neuroimaging (MR scans, landmarks and surface maps for deep subcortical structures, and FreeSurfer cortical parcellation and measurement data), cognitive (cognitive domain scores for crystallized intelligence, working memory, episodic memory, and executive function), clinical (demographic, sibling relationship, SAPS and SANS psychopathology), and genetic (20 polymorphisms) data, collected from more than 450 subjects, most with 2-year longitudinal follow-up. A neuroimaging mapping, analysis and visualization software tool, CAWorks, is also part of this resource. Moreover, in making our existing neuroimaging data along with the associated meta-data and computational tools publically accessible, we have established a web-based information retrieval portal that allows the user to efficiently search the collection. This research-ready dataset meaningfully combines neuroimaging data with other relevant information, and it can be used to help facilitate advancing neuroimaging research. It is our hope that this effort will help to overcome some of the commonly recognized technical barriers in advancing neuroimaging research such as lack of local organization and standard descriptions. PMID:24223551

Northwestern University Schizophrenia Data and Software Tool (NUSDAST).

PubMed

Wang, Lei; Kogan, Alex; Cobia, Derin; Alpert, Kathryn; Kolasny, Anthony; Miller, Michael I; Marcus, Daniel

2013-01-01

The schizophrenia research community has invested substantial resources on collecting, managing and sharing large neuroimaging datasets. As part of this effort, our group has collected high resolution magnetic resonance (MR) datasets from individuals with schizophrenia, their non-psychotic siblings, healthy controls and their siblings. This effort has resulted in a growing resource, the Northwestern University Schizophrenia Data and Software Tool (NUSDAST), an NIH-funded data sharing project to stimulate new research. This resource resides on XNAT Central, and it contains neuroimaging (MR scans, landmarks and surface maps for deep subcortical structures, and FreeSurfer cortical parcellation and measurement data), cognitive (cognitive domain scores for crystallized intelligence, working memory, episodic memory, and executive function), clinical (demographic, sibling relationship, SAPS and SANS psychopathology), and genetic (20 polymorphisms) data, collected from more than 450 subjects, most with 2-year longitudinal follow-up. A neuroimaging mapping, analysis and visualization software tool, CAWorks, is also part of this resource. Moreover, in making our existing neuroimaging data along with the associated meta-data and computational tools publically accessible, we have established a web-based information retrieval portal that allows the user to efficiently search the collection. This research-ready dataset meaningfully combines neuroimaging data with other relevant information, and it can be used to help facilitate advancing neuroimaging research. It is our hope that this effort will help to overcome some of the commonly recognized technical barriers in advancing neuroimaging research such as lack of local organization and standard descriptions.

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.

Automated support for experience-based software management

NASA Technical Reports Server (NTRS)

Valett, Jon D.

1992-01-01

To effectively manage a software development project, the software manager must have access to key information concerning a project's status. This information includes not only data relating to the project of interest, but also, the experience of past development efforts within the environment. This paper describes the concepts and functionality of a software management tool designed to provide this information. This tool, called the Software Management Environment (SME), enables the software manager to compare an ongoing development effort with previous efforts and with models of the 'typical' project within the environment, to predict future project status, to analyze a project's strengths and weaknesses, and to assess the project's quality. In order to provide these functions the tool utilizes a vast corporate memory that includes a data base of software metrics, a set of models and relationships that describe the software development environment, and a set of rules that capture other knowledge and experience of software managers within the environment. Integrating these major concepts into one software management tool, the SME is a model of the type of management tool needed for all software development organizations.

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

Navarro, Carmen; Martínez, Victor; Blanco, Armando; Cano, Carlos

2017-12-01

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization. ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality. © The Authors 2017. Published by Oxford University Press.

An Exact Formula for Calculating Inverse Radial Lens Distortions

PubMed Central

Drap, Pierre; Lefèvre, Julien

2016-01-01

This article presents a new approach to calculating the inverse of radial distortions. The method presented here provides a model of reverse radial distortion, currently modeled by a polynomial expression, that proposes another polynomial expression where the new coefficients are a function of the original ones. After describing the state of the art, the proposed method is developed. It is based on a formal calculus involving a power series used to deduce a recursive formula for the new coefficients. We present several implementations of this method and describe the experiments conducted to assess the validity of the new approach. Such an approach, non-iterative, using another polynomial expression, able to be deduced from the first one, can actually be interesting in terms of performance, reuse of existing software, or bridging between different existing software tools that do not consider distortion from the same point of view. PMID:27258288

Towards a mature measurement environment: Creating a software engineering research environment

NASA Technical Reports Server (NTRS)

Basili, Victor R.

1990-01-01

Software engineering researchers are building tools, defining methods, and models; however, there are problems with the nature and style of the research. The research is typically bottom-up, done in isolation so the pieces cannot be easily logically or physically integrated. A great deal of the research is essentially the packaging of a particular piece of technology with little indication of how the work would be integrated with other prices of research. The research is not aimed at solving the real problems of software engineering, i.e., the development and maintenance of quality systems in a productive manner. The research results are not evaluated or analyzed via experimentation or refined and tailored to the application environment. Thus, it cannot be easily transferred into practice. Because of these limitations we have not been able to understand the components of the discipline as a coherent whole and the relationships between various models of the process and product. What is needed is a top down experimental, evolutionary framework in which research can be focused, logically and physically integrated to produce quality software productively, and evaluated and tailored to the application environment. This implies the need for experimentation, which in turn implies the need for a laboratory that is associated with the artifact we are studying. This laboratory can only exist in an environment where software is being built, i.e., as part of a real software development and maintenance organization. Thus, we propose that Software Engineering Laboratory (SEL) type activities exist in all organizations to support software engineering research. We describe the SEL from a researcher's point of view, and discuss the corporate and government benefits of the SEL. The discussion focuses on the benefits to the research community.

Telepathology: design of a modular system.

PubMed

Brauchli, K; Christen, H; Meyer, P; Haroske, G; Meyer, W; Kunze, K D; Otto, R; Oberholzer, M

2000-01-01

Although telepathology systems have been developed for more than a decade, they are still not a widespread tool for routine diagnostic applications. Lacking interoperability, software that is not satisfying user needs as well as high costs have been identified as reasons. In this paper we would like to demonstrate that with a clear separation of the tasks required for a telepathology application, telepathology systems can be built in a modular way, where many modules can be implemented using standard software components. With such a modular design, systems can be easily adapted to changing user needs and new technological developments and it is easier to integrate modular systems into existing environments.

Software project management tools in global software development: a systematic mapping study.

PubMed

Chadli, Saad Yasser; Idri, Ali; Ros, Joaquín Nicolás; Fernández-Alemán, José Luis; de Gea, Juan M Carrillo; Toval, Ambrosio

2016-01-01

Global software development (GSD) which is a growing trend in the software industry is characterized by a highly distributed environment. Performing software project management (SPM) in such conditions implies the need to overcome new limitations resulting from cultural, temporal and geographic separation. The aim of this research is to discover and classify the various tools mentioned in literature that provide GSD project managers with support and to identify in what way they support group interaction. A systematic mapping study has been performed by means of automatic searches in five sources. We have then synthesized the data extracted and presented the results of this study. A total of 102 tools were identified as being used in SPM activities in GSD. We have classified these tools, according to the software life cycle process on which they focus and how they support the 3C collaboration model (communication, coordination and cooperation). The majority of the tools found are standalone tools (77%). A small number of platforms (8%) also offer a set of interacting tools that cover the software development lifecycle. Results also indicate that SPM areas in GSD are not adequately supported by corresponding tools and deserve more attention from tool builders.

Integrating and Managing Bim in GIS, Software Review

NASA Astrophysics Data System (ADS)

El Meouche, R.; Rezoug, M.; Hijazi, I.

2013-08-01

Since the advent of Computer-Aided Design (CAD) and Geographical Information System (GIS) tools, project participants have been increasingly leveraging these tools throughout the different phases of a civil infrastructure project. In recent years the number of GIS software that provides tools to enable the integration of Building information in geo context has risen sharply. More and more GIS software are added tools for this purposes and other software projects are regularly extending these tools. However, each software has its different strength and weakness and its purpose of use. This paper provides a thorough review to investigate the software capabilities and clarify its purpose. For this study, Autodesk Revit 2012 i.e. BIM editor software was used to create BIMs. In the first step, three building models were created, the resulted models were converted to BIM format and then the software was used to integrate it. For the evaluation of the software, general characteristics was studied such as the user interface, what formats are supported (import/export), and the way building information are imported.

A GIS-based framework for evaluating investments in fire management: Spatial allocation of recreation values

Treesearch

Kenneth A. Baerenklau; Armando González-Cabán; Catrina I. Páez; Edgard Chávez

2009-01-01

The U.S. Forest Service is responsible for developing tools to facilitate effective and efficient fire management on wildlands and urban-wildland interfaces. Existing GIS-based fire modeling software only permits estimation of the costs of fire prevention and mitigation efforts as well as the effects of those efforts on fire behavior. This research demonstrates how the...

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

ERIC Educational Resources Information Center

Weber, Jonathan

2006-01-01

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

Development and validation of an open source quantification tool for DSC-MRI studies.

PubMed

Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

2015-03-01

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

A workflow learning model to improve geovisual analytics utility

PubMed Central

Roth, Robert E; MacEachren, Alan M; McCabe, Craig A

2011-01-01

Introduction This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. Objectives The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. Methodology The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. Results/Conclusions In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009. PMID:21983545

A workflow learning model to improve geovisual analytics utility.

PubMed

Roth, Robert E; Maceachren, Alan M; McCabe, Craig A

2009-01-01

INTRODUCTION: This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. OBJECTIVES: The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. METHODOLOGY: The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

Crossing the chasm: how to develop weather and climate models for next generation computers?

NASA Astrophysics Data System (ADS)

Lawrence, Bryan N.; Rezny, Michael; Budich, Reinhard; Bauer, Peter; Behrens, Jörg; Carter, Mick; Deconinck, Willem; Ford, Rupert; Maynard, Christopher; Mullerworth, Steven; Osuna, Carlos; Porter, Andrew; Serradell, Kim; Valcke, Sophie; Wedi, Nils; Wilson, Simon

2018-05-01

Weather and climate models are complex pieces of software which include many individual components, each of which is evolving under pressure to exploit advances in computing to enhance some combination of a range of possible improvements (higher spatio-temporal resolution, increased fidelity in terms of resolved processes, more quantification of uncertainty, etc.). However, after many years of a relatively stable computing environment with little choice in processing architecture or programming paradigm (basically X86 processors using MPI for parallelism), the existing menu of processor choices includes significant diversity, and more is on the horizon. This computational diversity, coupled with ever increasing software complexity, leads to the very real possibility that weather and climate modelling will arrive at a chasm which will separate scientific aspiration from our ability to develop and/or rapidly adapt codes to the available hardware. In this paper we review the hardware and software trends which are leading us towards this chasm, before describing current progress in addressing some of the tools which we may be able to use to bridge the chasm. This brief introduction to current tools and plans is followed by a discussion outlining the scientific requirements for quality model codes which have satisfactory performance and portability, while simultaneously supporting productive scientific evolution. We assert that the existing method of incremental model improvements employing small steps which adjust to the changing hardware environment is likely to be inadequate for crossing the chasm between aspiration and hardware at a satisfactory pace, in part because institutions cannot have all the relevant expertise in house. Instead, we outline a methodology based on large community efforts in engineering and standardisation, which will depend on identifying a taxonomy of key activities - perhaps based on existing efforts to develop domain-specific languages, identify common patterns in weather and climate codes, and develop community approaches to commonly needed tools and libraries - and then collaboratively building up those key components. Such a collaborative approach will depend on institutions, projects, and individuals adopting new interdependencies and ways of working.

MatMRI and MatHIFU: software toolboxes for real-time monitoring and control of MR-guided HIFU

PubMed Central

2013-01-01

Background The availability of open and versatile software tools is a key feature to facilitate pre-clinical research for magnetic resonance imaging (MRI) and magnetic resonance-guided high-intensity focused ultrasound (MR-HIFU) and expedite clinical translation of diagnostic and therapeutic medical applications. In the present study, two customizable software tools that were developed at the Thunder Bay Regional Research Institute are presented for use with both MRI and MR-HIFU. Both tools operate in a MATLAB®; environment. The first tool is named MatMRI and enables real-time, dynamic acquisition of MR images with a Philips MRI scanner. The second tool is named MatHIFU and enables the execution and dynamic modification of user-defined treatment protocols with the Philips Sonalleve MR-HIFU therapy system to perform ultrasound exposures in MR-HIFU therapy applications. Methods MatMRI requires four basic steps: initiate communication, subscribe to MRI data, query for new images, and unsubscribe. MatMRI can also pause/resume the imaging and perform real-time updates of the location and orientation of images. MatHIFU requires four basic steps: initiate communication, prepare treatment protocol, and execute treatment protocol. MatHIFU can monitor the state of execution and, if required, modify the protocol in real time. Results Four applications were developed to showcase the capabilities of MatMRI and MatHIFU to perform pre-clinical research. Firstly, MatMRI was integrated with an existing small animal MR-HIFU system (FUS Instruments, Toronto, Ontario, Canada) to provide real-time temperature measurements. Secondly, MatMRI was used to perform T2-based MR thermometry in the bone marrow. Thirdly, MatHIFU was used to automate acoustic hydrophone measurements on a per-element basis of the 256-element transducer of the Sonalleve system. Finally, MatMRI and MatHIFU were combined to produce and image a heating pattern that recreates the word ‘HIFU’ in a tissue-mimicking heating phantom. Conclusions MatMRI and MatHIFU leverage existing MRI and MR-HIFU clinical platforms to facilitate pre-clinical research. MatMRI substantially simplifies the real-time acquisition and processing of MR data. MatHIFU facilitates the testing and characterization of new therapy applications using the Philips Sonalleve clinical MR-HIFU system. Under coordination with Philips Healthcare, both MatMRI and MatHIFU are intended to be freely available as open-source software packages to other research groups. PMID:25512856

Knowledge-Based Aircraft Automation: Managers Guide on the use of Artificial Intelligence for Aircraft Automation and Verification and Validation Approach for a Neural-Based Flight Controller

NASA Technical Reports Server (NTRS)

Broderick, Ron

1997-01-01

The ultimate goal of this report was to integrate the powerful tools of artificial intelligence into the traditional process of software development. To maintain the US aerospace competitive advantage, traditional aerospace and software engineers need to more easily incorporate the technology of artificial intelligence into the advanced aerospace systems being designed today. The future goal was to transition artificial intelligence from an emerging technology to a standard technology that is considered early in the life cycle process to develop state-of-the-art aircraft automation systems. This report addressed the future goal in two ways. First, it provided a matrix that identified typical aircraft automation applications conducive to various artificial intelligence methods. The purpose of this matrix was to provide top-level guidance to managers contemplating the possible use of artificial intelligence in the development of aircraft automation. Second, the report provided a methodology to formally evaluate neural networks as part of the traditional process of software development. The matrix was developed by organizing the discipline of artificial intelligence into the following six methods: logical, object representation-based, distributed, uncertainty management, temporal and neurocomputing. Next, a study of existing aircraft automation applications that have been conducive to artificial intelligence implementation resulted in the following five categories: pilot-vehicle interface, system status and diagnosis, situation assessment, automatic flight planning, and aircraft flight control. The resulting matrix provided management guidance to understand artificial intelligence as it applied to aircraft automation. The approach taken to develop a methodology to formally evaluate neural networks as part of the software engineering life cycle was to start with the existing software quality assurance standards and to change these standards to include neural network development. The changes were to include evaluation tools that can be applied to neural networks at each phase of the software engineering life cycle. The result was a formal evaluation approach to increase the product quality of systems that use neural networks for their implementation.

Software attribute visualization for high integrity software

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

Pollock, G.M.

1998-03-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

PubMed Central

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

Reference gene validation for RT-qPCR, a note on different available software packages.

PubMed

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use.

Software Users Manual (SUM): Extended Testability Analysis (ETA) Tool

NASA Technical Reports Server (NTRS)

Maul, William A.; Fulton, Christopher E.

2011-01-01

This software user manual describes the implementation and use the Extended Testability Analysis (ETA) Tool. The ETA Tool is a software program that augments the analysis and reporting capabilities of a commercial-off-the-shelf (COTS) testability analysis software package called the Testability Engineering And Maintenance System (TEAMS) Designer. An initial diagnostic assessment is performed by the TEAMS Designer software using a qualitative, directed-graph model of the system being analyzed. The ETA Tool utilizes system design information captured within the diagnostic model and testability analysis output from the TEAMS Designer software to create a series of six reports for various system engineering needs. The ETA Tool allows the user to perform additional studies on the testability analysis results by determining the detection sensitivity to the loss of certain sensors or tests. The ETA Tool was developed to support design and development of the NASA Ares I Crew Launch Vehicle. The diagnostic analysis provided by the ETA Tool was proven to be valuable system engineering output that provided consistency in the verification of system engineering requirements. This software user manual provides a description of each output report generated by the ETA Tool. The manual also describes the example diagnostic model and supporting documentation - also provided with the ETA Tool software release package - that were used to generate the reports presented in the manual

The Exoplanet Characterization ToolKit (ExoCTK)

NASA Astrophysics Data System (ADS)

Stevenson, Kevin; Fowler, Julia; Lewis, Nikole K.; Fraine, Jonathan; Pueyo, Laurent; Valenti, Jeff; Bruno, Giovanni; Filippazzo, Joseph; Hill, Matthew; Batalha, Natasha E.; Bushra, Rafia

2018-01-01

The success of exoplanet characterization depends critically on a patchwork of analysis tools and spectroscopic libraries that currently require extensive development and lack a centralized support system. Due to the complexity of spectroscopic analyses and initial time commitment required to become productive, there are currently a limited number of teams that are actively advancing the field. New teams with significant expertise, but without the proper tools, face prohibitively steep hills to climb before they can contribute. As a solution, we are developing an open-source, modular data analysis package in Python and a publicly facing web interface focused primarily on atmospheric characterization of exoplanets and exoplanet transit observation planning with JWST. The foundation of these software tools and libraries exist within pockets of the exoplanet community. Our project will gather these seedling tools and grow a robust, uniform, and well maintained exoplanet characterization toolkit.

A Tool Supporting Collaborative Data Analytics Workflow Design and Management

NASA Astrophysics Data System (ADS)

Zhang, J.; Bao, Q.; Lee, T. J.

2016-12-01

Collaborative experiment design could significantly enhance the sharing and adoption of the data analytics algorithms and models emerged in Earth science. Existing data-oriented workflow tools, however, are not suitable to support collaborative design of such a workflow, to name a few, to support real-time co-design; to track how a workflow evolves over time based on changing designs contributed by multiple Earth scientists; and to capture and retrieve collaboration knowledge on workflow design (discussions that lead to a design). To address the aforementioned challenges, we have designed and developed a technique supporting collaborative data-oriented workflow composition and management, as a key component toward supporting big data collaboration through the Internet. Reproducibility and scalability are two major targets demanding fundamental infrastructural support. One outcome of the project os a software tool, supporting an elastic number of groups of Earth scientists to collaboratively design and compose data analytics workflows through the Internet. Instead of recreating the wheel, we have extended an existing workflow tool VisTrails into an online collaborative environment as a proof of concept.

MNE Scan: Software for real-time processing of electrophysiological data.

PubMed

Esch, Lorenz; Sun, Limin; Klüber, Viktor; Lew, Seok; Baumgarten, Daniel; Grant, P Ellen; Okada, Yoshio; Haueisen, Jens; Hämäläinen, Matti S; Dinh, Christoph

2018-06-01

Magnetoencephalography (MEG) and Electroencephalography (EEG) are noninvasive techniques to study the electrophysiological activity of the human brain. Thus, they are well suited for real-time monitoring and analysis of neuronal activity. Real-time MEG/EEG data processing allows adjustment of the stimuli to the subject's responses for optimizing the acquired information especially by providing dynamically changing displays to enable neurofeedback. We introduce MNE Scan, an acquisition and real-time analysis software based on the multipurpose software library MNE-CPP. MNE Scan allows the development and application of acquisition and novel real-time processing methods in both research and clinical studies. The MNE Scan development follows a strict software engineering process to enable approvals required for clinical software. We tested the performance of MNE Scan in several device-independent use cases, including, a clinical epilepsy study, real-time source estimation, and Brain Computer Interface (BCI) application. Compared to existing tools we propose a modular software considering clinical software requirements expected by certification authorities. At the same time the software is extendable and freely accessible. We conclude that MNE Scan is the first step in creating a device-independent open-source software to facilitate the transition from basic neuroscience research to both applied sciences and clinical applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

In recent years many software tools and applications have appeared that offer procedures, scripts and algorithms to process and visualize ALS data. This variety of software tools and of "point cloud" processing methods contributed to the aim of this study: to assess algorithms available in various software tools that are used to classify LIDAR "point cloud" data, through a careful examination of Digital Elevation Models (DEMs) generated from LIDAR data on a base of these algorithms. The works focused on the most important available software tools: both commercial and open source ones. Two sites in a mountain area were selected for the study. The area of each site is 0.645 sq km. DEMs generated with analysed software tools ware compared with a reference dataset, generated using manual methods to eliminate non ground points. Surfaces were analysed using raster analysis. Minimum, maximum and mean differences between reference DEM and DEMs generated with analysed software tools were calculated, together with Root Mean Square Error. Differences between DEMs were also examined visually using transects along the grid axes in the test sites.

Lessons learned in deploying software estimation technology and tools

NASA Technical Reports Server (NTRS)

Panlilio-Yap, Nikki; Ho, Danny

1994-01-01

Developing a software product involves estimating various project parameters. This is typically done in the planning stages of the project when there is much uncertainty and very little information. Coming up with accurate estimates of effort, cost, schedule, and reliability is a critical problem faced by all software project managers. The use of estimation models and commercially available tools in conjunction with the best bottom-up estimates of software-development experts enhances the ability of a product development group to derive reasonable estimates of important project parameters. This paper describes the experience of the IBM Software Solutions (SWS) Toronto Laboratory in selecting software estimation models and tools and deploying their use to the laboratory's product development groups. It introduces the SLIM and COSTAR products, the software estimation tools selected for deployment to the product areas, and discusses the rationale for their selection. The paper also describes the mechanisms used for technology injection and tool deployment, and concludes with a discussion of important lessons learned in the technology and tool insertion process.

Using bio.tools to generate and annotate workbench tool descriptions

PubMed Central

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Evaluation of the efficiency and reliability of software generated by code generators

NASA Technical Reports Server (NTRS)

Schreur, Barbara

1994-01-01

There are numerous studies which show that CASE Tools greatly facilitate software development. As a result of these advantages, an increasing amount of software development is done with CASE Tools. As more software engineers become proficient with these tools, their experience and feedback lead to further development with the tools themselves. What has not been widely studied, however, is the reliability and efficiency of the actual code produced by the CASE Tools. This investigation considered these matters. Three segments of code generated by MATRIXx, one of many commercially available CASE Tools, were chosen for analysis: ETOFLIGHT, a portion of the Earth to Orbit Flight software, and ECLSS and PFMC, modules for Environmental Control and Life Support System and Pump Fan Motor Control, respectively.

WinHPC System Software | High-Performance Computing | NREL

Science.gov Websites

Software WinHPC System Software Learn about the software applications, tools, toolchains, and for industrial applications. Intel Compilers Development Tool, Toolchain Suite featuring an industry

NEURON and Python.

PubMed

Hines, Michael L; Davison, Andrew P; Muller, Eilif

2009-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

NEURON and Python

PubMed Central

Hines, Michael L.; Davison, Andrew P.; Muller, Eilif

2008-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications. PMID:19198661

[Application of microelectronics CAD tools to synthetic biology].

PubMed

Madec, Morgan; Haiech, Jacques; Rosati, Élise; Rezgui, Abir; Gendrault, Yves; Lallement, Christophe

2017-02-01

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process. Nevertheless, with the increasing complexity of biological circuits, this is no longer the case and a large number of computer aided design softwares have been developed in the past few years. These tools include languages for the behavioral description and the mathematical modelling of biological systems, simulators at different levels of abstraction, libraries of biological devices and circuit design automation algorithms. All of these tools already exist in other fields of engineering sciences, particularly in microelectronics. This is the approach that is put forward in this paper. © 2017 médecine/sciences – Inserm.

NSTX-U Advances in Real-Time C++11 on Linux

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

Erickson, Keith G.

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) willmore » serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.« less

NSTX-U Advances in Real-Time C++11 on Linux

DOE PAGES

Erickson, Keith G.

2015-08-14

Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) willmore » serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.« less

Installing and Setting Up the Git Software Tool on OS X | High-Performance

Science.gov Websites

Computing | NREL the Git Software Tool on OS X Installing and Setting Up the Git Software Tool on OS X Learn how to install the Git software tool on OS X for use with the Peregrine system. You can . Binary Installer for OS X - Easiest! You can download the latest version of git from http://git-scm.com

The use of emulator-based simulators for on-board software maintenance

NASA Astrophysics Data System (ADS)

Irvine, M. M.; Dartnell, A.

2002-07-01

Traditionally, onboard software maintenance activities within the space sector are performed using hardware-based facilities. These facilities are developed around the use of hardware emulation or breadboards containing target processors. Some sort of environment is provided around the hardware to support the maintenance actives. However, these environments are not easy to use to set-up the required test scenarios, particularly when the onboard software executes in a dynamic I/O environment, e.g. attitude control software, or data handling software. In addition, the hardware and/or environment may not support the test set-up required during investigations into software anomalies, e.g. raise spurious interrupt, fail memory, etc, and the overall "visibility" of the software executing may be limited. The Software Maintenance Simulator (SOMSIM) is a tool that can support the traditional maintenance facilities. The following list contains some of the main benefits that SOMSIM can provide: Low cost flexible extension to existing product - operational simulator containing software processor emulator; System-level high-fidelity test-bed in which software "executes"; Provides a high degree of control/configuration over the entire "system", including contingency conditions perhaps not possible with real hardware; High visibility and control over execution of emulated software. This paper describes the SOMSIM concept in more detail, and also describes the SOMSIM study being carried out for ESA/ESOC by VEGA IT GmbH.

Developing Teaching Material Software Assisted for Numerical Methods

NASA Astrophysics Data System (ADS)

Handayani, A. D.; Herman, T.; Fatimah, S.

2017-09-01

The NCTM vision shows the importance of two things in school mathematics, which is knowing the mathematics of the 21st century and the need to continue to improve mathematics education to answer the challenges of a changing world. One of the competencies associated with the great challenges of the 21st century is the use of help and tools (including IT), such as: knowing the existence of various tools for mathematical activity. One of the significant challenges in mathematical learning is how to teach students about abstract concepts. In this case, technology in the form of mathematics learning software can be used more widely to embed the abstract concept in mathematics. In mathematics learning, the use of mathematical software can make high level math activity become easier accepted by student. Technology can strengthen student learning by delivering numerical, graphic, and symbolic content without spending the time to calculate complex computing problems manually. The purpose of this research is to design and develop teaching materials software assisted for numerical method. The process of developing the teaching material starts from the defining step, the process of designing the learning material developed based on information obtained from the step of early analysis, learners, materials, tasks that support then done the design step or design, then the last step is the development step. The development of teaching materials software assisted for numerical methods is valid in content. While validator assessment for teaching material in numerical methods is good and can be used with little revision.

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

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

The Capabilities of the Graphical Observation Scheduling System (GROSS) as Used by the Astro-2 Spacelab Mission

NASA Technical Reports Server (NTRS)

Phillips, Shaun

1996-01-01

The Graphical Observation Scheduling System (GROSS) and its functionality and editing capabilities are reported on. The GROSS system was developed as a replacement for a suite of existing programs and associated processes with the aim of: providing a software tool that combines the functionality of several of the existing programs, and provides a Graphical User Interface (GUI) that gives greater data visibility and editing capabilities. It is considered that the improved editing capability provided by this approach enhanced the efficiency of the second astronomical Spacelab mission's (ASTRO-2) mission planning.

Conversion of IVA Human Computer Model to EVA Use and Evaluation and Comparison of the Result to Existing EVA Models

NASA Technical Reports Server (NTRS)

Hamilton, George S.; Williams, Jermaine C.

1998-01-01

This paper describes the methods, rationale, and comparative results of the conversion of an intravehicular (IVA) 3D human computer model (HCM) to extravehicular (EVA) use and compares the converted model to an existing model on another computer platform. The task of accurately modeling a spacesuited human figure in software is daunting: the suit restricts the human's joint range of motion (ROM) and does not have joints collocated with human joints. The modeling of the variety of materials needed to construct a space suit (e. g. metal bearings, rigid fiberglass torso, flexible cloth limbs and rubber coated gloves) attached to a human figure is currently out of reach of desktop computer hardware and software. Therefore a simplified approach was taken. The HCM's body parts were enlarged and the joint ROM was restricted to match the existing spacesuit model. This basic approach could be used to model other restrictive environments in industry such as chemical or fire protective clothing. In summary, the approach provides a moderate fidelity, usable tool which will run on current notebook computers.

Software for predictive microbiology and risk assessment: a description and comparison of tools presented at the ICPMF8 Software Fair.

PubMed

Tenenhaus-Aziza, Fanny; Ellouze, Mariem

2015-02-01

The 8th International Conference on Predictive Modelling in Food was held in Paris, France in September 2013. One of the major topics of this conference was the transfer of knowledge and tools between academics and stakeholders of the food sector. During the conference, a "Software Fair" was held to provide information and demonstrations of predictive microbiology and risk assessment software. This article presents an overall description of the 16 software tools demonstrated at the session and provides a comparison based on several criteria such as the modeling approach, the different modules available (e.g. databases, predictors, fitting tools, risk assessment tools), the studied environmental factors (temperature, pH, aw, etc.), the type of media (broth or food) and the number and type of the provided micro-organisms (pathogens and spoilers). The present study is a guide to help users select the software tools which are most suitable to their specific needs, before they test and explore the tool(s) in more depth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Toolpack mathematical software development environment

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

Osterweil, L.

1982-07-21

The purpose of this research project was to produce a well integrated set of tools for the support of numerical computation. The project entailed the specification, design and implementation of both a diversity of tools and an innovative tool integration mechanism. This large configuration of tightly integrated tools comprises an environment for numerical software development, and has been named Toolpack/IST (Integrated System of Tools). Following the creation of this environment in prototype form, the environment software was readied for widespread distribution by transitioning it to a development organization for systematization, documentation and distribution. It is expected that public release ofmore » Toolpack/IST will begin imminently and will provide a basis for evaluation of the innovative software approaches taken as well as a uniform set of development tools for the numerical software community.« less

Flexible Workflow Software enables the Management of an Increased Volume and Heterogeneity of Sensors, and evolves with the Expansion of Complex Ocean Observatory Infrastructures.

NASA Astrophysics Data System (ADS)

Tomlin, M. C.; Jenkyns, R.

2015-12-01

Ocean Networks Canada (ONC) collects data from observatories in the northeast Pacific, Salish Sea, Arctic Ocean, Atlantic Ocean, and land-based sites in British Columbia. Data are streamed, collected autonomously, or transmitted via satellite from a variety of instruments. The Software Engineering group at ONC develops and maintains Oceans 2.0, an in-house software system that acquires and archives data from sensors, and makes data available to scientists, the public, government and non-government agencies. The Oceans 2.0 workflow tool was developed by ONC to manage a large volume of tasks and processes required for instrument installation, recovery and maintenance activities. Since 2013, the workflow tool has supported 70 expeditions and grown to include 30 different workflow processes for the increasing complexity of infrastructures at ONC. The workflow tool strives to keep pace with an increasing heterogeneity of sensors, connections and environments by supporting versioning of existing workflows, and allowing the creation of new processes and tasks. Despite challenges in training and gaining mutual support from multidisciplinary teams, the workflow tool has become invaluable in project management in an innovative setting. It provides a collective place to contribute to ONC's diverse projects and expeditions and encourages more repeatable processes, while promoting interactions between the multidisciplinary teams who manage various aspects of instrument development and the data they produce. The workflow tool inspires documentation of terminologies and procedures, and effectively links to other tools at ONC such as JIRA, Alfresco and Wiki. Motivated by growing sensor schemes, modes of collecting data, archiving, and data distribution at ONC, the workflow tool ensures that infrastructure is managed completely from instrument purchase to data distribution. It integrates all areas of expertise and helps fulfill ONC's mandate to offer quality data to users.

Software development environments: Status and trends

NASA Technical Reports Server (NTRS)

Duffel, Larry E.

1988-01-01

Currently software engineers are the essential integrating factors tying several components together. The components consist of process, methods, computers, tools, support environments, and software engineers. The engineers today empower the tools versus the tools empowering the engineers. Some of the issues in software engineering are quality, managing the software engineering process, and productivity. A strategy to accomplish this is to promote the evolution of software engineering from an ad hoc, labor intensive activity to a managed, technology supported discipline. This strategy may be implemented by putting the process under management control, adopting appropriate methods, inserting the technology that provides automated support for the process and methods, collecting automated tools into an integrated environment and educating the personnel.

VennDIS: a JavaFX-based Venn and Euler diagram software to generate publication quality figures.

PubMed

Ignatchenko, Vladimir; Ignatchenko, Alexandr; Sinha, Ankit; Boutros, Paul C; Kislinger, Thomas

2015-04-01

Venn diagrams are graphical representations of the relationships among multiple sets of objects and are often used to illustrate similarities and differences among genomic and proteomic datasets. All currently existing tools for producing Venn diagrams evince one of two traits; they require expertise in specific statistical software packages (such as R), or lack the flexibility required to produce publication-quality figures. We describe a simple tool that addresses both shortcomings, Venn Diagram Interactive Software (VennDIS), a JavaFX-based solution for producing highly customizable, publication-quality Venn, and Euler diagrams of up to five sets. The strengths of VennDIS are its simple graphical user interface and its large array of customization options, including the ability to modify attributes such as font, style and position of the labels, background color, size of the circle/ellipse, and outline color. It is platform independent and provides real-time visualization of figure modifications. The created figures can be saved as XML files for future modification or exported as high-resolution images for direct use in publications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PREMER: a Tool to Infer Biological Networks.

PubMed

Villaverde, Alejandro F; Becker, Kolja; Banga, Julio R

2017-10-04

Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux and OSX (https://sites.google.com/site/premertoolbox/).

Fault tolerant testbed evaluation, phase 1

NASA Technical Reports Server (NTRS)

Caluori, V., Jr.; Newberry, T.

1993-01-01

In recent years, avionics systems development costs have become the driving factor in the development of space systems, military aircraft, and commercial aircraft. A method of reducing avionics development costs is to utilize state-of-the-art software application generator (autocode) tools and methods. The recent maturity of application generator technology has the potential to dramatically reduce development costs by eliminating software development steps that have historically introduced errors and the need for re-work. Application generator tools have been demonstrated to be an effective method for autocoding non-redundant, relatively low-rate input/output (I/O) applications on the Space Station Freedom (SSF) program; however, they have not been demonstrated for fault tolerant, high-rate I/O, flight critical environments. This contract will evaluate the use of application generators in these harsh environments. Using Boeing's quad-redundant avionics system controller as the target system, Space Shuttle Guidance, Navigation, and Control (GN&C) software will be autocoded, tested, and evaluated in the Johnson (Space Center) Avionics Engineering Laboratory (JAEL). The response of the autocoded system will be shown to match the response of the existing Shuttle General Purpose Computers (GPC's), thereby demonstrating the viability of using autocode techniques in the development of future avionics systems.

Integrating Online GIS into the K-12 Curricula: Lessons from the Development of a Collaborative GIS in Michigan

ERIC Educational Resources Information Center

Henry, Paul; Semple, Hugh

2012-01-01

GIS has shown promise in Project Based Learning (PBL) environments, but many obstacles exist in its integration into school curriculums. This article discusses the development and utilization of an online GIS tool that was created to illustrate that the perceptual gap between relevance and ease of use of GIS software can be bridged at the K-12…

Resilient Software Systems

DTIC Science & Technology

2015-06-01

and tools, called model-integrated computing ( MIC ) [3] relies on the use of domain-specific modeling languages for creating models of the system to be...hence giving reflective capabilities to it. We have followed the MIC method here: we designed a domain- specific modeling language for modeling...are produced one-off and not for the mass market , the scope for price reduction based on the market demands is non-existent. Processes to create

Opening Up Architectures of Software-Intensive Systems: A First Prototype Implementation

DTIC Science & Technology

2007-11-01

9 4.1.2 Sequence Diagram Viewer NetBeans Module .................................. 11 4.1.3 Limitations of Static Analysis...Viewer NetBeans module [18]. Note that there exist other tools which can statically reverse engineer sequence diagrams such as Borland Together [19...and the NetBeans UML Modeling module [20]. The reason those are not presented in this document is because their functionalities are very similar

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

Jonathan Helmus, Scott Collis

The Python-ARM Radar Toolkit (Py-ART) is a collection of radar quality control and retrieval codes which all work on two unifying Python objects: the PyRadar and PyGrid objects. By building ingests to several popular radar formats and then abstracting the interface Py-ART greatly simplifies data processing over several other available utilities. In addition Py-ART makes use of Numpy arrays as its primary storage mechanism enabling use of existing and extensive community software tools.

Candidate R&D Thrusts for the Software Technology Initiative.

DTIC Science & Technology

1981-05-01

computer-aided design and manufacturing efforts provide examples of multiple representations and multiple manipulation modes. R&D difficulties exist in...farfetched, but the potential payoffs are enormous. References Birk, J., and R. Kelley. Research Needed to Advance the State of Knowledge in Robotics . In...and specifica- tion languages would be benefical . This R&D effort may also result in fusion with management tools with which an acquisition manager

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation.

PubMed

Wolf, Beat; Kuonen, Pierre; Dandekar, Thomas; Atlan, David

2015-01-01

Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.

BEopt-CA (Ex) -- A Tool for Optimal Integration of EE/DR/ES+PV in Existing California Homes. Cooperative Research and Development Final Report, CRADA Number CRD-11-429

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

Christensen, Craig

Opportunities for combining energy efficiency, demand response, and energy storage with PV are often missed, because the required knowledge and expertise for these different technologies exist in separate organizations or individuals. Furthermore, there is a lack of quantitative tools to optimize energy efficiency, demand response and energy storage with PV, especially for existing buildings. Our goal is to develop a modeling tool, BEopt-CA (Ex), with capabilities to facilitate identification and implementation of a balanced integration of energy efficiency (EE), demand response (DR), and energy storage (ES) with photovoltaics (PV) within the residential retrofit market. To achieve this goal, we willmore » adapt and extend an existing tool -- BEopt -- that is designed to identify optimal combinations of efficiency and PV in new home designs. In addition, we will develop multifamily residential modeling capabilities for use in California, to facilitate integration of distributed solar power into the grid in order to maximize its value to California ratepayers. The project is follow-on research that leverages previous California Solar Initiative RD&D investment in the BEopt software. BEopt facilitates finding the least cost combination of energy efficiency and renewables to support integrated DSM (iDSM) and Zero Net Energy (ZNE) in California residential buildings. However, BEopt is currently focused on modeling single-family houses and does not include satisfactory capabilities for modeling multifamily homes. The project brings BEopt's existing modeling and optimization capabilities to multifamily buildings, including duplexes, triplexes, townhouses, flats, and low-rise apartment buildings.« less

MTpy - Python Tools for Magnetotelluric Data Processing and Analysis

NASA Astrophysics Data System (ADS)

Krieger, Lars; Peacock, Jared; Thiel, Stephan; Inverarity, Kent; Kirkby, Alison; Robertson, Kate; Soeffky, Paul; Didana, Yohannes

2014-05-01

We present the Python package MTpy, which provides functions for the processing, analysis, and handling of magnetotelluric (MT) data sets. MT is a relatively immature and not widely applied geophysical method in comparison to other geophysical techniques such as seismology. As a result, the data processing within the academic MT community is not thoroughly standardised and is often based on a loose collection of software, adapted to the respective local specifications. We have developed MTpy to overcome problems that arise from missing standards, and to provide a simplification of the general handling of MT data. MTpy is written in Python, and the open-source code is freely available from a GitHub repository. The setup follows the modular approach of successful geoscience software packages such as GMT or Obspy. It contains sub-packages and modules for the various tasks within the standard work-flow of MT data processing and interpretation. In order to allow the inclusion of already existing and well established software, MTpy does not only provide pure Python classes and functions, but also wrapping command-line scripts to run standalone tools, e.g. modelling and inversion codes. Our aim is to provide a flexible framework, which is open for future dynamic extensions. MTpy has the potential to promote the standardisation of processing procedures and at same time be a versatile supplement for existing algorithms. Here, we introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing, interpretation, and visualisation utilising MTpy on example data sets collected over different regions of Australia and the USA.

PSAMM: A Portable System for the Analysis of Metabolic Models

PubMed Central

Steffensen, Jon Lund; Dufault-Thompson, Keith; Zhang, Ying

2016-01-01

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies. PMID:26828591

Preparing WIND for the STEREO Mission

NASA Astrophysics Data System (ADS)

Schroeder, P.; Ogilve, K.; Szabo, A.; Lin, R.; Luhmann, J.

2006-05-01

The upcoming STEREO mission's IMPACT and PLASTIC investigations will provide the first opportunity for long duration, detailed observations of 1 AU magnetic field structures, plasma ions and electrons, suprathermal electrons, and energetic particles at points bracketing Earth's heliospheric location. Stereoscopic/3D information from the STEREO SECCHI imagers and SWAVES radio experiment will make it possible to use both multipoint and quadrature studies to connect interplanetary Coronal Mass Ejections (ICME) and solar wind structures to CMEs and coronal holes observed at the Sun. To fully exploit these unique data sets, tight integration with similarly equipped missions at L1 will be essential, particularly WIND and ACE. The STEREO mission is building novel data analysis tools to take advantage of the mission's scientific potential. These tools will require reliable access and a well-documented interface to the L1 data sets. Such an interface already exists for ACE through the ACE Science Center. We plan to provide a similar service for the WIND mission that will supplement existing CDAWeb services. Building on tools also being developed for STEREO, we will create a SOAP application program interface (API) which will allow both our STEREO/WIND/ACE interactive browser and third-party software to access WIND data as a seamless and integral part of the STEREO mission. The API will also allow for more advanced forms of data mining than currently available through other data web services. Access will be provided to WIND-specific data analysis software as well. The development of cross-spacecraft data analysis tools will allow a larger scientific community to combine STEREO's unique in-situ data with those of other missions, particularly the L1 missions, and, therefore, to maximize STEREO's scientific potential in gaining a greater understanding of the heliosphere.

A Concept for the One Degree Imager (ODI) Data Reduction Pipeline and Archiving System

NASA Astrophysics Data System (ADS)

Knezek, Patricia; Stobie, B.; Michael, S.; Valdes, F.; Marru, S.; Henschel, R.; Pierce, M.

2010-05-01

The One Degree Imager (ODI), currently being built by the WIYN Observatory, will provide tremendous possibilities for conducting diverse scientific programs. ODI will be a complex instrument, using non-conventional Orthogonal Transfer Array (OTA) detectors. Due to its large field of view, small pixel size, use of OTA technology, and expected frequent use, ODI will produce vast amounts of astronomical data. If ODI is to achieve its full potential, a data reduction pipeline must be developed. Long-term archiving must also be incorporated into the pipeline system to ensure the continued value of ODI data. This paper presents a concept for an ODI data reduction pipeline and archiving system. To limit costs and development time, our plan leverages existing software and hardware, including existing pipeline software, Science Gateways, Computational Grid & Cloud Technology, Indiana University's Data Capacitor and Massive Data Storage System, and TeraGrid compute resources. Existing pipeline software will be augmented to add functionality required to meet challenges specific to ODI, enhance end-user control, and enable the execution of the pipeline on grid resources including national grid resources such as the TeraGrid and Open Science Grid. The planned system offers consistent standard reductions and end-user flexibility when working with images beyond the initial instrument signature removal. It also gives end-users access to computational and storage resources far beyond what are typically available at most institutions. Overall, the proposed system provides a wide array of software tools and the necessary hardware resources to use them effectively.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

Software management tools: Lessons learned from use

NASA Technical Reports Server (NTRS)

Reifer, D. J.; Valett, J.; Knight, J.; Wenneson, G.

1985-01-01

Experience in inserting software project planning tools into more than 100 projects producing mission critical software are discussed. The problems the software project manager faces are listed along with methods and tools available to handle them. Experience is reported with the Project Manager's Workstation (PMW) and the SoftCost-R cost estimating package. Finally, the results of a survey, which looked at what could be done in the future to overcome the problems experienced and build a set of truly useful tools, are presented.

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

PubMed

Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

2017-08-15

Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Software phantom with realistic speckle modeling for validation of image analysis methods in echocardiography

NASA Astrophysics Data System (ADS)

Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten

2014-03-01

Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.

Symbolic Constraint Maintenance Grid

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

Version 3.1 of Symbolic Constraint Maintenance Grid (SCMG) is a software system that provides a general conceptual framework for utilizing pre-existing programming techniques to perform symbolic transformations of data. SCMG also provides a language (and an associated communication method and protocol) for representing constraints on the original non-symbolic data. SCMG provides a facility for exchanging information between numeric and symbolic components without knowing the details of the components themselves. In essence, it integrates symbolic software tools (for diagnosis, prognosis, and planning) with non-artificial-intelligence software. SCMG executes a process of symbolic summarization and monitoring of continuous time series data that are being abstractly represented as symbolic templates of information exchange. This summarization process enables such symbolic- reasoning computing systems as artificial- intelligence planning systems to evaluate the significance and effects of channels of data more efficiently than would otherwise be possible. As a result of the increased efficiency in representation, reasoning software can monitor more channels and is thus able to perform monitoring and control functions more effectively.

MFV-class: a multi-faceted visualization tool of object classes.

PubMed

Zhang, Zhi-meng; Pan, Yun-he; Zhuang, Yue-ting

2004-11-01

Classes are key software components in an object-oriented software system. In many industrial OO software systems, there are some classes that have complicated structure and relationships. So in the processes of software maintenance, testing, software reengineering, software reuse and software restructure, it is a challenge for software engineers to understand these classes thoroughly. This paper proposes a class comprehension model based on constructivist learning theory, and implements a software visualization tool (MFV-Class) to help in the comprehension of a class. The tool provides multiple views of class to uncover manifold facets of class contents. It enables visualizing three object-oriented metrics of classes to help users focus on the understanding process. A case study was conducted to evaluate our approach and the toolkit.

TaxI: a software tool for DNA barcoding using distance methods

PubMed Central

Steinke, Dirk; Vences, Miguel; Salzburger, Walter; Meyer, Axel

2005-01-01

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding. PMID:16214755

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

PubMed

Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

2016-09-02

Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNP(xl) for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNP(xl), represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

Standardizing Exoplanet Analysis with the Exoplanet Characterization Tool Kit (ExoCTK)

NASA Astrophysics Data System (ADS)

Fowler, Julia; Stevenson, Kevin B.; Lewis, Nikole K.; Fraine, Jonathan D.; Pueyo, Laurent; Bruno, Giovanni; Filippazzo, Joe; Hill, Matthew; Batalha, Natasha; Wakeford, Hannah; Bushra, Rafia

2018-06-01

Exoplanet characterization depends critically on analysis tools, models, and spectral libraries that are constantly under development and have no single source nor sense of unified style or methods. The complexity of spectroscopic analysis and initial time commitment required to become competitive is prohibitive to new researchers entering the field, as well as a remaining obstacle for established groups hoping to contribute in a comparable manner to their peers. As a solution, we are developing an open-source, modular data analysis package in Python and a publicly facing web interface including tools that address atmospheric characterization, transit observation planning with JWST, JWST corongraphy simulations, limb darkening, forward modeling, and data reduction, as well as libraries of stellar, planet, and opacity models. The foundation of these software tools and libraries exist within pockets of the exoplanet community, but our project will gather these seedling tools and grow a robust, uniform, and well-maintained exoplanet characterization toolkit.

ToxPredictor: a Toxicity Estimation Software Tool

EPA Science Inventory

The Computational Toxicology Team within the National Risk Management Research Laboratory has developed a software tool that will allow the user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be ac...

Dynamic visualization techniques for high consequence software

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

Pollock, G.M.

1998-02-01

This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification. The prototype tool is described along with the requirements constraint language after a brief literature review is presented. Examples of howmore » the tool can be used are also presented. In conclusion, the most significant advantage of this tool is to provide a first step in evaluating specification completeness, and to provide a more productive method for program comprehension and debugging. The expected payoff is increased software surety confidence, increased program comprehension, and reduced development and debugging time.« less

Bayesian networks for satellite payload testing

NASA Astrophysics Data System (ADS)

Przytula, Krzysztof W.; Hagen, Frank; Yung, Kar

1999-11-01

Satellite payloads are fast increasing in complexity, resulting in commensurate growth in cost of manufacturing and operation. A need exists for a software tool, which would assist engineers in production and operation of satellite systems. We have designed and implemented a software tool, which performs part of this task. The tool aids a test engineer in debugging satellite payloads during system testing. At this stage of satellite integration and testing both the tested payload and the testing equipment represent complicated systems consisting of a very large number of components and devices. When an error is detected during execution of a test procedure, the tool presents to the engineer a ranked list of potential sources of the error and a list of recommended further tests. The engineer decides this on this basis if to perform some of the recommended additional test or replace the suspect component. The tool has been installed in payload testing facility. The tool is based on Bayesian networks, a graphical method of representing uncertainty in terms of probabilistic influences. The Bayesian network was configured using detailed flow diagrams of testing procedures and block diagrams of the payload and testing hardware. The conditional and prior probability values were initially obtained from experts and refined in later stages of design. The Bayesian network provided a very informative model of the payload and testing equipment and inspired many new ideas regarding the future test procedures and testing equipment configurations. The tool is the first step in developing a family of tools for various phases of satellite integration and operation.

Bringing your tools to CyVerse Discovery Environment using Docker

PubMed Central

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse’s Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse’s production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use. PMID:27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

PubMed

Devisetty, Upendra Kumar; Kennedy, Kathleen; Sarando, Paul; Merchant, Nirav; Lyons, Eric

2016-01-01

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

Cloud-Based Computational Tools for Earth Science Applications

NASA Astrophysics Data System (ADS)

Arendt, A. A.; Fatland, R.; Howe, B.

2015-12-01

Earth scientists are increasingly required to think across disciplines and utilize a wide range of datasets in order to solve complex environmental challenges. Although significant progress has been made in distributing data, researchers must still invest heavily in developing computational tools to accommodate their specific domain. Here we document our development of lightweight computational data systems aimed at enabling rapid data distribution, analytics and problem solving tools for Earth science applications. Our goal is for these systems to be easily deployable, scalable and flexible to accommodate new research directions. As an example we describe "Ice2Ocean", a software system aimed at predicting runoff from snow and ice in the Gulf of Alaska region. Our backend components include relational database software to handle tabular and vector datasets, Python tools (NumPy, pandas and xray) for rapid querying of gridded climate data, and an energy and mass balance hydrological simulation model (SnowModel). These components are hosted in a cloud environment for direct access across research teams, and can also be accessed via API web services using a REST interface. This API is a vital component of our system architecture, as it enables quick integration of our analytical tools across disciplines, and can be accessed by any existing data distribution centers. We will showcase several data integration and visualization examples to illustrate how our system has expanded our ability to conduct cross-disciplinary research.

PD5: a general purpose library for primer design software.

PubMed

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

2013-01-01

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

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.

PubMed

Sun, Peng; Speicher, Nora K; Röttger, Richard; Guo, Jiong; Baumbach, Jan

2014-05-01

The explosion of the biological data has dramatically reformed today's biological research. The need to integrate and analyze high-dimensional biological data on a large scale is driving the development of novel bioinformatics approaches. Biclustering, also known as 'simultaneous clustering' or 'co-clustering', has been successfully utilized to discover local patterns in gene expression data and similar biomedical data types. Here, we contribute a new heuristic: 'Bi-Force'. It is based on the weighted bicluster editing model, to perform biclustering on arbitrary sets of biological entities, given any kind of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A comparative analysis of biclustering algorithms for gene expressiondata. Brief. Bioinform., 14:279-292.) and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, BiMax, Spectral, xMOTIFs and ISA. To this end, a suite of synthetic datasets as well as nine large gene expression datasets from Gene Expression Omnibus were analyzed. All resulting biclusters were subsequently investigated by Gene Ontology enrichment analysis to evaluate their biological relevance. The distinct theoretical foundation of Bi-Force (bicluster editing) is more powerful than strict biclustering. We thus outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used datasets are publicly available at http://biclue.mpi-inf.mpg.de. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Proceedings of the Ninth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1984-01-01

Experiences in measurement, utilization, and evaluation of software methodologies, models, and tools are discussed. NASA's involvement in ever larger and more complex systems, like the space station project, provides a motive for the support of software engineering research and the exchange of ideas in such forums. The topics of current SEL research are software error studies, experiments with software development, and software tools.

Slow magnetic monopoles search in NOvA

NASA Astrophysics Data System (ADS)

Antoshkin, Alexander; Frank, Martin

2018-04-01

The NOvA far detector is well suited for finding exotic particles due to its technical features (see [1]). One type of those exotic particles is a "slow" magnetic monopole. It is assumed that the energy deposition of such monopoles should be enough to be registered (see [2]). Measurement of the expected signals was performed on the NOvA test bench at JINR (see [3]). Result of this measurement allows us to perform slow monopole's research using NOvA software and hardware with high efficiency. As a whole, the research can lead to a discovery, or it can limit the existence of monopoles in a wide range of parameters, previously unreachable in other experiments (MACRO, SLIM, RICE, IceCube). Several special software tools have been developed. Slow Monopole Trigger has been created and implemented in the NOvA Data-Driven-Trigger system. Also, an online reconstruction algorithm has been developed and tested on 5% of the data. A technical description of these tools and current results of the analysis are presented in this work.

Performance evaluation of automated segmentation software on optical coherence tomography volume data

PubMed Central

Tian, Jing; Varga, Boglarka; Tatrai, Erika; Fanni, Palya; Somfai, Gabor Mark; Smiddy, William E.

2016-01-01

Over the past two decades a significant number of OCT segmentation approaches have been proposed in the literature. Each methodology has been conceived for and/or evaluated using specific datasets that do not reflect the complexities of the majority of widely available retinal features observed in clinical settings. In addition, there does not exist an appropriate OCT dataset with ground truth that reflects the realities of everyday retinal features observed in clinical settings. While the need for unbiased performance evaluation of automated segmentation algorithms is obvious, the validation process of segmentation algorithms have been usually performed by comparing with manual labelings from each study and there has been a lack of common ground truth. Therefore, a performance comparison of different algorithms using the same ground truth has never been performed. This paper reviews research-oriented tools for automated segmentation of the retinal tissue on OCT images. It also evaluates and compares the performance of these software tools with a common ground truth. PMID:27159849

Development of a competency mapping tool for undergraduate professional degree programmes, using mechanical engineering as a case study

NASA Astrophysics Data System (ADS)

Holmes, David W.; Sheehan, Madoc; Birks, Melanie; Smithson, John

2018-01-01

Mapping the curriculum of a professional degree to the associated competency standard ensures graduates have the competence to perform as professionals. Existing approaches to competence mapping vary greatly in depth, complexity, and effectiveness, and a standardised approach remains elusive. This paper describes a new mapping software tool that streamlines and standardises the competency mapping process. The available analytics facilitate ongoing programme review, management, and accreditation. The complete mapping and analysis of an Australian mechanical engineering degree programme is described as a case study. Each subject is mapped by evaluating the amount and depth of competence development present. Combining subject results then enables highly detailed programme level analysis. The mapping process is designed to be administratively light, with aspects of professional development embedded in the software. The effective competence mapping described in this paper enables quantification of learning within a professional degree programme, and provides a mechanism for holistic programme improvement.

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

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

Sweezy, Jeremy Ed

2016-01-21

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

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

2008-03-01

The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

Preliminary Development of an Object-Oriented Optimization Tool

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2011-01-01

The National Aeronautics and Space Administration Dryden Flight Research Center has developed a FORTRAN-based object-oriented optimization (O3) tool that leverages existing tools and practices and allows easy integration and adoption of new state-of-the-art software. The object-oriented framework can integrate the analysis codes for multiple disciplines, as opposed to relying on one code to perform analysis for all disciplines. Optimization can thus take place within each discipline module, or in a loop between the central executive module and the discipline modules, or both. Six sample optimization problems are presented. The first four sample problems are based on simple mathematical equations; the fifth and sixth problems consider a three-bar truss, which is a classical example in structural synthesis. Instructions for preparing input data for the O3 tool are presented.

Software Management Environment (SME): Components and algorithms

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1994-01-01

This document presents the components and algorithms of the Software Management Environment (SME), a management tool developed for the Software Engineering Branch (Code 552) of the Flight Dynamics Division (FDD) of the Goddard Space Flight Center (GSFC). The SME provides an integrated set of visually oriented experienced-based tools that can assist software development managers in managing and planning software development projects. This document describes and illustrates the analysis functions that underlie the SME's project monitoring, estimation, and planning tools. 'SME Components and Algorithms' is a companion reference to 'SME Concepts and Architecture' and 'Software Engineering Laboratory (SEL) Relationships, Models, and Management Rules.'

Supporting Interdisciplinary Collaboration Through Reusable Free Software. A Research Student Experience

NASA Astrophysics Data System (ADS)

Dimech, C.

2013-12-01

In this contribution, I present a critical evaluation of my experience as a research student conducting an interdisciplinary project that bridges the world of geoscience with that of astronomy. The major challenge consists in studying and modifying existing geophysical software to work with synthetic solar data not obtained by direct measurement but useful for testing and evaluation, and data released from the satellite HINODE and the Solar Dynamics Observatory. I have been fortunate to collaborate closely with multiple geoscientists keen to share their software codes and help me understand their implementations so I can extend the methodology to solve problems in solar physics. Moreover, two additional experiences have helped me develop my research and collaborative skills. First was an opportunity to involve an undergraduate student, and secondly, my participation at the GNU Hackers Meeting in Paris. Three aspects that need particular attention to enhance the collective productivity of any group of individuals keen to extend existing codes to achieve further interdisciplinary goals have been identified. (1) The production of easily reusable code that users can study and modify even when large sets of computations are involved. (2) The transformation of solutions into tools that are 100% free software. (3) The harmonisation of collaborative interactions that effectively tackle the two aforementioned tasks. Each one will be discussed in detail during this session based on my experience as a research student.

Harnessing Scientific Literature Reports for Pharmacovigilance

PubMed Central

Ripple, Anna; Tonning, Joseph; Munoz, Monica; Hasan, Rashedul; Ly, Thomas; Francis, Henry; Bodenreider, Olivier

2017-01-01

Summary Objectives We seek to develop a prototype software analytical tool to augment FDA regulatory reviewers’ capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool. Methods A prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use. Results All usability test participants cited the tool’s ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool’s automated literature search relative to a manual ‘all fields’ PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools. Conclusions Usability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction. PMID:28326432

Extending software repository hosting to code review and testing

NASA Astrophysics Data System (ADS)

Gonzalez Alvarez, A.; Aparicio Cotarelo, B.; Lossent, A.; Andersen, T.; Trzcinska, A.; Asbury, D.; Hłimyr, N.; Meinhard, H.

2015-12-01

We will describe how CERN's services around Issue Tracking and Version Control have evolved, and what the plans for the future are. We will describe the services main design, integration and structure, giving special attention to the new requirements from the community of users in terms of collaboration and integration tools and how we address this challenge when defining new services based on GitLab for collaboration to replace our current Gitolite service and Code Review and Jenkins for Continuous Integration. These new services complement the existing ones to create a new global "development tool stack" where each working group can place its particular development work-flow.

Improvement of Computer Software Quality through Software Automated Tools.

DTIC Science & Technology

1986-08-31

requirement for increased emphasis on software quality assurance has lead to the creation of various methods of verification and validation. Experience...result was a vast array of methods , systems, languages and automated tools to assist in the process. Given that the primary role of quality assurance is...Unfortunately, there is no single method , tool or technique that can insure accurate, reliable and cost effective software. Therefore, government and industry

Reviews of Instructional Software in Scholarly Journals: A Selected Bibliography.

ERIC Educational Resources Information Center

Bantz, David A.; And Others

This bibliography lists reviews of more than 100 instructional software packages, which are arranged alphabetically by discipline. Information provided for each entry includes the topical emphasis, type of software (i.e., simulation, tutorial, analysis tool, test generator, database, writing tool, drill, plotting tool, videodisc), the journal…

Modeling and MBL: Software Tools for Science.

ERIC Educational Resources Information Center

Tinker, Robert F.

Recent technological advances and new software packages put unprecedented power for experimenting and theory-building in the hands of students at all levels. Microcomputer-based laboratory (MBL) and model-solving tools illustrate the educational potential of the technology. These tools include modeling software and three MBL packages (which are…

Assistive Software Tools for Secondary-Level Students with Literacy Difficulties

ERIC Educational Resources Information Center

Lange, Alissa A.; McPhillips, Martin; Mulhern, Gerry; Wylie, Judith

2006-01-01

The present study assessed the compensatory effectiveness of four assistive software tools (speech synthesis, spellchecker, homophone tool, and dictionary) on literacy. Secondary-level students (N = 93) with reading difficulties completed computer-based tests of literacy skills. Training on their respective software followed for those assigned to…

Estimation of toxicity using a Java based software tool

EPA Science Inventory

A software tool has been developed that will allow a user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be accessed using a web browser (or alternatively downloaded and ran as a stand alone applic...

Software Construction and Analysis Tools for Future Space Missions

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Clancy, Daniel (Technical Monitor)

2002-01-01

NASA and its international partners will increasingly depend on software-based systems to implement advanced functions for future space missions, such as Martian rovers that autonomously navigate long distances exploring geographic features formed by surface water early in the planet's history. The software-based functions for these missions will need to be robust and highly reliable, raising significant challenges in the context of recent Mars mission failures attributed to software faults. After reviewing these challenges, this paper describes tools that have been developed at NASA Ames that could contribute to meeting these challenges; 1) Program synthesis tools based on automated inference that generate documentation for manual review and annotations for automated certification. 2) Model-checking tools for concurrent object-oriented software that achieve memorability through synergy with program abstraction and static analysis tools.

Software tool for portal dosimetry research.

PubMed

Vial, P; Hunt, P; Greer, P B; Oliver, L; Baldock, C

2008-09-01

This paper describes a software tool developed for research into the use of an electronic portal imaging device (EPID) to verify dose for intensity modulated radiation therapy (IMRT) beams. A portal dose image prediction (PDIP) model that predicts the EPID response to IMRT beams has been implemented into a commercially available treatment planning system (TPS). The software tool described in this work was developed to modify the TPS PDIP model by incorporating correction factors into the predicted EPID image to account for the difference in EPID response to open beam radiation and multileaf collimator (MLC) transmitted radiation. The processes performed by the software tool include; i) read the MLC file and the PDIP from the TPS, ii) calculate the fraction of beam-on time that each point in the IMRT beam is shielded by MLC leaves, iii) interpolate correction factors from look-up tables, iv) create a corrected PDIP image from the product of the original PDIP and the correction factors and write the corrected image to file, v) display, analyse, and export various image datasets. The software tool was developed using the Microsoft Visual Studio.NET framework with the C# compiler. The operation of the software tool was validated. This software provided useful tools for EPID dosimetry research, and it is being utilised and further developed in ongoing EPID dosimetry and IMRT dosimetry projects.

An Expertise Recommender using Web Mining

NASA Technical Reports Server (NTRS)

Joshi, Anupam; Chandrasekaran, Purnima; ShuYang, Michelle; Ramakrishnan, Ramya

2001-01-01

This report explored techniques to mine web pages of scientists to extract information regarding their expertise, build expertise chains and referral webs, and semi automatically combine this information with directory information services to create a recommender system that permits query by expertise. The approach included experimenting with existing techniques that have been reported in research literature in recent past , and adapted them as needed. In addition, software tools were developed to capture and use this information.

Ada Programming Support Environment (APSE) Evaluation and Validation (E&V) Team

DTIC Science & Technology

1991-12-31

standards. The purpose of the team was to assist the project in several ways. Raymond Szymanski of Wright Research Iand Development Center (WRDC, now...debuggers, program library systems, and compiler diagnostics. The test suite does not include explicit tests for the existence of language features . The...support software is a set of tools and procedures which assist in preparing and executing the test suite, in extracting data from the results of

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

Expert system development for commonality analysis in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1987-01-01

This report is a combination of foundational mathematics and software design. A mathematical model of the Commonality Analysis problem was developed and some important properties discovered. The complexity of the problem is described herein and techniques, both deterministic and heuristic, for reducing that complexity are presented. Weaknesses are pointed out in the existing software (System Commonality Analysis Tool) and several improvements are recommended. It is recommended that: (1) an expert system for guiding the design of new databases be developed; (2) a distributed knowledge base be created and maintained for the purpose of encoding the commonality relationships between design items in commonality databases; (3) a software module be produced which automatically generates commonality alternative sets from commonality databases using the knowledge associated with those databases; and (4) a more complete commonality analysis module be written which is capable of generating any type of feasible solution.

Globes from global data: Charting international research networks with the GRASS GIS r.out.polycones add-on module.

NASA Astrophysics Data System (ADS)

Löwe, Peter

2015-04-01

Many Free and Open Source Software (FOSS) tools have been created for the various application fields within geoscience. While FOSS allows re-implementation of functionalities in new environments by access to the original codebase, the easiest approach to build new software solutions for new problems is the combination or merging of existing software tools. Such mash-ups are implemented by embedding and encapsulating FOSS tools within each another, effectively focusing the use of the embedded software to the specific role it needs to perform in the given scenario, while ignoring all its other capabilities. GRASS GIS is a powerful and established FOSS GIS for raster, vector and volume data processing while the Generic Mapping Tools (GMT) are a suite of powerful Open Source mapping tools, which exceed the mapping capabilities of GRASS GIS. This poster reports on the new GRASS GIS add-on module r.out.polycones. It enables users to utilize non-continuous projections for map production within the GRASS production environment. This is implemented on the software level by encapsulating a subset of GMT mapping capabilities into a GRASS GIS (Version 6.x) add-on module. The module was developed at the German National Library of Science and Technology (TIB) to provide custom global maps of scientific collaboration networks, such as the DataCite consortium, the registration agency for Digital Object Identifiers (DOI) for research data. The GRASS GIS add-on module can be used for global mapping of raster data into a variety of non continuous sinosoidal projections, allowing the creation of printable biangles (gores) to be used for globe making. Due to the well structured modular nature of GRASS modules, technical follow-up work will focus on API-level Python-based integration in GRASS 7 [1]. Based on this, GMT based mapping capabilities in GRASS will be extended beyond non-continuous sinosoidal maps and advanced from raster-layers to content GRASS display monitors. References: [1] Petras, V., Petrasova, A., Chemin, Y., Zambelli, P., Landa, M., Gebbert, S., Neteler, N., Löwe, P.: Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7, Geophysical Research Abstracts Vol. 17, EGU2015-8142, 2015 (in preparation)

Dataflow Design Tool: User's Manual

NASA Technical Reports Server (NTRS)

Jones, Robert L., III

1996-01-01

The Dataflow Design Tool is a software tool for selecting a multiprocessor scheduling solution for a class of computational problems. The problems of interest are those that can be described with a dataflow graph and are intended to be executed repetitively on a set of identical processors. Typical applications include signal processing and control law problems. The software tool implements graph-search algorithms and analysis techniques based on the dataflow paradigm. Dataflow analyses provided by the software are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool provides performance optimization through the inclusion of artificial precedence constraints among the schedulable tasks. The user interface and tool capabilities are described. Examples are provided to demonstrate the analysis, scheduling, and optimization functions facilitated by the tool.

TCGA Expedition: A Data Acquisition and Management System for TCGA Data

PubMed Central

Chandran, Uma R.; Medvedeva, Olga P.; Barmada, M. Michael; Blood, Philip D.; Chakka, Anish; Luthra, Soumya; Ferreira, Antonio; Wong, Kim F.; Lee, Adrian V.; Zhang, Zhihui; Budden, Robert; Scott, J. Ray; Berndt, Annerose; Berg, Jeremy M.; Jacobson, Rebecca S.

2016-01-01

Background The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices. Results TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR) that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing; having locally accessible WGS BAM files has proven invaluable. Conclusion Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets. PMID:27788220

Data Publication and Interoperability for Long Tail Researchers via the Open Data Repository's (ODR) Data Publisher.

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R.; Downs, R. T.; Blake, D. F.; Fonda, M.; Pires, A.

2016-12-01

Working primarily with astrobiology researchers at NASA Ames, the Open Data Repository (ODR) has been conducting a software pilot to meet the varying needs of this multidisciplinary community. Astrobiology researchers often have small communities or operate individually with unique data sets that don't easily fit into existing database structures. The ODR constructed its Data Publisher software to allow researchers to create databases with common metadata structures and subsequently extend them to meet their individual needs and data requirements. The software accomplishes these tasks through a web-based interface that allows collaborative creation and revision of common metadata templates and individual extensions to these templates for custom data sets. This allows researchers to search disparate datasets based on common metadata established through the metadata tools, but still facilitates distinct analyses and data that may be stored alongside the required common metadata. The software produces web pages that can be made publicly available at the researcher's discretion so that users may search and browse the data in an effort to make interoperability and data discovery a human-friendly task while also providing semantic data for machine-based discovery. Once relevant data has been identified, researchers can utilize the built-in application programming interface (API) that exposes the data for machine-based consumption and integration with existing data analysis tools (e.g. R, MATLAB, Project Jupyter - http://jupyter.org). The current evolution of the project has created the Astrobiology Habitable Environments Database (AHED)[1] which provides an interface to databases connected through a common metadata core. In the next project phase, the goal is for small research teams and groups to be self-sufficient in publishing their research data to meet funding mandates and academic requirements as well as fostering increased data discovery and interoperability through human-readable and machine-readable interfaces. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, MSL. [1] B. Lafuente et al. (2016) AGU, submitted.

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.

PubMed

Johnson, Benjamin K; Scholz, Matthew B; Teal, Tracy K; Abramovitch, Robert B

2016-02-04

Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes. In spite of the numerous tools developed for each component of an RNA-seq analysis workflow, easy-to-use bacterially oriented workflow applications to combine multiple tools and automate the process are lacking. With many tools to choose from for each step, the task of identifying a specific tool, adapting the input/output options to the specific use-case, and integrating the tools into a coherent analysis pipeline is not a trivial endeavor, particularly for microbiologists with limited bioinformatics experience. To make bacterial RNA-seq data analysis more accessible, we developed a Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis (SPARTA). SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. SPARTA provides an easy-to-use bacterial RNA-seq transcriptional profiling workflow to identify differentially expressed genes between experimental conditions. This software will enable microbiologists with limited bioinformatics experience to analyze their data and integrate next generation sequencing (NGS) technologies into the classroom. The SPARTA software and tutorial are available at sparta.readthedocs.org.

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

PubMed Central

2012-01-01

Background Further advances in modern microscopy are leading to teravoxel-sized tiled 3D images at high resolution, thus increasing the dimension of the stitching problem of at least two orders of magnitude. The existing software solutions do not seem adequate to address the additional requirements arising from these datasets, such as the minimization of memory usage and the need to process just a small portion of data. Results We propose a free and fully automated 3D Stitching tool designed to match the special requirements coming out of teravoxel-sized tiled microscopy images that is able to stitch them in a reasonable time even on workstations with limited resources. The tool was tested on teravoxel-sized whole mouse brain images with micrometer resolution and it was also compared with the state-of-the-art stitching tools on megavoxel-sized publicy available datasets. This comparison confirmed that the solutions we adopted are suited for stitching very large images and also perform well on datasets with different characteristics. Indeed, some of the algorithms embedded in other stitching tools could be easily integrated in our framework if they turned out to be more effective on other classes of images. To this purpose, we designed a software architecture which separates the strategies that use efficiently memory resources from the algorithms which may depend on the characteristics of the acquired images. Conclusions TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed. We provide TeraStitcher both as standalone application and as plugin of the free software Vaa3D. PMID:23181553

Techniques to Access Databases and Integrate Data for Hydrologic Modeling

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

Whelan, Gene; Tenney, Nathan D.; Pelton, Mitchell A.

2009-06-17

This document addresses techniques to access and integrate data for defining site-specific conditions and behaviors associated with ground-water and surface-water radionuclide transport applicable to U.S. Nuclear Regulatory Commission reviews. Environmental models typically require input data from multiple internal and external sources that may include, but are not limited to, stream and rainfall gage data, meteorological data, hydrogeological data, habitat data, and biological data. These data may be retrieved from a variety of organizations (e.g., federal, state, and regional) and source types (e.g., HTTP, FTP, and databases). Available data sources relevant to hydrologic analyses for reactor licensing are identified and reviewed.more » The data sources described can be useful to define model inputs and parameters, including site features (e.g., watershed boundaries, stream locations, reservoirs, site topography), site properties (e.g., surface conditions, subsurface hydraulic properties, water quality), and site boundary conditions, input forcings, and extreme events (e.g., stream discharge, lake levels, precipitation, recharge, flood and drought characteristics). Available software tools for accessing established databases, retrieving the data, and integrating it with models were identified and reviewed. The emphasis in this review was on existing software products with minimal required modifications to enable their use with the FRAMES modeling framework. The ability of four of these tools to access and retrieve the identified data sources was reviewed. These four software tools were the Hydrologic Data Acquisition and Processing System (HDAPS), Integrated Water Resources Modeling System (IWRMS) External Data Harvester, Data for Environmental Modeling Environmental Data Download Tool (D4EM EDDT), and the FRAMES Internet Database Tools. The IWRMS External Data Harvester and the D4EM EDDT were identified as the most promising tools based on their ability to access and retrieve the required data, and their ability to integrate the data into environmental models using the FRAMES environment.« less

Implementing Earned Value Management in the CxP EVA Systems Project Office

NASA Technical Reports Server (NTRS)

Sorge, Les L.

2009-01-01

Earned Value Management (EVM), like project management, is as much art as it is science to develop an implementation plan for a project. This presentation will cover issues that were overcome and the implementation strategy to deploy Earned Value Management (EVM) within the Constellation Program (CxP), EVA Systems Project Office (ESPO), as well as discuss additional hurdles that currently prevent the organization from optimizing EVM. Each organization and each project within an organization needs to mold an EVM implementation plan around existing processes and tools, while at the same time revising those existing processes and tools as necessary to make them compatible with EVM. The ESPO EVM implementation covers work breakdown structure, organizational breakdown structure, control account, work/planning package development; integrated master schedule development using an integrated master plan; incorporating reporting requirements for existing funding process such as Planning, Programming, Budgeting, and Execution (PPBE) and JSC Internal Task Agreements (ITA); and interfacing with other software tools such as the Systems Applications and Products (SAP) accounting system and the CxP wInsight EVM analysis tool. However, there are always areas for improvement and EVM is no exception. As EVM continues to mature within the NASA CxP, these areas will continue to be worked to resolution to provide the Program Managers, Project Managers, and Control Account Managers the best EVM data possible to make informed decisions.

Technical Note: Harmonizing met-ocean model data via standard web services within small research groups

USGS Publications Warehouse

Signell, Richard; Camossi, E.

2016-01-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Technical note: Harmonising metocean model data via standard web services within small research groups

NASA Astrophysics Data System (ADS)

Signell, Richard P.; Camossi, Elena

2016-05-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Type Safe Extensible Programming

NASA Astrophysics Data System (ADS)

Chae, Wonseok

2009-10-01

Software products evolve over time. Sometimes they evolve by adding new features, and sometimes by either fixing bugs or replacing outdated implementations with new ones. When software engineers fail to anticipate such evolution during development, they will eventually be forced to re-architect or re-build from scratch. Therefore, it has been common practice to prepare for changes so that software products are extensible over their lifetimes. However, making software extensible is challenging because it is difficult to anticipate successive changes and to provide adequate abstraction mechanisms over potential changes. Such extensibility mechanisms, furthermore, should not compromise any existing functionality during extension. Software engineers would benefit from a tool that provides a way to add extensions in a reliable way. It is natural to expect programming languages to serve this role. Extensible programming is one effort to address these issues. In this thesis, we present type safe extensible programming using the MLPolyR language. MLPolyR is an ML-like functional language whose type system provides type-safe extensibility mechanisms at several levels. After presenting the language, we will show how these extensibility mechanisms can be put to good use in the context of product line engineering. Product line engineering is an emerging software engineering paradigm that aims to manage variations, which originate from successive changes in software.

Techniques and implementation of the embedded rule-based expert system using Ada

NASA Technical Reports Server (NTRS)

Liberman, Eugene M.; Jones, Robert E.

1991-01-01

Ada is becoming an increasingly popular programming language for large Government-funded software projects. Ada with its portability, transportability, and maintainability lends itself well to today's complex programming environment. In addition, expert systems have also assured a growing role in providing human-like reasoning capability and expertise for computer systems. The integration of expert system technology with Ada programming language, specifically a rule-based expert system using an ART-Ada (Automated Reasoning Tool for Ada) system shell is discussed. The NASA Lewis Research Center was chosen as a beta test site for ART-Ada. The test was conducted by implementing the existing Autonomous Power EXpert System (APEX), a Lisp-base power expert system, in ART-Ada. Three components, the rule-based expert system, a graphics user interface, and communications software make up SMART-Ada (Systems fault Management with ART-Ada). The main objective, to conduct a beta test on the ART-Ada rule-based expert system shell, was achieved. The system is operational. New Ada tools will assist in future successful projects. ART-Ada is one such tool and is a viable alternative to the straight Ada code when an application requires a rule-based or knowledge-based approach.

APM_GUI: analyzing particle movement on the cell membrane and determining confinement.

PubMed

Menchón, Silvia A; Martín, Mauricio G; Dotti, Carlos G

2012-02-20

Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,. Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with. APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

PubMed

Misirli, Göksel; Nguyen, Tramy; McLaughlin, James Alastair; Vaidyanathan, Prashant; Jones, Timothy S; Densmore, Douglas; Myers, Chris; Wipat, Anil

2018-06-05

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.

Performance Assessment and Translation of Physiologically Based Pharmacokinetic Models From acslX to Berkeley Madonna, MATLAB, and R Language: Oxytetracycline and Gold Nanoparticles As Case Examples.

PubMed

Lin, Zhoumeng; Jaberi-Douraki, Majid; He, Chunla; Jin, Shiqiang; Yang, Raymond S H; Fisher, Jeffrey W; Riviere, Jim E

2017-07-01

Many physiologically based pharmacokinetic (PBPK) models for environmental chemicals, drugs, and nanomaterials have been developed to aid risk and safety assessments using acslX. However, acslX has been rendered sunset since November 2015. Alternative modeling tools and tutorials are needed for future PBPK applications. This forum article aimed to: (1) demonstrate the performance of 4 PBPK modeling software packages (acslX, Berkeley Madonna, MATLAB, and R language) tested using 2 existing models (oxytetracycline and gold nanoparticles); (2) provide a tutorial of PBPK model code conversion from acslX to Berkeley Madonna, MATLAB, and R language; (3) discuss the advantages and disadvantages of each software package in the implementation of PBPK models in toxicology, and (4) share our perspective about future direction in this field. Simulation results of plasma/tissue concentrations/amounts of oxytetracycline and gold from different models were compared visually and statistically with linear regression analyses. Simulation results from the original models were correlated well with results from the recoded models, with time-concentration/amount curves nearly superimposable and determination coefficients of 0.86-1.00. Step-by-step explanations of the recoding of the models in different software programs are provided in the Supplementary Data. In summary, this article presents a tutorial of PBPK model code conversion for a small molecule and a nanoparticle among 4 software packages, and a performance comparison of these software packages in PBPK model implementation. This tutorial helps beginners learn PBPK modeling, provides suggestions for selecting a suitable tool for future projects, and may lead to the transition from acslX to alternative modeling tools. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A LEAN approach toward automated analysis and data processing of polymers using proton NMR spectroscopy.

PubMed

de Brouwer, Hans; Stegeman, Gerrit

2011-02-01

To maximize utilization of expensive laboratory instruments and to make most effective use of skilled human resources, the entire chain of data processing, calculation, and reporting that is needed to transform raw NMR data into meaningful results was automated. The LEAN process improvement tools were used to identify non-value-added steps in the existing process. These steps were eliminated using an in-house developed software package, which allowed us to meet the key requirement of improving quality and reliability compared with the existing process while freeing up valuable human resources and increasing productivity. Reliability and quality were improved by the consistent data treatment as performed by the software and the uniform administration of results. Automating a single NMR spectrophotometer led to a reduction in operator time of 35%, doubling of the annual sample throughput from 1400 to 2800, and reducing the turn around time from 6 days to less than 2. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

PubMed

Burdick, David B; Cavnor, Chris C; Handcock, Jeremy; Killcoyne, Sarah; Lin, Jake; Marzolf, Bruz; Ramsey, Stephen A; Rovira, Hector; Bressler, Ryan; Shmulevich, Ilya; Boyle, John

2010-07-14

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

PubMed Central

2010-01-01

Background High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Results Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. Conclusion The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services. PMID:20630057

Parallel software tools at Langley Research Center

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Tennille, Geoffrey M.; Lakeotes, Christopher D.; Randall, Donald P.; Arthur, Jarvis J.; Hammond, Dana P.; Mall, Gerald H.

1993-01-01

This document gives a brief overview of parallel software tools available on the Intel iPSC/860 parallel computer at Langley Research Center. It is intended to provide a source of information that is somewhat more concise than vendor-supplied material on the purpose and use of various tools. Each of the chapters on tools is organized in a similar manner covering an overview of the functionality, access information, how to effectively use the tool, observations about the tool and how it compares to similar software, known problems or shortfalls with the software, and reference documentation. It is primarily intended for users of the iPSC/860 at Langley Research Center and is appropriate for both the experienced and novice user.

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

Use of Google Earth to strengthen public health capacity and facilitate management of vector-borne diseases in resource-poor environments.

PubMed

Lozano-Fuentes, Saul; Elizondo-Quiroga, Darwin; Farfan-Ale, Jose Arturo; Loroño-Pino, Maria Alba; Garcia-Rejon, Julian; Gomez-Carro, Salvador; Lira-Zumbardo, Victor; Najera-Vazquez, Rosario; Fernandez-Salas, Ildefonso; Calderon-Martinez, Joaquin; Dominguez-Galera, Marco; Mis-Avila, Pedro; Morris, Natashia; Coleman, Michael; Moore, Chester G; Beaty, Barry J; Eisen, Lars

2008-09-01

Novel, inexpensive solutions are needed for improved management of vector-borne and other diseases in resource-poor environments. Emerging free software providing access to satellite imagery and simple editing tools (e.g. Google Earth) complement existing geographic information system (GIS) software and provide new opportunities for: (i) strengthening overall public health capacity through development of information for city infrastructures; and (ii) display of public health data directly on an image of the physical environment. We used freely accessible satellite imagery and a set of feature-making tools included in the software (allowing for production of polygons, lines and points) to generate information for city infrastructure and to display disease data in a dengue decision support system (DDSS) framework. Two cities in Mexico (Chetumal and Merida) were used to demonstrate that a basic representation of city infrastructure useful as a spatial backbone in a DDSS can be rapidly developed at minimal cost. Data layers generated included labelled polygons representing city blocks, lines representing streets, and points showing the locations of schools and health clinics. City blocks were colour-coded to show presence of dengue cases. The data layers were successfully imported in a format known as shapefile into a GIS software. The combination of Google Earth and free GIS software (e.g. HealthMapper, developed by WHO, and SIGEpi, developed by PAHO) has tremendous potential to strengthen overall public health capacity and facilitate decision support system approaches to prevention and control of vector-borne diseases in resource-poor environments.

pyLIMA: An Open-source Package for Microlensing Modeling. I. Presentation of the Software and Analysis of Single-lens Models

NASA Astrophysics Data System (ADS)

Bachelet, E.; Norbury, M.; Bozza, V.; Street, R.

2017-11-01

Microlensing is a unique tool, capable of detecting the “cold” planets between ˜1 and 10 au from their host stars and even unbound “free-floating” planets. This regime has been poorly sampled to date owing to the limitations of alternative planet-finding methods, but a watershed in discoveries is anticipated in the near future thanks to the planned microlensing surveys of WFIRST-AFTA and Euclid's Extended Mission. Of the many challenges inherent in these missions, the modeling of microlensing events will be of primary importance, yet it is often time-consuming, complex, and perceived as a daunting barrier to participation in the field. The large scale of future survey data products will require thorough but efficient modeling software, but, unlike other areas of exoplanet research, microlensing currently lacks a publicly available, well-documented package to conduct this type of analysis. We present version 1.0 of the python Lightcurve Identification and Microlensing Analysis (pyLIMA). This software is written in Python and uses existing packages as much as possible to make it widely accessible. In this paper, we describe the overall architecture of the software and the core modules for modeling single-lens events. To verify the performance of this software, we use it to model both real data sets from events published in the literature and generated test data produced using pyLIMA's simulation module. The results demonstrate that pyLIMA is an efficient tool for microlensing modeling. We will expand pyLIMA to consider more complex phenomena in the following papers.

The LINDSAY Virtual Human Project: an immersive approach to anatomy and physiology.

PubMed

Tworek, Janet K; Jamniczky, Heather A; Jacob, Christian; Hallgrímsson, Benedikt; Wright, Bruce

2013-01-01

The increasing number of digital anatomy teaching software packages challenges anatomy educators on how to best integrate these tools for teaching and learning. Realistically, there exists a complex interplay of design, implementation, politics, and learning needs in the development and integration of software for education, each of which may be further amplified by the somewhat siloed roles of programmers, faculty, and students. LINDSAY Presenter is newly designed software that permits faculty and students to model and manipulate three-dimensional anatomy presentations and images, while including embedded quizzes, links, and text-based content. A validated tool measuring impact across pedagogy, resources, interactivity, freedom, granularity, and factors outside the immediate learning event was used in conjunction with observation, field notes, and focus groups to critically examine the impact of attitudes and perceptions of all stakeholders in the early implementation of LINDSAY Presenter before and after a three-week trial period with the software. Results demonstrate that external, personal media usage, along with students' awareness of the need to apply anatomy to clinical professional situations drove expectations of LINDSAY Presenter. A focus on the software over learning, which can be expected during initial orientation, surprisingly remained after three weeks of use. The time-intensive investment required to create learning content is a detractor from user-generated content and may reflect the consumption nature of other forms of digital learning. Early excitement over new technologies needs to be tempered with clear understanding of what learning is afforded, and how these constructively support future application and integration into professional practice. Copyright © 2012 American Association of Anatomists.

A Quantitative Analysis of Open Source Software's Acceptability as Production-Quality Code

ERIC Educational Resources Information Center

Fischer, Michael

2011-01-01

The difficulty in writing defect-free software has been long acknowledged both by academia and industry. A constant battle occurs as developers seek to craft software that works within aggressive business schedules and deadlines. Many tools and techniques are used in attempt to manage these software projects. Software metrics are a tool that has…

Design and implementation of a general main axis controller for the ESO telescopes

NASA Astrophysics Data System (ADS)

Sandrock, Stefan; Di Lieto, Nicola; Pettazzi, Lorenzo; Erm, Toomas

2012-09-01

Most of the real-time control systems at the existing ESO telescopes were developed with "traditional" methods, using general purpose VMEbus electronics, and running applications that were coded by hand, mostly using the C programming language under VxWorks. As we are moving towards more modern design methods, we have explored a model-based design approach for real-time applications in the telescope area, and used the control algorithm of a standard telescope main axis as a first example. We wanted to have a clear work-flow that follows the "correct-by-construction" paradigm, where the implementation is testable in simulation on the development host, and where the testing time spent by debugging on target is minimized. It should respect the domains of control, electronics, and software engineers in the choice of tools. It should be a targetindependent approach so that the result could be deployed on various platforms. We have selected the Mathworks tools Simulink, Stateflow, and Embedded Coder for design and implementation, and LabVIEW with NI hardware for hardware-in-the-loop testing, all of which are widely used in industry. We describe how these tools have been used in order to model, simulate, and test the application. We also evaluate the benefits of this approach compared to the traditional method with respect to testing effort and maintainability. For a specific axis controller application we have successfully integrated the result into the legacy platform of the existing VLT software, as well as demonstrated how to use the same design for a new development with a completely different environment.

Feasibility of streamlining an interactive Bayesian-based diagnostic support tool designed for clinical practice

NASA Astrophysics Data System (ADS)

Chen, Po-Hao; Botzolakis, Emmanuel; Mohan, Suyash; Bryan, R. N.; Cook, Tessa

2016-03-01

In radiology, diagnostic errors occur either through the failure of detection or incorrect interpretation. Errors are estimated to occur in 30-35% of all exams and contribute to 40-54% of medical malpractice litigations. In this work, we focus on reducing incorrect interpretation of known imaging features. Existing literature categorizes cognitive bias leading a radiologist to an incorrect diagnosis despite having correctly recognized the abnormal imaging features: anchoring bias, framing effect, availability bias, and premature closure. Computational methods make a unique contribution, as they do not exhibit the same cognitive biases as a human. Bayesian networks formalize the diagnostic process. They modify pre-test diagnostic probabilities using clinical and imaging features, arriving at a post-test probability for each possible diagnosis. To translate Bayesian networks to clinical practice, we implemented an entirely web-based open-source software tool. In this tool, the radiologist first selects a network of choice (e.g. basal ganglia). Then, large, clearly labeled buttons displaying salient imaging features are displayed on the screen serving both as a checklist and for input. As the radiologist inputs the value of an extracted imaging feature, the conditional probabilities of each possible diagnosis are updated. The software presents its level of diagnostic discrimination using a Pareto distribution chart, updated with each additional imaging feature. Active collaboration with the clinical radiologist is a feasible approach to software design and leads to design decisions closely coupling the complex mathematics of conditional probability in Bayesian networks with practice.

Studying Axon-Astrocyte Functional Interactions by 3D Two-Photon Ca2+ Imaging: A Practical Guide to Experiments and "Big Data" Analysis.

PubMed

Savtchouk, Iaroslav; Carriero, Giovanni; Volterra, Andrea

2018-01-01

Recent advances in fast volumetric imaging have enabled rapid generation of large amounts of multi-dimensional functional data. While many computer frameworks exist for data storage and analysis of the multi-gigabyte Ca 2+ imaging experiments in neurons, they are less useful for analyzing Ca 2+ dynamics in astrocytes, where transients do not follow a predictable spatio-temporal distribution pattern. In this manuscript, we provide a detailed protocol and commentary for recording and analyzing three-dimensional (3D) Ca 2+ transients through time in GCaMP6f-expressing astrocytes of adult brain slices in response to axonal stimulation, using our recently developed tools to perform interactive exploration, filtering, and time-correlation analysis of the transients. In addition to the protocol, we release our in-house software tools and discuss parameters pertinent to conducting axonal stimulation/response experiments across various brain regions and conditions. Our software tools are available from the Volterra Lab webpage at https://wwwfbm.unil.ch/dnf/group/glia-an-active-synaptic-partner/member/volterra-andrea-volterra in the form of software plugins for Image J (NIH)-a de facto standard in scientific image analysis. Three programs are available: MultiROI_TZ_profiler for interactive graphing of several movable ROIs simultaneously, Gaussian_Filter5D for Gaussian filtering in several dimensions, and Correlation_Calculator for computing various cross-correlation parameters on voxel collections through time.

The mission events graphic generator software: A small tool with big results

NASA Technical Reports Server (NTRS)

Lupisella, Mark; Leibee, Jack; Scaffidi, Charles

1993-01-01

Utilization of graphics has long been a useful methodology for many aspects of spacecraft operations. A personal computer based software tool that implements straight-forward graphics and greatly enhances spacecraft operations is presented. This unique software tool is the Mission Events Graphic Generator (MEGG) software which is used in support of the Hubble Space Telescope (HST) Project. MEGG reads the HST mission schedule and generates a graphical timeline.

Computational challenges and human factors influencing the design and use of clinical research participant eligibility pre-screening tools

PubMed Central

2012-01-01

Background Clinical trials are the primary mechanism for advancing clinical care and evidenced-based practice, yet challenges with the recruitment of participants for such trials are widely recognized as a major barrier to these types of studies. Data warehouses (DW) store large amounts of heterogenous clinical data that can be used to enhance recruitment practices, but multiple challenges exist when using a data warehouse for such activities, due to the manner of collection, management, integration, analysis, and dissemination of the data. A critical step in leveraging the DW for recruitment purposes is being able to match trial eligibility criteria to discrete and semi-structured data types in the data warehouse, though trial eligibility criteria tend to be written without concern for their computability. We present the multi-modal evaluation of a web-based tool that can be used for pre-screening patients for clinical trial eligibility and assess the ability of this tool to be practically used for clinical research pre-screening and recruitment. Methods The study used a validation study, usability testing, and a heuristic evaluation to evaluate and characterize the operational characteristics of the software as well as human factors affecting its use. Results Clinical trials from the Division of Cardiology and the Department of Family Medicine were used for this multi-modal evaluation, which included a validation study, usability study, and a heuristic evaluation. From the results of the validation study, the software demonstrated a positive predictive value (PPV) of 54.12% and 0.7%, respectively, and a negative predictive value (NPV) of 73.3% and 87.5%, respectively, for two types of clinical trials. Heuristic principles concerning error prevention and documentation were characterized as the major usability issues during the heuristic evaluation. Conclusions This software is intended to provide an initial list of eligible patients to a clinical study coordinators, which provides a starting point for further eligibility screening by the coordinator. Because this software has a high “rule in” ability, meaning that it is able to remove patients who are not eligible for the study, the use of an automated tool built to leverage an existing enterprise DW can be beneficial to determining eligibility and facilitating clinical trial recruitment through pre-screening. While the results of this study are promising, further refinement and study of this and related approaches to automated eligibility screening, including comparison to other approaches and stakeholder perceptions, are needed and future studies are planned to address these needs. PMID:22646313

Computational challenges and human factors influencing the design and use of clinical research participant eligibility pre-screening tools.

PubMed

Pressler, Taylor R; Yen, Po-Yin; Ding, Jing; Liu, Jianhua; Embi, Peter J; Payne, Philip R O

2012-05-30

Clinical trials are the primary mechanism for advancing clinical care and evidenced-based practice, yet challenges with the recruitment of participants for such trials are widely recognized as a major barrier to these types of studies. Data warehouses (DW) store large amounts of heterogenous clinical data that can be used to enhance recruitment practices, but multiple challenges exist when using a data warehouse for such activities, due to the manner of collection, management, integration, analysis, and dissemination of the data. A critical step in leveraging the DW for recruitment purposes is being able to match trial eligibility criteria to discrete and semi-structured data types in the data warehouse, though trial eligibility criteria tend to be written without concern for their computability. We present the multi-modal evaluation of a web-based tool that can be used for pre-screening patients for clinical trial eligibility and assess the ability of this tool to be practically used for clinical research pre-screening and recruitment. The study used a validation study, usability testing, and a heuristic evaluation to evaluate and characterize the operational characteristics of the software as well as human factors affecting its use. Clinical trials from the Division of Cardiology and the Department of Family Medicine were used for this multi-modal evaluation, which included a validation study, usability study, and a heuristic evaluation. From the results of the validation study, the software demonstrated a positive predictive value (PPV) of 54.12% and 0.7%, respectively, and a negative predictive value (NPV) of 73.3% and 87.5%, respectively, for two types of clinical trials. Heuristic principles concerning error prevention and documentation were characterized as the major usability issues during the heuristic evaluation. This software is intended to provide an initial list of eligible patients to a clinical study coordinators, which provides a starting point for further eligibility screening by the coordinator. Because this software has a high "rule in" ability, meaning that it is able to remove patients who are not eligible for the study, the use of an automated tool built to leverage an existing enterprise DW can be beneficial to determining eligibility and facilitating clinical trial recruitment through pre-screening. While the results of this study are promising, further refinement and study of this and related approaches to automated eligibility screening, including comparison to other approaches and stakeholder perceptions, are needed and future studies are planned to address these needs.

User Studies: Developing Learning Strategy Tool Software for Children.

ERIC Educational Resources Information Center

Fitzgerald, Gail E.; Koury, Kevin A.; Peng, Hsinyi

This paper is a report of user studies for developing learning strategy tool software for children. The prototype software demonstrated is designed for children with learning and behavioral disabilities. The tools consist of easy-to-use templates for creating organizational, memory, and learning approach guides for use in classrooms and at home.…

MUST - An integrated system of support tools for research flight software engineering. [Multipurpose User-oriented Software Technology

NASA Technical Reports Server (NTRS)

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

1977-01-01

The objectives of NASA's MUST (Multipurpose User-oriented Software Technology) program at Langley Research Center are to cut the cost of producing software which effectively utilizes digital systems for flight research. These objectives will be accomplished by providing an integrated system of support software tools for use throughout the research flight software development process. A description of the overall MUST program and its progress toward the release of a first MUST system will be presented. This release includes: a special interactive user interface, a library of subroutines, assemblers, a compiler, automatic documentation tools, and a test and simulation system.

The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities in Assessing the Degradation of Cementitious Barriers - 13487

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

Flach, G.P.; Burns, H.H.; Langton, C.

2013-07-01

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up tomore » 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in K{sub d}/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software tools. Modification of the existing tools can provide many opportunities to bring defense in depth in prediction of the performance of cementitious barriers over time. (authors)« less

MOPEX: a software package for astronomical image processing and visualization

NASA Astrophysics Data System (ADS)

Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

2006-06-01

We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software package has been developed by a small group of software developers and scientists at the Spitzer Science Center. It is available for distribution at the Spitzer Science Center web page.

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

Tools for Administration of a UNIX-Based Network

NASA Technical Reports Server (NTRS)

LeClaire, Stephen; Farrar, Edward

2004-01-01

Several computer programs have been developed to enable efficient administration of a large, heterogeneous, UNIX-based computing and communication network that includes a variety of computers connected to a variety of subnetworks. One program provides secure software tools for administrators to create, modify, lock, and delete accounts of specific users. This program also provides tools for users to change their UNIX passwords and log-in shells. These tools check for errors. Another program comprises a client and a server component that, together, provide a secure mechanism to create, modify, and query quota levels on a network file system (NFS) mounted by use of the VERITAS File SystemJ software. The client software resides on an internal secure computer with a secure Web interface; one can gain access to the client software from any authorized computer capable of running web-browser software. The server software resides on a UNIX computer configured with the VERITAS software system. Directories where VERITAS quotas are applied are NFS-mounted. Another program is a Web-based, client/server Internet Protocol (IP) address tool that facilitates maintenance lookup of information about IP addresses for a network of computers.

Modeling biochemical transformation processes and information processing with Narrator.

PubMed

Mandel, Johannes J; Fuss, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-03-27

Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from http://www.narrator-tool.org.

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

PubMed

Aubrey, Wayne; Riley, Michael C; Young, Michael; King, Ross D; Oliver, Stephen G; Clare, Amanda

2015-01-01

Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation

PubMed Central

Aubrey, Wayne; Riley, Michael C.; Young, Michael; King, Ross D.; Oliver, Stephen G.; Clare, Amanda

2015-01-01

Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences), or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1) a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2) software to design the method’s primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs) from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome. PMID:26630677

XMI2USE: A Tool for Transforming XMI to USE Specifications

NASA Astrophysics Data System (ADS)

Sun, Wuliang; Song, Eunjee; Grabow, Paul C.; Simmonds, Devon M.

The UML-based Specification Environment (USE) tool supports syntactic analysis, type checking, consistency checking, and dynamic validation of invariants and pre-/post conditions specified in the Object Constraint Language (OCL). Due to its animation and analysis power, it is useful when checking critical non-functional properties such as security policies. However, the USE tool requires one to specify (i.e., "write") a model using its own textual language and does not allow one to import any model specification files created by other UML modeling tools. Hence, to make the best use of existing UML tools, we often create a model with OCL constraints using a modeling tool such as the IBM Rational Software Architect (RSA) and then use the USE tool for model validation. This approach, however, requires a manual transformation between the specifications of two different tool formats, which is error-prone and diminishes the benefit of automated model-level validations. In this paper, we describe our own implementation of a specification transformation engine that is based on the Model Driven Architecture (MDA) framework and currently supports automatic tool-level transformations from RSA to USE.

iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.

PubMed

Groppe, David M; Bickel, Stephan; Dykstra, Andrew R; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R; Lado, Fred A; Mehta, Ashesh D; Honey, Christopher J

2017-04-01

Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. It takes 30-60min of user time and 12-24h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. COMPARISON WITH EXISTING METHODS: iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg. Copyright © 2017 Elsevier B.V. All rights reserved.

Orbit Software Suite

NASA Technical Reports Server (NTRS)

Osgood, Cathy; Williams, Kevin; Gentry, Philip; Brownfield, Dana; Hallstrom, John; Stuit, Tim

2012-01-01

Orbit Software Suite is used to support a variety of NASA/DM (Dependable Multiprocessor) mission planning and analysis activities on the IPS (Intrusion Prevention System) platform. The suite of Orbit software tools (Orbit Design and Orbit Dynamics) resides on IPS/Linux workstations, and is used to perform mission design and analysis tasks corresponding to trajectory/ launch window, rendezvous, and proximity operations flight segments. A list of tools in Orbit Software Suite represents tool versions established during/after the Equipment Rehost-3 Project.

Software platform for simulation of a prototype proton CT scanner.

PubMed

Giacometti, Valentina; Bashkirov, Vladimir A; Piersimoni, Pierluigi; Guatelli, Susanna; Plautz, Tia E; Sadrozinski, Hartmut F-W; Johnson, Robert P; Zatserklyaniy, Andriy; Tessonnier, Thomas; Parodi, Katia; Rosenfeld, Anatoly B; Schulte, Reinhard W

2017-03-01

Proton computed tomography (pCT) is a promising imaging technique to substitute or at least complement x-ray CT for more accurate proton therapy treatment planning as it allows calculating directly proton relative stopping power from proton energy loss measurements. A proton CT scanner with a silicon-based particle tracking system and a five-stage scintillating energy detector has been completed. In parallel a modular software platform was developed to characterize the performance of the proposed pCT. The modular pCT software platform consists of (1) a Geant4-based simulation modeling the Loma Linda proton therapy beam line and the prototype proton CT scanner, (2) water equivalent path length (WEPL) calibration of the scintillating energy detector, and (3) image reconstruction algorithm for the reconstruction of the relative stopping power (RSP) of the scanned object. In this work, each component of the modular pCT software platform is described and validated with respect to experimental data and benchmarked against theoretical predictions. In particular, the RSP reconstruction was validated with both experimental scans, water column measurements, and theoretical calculations. The results show that the pCT software platform accurately reproduces the performance of the existing prototype pCT scanner with a RSP agreement between experimental and simulated values to better than 1.5%. The validated platform is a versatile tool for clinical proton CT performance and application studies in a virtual setting. The platform is flexible and can be modified to simulate not yet existing versions of pCT scanners and higher proton energies than those currently clinically available. © 2017 American Association of Physicists in Medicine.

47 CFR 73.9007 - Robustness requirements for covered demodulator products.

Code of Federal Regulations, 2010 CFR

2010-10-01

... RADIO SERVICES RADIO BROADCAST SERVICES Digital Broadcast Television Redistribution Control § 73.9007...-available tools or equipment also means specialized electronic tools or software tools that are widely... requirements set forth in this subpart. Such specialized electronic tools or software tools includes, but is...

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools.

PubMed

O'Callaghan, Sean; De Souza, David P; Isaac, Andrew; Wang, Qiao; Hodkinson, Luke; Olshansky, Moshe; Erwin, Tim; Appelbe, Bill; Tull, Dedreia L; Roessner, Ute; Bacic, Antony; McConville, Malcolm J; Likić, Vladimir A

2012-05-30

Gas chromatography-mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data tightly integrate data processing methods with graphical user interface facilitating interactive data processing. While interactive processing remains critically important in GC-MS applications, high-throughput studies increasingly dictate the need for command line tools, suitable for scripting of high-throughput, customized processing pipelines. PyMS comprises a library of functions for processing of instrument GC-MS data developed in Python. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX), noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. A novel common ion single quantitation algorithm allows automated, accurate quantitation of GC-MS electron impact (EI) fragmentation spectra when a large number of experiments are being analyzed. PyMS implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments. A set of specifically designed experiments was performed in-house and used to comparatively evaluate the performance of PyMS and three widely used software packages for GC-MS data processing (AMDIS, AnalyzerPro, and XCMS). PyMS is a novel software package for the processing of raw GC-MS data, particularly suitable for scripting of customized processing pipelines and for data processing in batch mode. PyMS provides limited graphical capabilities and can be used both for routine data processing and interactive/exploratory data analysis. In real-life GC-MS data processing scenarios PyMS performs as well or better than leading software packages. We demonstrate data processing scenarios simple to implement in PyMS, yet difficult to achieve with many conventional GC-MS data processing software. Automated sample processing and quantitation with PyMS can provide substantial time savings compared to more traditional interactive software systems that tightly integrate data processing with the graphical user interface.

An Assessment of Integrated Health Management (IHM) Frameworks

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

N. Lybeck; M. Tawfik; L. Bond

In order to meet the ever increasing demand for energy, the United States nuclear industry is turning to life extension of existing nuclear power plants (NPPs). Economically ensuring the safe, secure, and reliable operation of aging nuclear power plants presents many challenges. The 2009 Light Water Reactor Sustainability Workshop identified online monitoring of active and structural components as essential to the better understanding and management of the challenges posed by aging nuclear power plants. Additionally, there is increasing adoption of condition-based maintenance (CBM) for active components in NPPs. These techniques provide a foundation upon which a variety of advanced onlinemore » surveillance, diagnostic, and prognostic techniques can be deployed to continuously monitor and assess the health of NPP systems and components. The next step in the development of advanced online monitoring is to move beyond CBM to estimating the remaining useful life of active components using prognostic tools. Deployment of prognostic health management (PHM) on the scale of a NPP requires the use of an integrated health management (IHM) framework - a software product (or suite of products) used to manage the necessary elements needed for a complete implementation of online monitoring and prognostics. This paper provides a thoughtful look at the desirable functions and features of IHM architectures. A full PHM system involves several modules, including data acquisition, system modeling, fault detection, fault diagnostics, system prognostics, and advisory generation (operations and maintenance planning). The standards applicable to PHM applications are indentified and summarized. A list of evaluation criteria for PHM software products, developed to ensure scalability of the toolset to an environment with the complexity of a NPP, is presented. Fourteen commercially available PHM software products are identified and classified into four groups: research tools, PHM system development tools, deployable architectures, and peripheral tools.« less

Configuring the Orion Guidance, Navigation, and Control Flight Software for Automated Sequencing

NASA Technical Reports Server (NTRS)

Odegard, Ryan G.; Siliwinski, Tomasz K.; King, Ellis T.; Hart, Jeremy J.

2010-01-01

The Orion Crew Exploration Vehicle is being designed with greater automation capabilities than any other crewed spacecraft in NASA s history. The Guidance, Navigation, and Control (GN&C) flight software architecture is designed to provide a flexible and evolvable framework that accommodates increasing levels of automation over time. Within the GN&C flight software, a data-driven approach is used to configure software. This approach allows data reconfiguration and updates to automated sequences without requiring recompilation of the software. Because of the great dependency of the automation and the flight software on the configuration data, the data management is a vital component of the processes for software certification, mission design, and flight operations. To enable the automated sequencing and data configuration of the GN&C subsystem on Orion, a desktop database configuration tool has been developed. The database tool allows the specification of the GN&C activity sequences, the automated transitions in the software, and the corresponding parameter reconfigurations. These aspects of the GN&C automation on Orion are all coordinated via data management, and the database tool provides the ability to test the automation capabilities during the development of the GN&C software. In addition to providing the infrastructure to manage the GN&C automation, the database tool has been designed with capabilities to import and export artifacts for simulation analysis and documentation purposes. Furthermore, the database configuration tool, currently used to manage simulation data, is envisioned to evolve into a mission planning tool for generating and testing GN&C software sequences and configurations. A key enabler of the GN&C automation design, the database tool allows both the creation and maintenance of the data artifacts, as well as serving the critical role of helping to manage, visualize, and understand the data-driven parameters both during software development and throughout the life of the Orion project.

A requirements specification for a software design support system

NASA Technical Reports Server (NTRS)

Noonan, Robert E.

1988-01-01

Most existing software design systems (SDSS) support the use of only a single design methodology. A good SDSS should support a wide variety of design methods and languages including structured design, object-oriented design, and finite state machines. It might seem that a multiparadigm SDSS would be expensive in both time and money to construct. However, it is proposed that instead an extensible SDSS that directly implements only minimal database and graphical facilities be constructed. In particular, it should not directly implement tools to faciliate language definition and analysis. It is believed that such a system could be rapidly developed and put into limited production use, with the experience gained used to refine and evolve the systems over time.

Application of desktop computers in nuclear engineering education

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

Graves, H.W. Jr.

1990-01-01

Utilization of desktop computers in the academic environment is based on the same objectives as in the industrial environment - increased quality and efficiency. Desktop computers can be extremely useful teaching tools in two general areas: classroom demonstrations and homework assignments. Although differences in emphasis exist, tutorial programs share many characteristics with interactive software developed for the industrial environment. In the Reactor Design and Fuel Management course at the University of Maryland, several interactive tutorial programs provided by Energy analysis Software Service have been utilized. These programs have been designed to be sufficiently structured to permit an orderly, disciplined solutionmore » to the problem being solved, and yet be flexible enough to accommodate most problem solution options.« less

Technology Transfer Challenges for High-Assurance Software Engineering Tools

NASA Technical Reports Server (NTRS)

Koga, Dennis (Technical Monitor); Penix, John; Markosian, Lawrence Z.

2003-01-01

In this paper, we describe our experience with the challenges thar we are currently facing in our effort to develop advanced software verification and validation tools. We categorize these challenges into several areas: cost benefits modeling, tool usability, customer application domain, and organizational issues. We provide examples of challenges in each area and identrfj, open research issues in areas which limit our ability to transfer high-assurance software engineering tools into practice.

Caesy: A software tool for computer-aided engineering

NASA Technical Reports Server (NTRS)

Wette, Matt

1993-01-01

A new software tool, Caesy, is described. This tool provides a strongly typed programming environment for research in the development of algorithms and software for computer-aided control system design. A description of the user language and its implementation as they currently stand are presented along with a description of work in progress and areas of future work.

Software Tools for Battery Design | Transportation Research | NREL

Science.gov Websites

battery designers, developers, and manufacturers create affordable, high-performance lithium-ion (Li-ion Software Tools for Battery Design Software Tools for Battery Design Under the Computer-Aided ) batteries for next-generation electric-drive vehicles (EDVs). An image of a simulation of a battery pack

Using component technologies for web based wavelet enhanced mammographic image visualization.

PubMed

Sakellaropoulos, P; Costaridou, L; Panayiotakis, G

2000-01-01

The poor contrast detectability of mammography can be dealt with by domain specific software visualization tools. Remote desktop client access and time performance limitations of a previously reported visualization tool are addressed, aiming at more efficient visualization of mammographic image resources existing in web or PACS image servers. This effort is also motivated by the fact that at present, web browsers do not support domain-specific medical image visualization. To deal with desktop client access the tool was redesigned by exploring component technologies, enabling the integration of stand alone domain specific mammographic image functionality in a web browsing environment (web adaptation). The integration method is based on ActiveX Document Server technology. ActiveX Document is a part of Object Linking and Embedding (OLE) extensible systems object technology, offering new services in existing applications. The standard DICOM 3.0 part 10 compatible image-format specification Papyrus 3.0 is supported, in addition to standard digitization formats such as TIFF. The visualization functionality of the tool has been enhanced by including a fast wavelet transform implementation, which allows for real time wavelet based contrast enhancement and denoising operations. Initial use of the tool with mammograms of various breast structures demonstrated its potential in improving visualization of diagnostic mammographic features. Web adaptation and real time wavelet processing enhance the potential of the previously reported tool in remote diagnosis and education in mammography.

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

PubMed

Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

2010-09-21

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.

PubMed

Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

2015-01-01

A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.

Advanced space system analysis software. Technical, user, and programmer guide

NASA Technical Reports Server (NTRS)

Farrell, C. E.; Zimbelman, H. F.

1981-01-01

The LASS computer program provides a tool for interactive preliminary and conceptual design of LSS. Eight program modules were developed, including four automated model geometry generators, an associated mass properties module, an appendage synthesizer module, an rf analysis module, and an orbital transfer analysis module. The existing rigid body controls analysis module was modified to permit analysis of effects of solar pressure on orbital performance. A description of each module, user instructions, and programmer information are included.

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis.

PubMed

Van Doorslaer, Koenraad; Tan, Qina; Xirasagar, Sandhya; Bandaru, Sandya; Gopalan, Vivek; Mohamoud, Yasmin; Huyen, Yentram; McBride, Alison A

2013-01-01

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.

PubMed

Cope, A J; Richmond, P; James, S S; Gurney, K; Allerton, D J

2017-01-01

There is a growing requirement in computational neuroscience for tools that permit collaborative model building, model sharing, combining existing models into a larger system (multi-scale model integration), and are able to simulate models using a variety of simulation engines and hardware platforms. Layered XML model specification formats solve many of these problems, however they are difficult to write and visualise without tools. Here we describe a new graphical software tool, SpineCreator, which facilitates the creation and visualisation of layered models of point spiking neurons or rate coded neurons without requiring the need for programming. We demonstrate the tool through the reproduction and visualisation of published models and show simulation results using code generation interfaced directly into SpineCreator. As a unique application for the graphical creation of neural networks, SpineCreator represents an important step forward for neuronal modelling.

Image tools for UNIX

NASA Technical Reports Server (NTRS)

Banks, David C.

1994-01-01

This talk features two simple and useful tools for digital image processing in the UNIX environment. They are xv and pbmplus. The xv image viewer which runs under the X window system reads images in a number of different file formats and writes them out in different formats. The view area supports a pop-up control panel. The 'algorithms' menu lets you blur an image. The xv control panel also activates the color editor which displays the image's color map (if one exists). The xv image viewer is available through the internet. The pbmplus package is a set of tools designed to perform image processing from within a UNIX shell. The acronym 'pbm' stands for portable bit map. Like xv, the pbm plus tool can convert images from and to many different file formats. The source code and manual pages for pbmplus are also available through the internet. This software is in the public domain.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2005-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2006-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

Development of an Advanced Stimulation / Production Predictive Simulator for Enhanced Geothermal Systems

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

Pritchett, John W.

2015-04-15

There are several well-known obstacles to the successful deployment of EGS projects on a commercial scale, of course. EGS projects are expected to be deeper, on the average, than conventional “natural” geothermal reservoirs, and drilling costs are already a formidable barrier to conventional geothermal projects. Unlike conventional resources (which frequently announce their presence with natural manifestations such as geysers, hot springs and fumaroles), EGS prospects are likely to appear fairly undistinguished from the earth surface. And, of course, the probable necessity of fabricating a subterranean fluid circulation network to mine the heat from the rock (instead of simply relying onmore » natural, pre-existing permeable fractures) adds a significant degree of uncertainty to the prospects for success. Accordingly, the basic motivation for the work presented herein was to try to develop a new set of tools that would be more suitable for this purpose. Several years ago, the Department of Energy’s Geothermal Technologies Office recognized this need and funded a cost-shared grant to our company (then SAIC, now Leidos) to partner with Geowatt AG of Zurich, Switzerland and undertake the development of a new reservoir simulator that would be more suitable for EGS forecasting than the existing tools. That project has now been completed and a new numerical geothermal reservoir simulator has been developed. It is named “HeatEx” (for “Heat Extraction”) and is almost completely new, although its methodology owes a great deal to other previous geothermal software development efforts, including Geowatt’s “HEX-S” code, the STAR and SPFRAC simulators developed here at SAIC/Leidos, the MINC approach originally developed at LBNL, and tracer analysis software originally formulated at INEL. Furthermore, the development effort was led by engineers with many years of experience in using reservoir simulation software to make meaningful forecasts for real geothermal projects, not just software designers. It is hoped that, as a result, HeatEx will prove useful during the early stages of the development of EGS technology. The basic objective was to design a tool that could use field data that are likely to become available during the early phases of an EGS project (that is, during initial reconnaissance and fracture stimulation operations) to guide forecasts of the longer-term behavior of the system during production and heat-mining.« less

Methodology for automating software systems. Task 1 of the foundations for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1989-01-01

The early stages of a research program designed to establish an experimental research platform for software engineering are described. Major emphasis is placed on Computer Assisted Software Engineering (CASE). The Poor Man's CASE Tool is based on the Apple Macintosh system, employing available software including Focal Point II, Hypercard, XRefText, and Macproject. These programs are functional in themselves, but through advanced linking are available for operation from within the tool being developed. The research platform is intended to merge software engineering technology with artificial intelligence (AI). In the first prototype of the PMCT, however, the sections of AI are not included. CASE tools assist the software engineer in planning goals, routes to those goals, and ways to measure progress. The method described allows software to be synthesized instead of being written or built.

Computer implemented method, and apparatus for controlling a hand-held tool

NASA Technical Reports Server (NTRS)

Wagner, Kenneth William (Inventor); Taylor, James Clayton (Inventor)

1999-01-01

The invention described here in is a computer-implemented method and apparatus for controlling a hand-held tool. In particular, the control of a hand held tool is for the purpose of controlling the speed of a fastener interface mechanism and the torque applied to fasteners by the fastener interface mechanism of the hand-held tool and monitoring the operating parameters of the tool. The control is embodied in intool software embedded on a processor within the tool which also communicates with remote software. An operator can run the tool, or through the interaction of both software, operate the tool from a remote location, analyze data from a performance history recorded by the tool, and select various torque and speed parameters for each fastener.

Development of an Automatic Echo-counting Program for HROFFT Spectrograms

NASA Astrophysics Data System (ADS)

Noguchi, Kazuya; Yamamoto, Masa-Yuki

2008-06-01

Radio meteor observations by Ham-band beacon or FM radio broadcasts using “Ham-band Radio meteor Observation Fast Fourier Transform” (HROFFT) an automatic operating software have been performed widely in recent days. Previously, counting of meteor echoes on the spectrograms of radio meteor observation was performed manually by observers. In the present paper, we introduce an automatic meteor echo counting software application. Although output images of the HROFFT contain both the features of meteor echoes and those of various types of noises, a newly developed image processing technique has been applied, resulting in software that enables a useful auto-counting tool. There exists a slight error in the processing on spectrograms when the observation site is affected by many disturbing noises. Nevertheless, comparison between software and manual counting revealed an agreement of almost 90%. Therefore, we can easily obtain a dataset of detection time, duration time, signal strength, and Doppler shift of each meteor echo from the HROFFT spectrograms. Using this software, statistical analyses of meteor activities is based on the results obtained at many Ham-band Radio meteor Observation (HRO) sites throughout the world, resulting in a very useful “standard” for monitoring meteor stream activities in real time.

Constraints and Opportunities in GCM Model Development

NASA Technical Reports Server (NTRS)

Schmidt, Gavin; Clune, Thomas

2010-01-01

Over the past 30 years climate models have evolved from relatively simple representations of a few atmospheric processes to complex multi-disciplinary system models which incorporate physics from bottom of the ocean to the mesopause and are used for seasonal to multi-million year timescales. Computer infrastructure over that period has gone from punchcard mainframes to modern parallel clusters. Constraints of working within an ever evolving research code mean that most software changes must be incremental so as not to disrupt scientific throughput. Unfortunately, programming methodologies have generally not kept pace with these challenges, and existing implementations now present a heavy and growing burden on further model development as well as limiting flexibility and reliability. Opportunely, advances in software engineering from other disciplines (e.g. the commercial software industry) as well as new generations of powerful development tools can be incorporated by the model developers to incrementally and systematically improve underlying implementations and reverse the long term trend of increasing development overhead. However, these methodologies cannot be applied blindly, but rather must be carefully tailored to the unique characteristics of scientific software development. We will discuss the need for close integration of software engineers and climate scientists to find the optimal processes for climate modeling.

Distributed agile software development for the SKA

NASA Astrophysics Data System (ADS)

Wicenec, Andreas; Parsons, Rebecca; Kitaeff, Slava; Vinsen, Kevin; Wu, Chen; Nelson, Paul; Reed, David

2012-09-01

The SKA software will most probably be developed by many groups distributed across the globe and coming from dierent backgrounds, like industries and research institutions. The SKA software subsystems will have to cover a very wide range of dierent areas, but still they have to react and work together like a single system to achieve the scientic goals and satisfy the challenging data ow requirements. Designing and developing such a system in a distributed fashion requires proper tools and the setup of an environment to allow for ecient detection and tracking of interface and integration issues in particular in a timely way. Agile development can provide much faster feedback mechanisms and also much tighter collaboration between the customer (scientist) and the developer. Continuous integration and continuous deployment on the other hand can provide much faster feedback of integration issues from the system level to the subsystem developers. This paper describes the results obtained from trialing a potential SKA development environment based on existing science software development processes like ALMA, the expected distribution of the groups potentially involved in the SKA development and experience gained in the development of large scale commercial software projects.

Software engineering methodologies and tools

NASA Technical Reports Server (NTRS)

Wilcox, Lawrence M.

1993-01-01

Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

DigBody®: A new 3D modeling tool for nasal virtual surgery.

PubMed

Burgos, M A; Sanmiguel-Rojas, E; Singh, Narinder; Esteban-Ortega, F

2018-07-01

Recent studies have demonstrated that a significant number of surgical procedures for nasal airway obstruction (NAO) have a high rate of surgical failure. In part, this problem is due to the lack of reliable objective clinical parameters to aid surgeons during preoperative planning. Modeling tools that allow virtual surgery to be performed do exist, but all require direct manipulation of computed tomography (CT) or magnetic resonance imaging (MRI) data. Specialists in Rhinology have criticized these tools for their complex user interface, and have requested more intuitive, user-friendly and powerful software to make virtual surgery more accessible and realistic. In this paper we present a new virtual surgery software tool, DigBody ® . This new surgery module is integrated into the computational fluid dynamics (CFD) program MeComLand ® , which was developed exclusively to analyze nasal airflow. DigBody ® works directly with a 3D nasal model that mimics real surgery. Furthermore, this surgery module permits direct assessment of the operated cavity following virtual surgery by CFD simulation. The effectiveness of DigBody ® has been demonstrated by real surgery on two patients based on prior virtual operation results. Both subjects experienced excellent surgical outcomes with no residual nasal obstruction. This tool has great potential to aid surgeons in modeling potential surgical maneuvers, minimizing complications, and being confident that patients will receive optimal postoperative outcomes, validated by personalized CFD testing. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Karp, Peter D.

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manuallymore » curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.« less

Measurement of the area of venous ulcers using two software programs.

PubMed

Eberhardt, Thaís Dresch; Lima, Suzinara Beatriz Soares de; Lopes, Luis Felipe Dias; Borges, Eline de Lima; Weiller, Teresinha Heck; Fonseca, Graziele Gorete Portella da

2016-12-19

to compare the measurement area of venous ulcers using AutoCAD(r) and Image Tool software. this was an assessment of reproducibility tests conducted in a angiology clinic of a university hospital. Data were collected from 21 patients with venous ulcers, in the period from March to July of 2015, using a collection form and photograph of wounds. Five nurses (evaluators) of the hospital skin wound study group participated. The wounds were measured using both software programs. Data were analyzed using intraclass correlation coefficient, concordance correlation coefficient and Bland-Altman analysis. The study met the ethical aspects in accordance with current legislation. the size of ulcers varied widely, however, without significant difference between the measurements; an excellent intraclass and concordance correlation was found between both software programs, which seem to be more accurate when measuring a wound area >10 cm². the use of both software programs is appropriate for measurement of venous ulcers, appearing to be more accurate when used to measure a wound area > 10 cm². comparar a mensuração de área de úlceras venosas por meio dos softwares AutoCAD(r) e Image Tool. trata-se de um estudo de avaliação de reprodutibilidade de testes, realizado em um ambulatório de angiologia de um hospital universitário. Os dados foram coletados de 21 pacientes com úlceras venosas, no período de março a julho de 2015, por meio de formulário de coleta e fotografia das feridas. Cinco enfermeiros (avaliadores) do Grupo de Estudos de Lesões de Pele do hospital participaram da pesquisa. As feridas foram mensuradas em ambos os softwares. Os dados foram analisados por meio do Coeficiente de correlação intraclasse, Coeficiente de correlação de concordância e procedimento de Bland e Altman. A pesquisa respeitou os aspectos éticos de acordo com a legislação vigente. os tamanhos das úlceras apresentaram grande amplitude, porém, sem diferença significativa entre as mensurações, existe excelente correlação intraclasse e de concordância entre os softwares, os quais parecem ser mais precisos na mensuração de feridas com área > 10 cm². o uso de ambos os softwares é indicado para a mensuração de úlceras venosas, parecendo ser mais precisos quando utilizados para mensurar feridas com área > 10 cm². comparar la medida del área de úlceras venosas por medio de los softwares AutoCAD(r) e Image Tool. se trata de un estudio de evaluación de reproducibilidad de pruebas, realizado en un ambulatorio de angiología de un hospital universitario. Los datos fueron recolectados de 21 pacientes con úlceras venosas, en el período de marzo a julio de 2015, por medio de formulario de recolección y fotografías de las heridas. Cinco enfermeros (evaluadores) del Grupo de Estudios de Lesiones de Piel del hospital participaron de la investigación. Las heridas fueron medidas en ambos softwares. Los datos fueron analizados por medio de: Coeficiente de correlación intraclase, Coeficiente de correlación de concordancia y Procedimiento de Bland y Altman. La investigación respetó los aspectos éticos de acuerdo con la legislación vigente. los tamaños de las úlceras presentaron gran amplitud, sin embargo, sin diferencia significativa entre las medidas; existe excelente correlación intraclase y de concordancia entre los softwares, los que parecen ser más precisos en medidas de heridas con área > 10 cm². el uso de ambos softwares es indicado para medir úlceras venosas, pareciendo ser más precisos cuando utilizados para medir heridas con área > 10 cm².

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

PubMed

Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard

2015-01-01

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

ParseCNV integrative copy number variation association software with quality tracking

PubMed Central

Glessner, Joseph T.; Li, Jin; Hakonarson, Hakon

2013-01-01

A number of copy number variation (CNV) calling algorithms exist; however, comprehensive software tools for CNV association studies are lacking. We describe ParseCNV, unique software that takes CNV calls and creates probe-based statistics for CNV occurrence in both case–control design and in family based studies addressing both de novo and inheritance events, which are then summarized based on CNV regions (CNVRs). CNVRs are defined in a dynamic manner to allow for a complex CNV overlap while maintaining precise association region. Using this approach, we avoid failure to converge and non-monotonic curve fitting weaknesses of programs, such as CNVtools and CNVassoc, and although Plink is easy to use, it only provides combined CNV state probe-based statistics, not state-specific CNVRs. Existing CNV association methods do not provide any quality tracking information to filter confident associations, a key issue which is fully addressed by ParseCNV. In addition, uncertainty in CNV calls underlying CNV associations is evaluated to verify significant results, including CNV overlap profiles, genomic context, number of probes supporting the CNV and single-probe intensities. When optimal quality control parameters are followed using ParseCNV, 90% of CNVs validate by polymerase chain reaction, an often problematic stage because of inadequate significant association review. ParseCNV is freely available at http://parsecnv.sourceforge.net. PMID:23293001

ParseCNV integrative copy number variation association software with quality tracking.

PubMed

Glessner, Joseph T; Li, Jin; Hakonarson, Hakon

2013-03-01

A number of copy number variation (CNV) calling algorithms exist; however, comprehensive software tools for CNV association studies are lacking. We describe ParseCNV, unique software that takes CNV calls and creates probe-based statistics for CNV occurrence in both case-control design and in family based studies addressing both de novo and inheritance events, which are then summarized based on CNV regions (CNVRs). CNVRs are defined in a dynamic manner to allow for a complex CNV overlap while maintaining precise association region. Using this approach, we avoid failure to converge and non-monotonic curve fitting weaknesses of programs, such as CNVtools and CNVassoc, and although Plink is easy to use, it only provides combined CNV state probe-based statistics, not state-specific CNVRs. Existing CNV association methods do not provide any quality tracking information to filter confident associations, a key issue which is fully addressed by ParseCNV. In addition, uncertainty in CNV calls underlying CNV associations is evaluated to verify significant results, including CNV overlap profiles, genomic context, number of probes supporting the CNV and single-probe intensities. When optimal quality control parameters are followed using ParseCNV, 90% of CNVs validate by polymerase chain reaction, an often problematic stage because of inadequate significant association review. ParseCNV is freely available at http://parsecnv.sourceforge.net.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

PubMed

Helt, Gregg A; Nicol, John W; Erwin, Ed; Blossom, Eric; Blanchard, Steven G; Chervitz, Stephen A; Harmon, Cyrus; Loraine, Ann E

2009-08-25

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

Designing software for operational decision support through coloured Petri nets

NASA Astrophysics Data System (ADS)

Maggi, F. M.; Westergaard, M.

2017-05-01

Operational support provides, during the execution of a business process, replies to questions such as 'how do I end the execution of the process in the cheapest way?' and 'is my execution compliant with some expected behaviour?' These questions may be asked several times during a single execution and, to answer them, dedicated software components (the so-called operational support providers) need to be invoked. Therefore, an infrastructure is needed to handle multiple providers, maintain data between queries about the same execution and discard information when it is no longer needed. In this paper, we use coloured Petri nets (CPNs) to model and analyse software implementing such an infrastructure. This analysis is needed to clarify the requirements before implementation and to guarantee that the resulting software is correct. To this aim, we present techniques to represent and analyse state spaces with 250 million states on a normal PC. We show how the specified requirements have been implemented as a plug-in of the process mining tool ProM and how the operational support in ProM can be used in combination with an existing operational support provider.

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.

Modeling biochemical transformation processes and information processing with Narrator

PubMed Central

Mandel, Johannes J; Fuß, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-01-01

Background Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Conclusion Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from . PMID:17389034

Application of an evidence-based tool to evaluate health impacts of changes to the built environment.

PubMed

Ulmer, Jared M; Chapman, James E; Kershaw, Suzanne E; Campbell, Monica; Frank, Lawrence D

2014-07-11

To create and apply an empirically based health and greenhouse gas (GHG) impact assessment tool linking detailed measures of walkability and regional accessibility with travel, physical activity, health indicators and GHG emissions. Parcel land use and transportation system characteristics were calculated within a kilometre network buffer around each Toronto postal code. Built environment measures were linked with health and demographic characteristics from the Canadian Community Health Survey and travel behaviour from the Transportation Tomorrow Survey. Results were incorporated into an existing software tool and used to predict health-related indicators and GHG emissions for the Toronto West Don Lands Redevelopment. Walkability, regional accessibility, sidewalks, bike facilities and recreation facility access were positively associated with physical activity and negatively related to body weight, high blood pressure and transportation impacts. When applied to the West Don Lands, the software tool predicted a substantial shift from automobile use to walking, biking and transit. Walking and biking trips more than doubled, and transit trips increased by one third. Per capita automobile trips decreased by half, and vehicle kilometres travelled and GHG emissions decreased by 15% and 29%, respectively. The results presented are novel and among the first to link health outcomes with detailed built environment features in Canada. The resulting tool is the first of its kind in Canada. This tool can help policy-makers, land use and transportation planners, and health practitioners to evaluate built environment influences on health-related indicators and GHG emissions resulting from contrasting land use and transportation policies and actions.

Knowledge-based approach for generating target system specifications from a domain model

NASA Technical Reports Server (NTRS)

Gomaa, Hassan; Kerschberg, Larry; Sugumaran, Vijayan

1992-01-01

Several institutions in industry and academia are pursuing research efforts in domain modeling to address unresolved issues in software reuse. To demonstrate the concepts of domain modeling and software reuse, a prototype software engineering environment is being developed at George Mason University to support the creation of domain models and the generation of target system specifications. This prototype environment, which is application domain independent, consists of an integrated set of commercial off-the-shelf software tools and custom-developed software tools. This paper describes the knowledge-based tool that was developed as part of the environment to generate target system specifications from a domain model.

Use of a data warehouse at an academic medical center for clinical pathology quality improvement, education, and research

PubMed Central

Krasowski, Matthew D.; Schriever, Andy; Mathur, Gagan; Blau, John L.; Stauffer, Stephanie L.; Ford, Bradley A.

2015-01-01

Background: Pathology data contained within the electronic health record (EHR), and laboratory information system (LIS) of hospitals represents a potentially powerful resource to improve clinical care. However, existing reporting tools within commercial EHR and LIS software may not be able to efficiently and rapidly mine data for quality improvement and research applications. Materials and Methods: We present experience using a data warehouse produced collaboratively between an academic medical center and a private company. The data warehouse contains data from the EHR, LIS, admission/discharge/transfer system, and billing records and can be accessed using a self-service data access tool known as Starmaker. The Starmaker software allows users to use complex Boolean logic, include and exclude rules, unit conversion and reference scaling, and value aggregation using a straightforward visual interface. More complex queries can be achieved by users with experience with Structured Query Language. Queries can use biomedical ontologies such as Logical Observation Identifiers Names and Codes and Systematized Nomenclature of Medicine. Result: We present examples of successful searches using Starmaker, falling mostly in the realm of microbiology and clinical chemistry/toxicology. The searches were ones that were either very difficult or basically infeasible using reporting tools within the EHR and LIS used in the medical center. One of the main strengths of Starmaker searches is rapid results, with typical searches covering 5 years taking only 1–2 min. A “Run Count” feature quickly outputs the number of cases meeting criteria, allowing for refinement of searches before downloading patient-identifiable data. The Starmaker tool is available to pathology residents and fellows, with some using this tool for quality improvement and scholarly projects. Conclusion: A data warehouse has significant potential for improving utilization of clinical pathology testing. Software that can access data warehouse using a straightforward visual interface can be incorporated into pathology training programs. PMID:26284156