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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-05

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

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

NASA Technical Reports Server (NTRS)

Campbell, R. H.; Badger, W.; Beckman, C. S.; Beshers, G.; Hammerslag, D.; Kimball, J.; Kirslis, P. A.; Render, H.; Richards, P.; Terwilliger, R.

1984-01-01

The project to automate the management of software production systems is described. 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. Several major components of the SAGA system are completed to prototype form. The construction methods are described.

Pre- and Post-Processing Tools to Streamline the CFD Process

NASA Technical Reports Server (NTRS)

Dorney, Suzanne Miller

2002-01-01

This viewgraph presentation provides information on software development tools to facilitate the use of CFD (Computational Fluid Dynamics) codes. The specific CFD codes FDNS and CORSAIR are profiled, and uses for software development tools with these codes during pre-processing, interim-processing, and post-processing are explained.

Integrating automated structured analysis and design with Ada programming support environments

NASA Technical Reports Server (NTRS)

Hecht, Alan; Simmons, Andy

1986-01-01

Ada Programming Support Environments (APSE) include many powerful tools that address the implementation of Ada code. These tools do not address the entire software development process. Structured analysis is a methodology that addresses the creation of complete and accurate system specifications. Structured design takes a specification and derives a plan to decompose the system subcomponents, and provides heuristics to optimize the software design to minimize errors and maintenance. It can also produce the creation of useable modules. Studies have shown that most software errors result from poor system specifications, and that these errors also become more expensive to fix as the development process continues. Structured analysis and design help to uncover error in the early stages of development. The APSE tools help to insure that the code produced is correct, and aid in finding obscure coding errors. However, they do not have the capability to detect errors in specifications or to detect poor designs. An automated system for structured analysis and design TEAMWORK, which can be integrated with an APSE to support software systems development from specification through implementation is described. These tools completement each other to help developers improve quality and productivity, as well as to reduce development and maintenance costs. Complete system documentation and reusable code also resultss from the use of these tools. Integrating an APSE with automated tools for structured analysis and design provide capabilities and advantages beyond those realized with any of these systems used by themselves.

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

NASA Technical Reports Server (NTRS)

Leucht, Kurt W.; Semmel, Glenn S.

2008-01-01

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

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.

USE OF COMPUTER-AIDED PROCESS ENGINEERING TOOL IN POLLUTION PREVENTION

EPA Science Inventory

Computer-Aided Process Engineering has become established in industry as a design tool. With the establishment of the CAPE-OPEN software specifications for process simulation environments. CAPE-OPEN provides a set of "middleware" standards that enable software developers to acces...

Early Childhood Educational Software: Specific Features and Issues of Localization

ERIC Educational Resources Information Center

Nikolopoulou, Kleopatra

2007-01-01

The computer has now become a recognized tool in the education of young children and when used appropriately can reinforce their learning experiences. This paper reviews specific features (relating to pedagogic design, software content and user-interface design) of early childhood educational software and discusses issues in favor of its…

OEXP Analysis Tools Workshop

NASA Technical Reports Server (NTRS)

Garrett, L. Bernard; Wright, Robert L.; Badi, Deborah; Findlay, John T.

1988-01-01

This publication summarizes the software needs and available analysis tools presented at the OEXP Analysis Tools Workshop held at the NASA Langley Research Center, Hampton, Virginia on June 21 to 22, 1988. The objective of the workshop was to identify available spacecraft system (and subsystem) analysis and engineering design tools, and mission planning and analysis software that could be used for various NASA Office of Exploration (code Z) studies, specifically lunar and Mars missions.

Object-oriented design of medical imaging software.

PubMed

Ligier, Y; Ratib, O; Logean, M; Girard, C; Perrier, R; Scherrer, J R

1994-01-01

A special software package for interactive display and manipulation of medical images was developed at the University Hospital of Geneva, as part of a hospital wide Picture Archiving and Communication System (PACS). This software package, called Osiris, was especially designed to be easily usable and adaptable to the needs of noncomputer-oriented physicians. The Osiris software has been developed to allow the visualization of medical images obtained from any imaging modality. It provides generic manipulation tools, processing tools, and analysis tools more specific to clinical applications. This software, based on an object-oriented paradigm, is portable and extensible. Osiris is available on two different operating systems: the Unix X-11/OSF-Motif based workstations, and the Macintosh family.

BS-virus-finder: virus integration calling using bisulfite sequencing data.

PubMed

Gao, Shengjie; Hu, Xuesong; Xu, Fengping; Gao, Changduo; Xiong, Kai; Zhao, Xiao; Chen, Haixiao; Zhao, Shancen; Wang, Mengyao; Fu, Dongke; Zhao, Xiaohui; Bai, Jie; Mao, Likai; Li, Bo; Wu, Song; Wang, Jian; Li, Shengbin; Yang, Huangming; Bolund, Lars; Pedersen, Christian N S

2018-01-01

DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data. © The Authors 2017. Published by Oxford University Press.

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.

Teaching meta-analysis using MetaLight.

PubMed

Thomas, James; Graziosi, Sergio; Higgins, Steve; Coe, Robert; Torgerson, Carole; Newman, Mark

2012-10-18

Meta-analysis is a statistical method for combining the results of primary studies. It is often used in systematic reviews and is increasingly a method and topic that appears in student dissertations. MetaLight is a freely available software application that runs simple meta-analyses and contains specific functionality to facilitate the teaching and learning of meta-analysis. While there are many courses and resources for meta-analysis available and numerous software applications to run meta-analyses, there are few pieces of software which are aimed specifically at helping those teaching and learning meta-analysis. Valuable teaching time can be spent learning the mechanics of a new software application, rather than on the principles and practices of meta-analysis. We discuss ways in which the MetaLight tool can be used to present some of the main issues involved in undertaking and interpreting a meta-analysis. While there are many software tools available for conducting meta-analysis, in the context of a teaching programme such software can require expenditure both in terms of money and in terms of the time it takes to learn how to use it. MetaLight was developed specifically as a tool to facilitate the teaching and learning of meta-analysis and we have presented here some of the ways it might be used in a training situation.

The CSSIAR v.1.00 Software: A new tool based on SIAR to assess soil redistribution using Compound Specific Stable Isotopes

NASA Astrophysics Data System (ADS)

Sergio, de los Santos-Villalobos; Claudio, Bravo-Linares; dos Anjos Roberto, Meigikos; Renan, Cardoso; Max, Gibbs; Andrew, Swales; Lionel, Mabit; Gerd, Dercon

Soil erosion is one of the biggest challenges for food production around the world. Many techniques have been used to evaluate and mitigate soil degradation. Nowadays isotopic techniques are becoming a powerful tool to assess soil apportionment. One of the innovative techniques used is the Compound Specific Stable Isotopes (CSSI) analysis, which has been used to track down sediments and specify their sources by the isotopic signature of δ13 C in specific fatty acids. The application of this technique on soil apportionment has been recently developed, however there is a lack of user-friendly Software for data processing and interpretation. The aim of this article is to introduce a new open source tool for working with data sets generated by the use of the CSSI technique to assess soil apportionment, called the CSSIARv1.00 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.

Public Domain Generic Tools: An Overview.

ERIC Educational Resources Information Center

Erjavec, Tomaz

This paper presents an introduction to language engineering software, especially for computerized language and text corpora. The focus of the paper is on small and relatively independent pieces of software designed for specific, often low-level language analysis tasks, and on tools in the public domain. Discussion begins with the application of…

Finding the Right Educational Software for Your Child.

ERIC Educational Resources Information Center

Moore, Jack

1990-01-01

Ideas are presented for identifying, evaluating, and selecting instructional software for children with special needs. The article notes several library research tools as sources of information and lists specific questions to consider when evaluating software. (JDD)

Scalable collaborative risk management technology for complex critical systems

NASA Technical Reports Server (NTRS)

Campbell, Scott; Torgerson, Leigh; Burleigh, Scott; Feather, Martin S.; Kiper, James D.

2004-01-01

We describe here our project and plans to develop methods, software tools, and infrastructure tools to address challenges relating to geographically distributed software development. Specifically, this work is creating an infrastructure that supports applications working over distributed geographical and organizational domains and is using this infrastructure to develop a tool that supports project development using risk management and analysis techniques where the participants are not collocated.

Achieving Better Buying Power for Mobile Open Architecture Software Systems Through Diverse Acquisition Scenarios

DTIC Science & Technology

2016-04-30

software (OSS) and proprietary (CSS) software elements or remote services (Scacchi, 2002, 2010), eventually including recent efforts to support Web ...specific platforms, including those operating on secured Web /mobile devices.  Common Development Technology provides AC development tools and common...transition to OA systems and OSS software elements, specifically for Web and Mobile devices within the realm of C3CB. OA, Open APIs, OSS, and CSS OA

Luigi Gentile Polese | NREL

Science.gov Websites

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

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.

A high order approach to flight software development and testing

NASA Technical Reports Server (NTRS)

Steinbacher, J.

1981-01-01

The use of a software development facility is discussed as a means of producing a reliable and maintainable ECS software system, and as a means of providing efficient use of the ECS hardware test facility. Principles applied to software design are given, including modularity, abstraction, hiding, and uniformity. The general objectives of each phase of the software life cycle are also given, including testing, maintenance, code development, and requirement specifications. Software development facility tools are summarized, and tool deficiencies recognized in the code development and testing phases are considered. Due to limited lab resources, the functional simulation capabilities may be indispensable in the testing phase.

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.

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.

Computer Software Configuration Item-Specific Flight Software Image Transfer Script Generator

NASA Technical Reports Server (NTRS)

Bolen, Kenny; Greenlaw, Ronald

2010-01-01

A K-shell UNIX script enables the International Space Station (ISS) Flight Control Team (FCT) operators in NASA s Mission Control Center (MCC) in Houston to transfer an entire or partial computer software configuration item (CSCI) from a flight software compact disk (CD) to the onboard Portable Computer System (PCS). The tool is designed to read the content stored on a flight software CD and generate individual CSCI transfer scripts that are capable of transferring the flight software content in a given subdirectory on the CD to the scratch directory on the PCS. The flight control team can then transfer the flight software from the PCS scratch directory to the Electronically Erasable Programmable Read Only Memory (EEPROM) of an ISS Multiplexer/ Demultiplexer (MDM) via the Indirect File Transfer capability. The individual CSCI scripts and the CSCI Specific Flight Software Image Transfer Script Generator (CFITSG), when executed a second time, will remove all components from their original execution. The tool will identify errors in the transfer process and create logs of the transferred software for the purposes of configuration management.

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.

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.

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

A Software Engineering Environment for the Navy.

DTIC Science & Technology

1982-03-31

Engineering Pr.cess . - 55 ?art II: Description of A Software Engineering Env.Lonnmeut 1. Data Base ........................................ 7 -3 L.I...Methodology to Tool 1-54 2.2.2.2-6 Flow of Management: Activity to Methodology to Tool 21- 55 2.2.2.2-7 Pipelining for Activity-Specific Tools 11-56 A.1.1-1 A...testing techniques. 2.2. 2 Methodciogies and Tools: Correctness Analysis Pai e T- 4Metboioioo ies aews - Pev2.ews Jeicrmine the in ernai ’ Qolc .. ness and

Integrated Systems Health Management (ISHM) Toolkit

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Environmental databases and other computerized information tools

NASA Technical Reports Server (NTRS)

Clark-Ingram, Marceia

1995-01-01

Increasing environmental legislation has brought about the development of many new environmental databases and software application packages to aid in the quest for environmental compliance. These databases and software packages are useful tools and applicable to a wide range of environmental areas from atmospheric modeling to materials replacement technology. The great abundance of such products and services can be very overwhelming when trying to identify the tools which best meet specific needs. This paper will discuss the types of environmental databases and software packages available. This discussion will also encompass the affected environmental areas of concern, product capabilities, and hardware requirements for product utilization.

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

DTIC Science & Technology

1994-03-01

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

Revisiting Information Technology tools serving authorship and editorship: a case-guided tutorial to statistical analysis and plagiarism detection

PubMed Central

Bamidis, P D; Lithari, C; Konstantinidis, S T

2010-01-01

With the number of scientific papers published in journals, conference proceedings, and international literature ever increasing, authors and reviewers are not only facilitated with an abundance of information, but unfortunately continuously confronted with risks associated with the erroneous copy of another's material. In parallel, Information Communication Technology (ICT) tools provide to researchers novel and continuously more effective ways to analyze and present their work. Software tools regarding statistical analysis offer scientists the chance to validate their work and enhance the quality of published papers. Moreover, from the reviewers and the editor's perspective, it is now possible to ensure the (text-content) originality of a scientific article with automated software tools for plagiarism detection. In this paper, we provide a step-bystep demonstration of two categories of tools, namely, statistical analysis and plagiarism detection. The aim is not to come up with a specific tool recommendation, but rather to provide useful guidelines on the proper use and efficiency of either category of tools. In the context of this special issue, this paper offers a useful tutorial to specific problems concerned with scientific writing and review discourse. A specific neuroscience experimental case example is utilized to illustrate the young researcher's statistical analysis burden, while a test scenario is purpose-built using open access journal articles to exemplify the use and comparative outputs of seven plagiarism detection software pieces. PMID:21487489

Revisiting Information Technology tools serving authorship and editorship: a case-guided tutorial to statistical analysis and plagiarism detection.

PubMed

Bamidis, P D; Lithari, C; Konstantinidis, S T

2010-12-01

With the number of scientific papers published in journals, conference proceedings, and international literature ever increasing, authors and reviewers are not only facilitated with an abundance of information, but unfortunately continuously confronted with risks associated with the erroneous copy of another's material. In parallel, Information Communication Technology (ICT) tools provide to researchers novel and continuously more effective ways to analyze and present their work. Software tools regarding statistical analysis offer scientists the chance to validate their work and enhance the quality of published papers. Moreover, from the reviewers and the editor's perspective, it is now possible to ensure the (text-content) originality of a scientific article with automated software tools for plagiarism detection. In this paper, we provide a step-bystep demonstration of two categories of tools, namely, statistical analysis and plagiarism detection. The aim is not to come up with a specific tool recommendation, but rather to provide useful guidelines on the proper use and efficiency of either category of tools. In the context of this special issue, this paper offers a useful tutorial to specific problems concerned with scientific writing and review discourse. A specific neuroscience experimental case example is utilized to illustrate the young researcher's statistical analysis burden, while a test scenario is purpose-built using open access journal articles to exemplify the use and comparative outputs of seven plagiarism detection software pieces.

Collaborative Software Development in Support of Fast Adaptive AeroSpace Tools (FAAST)

NASA Technical Reports Server (NTRS)

Kleb, William L.; Nielsen, Eric J.; Gnoffo, Peter A.; Park, Michael A.; Wood, William A.

2003-01-01

A collaborative software development approach is described. The software product is an adaptation of proven computational capabilities combined with new capabilities to form the Agency's next generation aerothermodynamic and aerodynamic analysis and design tools. To efficiently produce a cohesive, robust, and extensible software suite, the approach uses agile software development techniques; specifically, project retrospectives, the Scrum status meeting format, and a subset of Extreme Programming's coding practices are employed. Examples are provided which demonstrate the substantial benefits derived from employing these practices. Also included is a discussion of issues encountered when porting legacy Fortran 77 code to Fortran 95 and a Fortran 95 coding standard.

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

NASA Technical Reports Server (NTRS)

Zenie, Alexandre; Luguern, Jean-Pierre

1987-01-01

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages.

Automated real-time software development

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Software engineering and Ada in design

NASA Technical Reports Server (NTRS)

Oneill, Don

1986-01-01

Modern software engineering promises significant reductions in software costs and improvements in software quality. The Ada language is the focus for these software methodology and tool improvements. The IBM FSD approach, including the software engineering practices that guide the systematic design and development of software products and the management of the software process are examined. The revised Ada design language adaptation is revealed. This four level design methodology is detailed including the purpose of each level, the management strategy that integrates the software design activity with the program milestones, and the technical strategy that maps the Ada constructs to each level of design. A complete description of each design level is provided along with specific design language recording guidelines for each level. Finally, some testimony is offered on education, tools, architecture, and metrics resulting from project use of the four level Ada design language adaptation.

Presenting an Evaluation Model for the Cancer Registry Software.

PubMed

Moghaddasi, Hamid; Asadi, Farkhondeh; Rabiei, Reza; Rahimi, Farough; Shahbodaghi, Reihaneh

2017-12-01

As cancer is increasingly growing, cancer registry is of great importance as the main core of cancer control programs, and many different software has been designed for this purpose. Therefore, establishing a comprehensive evaluation model is essential to evaluate and compare a wide range of such software. In this study, the criteria of the cancer registry software have been determined by studying the documents and two functional software of this field. The evaluation tool was a checklist and in order to validate the model, this checklist was presented to experts in the form of a questionnaire. To analyze the results of validation, an agreed coefficient of %75 was determined in order to apply changes. Finally, when the model was approved, the final version of the evaluation model for the cancer registry software was presented. The evaluation model of this study contains tool and method of evaluation. The evaluation tool is a checklist including the general and specific criteria of the cancer registry software along with their sub-criteria. The evaluation method of this study was chosen as a criteria-based evaluation method based on the findings. The model of this study encompasses various dimensions of cancer registry software and a proper method for evaluating it. The strong point of this evaluation model is the separation between general criteria and the specific ones, while trying to fulfill the comprehensiveness of the criteria. Since this model has been validated, it can be used as a standard to evaluate the cancer registry software.

Learning Theories Applied to Teaching Technology: Constructivism versus Behavioral Theory for Instructing Multimedia Software Programs

ERIC Educational Resources Information Center

Reed, Cajah S.

2012-01-01

This study sought to find evidence for a beneficial learning theory to teach computer software programs. Additionally, software was analyzed for each learning theory's applicability to resolve whether certain software requires a specific method of education. The results are meant to give educators more effective teaching tools, so students…

Automating software design system DESTA

NASA Technical Reports Server (NTRS)

Lovitsky, Vladimir A.; Pearce, Patricia D.

1992-01-01

'DESTA' is the acronym for the Dialogue Evolutionary Synthesizer of Turnkey Algorithms by means of a natural language (Russian or English) functional specification of algorithms or software being developed. DESTA represents the computer-aided and/or automatic artificial intelligence 'forgiving' system which provides users with software tools support for algorithm and/or structured program development. The DESTA system is intended to provide support for the higher levels and earlier stages of engineering design of software in contrast to conventional Computer Aided Design (CAD) systems which provide low level tools for use at a stage when the major planning and structuring decisions have already been taken. DESTA is a knowledge-intensive system. The main features of the knowledge are procedures, functions, modules, operating system commands, batch files, their natural language specifications, and their interlinks. The specific domain for the DESTA system is a high level programming language like Turbo Pascal 6.0. The DESTA system is operational and runs on an IBM PC computer.

Tool Use Within NASA Software Quality Assurance

NASA Technical Reports Server (NTRS)

Shigeta, Denise; Port, Dan; Nikora, Allen P.; Wilf, Joel

2013-01-01

As space mission software systems become larger and more complex, it is increasingly important for the software assurance effort to have the ability to effectively assess both the artifacts produced during software system development and the development process itself. Conceptually, assurance is a straightforward idea - it is the result of activities carried out by an organization independent of the software developers to better inform project management of potential technical and programmatic risks, and thus increase management's confidence in the decisions they ultimately make. In practice, effective assurance for large, complex systems often entails assessing large, complex software artifacts (e.g., requirements specifications, architectural descriptions) as well as substantial amounts of unstructured information (e.g., anomaly reports resulting from testing activities during development). In such an environment, assurance engineers can benefit greatly from appropriate tool support. In order to do so, an assurance organization will need accurate and timely information on the tool support available for various types of assurance activities. In this paper, we investigate the current use of tool support for assurance organizations within NASA, and describe on-going work at JPL for providing assurance organizations with the information about tools they need to use them effectively.

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.

Multidisciplinary and Active/Collaborative Approaches in Teaching Requirements Engineering

ERIC Educational Resources Information Center

Rosca, Daniela

2005-01-01

The requirements engineering course is a core component of the curriculum for the Master's in Software Engineering programme, at Monmouth University (MU). It covers the process, methods and tools specific to this area, together with the corresponding software quality issues. The need to produce software engineers with strong teamwork and…

Scalability Assessments for the Malicious Activity Simulation Tool (MAST)

DTIC Science & Technology

2012-09-01

the scalability characteristics of MAST. Specifically, we show that an exponential increase in clients using the MAST software does not impact...an exponential increase in clients using the MAST software does not impact network and system resources significantly. Additionally, we...31 1. Hardware .....................................31 2. Software .....................................32 3. Common PC

IPAT: a freely accessible software tool for analyzing multiple patent documents with inbuilt landscape visualizer.

PubMed

Ajay, Dara; Gangwal, Rahul P; Sangamwar, Abhay T

2015-01-01

Intelligent Patent Analysis Tool (IPAT) is an online data retrieval tool, operated based on text mining algorithm to extract specific patent information in a predetermined pattern into an Excel sheet. The software is designed and developed to retrieve and analyze technology information from multiple patent documents and generate various patent landscape graphs and charts. The software is C# coded in visual studio 2010, which extracts the publicly available patent information from the web pages like Google Patent and simultaneously study the various technology trends based on user-defined parameters. In other words, IPAT combined with the manual categorization will act as an excellent technology assessment tool in competitive intelligence and due diligence for predicting the future R&D forecast.

Annotated bibliography of Software Engineering Laboratory literature

NASA Technical Reports Server (NTRS)

Morusiewicz, Linda; Valett, Jon D.

1991-01-01

An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. All materials have been grouped into eight general subject areas for easy reference: The Software Engineering Laboratory; The Software Engineering Laboratory: Software Development Documents; Software Tools; Software Models; Software Measurement; Technology Evaluations; Ada Technology; and Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

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.

Validation, reliability, and specificity of CliniCom™ Psychiatric Assessment Software.

PubMed

Handal, Nelson; LePage, James; Dayley, Philip; Baldwin, Barbara; Roeser, Amellia; Kay, Joni; Theobald, Heather Ann; Nellamattathil, Michael; Drotar, Scott; Weir, Connor; Tindell, Neil; Tice, Kevin

2018-07-01

The purpose of this study was to determine the specificity and reproducibility of CliniCom™ Psychiatric Assessment Software to appropriately diagnose five prevalent mental health disorders. This online assessment tool incorporates proprietary algorithms for its propensity assessment. Unlike other questionnaires, which require a survey per specific mental disorder, CliniCom can simultaneously assess multiple mental disorders for an individual. CliniCom was concordant with other commonly used assessment tools in diagnosing five prevalent disorders including: Attention Deficit and Hyperactivity Disorder, Generalized Anxiety Disorder, Major Depressive Disorder, Obsessive Compulsive Disorder, and Social Phobia. The online tool was overall 78% concordant in diagnosing the same disorder during a test-retest analysis. When subjects exhibited two, three, or four disorders, the tool was less consistent in diagnosing the same set of disorders during the test-retest analysis (53% concordant). However, if evaluated as individual disorders within subjects, the more persistent disorders had a higher rate of concordance: MDD (83.3%), ADHD (81.0%), and OCD (68.4%). This study proposes CliniCom as an online assessment tool that demonstrates specificity in identifying specific psychiatric conditions and shows reproducibility over multiple administrations. Copyright © 2018 Elsevier B.V. All rights reserved.

Proposal for constructing an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Sims, Michael H.; Podolak, Esther; Mckay, Christopher P.; Thompson, David E.

1990-01-01

Scientific model building can be a time intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing and using models. The proposed tool will include an interactive intelligent graphical interface and a high level, domain specific, modeling language. As a testbed for this research, we propose development of a software prototype in the domain of planetary atmospheric modeling.

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.

Using SFOC to fly the Magellan Venus mapping mission

NASA Technical Reports Server (NTRS)

Bucher, Allen W.; Leonard, Robert E., Jr.; Short, Owen G.

1993-01-01

Traditionally, spacecraft flight operations at the Jet Propulsion Laboratory (JPL) have been performed by teams of spacecraft experts utilizing ground software designed specifically for the current mission. The Jet Propulsion Laboratory set out to reduce the cost of spacecraft mission operations by designing ground data processing software that could be used by multiple spacecraft missions, either sequentially or concurrently. The Space Flight Operations Center (SFOC) System was developed to provide the ground data system capabilities needed to monitor several spacecraft simultaneously and provide enough flexibility to meet the specific needs of individual projects. The Magellan Spacecraft Team utilizes the SFOC hardware and software designed for engineering telemetry analysis, both real-time and non-real-time. The flexibility of the SFOC System has allowed the spacecraft team to integrate their own tools with SFOC tools to perform the tasks required to operate a spacecraft mission. This paper describes how the Magellan Spacecraft Team is utilizing the SFOC System in conjunction with their own software tools to perform the required tasks of spacecraft event monitoring as well as engineering data analysis and trending.

Pointo - a Low Cost Solution to Point Cloud Processing

NASA Astrophysics Data System (ADS)

Houshiar, H.; Winkler, S.

2017-11-01

With advance in technology access to data especially 3D point cloud data becomes more and more an everyday task. 3D point clouds are usually captured with very expensive tools such as 3D laser scanners or very time consuming methods such as photogrammetry. Most of the available softwares for 3D point cloud processing are designed for experts and specialists in this field and are usually very large software packages containing variety of methods and tools. This results in softwares that are usually very expensive to acquire and also very difficult to use. Difficulty of use is caused by complicated user interfaces that is required to accommodate a large list of features. The aim of these complex softwares is to provide a powerful tool for a specific group of specialist. However they are not necessary required by the majority of the up coming average users of point clouds. In addition to complexity and high costs of these softwares they generally rely on expensive and modern hardware and only compatible with one specific operating system. Many point cloud customers are not point cloud processing experts or willing to spend the high acquisition costs of these expensive softwares and hardwares. In this paper we introduce a solution for low cost point cloud processing. Our approach is designed to accommodate the needs of the average point cloud user. To reduce the cost and complexity of software our approach focuses on one functionality at a time in contrast with most available softwares and tools that aim to solve as many problems as possible at the same time. Our simple and user oriented design improve the user experience and empower us to optimize our methods for creation of an efficient software. In this paper we introduce Pointo family as a series of connected softwares to provide easy to use tools with simple design for different point cloud processing requirements. PointoVIEWER and PointoCAD are introduced as the first components of the Pointo family to provide a fast and efficient visualization with the ability to add annotation and documentation to the point clouds.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

PubMed

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

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.

Analysis and specification tools in relation to the APSE

NASA Technical Reports Server (NTRS)

Hendricks, John W.

1986-01-01

Ada and the Ada Programming Support Environment (APSE) specifically address the phases of the system/software life cycle which follow after the user's problem was translated into system and software development specifications. The waterfall model of the life cycle identifies the analysis and requirements definition phases as preceeding program design and coding. Since Ada is a programming language and the APSE is a programming support environment, they are primarily targeted to support program (code) development, tecting, and maintenance. The use of Ada based or Ada related specification languages (SLs) and program design languages (PDLs) can extend the use of Ada back into the software design phases of the life cycle. Recall that the standardization of the APSE as a programming support environment is only now happening after many years of evolutionary experience with diverse sets of programming support tools. Restricting consideration to one, or even a few chosen specification and design tools, could be a real mistake for an organization or a major project such as the Space Station, which will need to deal with an increasingly complex level of system problems. To require that everything be Ada-like, be implemented in Ada, run directly under the APSE, and fit into a rigid waterfall model of the life cycle would turn a promising support environment into a straight jacket for progress.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1993-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a testbed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1992-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a test bed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Annotated bibliography of software engineering laboratory literature

NASA Technical Reports Server (NTRS)

Buhler, Melanie; Valett, Jon

1989-01-01

An annotated bibliography is presented of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. The bibliography was updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials were grouped into eight general subject areas for easy reference: (1) The Software Engineering Laboratory; (2) The Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

The GenABEL Project for statistical genomics.

PubMed

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

2016-01-01

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

Specification Improvement Through Analysis of Proof Structure (SITAPS): High Assurance Software Development

DTIC Science & Technology

2016-02-01

proof in mathematics. For example, consider the proof of the Pythagorean Theorem illustrated at: http://www.cut-the-knot.org/ pythagoras / where 112...methods and tools have made significant progress in their ability to model software designs and prove correctness theorems about the systems modeled...assumption criticality” or “ theorem root set size” SITAPS detects potentially brittle verification cases. SITAPS provides tools and techniques that

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

NASA Astrophysics Data System (ADS)

Martinengo, Chiara; Curatelli, Francesco

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

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications

PubMed Central

Bajorath, Jurgen

2012-01-01

We have generated a number of  compound data sets and programs for different types of applications in pharmaceutical research. These data sets and programs were originally designed for our research projects and are made publicly available. Without consulting original literature sources, it is difficult to understand specific features of data sets and software tools, basic ideas underlying their design, and applicability domains. Currently, 30 different entries are available for download from our website. In this data article, we provide an overview of the data and tools we make available and designate the areas of research for which they should be useful. For selected data sets and methods/programs, detailed descriptions are given. This article should help interested readers to select data and tools for specific computational investigations. PMID:24358818

Comparison of BrainTool to other UML modeling and model transformation tools

NASA Astrophysics Data System (ADS)

Nikiforova, Oksana; Gusarovs, Konstantins

2017-07-01

In the last 30 years there were numerous model generated software systems offered targeting problems with the development productivity and the resulting software quality. CASE tools developed due today's date are being advertised as having "complete code-generation capabilities". Nowadays the Object Management Group (OMG) is calling similar arguments in regards to the Unified Modeling Language (UML) models at different levels of abstraction. It is being said that software development automation using CASE tools enables significant level of automation. Actual today's CASE tools are usually offering a combination of several features starting with a model editor and a model repository for a traditional ones and ending with code generator (that could be using a scripting or domain-specific (DSL) language), transformation tool to produce the new artifacts from the manually created and transformation definition editor to define new transformations for the most advanced ones. Present paper contains the results of CASE tool (mainly UML editors) comparison against the level of the automation they are offering.

Review of Software Tools for Design and Analysis of Large scale MRM Proteomic Datasets

PubMed Central

Colangelo, Christopher M.; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-01-01

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. PMID:23702368

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.

Family-Based Benchmarking of Copy Number Variation Detection Software.

PubMed

Nutsua, Marcel Elie; Fischer, Annegret; Nebel, Almut; Hofmann, Sylvia; Schreiber, Stefan; Krawczak, Michael; Nothnagel, Michael

2015-01-01

The analysis of structural variants, in particular of copy-number variations (CNVs), has proven valuable in unraveling the genetic basis of human diseases. Hence, a large number of algorithms have been developed for the detection of CNVs in SNP array signal intensity data. Using the European and African HapMap trio data, we undertook a comparative evaluation of six commonly used CNV detection software tools, namely Affymetrix Power Tools (APT), QuantiSNP, PennCNV, GLAD, R-gada and VEGA, and assessed their level of pair-wise prediction concordance. The tool-specific CNV prediction accuracy was assessed in silico by way of intra-familial validation. Software tools differed greatly in terms of the number and length of the CNVs predicted as well as the number of markers included in a CNV. All software tools predicted substantially more deletions than duplications. Intra-familial validation revealed consistently low levels of prediction accuracy as measured by the proportion of validated CNVs (34-60%). Moreover, up to 20% of apparent family-based validations were found to be due to chance alone. Software using Hidden Markov models (HMM) showed a trend to predict fewer CNVs than segmentation-based algorithms albeit with greater validity. PennCNV yielded the highest prediction accuracy (60.9%). Finally, the pairwise concordance of CNV prediction was found to vary widely with the software tools involved. We recommend HMM-based software, in particular PennCNV, rather than segmentation-based algorithms when validity is the primary concern of CNV detection. QuantiSNP may be used as an additional tool to detect sets of CNVs not detectable by the other tools. Our study also reemphasizes the need for laboratory-based validation, such as qPCR, of CNVs predicted in silico.

Computer-aided system design

NASA Technical Reports Server (NTRS)

Walker, Carrie K.

1991-01-01

A technique has been developed for combining features of a systems architecture design and assessment tool and a software development tool. This technique reduces simulation development time and expands simulation detail. The Architecture Design and Assessment System (ADAS), developed at the Research Triangle Institute, is a set of computer-assisted engineering tools for the design and analysis of computer systems. The ADAS system is based on directed graph concepts and supports the synthesis and analysis of software algorithms mapped to candidate hardware implementations. Greater simulation detail is provided by the ADAS functional simulator. With the functional simulator, programs written in either Ada or C can be used to provide a detailed description of graph nodes. A Computer-Aided Software Engineering tool developed at the Charles Stark Draper Laboratory (CSDL CASE) automatically generates Ada or C code from engineering block diagram specifications designed with an interactive graphical interface. A technique to use the tools together has been developed, which further automates the design process.

Developing Formal Object-oriented Requirements Specifications: A Model, Tool and Technique.

ERIC Educational Resources Information Center

Jackson, Robert B.; And Others

1995-01-01

Presents a formal object-oriented specification model (OSS) for computer software system development that is supported by a tool that automatically generates a prototype from an object-oriented analysis model (OSA) instance, lets the user examine the prototype, and permits the user to refine the OSA model instance to generate a requirements…

Software engineering project management - A state-of-the-art report

NASA Technical Reports Server (NTRS)

Thayer, R. H.; Lehman, J. H.

1977-01-01

The management of software engineering projects in the aerospace industry was investigated. The survey assessed such features as contract type, specification preparation techniques, software documentation required by customers, planning and cost-estimating, quality control, the use of advanced program practices, software tools and test procedures, the education levels of project managers, programmers and analysts, work assignment, automatic software monitoring capabilities, design and coding reviews, production times, success rates, and organizational structure of the projects.

Software reliability through fault-avoidance and fault-tolerance

NASA Technical Reports Server (NTRS)

Vouk, Mladen A.; Mcallister, David F.

1993-01-01

Strategies and tools for the testing, risk assessment and risk control of dependable software-based systems were developed. Part of this project consists of studies to enable the transfer of technology to industry, for example the risk management techniques for safety-concious systems. Theoretical investigations of Boolean and Relational Operator (BRO) testing strategy were conducted for condition-based testing. The Basic Graph Generation and Analysis tool (BGG) was extended to fully incorporate several variants of the BRO metric. Single- and multi-phase risk, coverage and time-based models are being developed to provide additional theoretical and empirical basis for estimation of the reliability and availability of large, highly dependable software. A model for software process and risk management was developed. The use of cause-effect graphing for software specification and validation was investigated. Lastly, advanced software fault-tolerance models were studied to provide alternatives and improvements in situations where simple software fault-tolerance strategies break down.

Towards Archetypes-Based Software Development

NASA Astrophysics Data System (ADS)

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

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

Navigating freely-available software tools for metabolomics analysis.

PubMed

Spicer, Rachel; Salek, Reza M; Moreno, Pablo; Cañueto, Daniel; Steinbeck, Christoph

2017-01-01

The field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics software tools. The diversity of experimental designs and instrumental technologies used for metabolomics has led to the need for distinct data analysis methods and the development of many software tools. To compile a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics. The most widely used tools were selected for inclusion in the review by either ≥ 50 citations on Web of Science (as of 08/09/16) or the use of the tool being reported in the recent Metabolomics Society survey. Tools were then categorised by the type of instrumental data (i.e. LC-MS, GC-MS or NMR) and the functionality (i.e. pre- and post-processing, statistical analysis, workflow and other functions) they are designed for. A comprehensive list of the most used tools was compiled. Each tool is discussed within the context of its application domain and in relation to comparable tools of the same domain. An extended list including additional tools is available at https://github.com/RASpicer/MetabolomicsTools which is classified and searchable via a simple controlled vocabulary. This review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality. As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.

Introducing the CUAHSI Hydrologic Information System Desktop Application (HydroDesktop) and Open Development Community

NASA Astrophysics Data System (ADS)

Ames, D.; Kadlec, J.; Horsburgh, J. S.; Maidment, D. R.

2009-12-01

The Consortium of Universities for the Advancement of Hydrologic Sciences (CUAHSI) Hydrologic Information System (HIS) project includes extensive development of data storage and delivery tools and standards including WaterML (a language for sharing hydrologic data sets via web services); and HIS Server (a software tool set for delivering WaterML from a server); These and other CUASHI HIS tools have been under development and deployment for several years and together, present a relatively complete software “stack” to support the consistent storage and delivery of hydrologic and other environmental observation data. This presentation describes the development of a new HIS software tool called “HydroDesktop” and the development of an online open source software development community to update and maintain the software. HydroDesktop is a local (i.e. not server-based) client side software tool that ultimately will run on multiple operating systems and will provide a highly usable level of access to HIS services. The software provides many key capabilities including data query, map-based visualization, data download, local data maintenance, editing, graphing, data export to selected model-specific data formats, linkage with integrated modeling systems such as OpenMI, and ultimately upload to HIS servers from the local desktop software. As the software is presently in the early stages of development, this presentation will focus on design approach and paradigm and is viewed as an opportunity to encourage participation in the open development community. Indeed, recognizing the value of community based code development as a means of ensuring end-user adoption, this project has adopted an “iterative” or “spiral” software development approach which will be described in this presentation.

What's New in Software? Computers and the Writing Process: Strategies That Work.

ERIC Educational Resources Information Center

Ellsworth, Nancy J.

1990-01-01

The computer can be a powerful tool to help students who are having difficulty learning the skills of prewriting, composition, revision, and editing. Specific software is suggested for each phase, as well as for classroom publishing. (Author/JDD)

Evolution of the phase 2 preparation and observation tools at ESO

NASA Astrophysics Data System (ADS)

Dorigo, D.; Amarand, B.; Bierwirth, T.; Jung, Y.; Santos, P.; Sogni, F.; Vera, I.

2012-09-01

Throughout the course of many years of observations at the VLT, the phase 2 software applications supporting the specification, execution and reporting of observations have been continuously improved and refined. Specifically the introduction of astronomical surveys propelled the creation of new tools to express more sophisticated, longer-term observing strategies often consisting of several hundreds of observations. During the execution phase, such survey programs compete with other service and visitor mode observations and a number of constraints have to be considered. In order to maximize telescope utilization and execute all programs in a fair way, new algorithms have been developed to prioritize observable OBs taking into account both current and future constraints (e.g. OB time constraints, technical telescope time) and suggest the next OB to be executed. As a side effect, a higher degree of observation automation enables operators to run telescopes mostly autonomously with little supervision by a support astronomer. We describe the new tools that have been deployed and the iterative and incremental software development process applied to develop them. We present our key software technologies used so far and discuss potential future evolution both in terms of features as well as software technologies.

VLSI synthesis of digital application specific neural networks

NASA Technical Reports Server (NTRS)

Beagles, Grant; Winters, Kel

1991-01-01

Neural networks tend to fall into two general categories: (1) software simulations, or (2) custom hardware that must be trained. The scope of this project is the merger of these two classifications into a system whereby a software model of a network is trained to perform a specific task and the results used to synthesize a standard cell realization of the network using automated tools.

Annotated bibliography of software engineering laboratory literature

NASA Technical Reports Server (NTRS)

Groves, Paula; Valett, Jon

1990-01-01

An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: the Software Engineering Laboratory; the Software Engineering Laboratory-software development documents; software tools; software models; software measurement; technology evaluations; Ada technology; and data collection. Subject and author indexes further classify these documents by specific topic and individual author.

The GenABEL Project for statistical genomics

PubMed Central

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

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment.

PubMed

Forkert, N D; Cheng, B; Kemmling, A; Thomalla, G; Fiehler, J

2014-01-01

The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation. Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses. For reliability evaluation, the described software tool was used by two observers for quantitative analysis of 15 datasets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used. Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

Production of Reliable Flight Crucial Software: Validation Methods Research for Fault Tolerant Avionics and Control Systems Sub-Working Group Meeting

NASA Technical Reports Server (NTRS)

Dunham, J. R. (Editor); Knight, J. C. (Editor)

1982-01-01

The state of the art in the production of crucial software for flight control applications was addressed. The association between reliability metrics and software is considered. Thirteen software development projects are discussed. A short term need for research in the areas of tool development and software fault tolerance was indicated. For the long term, research in format verification or proof methods was recommended. Formal specification and software reliability modeling, were recommended as topics for both short and long term research.

Comparative exploration of multidimensional flow cytometry software: a model approach evaluating T cell polyfunctional behavior.

PubMed

Spear, Timothy T; Nishimura, Michael I; Simms, Patricia E

2017-08-01

Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s). Here, we comparatively assess various multidimensional flow cytometry software packages for their ability to answer a specific biologic question and provide graphical representation output suitable for publication, as well as their ease of use and cost. We assessed polyfunctional potential of TCR-transduced T cells, serving as a model evaluation, using multidimensional flow cytometry to analyze 6 intracellular cytokines and degranulation on a per-cell basis. Analysis of 7 parameters resulted in 128 possible combinations of positivity/negativity, far too complex for basic flow cytometry software to analyze fully. Various software packages were used, analysis methods used in each described, and representative output displayed. Of the tools investigated, automated classification of cellular expression by nonlinear stochastic embedding (ACCENSE) and coupled analysis in Pestle/simplified presentation of incredibly complex evaluations (SPICE) provided the most user-friendly manipulations and readable output, evaluating effects of altered antigen-specific stimulation on T cell polyfunctionality. This detailed approach may serve as a model for other investigators/SRLs in selecting the most appropriate software to analyze complex flow cytometry datasets. Further development and awareness of available tools will help guide proper data analysis to answer difficult biologic questions arising from incredibly complex datasets. © Society for Leukocyte Biology.

Portable image-manipulation software: what is the extra development cost?

PubMed

Ligier, Y; Ratib, O; Funk, M; Perrier, R; Girard, C; Logean, M

1992-08-01

A hospital-wide picture archiving and communication system (PACS) project is currently under development at the University Hospital of Geneva. The visualization and manipulation of images provided by different imaging modalities constitutes one of the most challenging component of a PACS. It was necessary to provide this visualization software on a number of types of workstations because of the varying requirements imposed by the range of clinical uses it must serve. The user interface must be the same, independent of the underlying workstation. In addition to a standard set of image-manipulation and processing tools, there is a need for more specific clinical tools that can be easily adapted to specific medical requirements. To achieve this goal, it was elected to develop a modular and portable software called OSIRIS. This software is available on two different operating systems (the UNIX standard X-11/OSF-Motif based workstations and the Macintosh family) and can be easily ported to other systems. The extra effort required to design such software in a modular and portable way was worthwhile because it resulted in a platform that can be easily expanded and adapted to a variety of specific clinical applications. Its portability allows users to benefit from the rapidly evolving workstation technology and to adapt the performance to suit their needs.

Rotorcraft Conceptual Design Environment

DTIC Science & Technology

2009-10-01

systems engineering design tool sets. The DaVinci Project vision is to develop software architecture and tools specifically for acquisition system...enable movement of that information to and from analyses. Finally, a recently developed rotorcraft system analysis tool is described. Introduction...information to and from analyses. Finally, a recently developed rotorcraft system analysis tool is described. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION

An overview of very high level software design methods

NASA Technical Reports Server (NTRS)

Asdjodi, Maryam; Hooper, James W.

1988-01-01

Very High Level design methods emphasize automatic transfer of requirements to formal design specifications, and/or may concentrate on automatic transformation of formal design specifications that include some semantic information of the system into machine executable form. Very high level design methods range from general domain independent methods to approaches implementable for specific applications or domains. Applying AI techniques, abstract programming methods, domain heuristics, software engineering tools, library-based programming and other methods different approaches for higher level software design are being developed. Though one finds that a given approach does not always fall exactly in any specific class, this paper provides a classification for very high level design methods including examples for each class. These methods are analyzed and compared based on their basic approaches, strengths and feasibility for future expansion toward automatic development of software systems.

Evidence of absence (v2.0) software user guide

USGS Publications Warehouse

Dalthorp, Daniel; Huso, Manuela; Dail, David

2017-07-06

Evidence of Absence software (EoA) is a user-friendly software application for estimating bird and bat fatalities at wind farms and for designing search protocols. The software is particularly useful in addressing whether the number of fatalities is below a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The software also includes tools (1) for estimating carcass persistence distributions and searcher efficiency parameters ( and ) from field trials, (2) for projecting future mortality based on past monitoring data, and (3) for exploring the potential consequences of various choices in the design of long-term incidental take permits for protected species. The software was designed specifically for cases where tolerance for mortality is low and carcass counts are small or even 0, but the tools also may be used for mortality estimates when carcass counts are large.

Review of software tools for design and analysis of large scale MRM proteomic datasets.

PubMed

Colangelo, Christopher M; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-06-15

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

ReGaTE: Registration of Galaxy Tools in Elixir

PubMed Central

Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-01-01

Abstract Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE. PMID:28402416

Proceedings of the Workshop on software tools for distributed intelligent control systems

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

Herget, C.J.

1990-09-01

The Workshop on Software Tools for Distributed Intelligent Control Systems was organized by Lawrence Livermore National Laboratory for the United States Army Headquarters Training and Doctrine Command and the Defense Advanced Research Projects Agency. The goals of the workshop were to the identify the current state of the art in tools which support control systems engineering design and implementation, identify research issues associated with writing software tools which would provide a design environment to assist engineers in multidisciplinary control design and implementation, formulate a potential investment strategy to resolve the research issues and develop public domain code which can formmore » the core of more powerful engineering design tools, and recommend test cases to focus the software development process and test associated performance metrics. Recognizing that the development of software tools for distributed intelligent control systems will require a multidisciplinary effort, experts in systems engineering, control systems engineering, and compute science were invited to participate in the workshop. In particular, experts who could address the following topics were selected: operating systems, engineering data representation and manipulation, emerging standards for manufacturing data, mathematical foundations, coupling of symbolic and numerical computation, user interface, system identification, system representation at different levels of abstraction, system specification, system design, verification and validation, automatic code generation, and integration of modular, reusable code.« less

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.

Building Safer Systems With SpecTRM

NASA Technical Reports Server (NTRS)

2003-01-01

System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.System safety, an integral component in software development, often poses a challenge to engineers designing computer-based systems. While the relaxed constraints on software design allow for increased power and flexibility, this flexibility introduces more possibilities for error. As a result, system engineers must identify the design constraints necessary to maintain safety and ensure that the system and software design enforces them. Safeware Engineering Corporation, of Seattle, Washington, provides the information, tools, and techniques to accomplish this task with its Specification Tools and Requirements Methodology (SpecTRM). NASA assisted in developing this engineering toolset by awarding the company several Small Business Innovation Research (SBIR) contracts with Ames Research Center and Langley Research Center. The technology benefits NASA through its applications for Space Station rendezvous and docking. SpecTRM aids system and software engineers in developing specifications for large, complex safety critical systems. The product enables engineers to find errors early in development so that they can be fixed with the lowest cost and impact on the system design. SpecTRM traces both the requirements and design rationale (including safety constraints) throughout the system design and documentation, allowing engineers to build required system properties into the design from the beginning, rather than emphasizing assessment at the end of the development process when changes are limited and costly.

Recent developments in software tools for high-throughput in vitro ADME support with high-resolution MS.

PubMed

Paiva, Anthony; Shou, Wilson Z

2016-08-01

The last several years have seen the rapid adoption of the high-resolution MS (HRMS) for bioanalytical support of high throughput in vitro ADME profiling. Many capable software tools have been developed and refined to process quantitative HRMS bioanalysis data for ADME samples with excellent performance. Additionally, new software applications specifically designed for quan/qual soft spot identification workflows using HRMS have greatly enhanced the quality and efficiency of the structure elucidation process for high throughput metabolite ID in early in vitro ADME profiling. Finally, novel approaches in data acquisition and compression, as well as tools for transferring, archiving and retrieving HRMS data, are being continuously refined to tackle the issue of large data file size typical for HRMS analyses.

Experiences with a generator tool for building clinical application modules.

PubMed

Kuhn, K A; Lenz, R; Elstner, T; Siegele, H; Moll, R

2003-01-01

To elaborate main system characteristics and relevant deployment experiences for the health information system (HIS) Orbis/OpenMed, which is in widespread use in Germany, Austria, and Switzerland. In a deployment phase of 3 years in a 1.200 bed university hospital, where the system underwent significant improvements, the system's functionality and its software design have been analyzed in detail. We focus on an integrated CASE tool for generating embedded clinical applications and for incremental system evolution. We present a participatory and iterative software engineering process developed for efficient utilization of such a tool. The system's functionality is comparable to other commercial products' functionality; its components are embedded in a vendor-specific application framework, and standard interfaces are being used for connecting subsystems. The integrated generator tool is a remarkable feature; it became a key factor of our project. Tool generated applications are workflow enabled and embedded into the overall data base schema. Rapid prototyping and iterative refinement are supported, so application modules can be adapted to the users' work practice. We consider tools supporting an iterative and participatory software engineering process highly relevant for health information system architects. The potential of a system to continuously evolve and to be effectively adapted to changing needs may be more important than sophisticated but hard-coded HIS functionality. More work will focus on HIS software design and on software engineering. Methods and tools are needed for quick and robust adaptation of systems to health care processes and changing requirements.

Modular Analytical Multicomponent Analysis in Gas Sensor Aarrays

PubMed Central

Chaiyboun, Ali; Traute, Rüdiger; Kiesewetter, Olaf; Ahlers, Simon; Müller, Gerhard; Doll, Theodor

2006-01-01

A multi-sensor system is a chemical sensor system which quantitatively and qualitatively records gases with a combination of cross-sensitive gas sensor arrays and pattern recognition software. This paper addresses the issue of data analysis for identification of gases in a gas sensor array. We introduce a software tool for gas sensor array configuration and simulation. It concerns thereby about a modular software package for the acquisition of data of different sensors. A signal evaluation algorithm referred to as matrix method was used specifically for the software tool. This matrix method computes the gas concentrations from the signals of a sensor array. The software tool was used for the simulation of an array of five sensors to determine gas concentration of CH4, NH3, H2, CO and C2H5OH. The results of the present simulated sensor array indicate that the software tool is capable of the following: (a) identify a gas independently of its concentration; (b) estimate the concentration of the gas, even if the system was not previously exposed to this concentration; (c) tell when a gas concentration exceeds a certain value. A gas sensor data base was build for the configuration of the software. With the data base one can create, generate and manage scenarios and source files for the simulation. With the gas sensor data base and the simulation software an on-line Web-based version was developed, with which the user can configure and simulate sensor arrays on-line.

Share Repository Framework: Component Specification and Otology

DTIC Science & Technology

2008-04-23

Palantir Technologies has created one such software application to support the DoD intelligence community by providing robust capabilities for...managing data from various sources. The Palantir tool is based on user-defined ontologies and supports multiple representation and analysis 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.

PHARMAVIRTUA: Educational Software for Teaching and Learning Basic Pharmacology

ERIC Educational Resources Information Center

Fidalgo-Neto, Antonio Augusto; Alberto, Anael Viana Pinto; Bonavita, André Gustavo Calvano; Bezerra, Rômulo José Soares; Berçot, Felipe Faria; Lopes, Renato Matos; Alves, Luiz Anastacio

2014-01-01

Information and communication technologies have become important tools for teaching scientific subjects such as anatomy and histology as well as other, nondescriptive subjects like physiology and pharmacology. Software has been used to facilitate the learning of specific concepts at the cellular and molecular levels in the biological and health…

Workflow-Based Software Development Environment

NASA Technical Reports Server (NTRS)

Izygon, Michel E.

2013-01-01

The Software Developer's Assistant (SDA) helps software teams more efficiently and accurately conduct or execute software processes associated with NASA mission-critical software. SDA is a process enactment platform that guides software teams through project-specific standards, processes, and procedures. Software projects are decomposed into all of their required process steps or tasks, and each task is assigned to project personnel. SDA orchestrates the performance of work required to complete all process tasks in the correct sequence. The software then notifies team members when they may begin work on their assigned tasks and provides the tools, instructions, reference materials, and supportive artifacts that allow users to compliantly perform the work. A combination of technology components captures and enacts any software process use to support the software lifecycle. It creates an adaptive workflow environment that can be modified as needed. SDA achieves software process automation through a Business Process Management (BPM) approach to managing the software lifecycle for mission-critical projects. It contains five main parts: TieFlow (workflow engine), Business Rules (rules to alter process flow), Common Repository (storage for project artifacts, versions, history, schedules, etc.), SOA (interface to allow internal, GFE, or COTS tools integration), and the Web Portal Interface (collaborative web environment

Integrating interface slicing into software engineering processes

NASA Technical Reports Server (NTRS)

Beck, Jon

1993-01-01

Interface slicing is a tool which was developed to facilitate software engineering. As previously presented, it was described in terms of its techniques and mechanisms. The integration of interface slicing into specific software engineering activities is considered by discussing a number of potential applications of interface slicing. The applications discussed specifically address the problems, issues, or concerns raised in a previous project. Because a complete interface slicer is still under development, these applications must be phrased in future tenses. Nonetheless, the interface slicing techniques which were presented can be implemented using current compiler and static analysis technology. Whether implemented as a standalone tool or as a module in an integrated development or reverse engineering environment, they require analysis no more complex than that required for current system development environments. By contrast, conventional slicing is a methodology which, while showing much promise and intuitive appeal, has yet to be fully implemented in a production language environment despite 12 years of development.

Process Based on SysML for New Launchers System and Software Developments

NASA Astrophysics Data System (ADS)

Hiron, Emmanuel; Miramont, Philippe

2010-08-01

The purpose of this paper is to present the Astrium-ST engineering process based on SysML. This process is currently set-up in the frame of common CNES /Astrium-ST R&T studies related to the Ariane 5 electrical system and flight software modelling. The tool used to set up this process is Rhapsody release 7.3 from IBM-Software firm [1]. This process focuses on the system engineering phase dedicated to Software with the objective to generate both System documents (sequential system design and flight control) and Software specifications.

Annotated bibliography of Software Engineering Laboratory literature

NASA Technical Reports Server (NTRS)

1985-01-01

An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is presented. More than 100 publications are summarized. These publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials are grouped into five general subject areas for easy reference: (1) the software engineering laboratory; (2) software tools; (3) models and measures; (4) technology evaluations; and (5) data collection. An index further classifies these documents by specific topic.

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

2017-03-01

Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

ControlShell - A real-time software framework

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

General guidelines for biomedical software development

PubMed Central

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

2017-01-01

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

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

statistical packages and software for screen layout. These items work at a higher level than another category of prototyping tool, program generators... Program generators are software packages which, when given specifications, produce source listings, usually in a high order language such as COBCL...with users and this will not happen if he must stop to develcp a detailed program . [Ref. 241] Hardware as well as software should be considered in

ReGaTE: Registration of Galaxy Tools in Elixir.

PubMed

Doppelt-Azeroual, Olivia; Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-06-01

Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE . © The Author 2017. Published by Oxford University Press.

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.

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

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.

PubMed

Prior, Fred W; Erickson, Bradley J; Tarbox, Lawrence

2007-11-01

The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.

Design and implementation of the mobility assessment tool: software description.

PubMed

Barnard, Ryan T; Marsh, Anthony P; Rejeski, Walter Jack; Pecorella, Anthony; Ip, Edward H

2013-07-23

In previous work, we described the development of an 81-item video-animated tool for assessing mobility. In response to criticism levied during a pilot study of this tool, we sought to develop a new version built upon a flexible framework for designing and administering the instrument. Rather than constructing a self-contained software application with a hard-coded instrument, we designed an XML schema capable of describing a variety of psychometric instruments. The new version of our video-animated assessment tool was then defined fully within the context of a compliant XML document. Two software applications--one built in Java, the other in Objective-C for the Apple iPad--were then built that could present the instrument described in the XML document and collect participants' responses. Separating the instrument's definition from the software application implementing it allowed for rapid iteration and easy, reliable definition of variations. Defining instruments in a software-independent XML document simplifies the process of defining instruments and variations and allows a single instrument to be deployed on as many platforms as there are software applications capable of interpreting the instrument, thereby broadening the potential target audience for the instrument. Continued work will be done to further specify and refine this type of instrument specification with a focus on spurring adoption by researchers in gerontology and geriatric medicine.

Design and implementation of the mobility assessment tool: software description

PubMed Central

2013-01-01

Background In previous work, we described the development of an 81-item video-animated tool for assessing mobility. In response to criticism levied during a pilot study of this tool, we sought to develop a new version built upon a flexible framework for designing and administering the instrument. Results Rather than constructing a self-contained software application with a hard-coded instrument, we designed an XML schema capable of describing a variety of psychometric instruments. The new version of our video-animated assessment tool was then defined fully within the context of a compliant XML document. Two software applications—one built in Java, the other in Objective-C for the Apple iPad—were then built that could present the instrument described in the XML document and collect participants’ responses. Separating the instrument’s definition from the software application implementing it allowed for rapid iteration and easy, reliable definition of variations. Conclusions Defining instruments in a software-independent XML document simplifies the process of defining instruments and variations and allows a single instrument to be deployed on as many platforms as there are software applications capable of interpreting the instrument, thereby broadening the potential target audience for the instrument. Continued work will be done to further specify and refine this type of instrument specification with a focus on spurring adoption by researchers in gerontology and geriatric medicine. PMID:23879716

Generalized Information Architecture for Managing Requirements in IBM?s Rational DOORS(r) Application.

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

Aragon, Kathryn M.; Eaton, Shelley M.; McCornack, Marjorie Turner

When a requirements engineering effort fails to meet expectations, often times the requirements management tool is blamed. Working with numerous project teams at Sandia National Laboratories over the last fifteen years has shown us that the tool is rarely the culprit; usually it is the lack of a viable information architecture with well- designed processes to support requirements engineering. This document illustrates design concepts with rationale, as well as a proven information architecture to structure and manage information in support of requirements engineering activities for any size or type of project. This generalized information architecture is specific to IBM's Rationalmore » DOORS (Dynamic Object Oriented Requirements System) software application, which is the requirements management tool in Sandia's CEE (Common Engineering Environment). This generalized information architecture can be used as presented or as a foundation for designing a tailored information architecture for project-specific needs. It may also be tailored for another software tool. Version 1.0 4 November 201« less

Quantitative Measures for Software Independent Verification and Validation

NASA Technical Reports Server (NTRS)

Lee, Alice

1996-01-01

As software is maintained or reused, it undergoes an evolution which tends to increase the overall complexity of the code. To understand the effects of this, we brought in statistics experts and leading researchers in software complexity, reliability, and their interrelationships. These experts' project has resulted in our ability to statistically correlate specific code complexity attributes, in orthogonal domains, to errors found over time in the HAL/S flight software which flies in the Space Shuttle. Although only a prototype-tools experiment, the result of this research appears to be extendable to all other NASA software, given appropriate data similar to that logged for the Shuttle onboard software. Our research has demonstrated that a more complete domain coverage can be mathematically demonstrated with the approach we have applied, thereby ensuring full insight into the cause-and-effects relationship between the complexity of a software system and the fault density of that system. By applying the operational profile we can characterize the dynamic effects of software path complexity under this same approach We now have the ability to measure specific attributes which have been statistically demonstrated to correlate to increased error probability, and to know which actions to take, for each complexity domain. Shuttle software verifiers can now monitor the changes in the software complexity, assess the added or decreased risk of software faults in modified code, and determine necessary corrections. The reports, tool documentation, user's guides, and new approach that have resulted from this research effort represent advances in the state of the art of software quality and reliability assurance. Details describing how to apply this technique to other NASA code are contained in this document.

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

PubMed Central

Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

2010-01-01

Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software. PMID:20190053

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

PubMed

Meereis, Florian; Kaufmann, Michael

2004-10-15

The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Planetary Data Workshop, Part 2

NASA Technical Reports Server (NTRS)

1984-01-01

Technical aspects of the Planetary Data System (PDS) are addressed. Methods and tools for maintaining and accessing large, complex sets of data are discussed. The specific software and applications needed for processing imaging and non-imaging science data are reviewed. The need for specific software that provides users with information on the location and geometry of scientific observations is discussed. Computer networks and user interface to the PDS are covered along with Computer hardware available to this data system.

Simulink/PARS Integration Support

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

Vacaliuc, B.; Nakhaee, N.

2013-12-18

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

Requirements Specification Language (RSL) and supporting tools

NASA Technical Reports Server (NTRS)

Frincke, Deborah; Wolber, Dave; Fisher, Gene; Cohen, Gerald C.

1992-01-01

This document describes a general purpose Requirement Specification Language (RSL). RSL is a hybrid of features found in several popular requirement specification languages. The purpose of RSL is to describe precisely the external structure of a system comprised of hardware, software, and human processing elements. To overcome the deficiencies of informal specification languages, RSL includes facilities for mathematical specification. Two RSL interface tools are described. The Browser view contains a complete document with all details of the objects and operations. The Dataflow view is a specialized, operation-centered depiction of a specification that shows how specified operations relate in terms of inputs and outputs.

Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

PubMed

Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

2013-01-01

Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

From Verified Models to Verifiable Code

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

Global GIS database; digital atlas of South Pacific

USGS Publications Warehouse

Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

2001-01-01

This CD-ROM contains a digital atlas of the countries of the South Pacific. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included.

Global GIS database; digital atlas of Africa

USGS Publications Warehouse

Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

2001-01-01

This CD-ROM contains a digital atlas of the countries of Africa. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make this atlas easier to use, are also included.

Global GIS database; digital atlas of South Asia

USGS Publications Warehouse

Hearn, P.P.; Hare, T.M.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

2001-01-01

This CD-ROM contains a digital atlas of the countries of South Asia. This atlas is part of a global database compiled from USGS and other data sources at a nominal scale 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included.

An experience of qualified preventive screening: shiraz smart screening software.

PubMed

Islami Parkoohi, Parisa; Zare, Hashem; Abdollahifard, Gholamreza

2015-01-01

Computerized preventive screening software is a cost effective intervention tool to address non-communicable chronic diseases. Shiraz Smart Screening Software (SSSS) was developed as an innovative tool for qualified screening. It allows simultaneous smart screening of several high-burden chronic diseases and supports reminder notification functionality. The extent in which SSSS affects screening quality is also described. Following software development, preventive screening and annual health examinations of 261 school staff (Medical School of Shiraz, Iran) was carried out in a software-assisted manner. To evaluate the quality of the software-assisted screening, we used quasi-experimental study design and determined coverage, irregular attendance and inappropriateness proportions in relation with the manual and software-assisted screening as well as the corresponding number of requested tests. In manual screening method, 27% of employees were covered (with 94% irregular attendance) while by software-assisted screening, the coverage proportion was 79% (attendance status will clear after the specified time). The frequency of inappropriate screening test requests, before the software implementation, was 41.37% for fasting plasma glucose, 41.37% for lipid profile, 0.84% for occult blood, 0.19% for flexible sigmoidoscopy/colonoscopy, 35.29% for Pap smear, 19.20% for mammography and 11.2% for prostate specific antigen. All of the above were corrected by the software application. In total, 366 manual screening and 334 software-assisted screening tests were requested. SSSS is an innovative tool to improve the quality of preventive screening plans in terms of increased screening coverage, reduction in inappropriateness and the total number of requested tests.

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

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

Software Tool Integrating Data Flow Diagrams and Petri Nets

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Tavana, Madjid

2010-01-01

Data Flow Diagram - Petri Net (DFPN) is a software tool for analyzing other software to be developed. The full name of this program reflects its design, which combines the benefit of data-flow diagrams (which are typically favored by software analysts) with the power and precision of Petri-net models, without requiring specialized Petri-net training. (A Petri net is a particular type of directed graph, a description of which would exceed the scope of this article.) DFPN assists a software analyst in drawing and specifying a data-flow diagram, then translates the diagram into a Petri net, then enables graphical tracing of execution paths through the Petri net for verification, by the end user, of the properties of the software to be developed. In comparison with prior means of verifying the properties of software to be developed, DFPN makes verification by the end user more nearly certain, thereby making it easier to identify and correct misconceptions earlier in the development process, when correction is less expensive. After the verification by the end user, DFPN generates a printable system specification in the form of descriptions of processes and data.

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

Morphogenic designer--an efficient tool to digitally design tooth forms.

PubMed

Hajtó, J; Marinescu, C; Silva, N R F A

2014-01-01

Different digital software tools are available today for the purpose of designing anatomically correct anterior and posterior restorations. The current concepts present weaknesses, which can be potentially addressed by more advanced modeling tools, such as the ones already available in professional CAD (Computer Aided Design) graphical software. This study describes the morphogenic designer (MGD) as an efficient and easy method for digitally designing tooth forms for the anterior and posterior dentition. Anterior and posterior tooth forms were selected from a collection of digitalized natural teeth and subjectively assessed as "average". The models in the form of STL files were filtered, cleaned, idealized, and re-meshed to match the specifications of the software used. The shapes were then imported as wavefront ".obj" model into Modo 701, software built for modeling, texturing, visualization, and animation. In order to create a parametric design system, intentional interactive deformations were performed on the average tooth shapes and then further defined as morph targets. By combining various such parameters, several tooth shapes were formed virtually and their images presented. MGD proved to be a versatile and powerful tool for the purpose of esthetic and functional digital crown designs.

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.

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.

NASAL-Geom, a free upper respiratory tract 3D model reconstruction software

NASA Astrophysics Data System (ADS)

Cercos-Pita, J. L.; Cal, I. R.; Duque, D.; de Moreta, G. Sanjuán

2018-02-01

The tool NASAL-Geom, a free upper respiratory tract 3D model reconstruction software, is here described. As a free software, researchers and professionals are welcome to obtain, analyze, improve and redistribute it, potentially increasing the rate of development, and reducing at the same time ethical conflicts regarding medical applications which cannot be analyzed. Additionally, the tool has been optimized for the specific task of reading upper respiratory tract Computerized Tomography scans, and producing 3D geometries. The reconstruction process is divided into three stages: preprocessing (including Metal Artifact Reduction, noise removal, and feature enhancement), segmentation (where the nasal cavity is identified), and 3D geometry reconstruction. The tool has been automatized (i.e. no human intervention is required) a critical feature to avoid bias in the reconstructed geometries. The applied methodology is discussed, as well as the program robustness and precision.

Intelligent Systems and Advanced User Interfaces for Design, Operation, and Maintenance of Command Management Systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1998-01-01

Historically Command Management Systems (CMS) have been large, expensive, spacecraft-specific software systems that were costly to build, operate, and maintain. Current and emerging hardware, software, and user interface technologies may offer an opportunity to facilitate the initial formulation and design of a spacecraft-specific CMS as well as a to develop a more generic or a set of core components for CMS systems. Current MOC (mission operations center) hardware and software include Unix workstations, the C/C++ and Java programming languages, and X and Java window interfaces representations. This configuration provides the power and flexibility to support sophisticated systems and intelligent user interfaces that exploit state-of-the-art technologies in human-machine systems engineering, decision making, artificial intelligence, and software engineering. One of the goals of this research is to explore the extent to which technologies developed in the research laboratory can be productively applied in a complex system such as spacecraft command management. Initial examination of some of the issues in CMS design and operation suggests that application of technologies such as intelligent planning, case-based reasoning, design and analysis tools from a human-machine systems engineering point of view (e.g., operator and designer models) and human-computer interaction tools, (e.g., graphics, visualization, and animation), may provide significant savings in the design, operation, and maintenance of a spacecraft-specific CMS as well as continuity for CMS design and development across spacecraft with varying needs. The savings in this case is in software reuse at all stages of the software engineering process.

PC Software graphics tool for conceptual design of space/planetary electrical power systems

NASA Technical Reports Server (NTRS)

Truong, Long V.

1995-01-01

This paper describes the Decision Support System (DSS), a personal computer software graphics tool for designing conceptual space and/or planetary electrical power systems. By using the DSS, users can obtain desirable system design and operating parameters, such as system weight, electrical distribution efficiency, and bus power. With this tool, a large-scale specific power system was designed in a matter of days. It is an excellent tool to help designers make tradeoffs between system components, hardware architectures, and operation parameters in the early stages of the design cycle. The DSS is a user-friendly, menu-driven tool with online help and a custom graphical user interface. An example design and results are illustrated for a typical space power system with multiple types of power sources, frequencies, energy storage systems, and loads.

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

PubMed Central

2012-01-01

Background Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the number and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such analysis usually makes this a time-consuming and very difficult task for users, especially when the primers have a large number of hits. Furthermore, although the BLAST program has been widely used for primer target detection, it is in fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necessarily return complete match information over the entire primer range. Results We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers. This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers. Conclusions We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the specificity threshold and other primer properties. This tool is publicly available at http://www.ncbi.nlm.nih.gov/tools/primer-blast. PMID:22708584

Open access for ALICE analysis based on virtualization technology

NASA Astrophysics Data System (ADS)

Buncic, P.; Gheata, M.; Schutz, Y.

2015-12-01

Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system.

Multiobjective optimization of hybrid regenerative life support technologies. Topic D: Technology Assessment

NASA Technical Reports Server (NTRS)

Manousiouthakis, Vasilios

1995-01-01

We developed simple mathematical models for many of the technologies constituting the water reclamation system in a space station. These models were employed for subsystem optimization and for the evaluation of the performance of individual water reclamation technologies, by quantifying their operational 'cost' as a linear function of weight, volume, and power consumption. Then we performed preliminary investigations on the performance improvements attainable by simple hybrid systems involving parallel combinations of technologies. We are developing a software tool for synthesizing a hybrid water recovery system (WRS) for long term space missions. As conceptual framework, we are employing the state space approach. Given a number of available technologies and the mission specifications, the state space approach would help design flowsheets featuring optimal process configurations, including those that feature stream connections in parallel, series, or recycles. We visualize this software tool to function as follows: given the mission duration, the crew size, water quality specifications, and the cost coefficients, the software will synthesize a water recovery system for the space station. It should require minimal user intervention. The following tasks need to be solved for achieving this goal: (1) formulate a problem statement that will be used to evaluate the advantages of a hybrid WRS over a single technology WBS; (2) model several WRS technologies that can be employed in the space station; (3) propose a recycling network design methodology (since the WRS synthesis task is a recycling network design problem, it is essential to employ a systematic method in synthesizing this network); (4) develop a software implementation for this design methodology, design a hybrid system using this software, and compare the resulting WRS with a base-case WRS; and (5) create a user-friendly interface for this software tool.

Role of Hsp90 in Androgen-Refractory Prostate Cancer

DTIC Science & Technology

2010-03-01

designed siRNA sequence using Intergrated DNA Technologies RNAi online software tool (IDT, Coralville, IA). The sequence of siRNA specific for...proliferation and production of prostate-specific antigen in androgen-sensitive pros- tatic cancer cells, LNCaP, by dihydrotestosterone. Endocrinology 136

A Software Tool for the Annotation of Embolic Events in Echo Doppler Audio Signals

PubMed Central

Pierleoni, Paola; Maurizi, Lorenzo; Palma, Lorenzo; Belli, Alberto; Valenti, Simone; Marroni, Alessandro

2017-01-01

The use of precordial Doppler monitoring to prevent decompression sickness (DS) is well known by the scientific community as an important instrument for early diagnosis of DS. However, the timely and correct diagnosis of DS without assistance from diving medical specialists is unreliable. Thus, a common protocol for the manual annotation of echo Doppler signals and a tool for their automated recording and annotation are necessary. We have implemented original software for efficient bubble appearance annotation and proposed a unified annotation protocol. The tool auto-sets the response time of human “bubble examiners,” performs playback of the Doppler file by rendering it independent of the specific audio player, and enables the annotation of individual bubbles or multiple bubbles known as “showers.” The tool provides a report with an optimized data structure and estimates the embolic risk level according to the Extended Spencer Scale. The tool is built in accordance with ISO/IEC 9126 on software quality and has been projected and tested with assistance from the Divers Alert Network (DAN) Europe Foundation, which employs this tool for its diving data acquisition campaigns. PMID:29242701

BanTeC: a software tool for management of corneal transplantation.

PubMed

López-Alvarez, P; Caballero, F; Trias, J; Cortés, U; López-Navidad, A

2005-11-01

Until recently, all cornea information at our tissue bank was managed manually, no specific database or computer tool had been implemented to provide electronic versions of documents and medical reports. The main objective of the BanTeC project was therefore to create a computerized system to integrate and classify all the information and documents used in the center in order to facilitate management of retrieved, transplanted corneal tissues. We used the Windows platform to develop the project. Microsoft Access and Microsoft Jet Engine were used at the database level and Data Access Objects was the chosen data access technology. In short, the BanTeC software seeks to computerize the tissue bank. All the initial stages of the development have now been completed, from specification of needs, program design and implementation of the software components, to the total integration of the final result in the real production environment. BanTeC will allow the generation of statistical reports for analysis to improve our performance.

Image manipulation software portable on different hardware platforms: what is the cost?

NASA Astrophysics Data System (ADS)

Ligier, Yves; Ratib, Osman M.; Funk, Matthieu; Perrier, Rene; Girard, Christian; Logean, Marianne

1992-07-01

A hospital wide PACS project is currently under development at the University Hospital of Geneva. The visualization and manipulation of images provided by different imaging modalities constitutes one of the most challenging components of a PACS. Because there are different requirements depending on the clinical usage, it was necessary for such a visualization software to be provided on different types of workstations in different sectors of the PACS. The user interface has to be the same independently of the underlying workstation. Beside, in addition to a standard set of image manipulation and processing tools there is a need for more specific clinical tools that should be easily adapted to specific medical requirements. To achieve operating and windowing systems: the standard Unix/X-11/OSF-Motif based workstations and the Macintosh family and should be easily ported on other systems. This paper describes the design of such a system and discusses the extra cost and efforts involved in the development of a portable and easily expandable software.

Self-service for software development projects and HPC activities

NASA Astrophysics Data System (ADS)

Husejko, M.; Høimyr, N.; Gonzalez, A.; Koloventzos, G.; Asbury, D.; Trzcinska, A.; Agtzidis, I.; Botrel, G.; Otto, J.

2014-05-01

This contribution describes how CERN has implemented several essential tools for agile software development processes, ranging from version control (Git) to issue tracking (Jira) and documentation (Wikis). Running such services in a large organisation like CERN requires many administrative actions both by users and service providers, such as creating software projects, managing access rights, users and groups, and performing tool-specific customisation. Dealing with these requests manually would be a time-consuming task. Another area of our CERN computing services that has required dedicated manual support has been clusters for specific user communities with special needs. Our aim is to move all our services to a layered approach, with server infrastructure running on the internal cloud computing infrastructure at CERN. This contribution illustrates how we plan to optimise the management of our of services by means of an end-user facing platform acting as a portal into all the related services for software projects, inspired by popular portals for open-source developments such as Sourceforge, GitHub and others. Furthermore, the contribution will discuss recent activities with tests and evaluations of High Performance Computing (HPC) applications on different hardware and software stacks, and plans to offer a dynamically scalable HPC service at CERN, based on affordable hardware.

BYMUR software: a free and open source tool for quantifying and visualizing multi-risk analyses

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Selva, Jacopo

2013-04-01

The BYMUR software aims to provide an easy-to-use open source tool for both computing multi-risk and managing/visualizing/comparing all the inputs (e.g. hazard, fragilities and exposure) as well as the corresponding results (e.g. risk curves, risk indexes). For all inputs, a complete management of inter-model epistemic uncertainty is considered. The BYMUR software will be one of the final products provided by the homonymous ByMuR project (http://bymur.bo.ingv.it/) funded by Italian Ministry of Education, Universities and Research (MIUR), focused to (i) provide a quantitative and objective general method for a comprehensive long-term multi-risk analysis in a given area, accounting for inter-model epistemic uncertainty through Bayesian methodologies, and (ii) apply the methodology to seismic, volcanic and tsunami risks in Naples (Italy). More specifically, the BYMUR software will be able to separately account for the probabilistic hazard assessment of different kind of hazardous phenomena, the relative (time-dependent/independent) vulnerabilities and exposure data, and their possible (predefined) interactions: the software will analyze these inputs and will use them to estimate both single- and multi- risk associated to a specific target area. In addition, it will be possible to connect the software to further tools (e.g., a full hazard analysis), allowing a dynamic I/O of results. The use of Python programming language guarantees that the final software will be open source and platform independent. Moreover, thanks to the integration of some most popular and rich-featured Python scientific modules (Numpy, Matplotlib, Scipy) with the wxPython graphical user toolkit, the final tool will be equipped with a comprehensive Graphical User Interface (GUI) able to control and visualize (in the form of tables, maps and/or plots) any stage of the multi-risk analysis. The additional features of importing/exporting data in MySQL databases and/or standard XML formats (for instance, the global standards defined in the frame of GEM project for seismic hazard and risk) will grant the interoperability with other FOSS software and tools and, at the same time, to be on hand of the geo-scientific community. An already available example of connection is represented by the BET_VH(**) tool, which probabilistic volcanic hazard outputs will be used as input for BYMUR. Finally, the prototype version of BYMUR will be used for the case study of the municipality of Naples, by considering three different natural hazards (volcanic eruptions, earthquakes and tsunamis) and by assessing the consequent long-term risk evaluation. (**)BET_VH (Bayesian Event Tree for Volcanic Hazard) is probabilistic tool for long-term volcanic hazard assessment, recently re-designed and adjusted to be run on the Vhub cyber-infrastructure, a free web-based collaborative tool in volcanology research (see http://vhub.org/resources/betvh).

Strengthening Software Authentication with the ROSE Software Suite

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

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

Rotorcraft Optimization Tools: Incorporating Rotorcraft Design Codes into Multi-Disciplinary Design, Analysis, and Optimization

NASA Technical Reports Server (NTRS)

Meyn, Larry A.

2018-01-01

One of the goals of NASA's Revolutionary Vertical Lift Technology Project (RVLT) is to provide validated tools for multidisciplinary design, analysis and optimization (MDAO) of vertical lift vehicles. As part of this effort, the software package, RotorCraft Optimization Tools (RCOTOOLS), is being developed to facilitate incorporating key rotorcraft conceptual design codes into optimizations using the OpenMDAO multi-disciplinary optimization framework written in Python. RCOTOOLS, also written in Python, currently supports the incorporation of the NASA Design and Analysis of RotorCraft (NDARC) vehicle sizing tool and the Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics II (CAMRAD II) analysis tool into OpenMDAO-driven optimizations. Both of these tools use detailed, file-based inputs and outputs, so RCOTOOLS provides software wrappers to update input files with new design variable values, execute these codes and then extract specific response variable values from the file outputs. These wrappers are designed to be flexible and easy to use. RCOTOOLS also provides several utilities to aid in optimization model development, including Graphical User Interface (GUI) tools for browsing input and output files in order to identify text strings that are used to identify specific variables as optimization input and response variables. This paper provides an overview of RCOTOOLS and its use

Visual programming for next-generation sequencing data analytics.

PubMed

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

OsiriX: an open-source software for navigating in multidimensional DICOM images.

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

Applications of Formal Methods to Specification and Safety of Avionics Software

NASA Technical Reports Server (NTRS)

Hoover, D. N.; Guaspari, David; Humenn, Polar

1996-01-01

This report treats several topics in applications of formal methods to avionics software development. Most of these topics concern decision tables, an orderly, easy-to-understand format for formally specifying complex choices among alternative courses of action. The topics relating to decision tables include: generalizations fo decision tables that are more concise and support the use of decision tables in a refinement-based formal software development process; a formalism for systems of decision tables with behaviors; an exposition of Parnas tables for users of decision tables; and test coverage criteria and decision tables. We outline features of a revised version of ORA's decision table tool, Tablewise, which will support many of the new ideas described in this report. We also survey formal safety analysis of specifications and software.

Using Rose and Compass for Authentication

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

White, G

2009-07-09

Many recent non-proliferation software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project. ROSEmore » is an LLNL-developed robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. It continues to be extended to support the automated analysis of binaries (x86, ARM, and PowerPC). We continue to extend ROSE to address a number of security specific requirements and apply it to software authentication for non-proliferation projects. We will give an update on the status of our work.« less

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

Pipe Flow Simulation Software: A Team Approach to Solve an Engineering Education Problem.

ERIC Educational Resources Information Center

Engel, Renata S.; And Others

1996-01-01

A computer simulation program for use in the study of fluid mechanics is described. The package is an interactive tool to explore the fluid flow characteristics of a pipe system by manipulating the physical construction of the system. The motivation, software design requirements, and specific details on how its objectives were met are presented.…

Simulation Software's Effect on College Students Spreadsheet Project Scores

ERIC Educational Resources Information Center

Atkinson, J. Kirk; Thrasher, Evelyn H.; Coleman, Phillip D.

2011-01-01

The purpose of this study is to explore the potential impact of support materials on student spreadsheet skill acquisition. Specifically, this study examines the use of an online spreadsheet simulation tool versus a printed book across two independent student groups. This study hypothesizes that the online spreadsheet simulation tool will have a…

New direction in CAD tools

NASA Technical Reports Server (NTRS)

Peterson, S.

1990-01-01

Chip and software development communities are concerned with the runaway pace of chip development and the monumental problems which can quickly accumulate and overwhelm those charged with the task of IC development. This 'weight' must be transferred from the shoulders of the human developers to the software tools which assimilate and control the defining data of the development process. This paper details many of the problems which are being resolved by reviewing the obstacles and resultant advancements which the industry has made. Specifically, it will describe many of the things which are being done in one company to provide this much-needed relief.

Software development without languages

NASA Technical Reports Server (NTRS)

Osborne, Haywood S.

1988-01-01

Automatic programming generally involves the construction of a formal specification; i.e., one which allows unambiguous interpretation by tools for the subsequent production of the corresponding software. Previous practical efforts in this direction have focused on the serious problems of: (1) designing the optimum specification language; and (2) mapping (translating or compiling) from this specification language to the program itself. The approach proposed bypasses the above problems. It postulates that the specification proper should be an intermediate form, with the sole function of containing information sufficient to facilitate construction of programs and also of matching documentation. Thus, the means of forming the intermediary becomes a human factors task rather than a linguistic one; human users will read documents generated from the specification, rather than the specification itself.

Software Requirements Specification for Lunar IceCube

NASA Astrophysics Data System (ADS)

Glaser-Garbrick, Michael R.

Lunar IceCube is a 6U satellite that will orbit the moon to measure water volatiles as a function of position, altitude, and time, and measure in its various phases. Lunar IceCube, is a collaboration between Morehead State University, Vermont Technical University, Busek, and NASA. The Software Requirements Specification will serve as contract between the overall team and the developers of the flight software. It will provide a system's overview of the software that will be developed for Lunar IceCube, in that it will detail all of the interconnects and protocols for each subsystem's that Lunar IceCube will utilize. The flight software will be written in SPARK to the fullest extent, due to SPARK's unique ability to make software free of any errors. The LIC flight software does make use of a general purpose, reusable application framework called CubedOS. This framework imposes some structuring requirements on the architecture and design of the flight software, but it does not impose any high level requirements. It will also detail the tools that we will be using for Lunar IceCube, such as why we will be utilizing VxWorks.

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.

An Automated Method for Identifying Inconsistencies within Diagrammatic Software Requirements Specifications

NASA Technical Reports Server (NTRS)

Zhang, Zhong

1997-01-01

The development of large-scale, composite software in a geographically distributed environment is an evolutionary process. Often, in such evolving systems, striving for consistency is complicated by many factors, because development participants have various locations, skills, responsibilities, roles, opinions, languages, terminology and different degrees of abstraction they employ. This naturally leads to many partial specifications or viewpoints. These multiple views on the system being developed usually overlap. From another aspect, these multiple views give rise to the potential for inconsistency. Existing CASE tools do not efficiently manage inconsistencies in distributed development environment for a large-scale project. Based on the ViewPoints framework the WHERE (Web-Based Hypertext Environment for requirements Evolution) toolkit aims to tackle inconsistency management issues within geographically distributed software development projects. Consequently, WHERE project helps make more robust software and support software assurance process. The long term goal of WHERE tools aims to the inconsistency analysis and management in requirements specifications. A framework based on Graph Grammar theory and TCMJAVA toolkit is proposed to detect inconsistencies among viewpoints. This systematic approach uses three basic operations (UNION, DIFFERENCE, INTERSECTION) to study the static behaviors of graphic and tabular notations. From these operations, subgraphs Query, Selection, Merge, Replacement operations can be derived. This approach uses graph PRODUCTIONS (rewriting rules) to study the dynamic transformations of graphs. We discuss the feasibility of implementation these operations. Also, We present the process of porting original TCM (Toolkit for Conceptual Modeling) project from C++ to Java programming language in this thesis. A scenario based on NASA International Space Station Specification is discussed to show the applicability of our approach. Finally, conclusion and future work about inconsistency management issues in WHERE project will be summarized.

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

NOTE: MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

NASA Astrophysics Data System (ADS)

Alexander, A.; DeBlois, F.; Stroian, G.; Al-Yahya, K.; Heath, E.; Seuntjens, J.

2007-07-01

Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM_RT, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform-independent, large-scale MC treatment planning for different treatment sites. Patient recalculations were performed to validate the software and ensure proper functionality.

IMCS reflight certification requirements and design specifications

NASA Technical Reports Server (NTRS)

1984-01-01

The requirements for reflight certification are established. Software requirements encompass the software programs that are resident in the PCC, DEP, PDSS, EC, or any related GSE. A design approach for the reflight software packages is recommended. These designs will be of sufficient detail to permit the implementation of reflight software. The PDSS/IMC Reflight Certification system provides the tools and mechanisms for the user to perform the reflight certification test procedures, test data capture, test data display, and test data analysis. The system as defined will be structured to permit maximum automation of reflight certification procedures and test data analysis.

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.

Data Analysis with Graphical Models: Software Tools

NASA Technical Reports Server (NTRS)

Buntine, Wray L.

1994-01-01

Probabilistic graphical models (directed and undirected Markov fields, and combined in chain graphs) are used widely in expert systems, image processing and other areas as a framework for representing and reasoning with probabilities. They come with corresponding algorithms for performing probabilistic inference. This paper discusses an extension to these models by Spiegelhalter and Gilks, plates, used to graphically model the notion of a sample. This offers a graphical specification language for representing data analysis problems. When combined with general methods for statistical inference, this also offers a unifying framework for prototyping and/or generating data analysis algorithms from graphical specifications. This paper outlines the framework and then presents some basic tools for the task: a graphical version of the Pitman-Koopman Theorem for the exponential family, problem decomposition, and the calculation of exact Bayes factors. Other tools already developed, such as automatic differentiation, Gibbs sampling, and use of the EM algorithm, make this a broad basis for the generation of data analysis software.

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/

Leveraging Modeling Approaches: Reaction Networks and Rules

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high resolution and/or high throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatio-temporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks – the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks. PMID:22161349

Leveraging modeling approaches: reaction networks and rules.

PubMed

Blinov, Michael L; Moraru, Ion I

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.

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.

ESA's tools for internal charging

NASA Astrophysics Data System (ADS)

Sorensen, J.; Rodgers, D. J.; Ryden, K. A.; Latham, P. M.; Wrenn, G. L.; Levy, L.; Panabiere, G.

2000-06-01

Electrostatic discharges, caused by bulk charging of spacecraft insulating materials, are a major cause of satellite anomalies. A quantitative knowledge of the charge build-up is essential in order to eliminate these problems in the design stage. This is a presentation of ESA's tools to assess whether a given structure is liable to experience electrostatic discharges or not. A study has been made of the physical phenomenon, and an engineering specification has been created to be used to assess a structure for potential discharge problems. The specification has been implemented in a new software DICTAT. The implementation of tests in dedicated facilities is an important part of the specification, and tests have been performed to validate the new tool.

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

Cost Estimating Cases: Educational Tools for Cost Analysts

DTIC Science & Technology

1993-09-01

only appropriate documentation should be provided. In other words, students should not submit all of the documentation possible using ACEIT , only that...case was their lack of understanding of the ACEIT software used to conduct the estimate. Specifically, many students misinterpreted the cost...estimating relationships (CERs) embedded in the 49 software. Additionally, few of the students were able to properly organize the ACEIT documentation output

Development of a software safety process and a case study of its use

NASA Technical Reports Server (NTRS)

Knight, John C.

1993-01-01

The goal of this research is to continue the development of a comprehensive approach to software safety and to evaluate the approach with a case study. The case study is a major part of the project, and it involves the analysis of a specific safety-critical system from the medical equipment domain. The particular application being used was selected because of the availability of a suitable candidate system. We consider the results to be generally applicable and in no way particularly limited by the domain. The research is concentrating on issues raised by the specification and verification phases of the software lifecycle since they are central to our previously-developed rigorous definitions of software safety. The theoretical research is based on our framework of definitions for software safety. In the area of specification, the main topics being investigated are the development of techniques for building system fault trees that correctly incorporate software issues and the development of rigorous techniques for the preparation of software safety specifications. The research results are documented. Another area of theoretical investigation is the development of verification methods tailored to the characteristics of safety requirements. Verification of the correct implementation of the safety specification is central to the goal of establishing safe software. The empirical component of this research is focusing on a case study in order to provide detailed characterizations of the issues as they appear in practice, and to provide a testbed for the evaluation of various existing and new theoretical results, tools, and techniques. The Magnetic Stereotaxis System is summarized.

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

Belley, M; Schmidt, M; Knutson, N

Purpose: Physics second-checks for external beam radiation therapy are performed, in-part, to verify that the machine parameters in the Record-and-Verify (R&V) system that will ultimately be sent to the LINAC exactly match the values initially calculated by the Treatment Planning System (TPS). While performing the second-check, a large portion of the physicists’ time is spent navigating and arranging display windows to locate and compare the relevant numerical values (MLC position, collimator rotation, field size, MU, etc.). Here, we describe the development of a software tool that guides the physicist by aggregating and succinctly displaying machine parameter data relevant to themore » physics second-check process. Methods: A data retrieval software tool was developed using Python to aggregate data and generate a list of machine parameters that are commonly verified during the physics second-check process. This software tool imported values from (i) the TPS RT Plan DICOM file and (ii) the MOSAIQ (R&V) Structured Query Language (SQL) database. The machine parameters aggregated for this study included: MLC positions, X&Y jaw positions, collimator rotation, gantry rotation, MU, dose rate, wedges and accessories, cumulative dose, energy, machine name, couch angle, and more. Results: A GUI interface was developed to generate a side-by-side display of the aggregated machine parameter values for each field, and presented to the physicist for direct visual comparison. This software tool was tested for 3D conformal, static IMRT, sliding window IMRT, and VMAT treatment plans. Conclusion: This software tool facilitated the data collection process needed in order for the physicist to conduct a second-check, thus yielding an optimized second-check workflow that was both more user friendly and time-efficient. Utilizing this software tool, the physicist was able to spend less time searching through the TPS PDF plan document and the R&V system and focus the second-check efforts on assessing the patient-specific plan-quality.« less

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.

A benchmarking tool to evaluate computer tomography perfusion infarct core predictions against a DWI standard.

PubMed

Cereda, Carlo W; Christensen, Søren; Campbell, Bruce Cv; Mishra, Nishant K; Mlynash, Michael; Levi, Christopher; Straka, Matus; Wintermark, Max; Bammer, Roland; Albers, Gregory W; Parsons, Mark W; Lansberg, Maarten G

2016-10-01

Differences in research methodology have hampered the optimization of Computer Tomography Perfusion (CTP) for identification of the ischemic core. We aim to optimize CTP core identification using a novel benchmarking tool. The benchmarking tool consists of an imaging library and a statistical analysis algorithm to evaluate the performance of CTP. The tool was used to optimize and evaluate an in-house developed CTP-software algorithm. Imaging data of 103 acute stroke patients were included in the benchmarking tool. Median time from stroke onset to CT was 185 min (IQR 180-238), and the median time between completion of CT and start of MRI was 36 min (IQR 25-79). Volumetric accuracy of the CTP-ROIs was optimal at an rCBF threshold of <38%; at this threshold, the mean difference was 0.3 ml (SD 19.8 ml), the mean absolute difference was 14.3 (SD 13.7) ml, and CTP was 67% sensitive and 87% specific for identification of DWI positive tissue voxels. The benchmarking tool can play an important role in optimizing CTP software as it provides investigators with a novel method to directly compare the performance of alternative CTP software packages. © The Author(s) 2015.

TBell: A mathematical tool for analyzing decision tables

NASA Technical Reports Server (NTRS)

Hoover, D. N.; Chen, Zewei

1994-01-01

This paper describes the development of mathematical theory and software to analyze specifications that are developed using decision tables. A decision table is a tabular format for specifying a complex set of rules that chooses one of a number of alternative actions. The report also describes a prototype tool, called TBell, that automates certain types of analysis.

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

MAMA User Guide v2.0.1

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

Gaschen, Brian Keith; Bloch, Jeffrey Joseph; Porter, Reid

Morphological signatures of bulk SNM materials have significant promise, but these potential signatures are not fully utilized. This document describes software tools, collectively called the MAMA (Morphological Analysis for Material Attribution) software that can help provide robust and accurate quantification of morphological features in bulk material microscopy images (Optical, SEM). Although many of the specific tools are not unique to Mama, the software package has been designed specifically for nuclear material morphological analysis, and is at a point where it can be easily adapted (by Los Alamos or by collaborators) in response to new, different, or changing forensics needs. Themore » current release of the MAMA software only includes the image quantification, descriptions, and annotation functionality. Only limited information on a sample, its pedigree, and its chemistry are recorded inside this part of the software. This was decision based on initial feedback and the fact that there are several analytical chemistry databases being developed within the community. Currently MAMA is a standalone program that can export quantification results in a basic text format that can be imported into other programs such as Excel and Access. There is also a basic report generating feature that produces HTML formatted pages of the same information. We will be working with collaborators to provide better integration of MAMA into their particular systems, databases and workflows.« less

SafetyAnalyst

DOT National Transportation Integrated Search

2009-01-01

This booklet provides an overview of SafetyAnalyst. SafetyAnalyst is a set of software tools under development to help State and local highway agencies advance their programming of site-specific safety improvements. SafetyAnalyst will incorporate sta...

RSAT 2015: Regulatory Sequence Analysis Tools

PubMed Central

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-01-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632

Internet MEMS design tools based on component technology

NASA Astrophysics Data System (ADS)

Brueck, Rainer; Schumer, Christian

1999-03-01

The micro electromechanical systems (MEMS) industry in Europe is characterized by small and medium sized enterprises specialized on products to solve problems in specific domains like medicine, automotive sensor technology, etc. In this field of business the technology driven design approach known from micro electronics is not appropriate. Instead each design problem aims at its own, specific technology to be used for the solution. The variety of technologies at hand, like Si-surface, Si-bulk, LIGA, laser, precision engineering requires a huge set of different design tools to be available. No single SME can afford to hold licenses for all these tools. This calls for a new and flexible way of designing, implementing and distributing design software. The Internet provides a flexible manner of offering software access along with methodologies of flexible licensing e.g. on a pay-per-use basis. New communication technologies like ADSL, TV cable of satellites as carriers promise to offer a bandwidth sufficient even for interactive tools with graphical interfaces in the near future. INTERLIDO is an experimental tool suite for process specification and layout verification for lithography based MEMS technologies to be accessed via the Internet. The first version provides a Java implementation even including a graphical editor for process specification. Currently, a new version is brought into operation that is based on JavaBeans component technology. JavaBeans offers the possibility to realize independent interactive design assistants, like a design rule checking assistants, a process consistency checking assistants, a technology definition assistants, a graphical editor assistants, etc. that may reside distributed over the Internet, communicating via Internet protocols. Each potential user thus is able to configure his own dedicated version of a design tool set dedicated to the requirements of the current problem to be solved.

Automatic Certification of Kalman Filters for Reliable Code Generation

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

PubMed

Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C

2017-01-01

Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

Use of Automated Testing to Facilitate Affordable Design of Military Systems

DTIC Science & Technology

2015-04-30

momentum across the Navy and DoD. This initiative is no new big bang /silver bullet; it simply focuses on lowering the cost and risk of government...University of Minnesota. He has developed several specification languages, software tools for computer-aided software design, and fundamental theory ...review of lessons learned and recommendations for further enhancements are discussed. Overview: The Testing Challenge Infinity Is a Big Place The

Web-based software tool for constraint-based design specification of synthetic biological systems.

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

A new software tool for 3D motion analyses of the musculo-skeletal system.

PubMed

Leardini, A; Belvedere, C; Astolfi, L; Fantozzi, S; Viceconti, M; Taddei, F; Ensini, A; Benedetti, M G; Catani, F

2006-10-01

Many clinical and biomechanical research studies, particularly in orthopaedics, nowadays involve forms of movement analysis. Gait analysis, video-fluoroscopy of joint replacement, pre-operative planning, surgical navigation, and standard radiostereometry would require tools for easy access to three-dimensional graphical representations of rigid segment motion. Relevant data from this variety of sources need to be organised in structured forms. Registration, integration, and synchronisation of segment position data are additional necessities. With this aim, the present work exploits the features of a software tool recently developed within a EU-funded project ('Multimod') in a series of different research studies. Standard and advanced gait analysis on a normal subject, in vivo fluoroscopy-based three-dimensional motion of a replaced knee joint, patellar and ligament tracking on a knee specimen by a surgical navigation system, stem-to-femur migration pattern on a patient operated on total hip replacement, were analysed with standard techniques and all represented by this innovative software tool. Segment pose data were eventually obtained from these different techniques, and were successfully imported and organised in a hierarchical tree within the tool. Skeletal bony segments, prosthesis component models and ligament links were registered successfully to corresponding marker position data for effective three-dimensional animations. These were shown in various combinations, in different views, from different perspectives, according to possible specific research interests. Bioengineering and medical professionals would be much facilitated in the interpretation of the motion analysis measurements necessary in their research fields, and would benefit therefore from this software tool.

The "neuro-mapping locator" software. A real-time intraoperative objective paraesthesia mapping tool to evaluate paraesthesia coverage of the painful zone in patients undergoing spinal cord stimulation lead implantation.

PubMed

Guetarni, F; Rigoard, P

2015-03-01

Conventional spinal cord stimulation (SCS) generates paraesthesia, as the efficacy of this technique is based on the relationship between the paraesthesia provided by SCS on the painful zone and an analgesic effect on the stimulated zone. Although this basic postulate is based on clinical evidence, it is clear that this relationship has never been formally demonstrated by scientific studies. There is a need for objective evaluation tools ("transducers") to transpose electrical signals to clinical effects and to guide therapeutic choices. We have developed a software at Poitiers University hospital allowing real-time objective mapping of the paraesthesia generated by SCS lead placement and programming during the implantation procedure itself, on a touch screen interface. The purpose of this article is to describe this intraoperative mapping software, in terms of its concept and technical aspects. The Neuro-Mapping Locator (NML) software is dedicated to patients with failed back surgery syndrome, candidates for SCS lead implantation, to actively participate in the implantation procedure. Real-time geographical localization of the paraesthesia generated by percutaneous or multicolumn surgical SCS lead implanted under awake anaesthesia allows intraoperative lead programming and possibly lead positioning to be modified with the patient's cooperation. Software updates should enable us to refine objectives related to the use of this tool and minimize observational biases. The ultimate goals of NML software should not be limited to optimize one specific device implantation in a patient but also allow to compare instantaneously various stimulation strategies, by characterizing new technical parameters as "coverage efficacy" and "device specificity" on selected subgroups of patients. Another longer-term objective would be to organize these predictive factors into computer science ontologies, which could constitute robust and helpful data for device selection and programming of tomorrow's neurostimulators. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

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

NASA Technical Reports Server (NTRS)

2008-01-01

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

Computer-aided diagnosis software for vulvovaginal candidiasis detection from Pap smear images.

PubMed

Momenzadeh, Mohammadreza; Vard, Alireza; Talebi, Ardeshir; Mehri Dehnavi, Alireza; Rabbani, Hossein

2018-01-01

Vulvovaginal candidiasis (VVC) is a common gynecologic infection and it occurs when there is overgrowth of the yeast called Candida. VVC diagnosis is usually done by observing a Pap smear sample under a microscope and searching for the conidium and mycelium components of Candida. This manual method is time consuming, subjective and tedious. Any diagnosis tools that detect VVC, semi- or full-automatically, can be very helpful to pathologists. This article presents a computer aided diagnosis (CAD) software to improve human diagnosis of VVC from Pap smear samples. The proposed software is designed based on phenotypic and morphology features of the Candida in Pap smear sample images. This software provide a user-friendly interface which consists of a set of image processing tools and analytical results that helps to detect Candida and determine severity of illness. The software was evaluated on 200 Pap smear sample images and obtained specificity of 91.04% and sensitivity of 92.48% to detect VVC. As a result, the use of the proposed software reduces diagnostic time and can be employed as a second objective opinion for pathologists. © 2017 Wiley Periodicals, Inc.

Vocabulary Notebook: A Digital Solution to General and Specific Vocabulary Learning Problems in a CLIL Context

ERIC Educational Resources Information Center

Bazo, Plácido; Rodríguez, Romén; Fumero, Dácil

2016-01-01

In this paper, we will introduce an innovative software platform that can be especially useful in a Content and Language Integrated Learning (CLIL) context. This tool is called Vocabulary Notebook, and has been developed to solve all the problems that traditional (paper) vocabulary notebooks have. This tool keeps focus on the personalisation of…

Blogs and Wikis as Instructional Tools: A Social Software Adaptation of Just-in-Time Teaching

ERIC Educational Resources Information Center

Higdon, Jude; Topaz, Chad

2009-01-01

Just-in-Time Teaching (JiTT) methodology uses Web-based tools to gather student responses to questions on preclass reading assignments. However, the technological requirements of JiTT and the content-specific nature of the questions may prevent some instructors from implementing it. Our own JiTT implementation uses publicly and freely available…

MATISSE: A novel tool to access, visualize and analyse data from planetary exploration missions

NASA Astrophysics Data System (ADS)

Zinzi, A.; Capria, M. T.; Palomba, E.; Giommi, P.; Antonelli, L. A.

2016-04-01

The increasing number and complexity of planetary exploration space missions require new tools to access, visualize and analyse data to improve their scientific return. ASI Science Data Center (ASDC) addresses this request with the web-tool MATISSE (Multi-purpose Advanced Tool for the Instruments of the Solar System Exploration), allowing the visualization of single observation or real-time computed high-order products, directly projected on the three-dimensional model of the selected target body. Using MATISSE it will be no longer needed to download huge quantity of data or to write down a specific code for every instrument analysed, greatly encouraging studies based on joint analysis of different datasets. In addition the extremely high-resolution output, to be used offline with a Python-based free software, together with the files to be read with specific GIS software, makes it a valuable tool to further process the data at the best spatial accuracy available. MATISSE modular structure permits addition of new missions or tasks and, thanks to dedicated future developments, it would be possible to make it compliant to the Planetary Virtual Observatory standards currently under definition. In this context the recent development of an interface to the NASA ODE REST API by which it is possible to access to public repositories is set.

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

SU-E-T-211: Comparison of Seven New TrueBeam Linacs with Enhanced Beam Data Conformance Using a Beam Comparison Software Tool

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

Grzetic, S; Hessler, J; Gupta, N

2015-06-15

Purpose: To develop an independent software tool to assist in commissioning linacs with enhanced beam conformance, as well as perform ongoing QA for dosimetrically equivalent linacs. Methods: Linac manufacturers offer enhanced beam conformance as an option to allow for clinics to complete commissioning efficiently, as well as implement dosimetrically equivalent linacs. The specification for enhanced conformance includes PDD as well as profiles within 80% FWHM. Recently, we commissioned seven Varian TrueBeam linacs with enhanced beam conformance. We developed a software tool in Visual Basic to allow us to load the reference beam data and compare our beam data during commissioningmore » to evaluate enhanced beam conformance. This tool also allowed us to upload our beam data used for commissioning our dosimetrically equivalent beam models to compare and tweak each of our linac beams to match our modelled data in Varian’s Eclipse TPS. This tool will also be used during annual QA of the linacs to compare our beam data to our baseline data, as required by TG-142. Results: Our software tool was used to check beam conformance for seven TrueBeam linacs that we commissioned in the past six months. Using our tool we found that the factory conformed linacs showed up to 3.82% difference in their beam profile data upon installation. Using our beam comparison tool, we were able to adjust the energy and profiles of our beams to accomplish a better than 1.00% point by point data conformance. Conclusion: The availability of quantitative comparison tools is essential to accept and commission linacs with enhanced beam conformance, as well as to beam match multiple linacs. We further intend to use the same tool to ensure our beam data conforms to the commissioning beam data during our annual QA in keeping with the requirements of TG-142.« less

KSC Space Station Operations Language (SSOL)

NASA Technical Reports Server (NTRS)

1985-01-01

The Space Station Operations Language (SSOL) will serve a large community of diverse users dealing with the integration and checkout of Space Station modules. Kennedy Space Center's plan to achieve Level A specification of the SSOL system, encompassing both its language and its automated support environment, is presented in the format of a briefing. The SSOL concept is a collection of fundamental elements that span languages, operating systems, software development, software tools and several user classes. The approach outlines a thorough process that combines the benefits of rapid prototyping with a coordinated requirements gathering effort, yielding a Level A specification of the SSOL requirements.

Collected software engineering papers, volume 8

NASA Technical Reports Server (NTRS)

1990-01-01

A collection of selected technical papers produced by participants in the Software Engineering Laboratory (SEL) during the period November 1989 through October 1990 is presented. The purpose of the document is to make available, in one reference, some results of SEL research that originally appeared in a number of different forums. Although these papers cover several topics related to software engineering, they do not encompass the entire scope of SEL activities and interests. Additional information about the SEL and its research efforts may be obtained from the sources listed in the bibliography. The seven presented papers are grouped into four major categories: (1) experimental research and evaluation of software measurement; (2) studies on models for software reuse; (3) a software tool evaluation; and (4) Ada technology and studies in the areas of reuse and specification.

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.

Dynamic Hurricane Data Analysis Tool

NASA Technical Reports Server (NTRS)

Knosp, Brian W.; Li, Peggy; Vu, Quoc A.

2009-01-01

A dynamic hurricane data analysis tool allows users of the JPL Tropical Cyclone Information System (TCIS) to analyze data over a Web medium. The TCIS software is described in the previous article, Tropical Cyclone Information System (TCIS) (NPO-45748). This tool interfaces with the TCIS database to pull in data from several different atmospheric and oceanic data sets, both observed by instruments. Users can use this information to generate histograms, maps, and profile plots for specific storms. The tool also displays statistical values for the user-selected parameter for the mean, standard deviation, median, minimum, and maximum values. There is little wait time, allowing for fast data plots over date and spatial ranges. Users may also zoom-in for a closer look at a particular spatial range. This is version 1 of the software. Researchers will use the data and tools on the TCIS to understand hurricane processes, improve hurricane forecast models and identify what types of measurements the next generation of instruments will need to collect.

Construction of integrated case environments.

PubMed

Losavio, Francisca; Matteo, Alfredo; Pérez, María

2003-01-01

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

75 FR 5328 - Agency Information Collection Request; 60-Day Public Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-02

... center (REC) will be provided with a customer relationship management (CRM) software tool, which they... selecting a CRM vendor. Once this is completed it will submit the specific reports for clearance. [[Page...

Use of three-dimensional computer graphic animation to illustrate cleft lip and palate surgery.

PubMed

Cutting, C; Oliker, A; Haring, J; Dayan, J; Smith, D

2002-01-01

Three-dimensional (3D) computer animation is not commonly used to illustrate surgical techniques. This article describes the surgery-specific processes that were required to produce animations to teach cleft lip and palate surgery. Three-dimensional models were created using CT scans of two Chinese children with unrepaired clefts (one unilateral and one bilateral). We programmed several custom software tools, including an incision tool, a forceps tool, and a fat tool. Three-dimensional animation was found to be particularly useful for illustrating surgical concepts. Positioning the virtual "camera" made it possible to view the anatomy from angles that are impossible to obtain with a real camera. Transparency allows the underlying anatomy to be seen during surgical repair while maintaining a view of the overlaying tissue relationships. Finally, the representation of motion allows modeling of anatomical mechanics that cannot be done with static illustrations. The animations presented in this article can be viewed on-line at http://www.smiletrain.org/programs/virtual_surgery2.htm. Sophisticated surgical procedures are clarified with the use of 3D animation software and customized software tools. The next step in the development of this technology is the creation of interactive simulators that recreate the experience of surgery in a safe, digital environment. Copyright 2003 Wiley-Liss, Inc.

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

PubMed

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

2011-01-01

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

Air Data Report Improves Flight Safety

NASA Technical Reports Server (NTRS)

2007-01-01

NASA's Aviation Safety Program in the NASA Aeronautics Research Mission Directorate, which seeks to make aviation safer by developing tools for flight data analysis and interpretation and then by transferring these tools to the aviation industry, sponsored the development of Morning Report software. The software, created at Ames Research Center with the assistance of the Pacific Northwest National Laboratory, seeks to detect atypicalities without any predefined parameters-it spots deviations and highlights them. In 2004, Sagem Avionics Inc. entered a licensing agreement with NASA for the commercialization of the Morning Report software, and also licensed the NASA Aviation Data Integration System (ADIS) tool, which allows for the integration of data from disparate sources into the flight data analysis process. Sagem Avionics incorporated the Morning Report tool into its AGS product, a comprehensive flight operations monitoring system that helps users detect irregular or divergent practices, technical flaws, and problems that might develop when aircraft operate outside of normal procedures. Sagem developed AGS in collaboration with airlines, so that the system takes into account their technical evolutions and needs, and each airline is able to easily perform specific treatments and to build its own flight data analysis system. Further, the AGS is designed to support any aircraft and flight data recorders.

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

A Clinical Reasoning Tool for Virtual Patients: Design-Based Research Study.

PubMed

Hege, Inga; Kononowicz, Andrzej A; Adler, Martin

2017-11-02

Clinical reasoning is a fundamental process medical students have to learn during and after medical school. Virtual patients (VP) are a technology-enhanced learning method to teach clinical reasoning. However, VP systems do not exploit their full potential concerning the clinical reasoning process; for example, most systems focus on the outcome and less on the process of clinical reasoning. Keeping our concept grounded in a former qualitative study, we aimed to design and implement a tool to enhance VPs with activities and feedback, which specifically foster the acquisition of clinical reasoning skills. We designed the tool by translating elements of a conceptual clinical reasoning learning framework into software requirements. The resulting clinical reasoning tool enables learners to build their patient's illness script as a concept map when they are working on a VP scenario. The student's map is compared with the experts' reasoning at each stage of the VP, which is technically enabled by using Medical Subject Headings, which is a comprehensive controlled vocabulary published by the US National Library of Medicine. The tool is implemented using Web technologies, has an open architecture that enables its integration into various systems through an open application program interface, and is available under a Massachusetts Institute of Technology license. We conducted usability tests following a think-aloud protocol and a pilot field study with maps created by 64 medical students. The results show that learners interact with the tool but create less nodes and connections in the concept map than an expert. Further research and usability tests are required to analyze the reasons. The presented tool is a versatile, systematically developed software component that specifically supports the clinical reasoning skills acquisition. It can be plugged into VP systems or used as stand-alone software in other teaching scenarios. The modular design allows an extension with new feedback mechanisms and learning analytics algorithms. ©Inga Hege, Andrzej A Kononowicz, Martin Adler. Originally published in JMIR Medical Education (http://mededu.jmir.org), 02.11.2017.

Trade Space Specification Tool (TSST) for Rapid Mission Architecture (Version 1.2)

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Schrock, Mitchell; Borden, Chester S.; Moeller, Robert C.

2013-01-01

Trade Space Specification Tool (TSST) is designed to capture quickly ideas in the early spacecraft and mission architecture design and categorize them into trade space dimensions and options for later analysis. It is implemented as an Eclipse RCP Application, which can be run as a standalone program. Users rapidly create concept items with single clicks on a graphical canvas, and can organize and create linkages between the ideas using drag-and-drop actions within the same graphical view. Various views such as a trade view, rules view, and architecture view are provided to help users to visualize the trade space. This software can identify, explore, and assess aspects of the mission trade space, as well as capture and organize linkages/dependencies between trade space components. The tool supports a user-in-the-loop preliminary logical examination and filtering of trade space options to help identify which paths in the trade space are feasible (and preferred) and what analyses need to be done later with executable models. This tool provides multiple user views of the trade space to guide the analyst/team to facilitate interpretation and communication of the trade space components and linkages, identify gaps in combining and selecting trade space options, and guide user decision-making for which combinations of architectural options should be pursued for further evaluation. This software provides an environment to capture mission trade space elements rapidly and assist users for their architecture analysis. This is primarily focused on mission and spacecraft architecture design, rather than general-purpose design application. In addition, it provides more flexibility to create concepts and organize the ideas. The software is developed as an Eclipse plug-in and potentially can be integrated with other Eclipse-based tools.

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies.

PubMed

Barnes, Samuel R; Ng, Thomas S C; Santa-Maria, Naomi; Montagne, Axel; Zlokovic, Berislav V; Jacobs, Russell E

2015-06-16

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at https://github.com/petmri/ROCKETSHIP .

ELISA, a demonstrator environment for information systems architecture design

NASA Technical Reports Server (NTRS)

Panem, Chantal

1994-01-01

This paper describes an approach of reusability of software engineering technology in the area of ground space system design. System engineers have lots of needs similar to software developers: sharing of a common data base, capitalization of knowledge, definition of a common design process, communication between different technical domains. Moreover system designers need to simulate dynamically their system as early as possible. Software development environments, methods and tools now become operational and widely used. Their architecture is based on a unique object base, a set of common management services and they host a family of tools for each life cycle activity. In late '92, CNES decided to develop a demonstrative software environment supporting some system activities. The design of ground space data processing systems was chosen as the application domain. ELISA (Integrated Software Environment for Architectures Specification) was specified as a 'demonstrator', i.e. a sufficient basis for demonstrations, evaluation and future operational enhancements. A process with three phases was implemented: system requirements definition, design of system architectures models, and selection of physical architectures. Each phase is composed of several activities that can be performed in parallel, with the provision of Commercial Off the Shelves Tools. ELISA has been delivered to CNES in January 94, currently used for demonstrations and evaluations on real projects (e.g. SPOT4 Satellite Control Center). It is on the way of new evolutions.

Atropos: specific, sensitive, and speedy trimming of sequencing reads.

PubMed

Didion, John P; Martin, Marcel; Collins, Francis S

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

Atropos: specific, sensitive, and speedy trimming of sequencing reads

PubMed Central

Collins, Francis S.

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

Cementitious Barriers Partnership FY2013 End-Year Report

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

Flach, G. P.; Langton, C. A.; Burns, H. H.

2013-11-01

In FY2013, the Cementitious Barriers Partnership (CBP) demonstrated continued tangible progress toward fulfilling the objective of developing a set of software tools to improve understanding and prediction of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. In November 2012, the CBP released “Version 1.0” of the CBP Software Toolbox, a suite of software for simulating reactive transport in cementitious materials and important degradation phenomena. In addition, the CBP completed development of new software for the “Version 2.0” Toolbox to be released in early FY2014 and demonstrated use of the Version 1.0 Toolbox on DOEmore » applications. The current primary software components in both Versions 1.0 and 2.0 are LeachXS/ORCHESTRA, STADIUM, and a GoldSim interface for probabilistic analysis of selected degradation scenarios. The CBP Software Toolbox Version 1.0 supports analysis of external sulfate attack (including damage mechanics), carbonation, and primary constituent leaching. Version 2.0 includes the additional analysis of chloride attack and dual regime flow and contaminant migration in fractured and non-fractured cementitious material. The LeachXS component embodies an extensive material property measurements database along with chemical speciation and reactive mass transport simulation cases with emphasis on leaching of major, trace and radionuclide constituents from cementitious materials used in DOE facilities, such as Saltstone (Savannah River) and Cast Stone (Hanford), tank closure grouts, and barrier concretes. STADIUM focuses on the physical and structural service life of materials and components based on chemical speciation and reactive mass transport of major cement constituents and aggressive species (e.g., chloride, sulfate, etc.). THAMES is a planned future CBP Toolbox component focused on simulation of the microstructure of cementitious materials and calculation of resultant hydraulic and constituent mass transfer parameters needed in modeling. Two CBP software demonstrations were conducted in FY2013, one to support the Saltstone Disposal Facility (SDF) at SRS and the other on a representative Hanford high-level waste tank. The CBP Toolbox demonstration on the SDF provided analysis on the most probable degradation mechanisms to the cementitious vault enclosure caused by sulfate and carbonation ingress. This analysis was documented and resulted in the issuance of a SDF Performance Assessment Special Analysis by Liquid Waste Operations this fiscal year. The two new software tools supporting chloride attack and dual-regime flow will provide additional degradation tools to better evaluate performance of DOE and commercial cementitious barriers. The CBP SRNL experimental program produced two patent applications and field data that will be used in the development and calibration of CBP software tools being developed in FY2014. The CBP software and simulation tools varies from other efforts in that all the tools are based upon specific and relevant experimental research of cementitious materials utilized in DOE applications. The CBP FY2013 program involved continuing research to improve and enhance the simulation tools as well as developing new tools that model other key degradation phenomena not addressed in Version 1.0. Also efforts to continue to verify the various simulation tools through laboratory experiments and analysis of field specimens are ongoing and will continue into FY2014 to quantify and reduce the uncertainty associated with performance assessments. This end-year report summarizes FY2013 software development efforts and the various experimental programs that are providing data for calibration and validation of the CBP developed software.« less

Regulatory sequence analysis tools.

PubMed

van Helden, Jacques

2003-07-01

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.

Presenting an evaluation model of the trauma registry software.

PubMed

Asadi, Farkhondeh; Paydar, Somayeh

2018-04-01

Trauma is a major cause of 10% death in the worldwide and is considered as a global concern. This problem has made healthcare policy makers and managers to adopt a basic strategy in this context. Trauma registry has an important and basic role in decreasing the mortality and the disabilities due to injuries resulted from trauma. Today, different software are designed for trauma registry. Evaluation of this software improves management, increases efficiency and effectiveness of these systems. Therefore, the aim of this study is to present an evaluation model for trauma registry software. The present study is an applied research. In this study, general and specific criteria of trauma registry software were identified by reviewing literature including books, articles, scientific documents, valid websites and related software in this domain. According to general and specific criteria and related software, a model for evaluating trauma registry software was proposed. Based on the proposed model, a checklist designed and its validity and reliability evaluated. Mentioned model by using of the Delphi technique presented to 12 experts and specialists. To analyze the results, an agreed coefficient of %75 was determined in order to apply changes. Finally, when the model was approved by the experts and professionals, the final version of the evaluation model for the trauma registry software was presented. For evaluating of criteria of trauma registry software, two groups were presented: 1- General criteria, 2- Specific criteria. General criteria of trauma registry software were classified into four main categories including: 1- usability, 2- security, 3- maintainability, and 4-interoperability. Specific criteria were divided into four main categories including: 1- data submission and entry, 2- reporting, 3- quality control, 4- decision and research support. The presented model in this research has introduced important general and specific criteria of trauma registry software and sub criteria related to each main criteria separately. This model was validated by experts in this field. Therefore, this model can be used as a comprehensive model and a standard evaluation tool for measuring efficiency and effectiveness and performance improvement of trauma registry software. Copyright © 2018 Elsevier B.V. All rights reserved.

EOSCUBE: A Constraint Database System for High-Level Specification and Efficient Generation of EOSDIS Products. Phase 1; Proof-of-Concept

NASA Technical Reports Server (NTRS)

Brodsky, Alexander; Segal, Victor E.

1999-01-01

The EOSCUBE constraint database system is designed to be a software productivity tool for high-level specification and efficient generation of EOSDIS and other scientific products. These products are typically derived from large volumes of multidimensional data which are collected via a range of scientific instruments.

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…

A new spatial multi-criteria decision support tool for site selection for implementation of managed aquifer recharge.

PubMed

Rahman, M Azizur; Rusteberg, Bernd; Gogu, R C; Lobo Ferreira, J P; Sauter, Martin

2012-05-30

This study reports the development of a new spatial multi-criteria decision analysis (SMCDA) software tool for selecting suitable sites for Managed Aquifer Recharge (MAR) systems. The new SMCDA software tool functions based on the combination of existing multi-criteria evaluation methods with modern decision analysis techniques. More specifically, non-compensatory screening, criteria standardization and weighting, and Analytical Hierarchy Process (AHP) have been combined with Weighted Linear Combination (WLC) and Ordered Weighted Averaging (OWA). This SMCDA tool may be implemented with a wide range of decision maker's preferences. The tool's user-friendly interface helps guide the decision maker through the sequential steps for site selection, those steps namely being constraint mapping, criteria hierarchy, criteria standardization and weighting, and criteria overlay. The tool offers some predetermined default criteria and standard methods to increase the trade-off between ease-of-use and efficiency. Integrated into ArcGIS, the tool has the advantage of using GIS tools for spatial analysis, and herein data may be processed and displayed. The tool is non-site specific, adaptive, and comprehensive, and may be applied to any type of site-selection problem. For demonstrating the robustness of the new tool, a case study was planned and executed at Algarve Region, Portugal. The efficiency of the SMCDA tool in the decision making process for selecting suitable sites for MAR was also demonstrated. Specific aspects of the tool such as built-in default criteria, explicit decision steps, and flexibility in choosing different options were key features, which benefited the study. The new SMCDA tool can be augmented by groundwater flow and transport modeling so as to achieve a more comprehensive approach to the selection process for the best locations of the MAR infiltration basins, as well as the locations of recovery wells and areas of groundwater protection. The new spatial multicriteria analysis tool has already been implemented within the GIS based Gabardine decision support system as an innovative MAR planning tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

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

2012-04-23

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

Earthdata User Interface Patterns: Building Usable Web Interfaces Through a Shared UI Pattern Library

NASA Astrophysics Data System (ADS)

Siarto, J.

2014-12-01

As more Earth science software tools and services move to the web--the design and usability of those tools become ever more important. A good user interface is becoming expected and users are becoming increasingly intolerant of websites and web applications that work against them. The Earthdata UI Pattern Library attempts to give these scientists and developers the design tools they need to make usable, compelling user interfaces without the associated overhead of using a full design team. Patterns are tested and functional user interface elements targeted specifically at the Earth science community and will include web layouts, buttons, tables, typography, iconography, mapping and visualization/graphing widgets. These UI elements have emerged as the result of extensive user testing, research and software development within the NASA Earthdata team over the past year.

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

Guidelines for testing and release procedures

NASA Technical Reports Server (NTRS)

Molari, R.; Conway, M.

1984-01-01

Guidelines and procedures are recommended for the testing and release of the types of computer software efforts commonly performed at NASA/Ames Research Center. All recommendations are based on the premise that testing and release activities must be specifically selected for the environment, size, and purpose of each individual software project. Guidelines are presented for building a Test Plan and using formal Test Plan and Test Care Inspections on it. Frequent references are made to NASA/Ames Guidelines for Software Inspections. Guidelines are presented for selecting an Overall Test Approach and for each of the four main phases of testing: (1) Unit Testing of Components, (2) Integration Testing of Components, (3) System Integration Testing, and (4) Acceptance Testing. Tools used for testing are listed, including those available from operating systems used at Ames, specialized tools which can be developed, unit test drivers, stub module generators, and the use of format test reporting schemes.

Systems Engineering and Integration (SE and I)

NASA Technical Reports Server (NTRS)

Chevers, ED; Haley, Sam

1990-01-01

The issue of technology advancement and future space transportation vehicles is addressed. The challenge is to develop systems which can be evolved and improved in small incremental steps where each increment reduces present cost, improves, reliability, or does neither but sets the stage for a second incremental upgrade that does. Future requirements are interface standards for commercial off the shelf products to aid in the development of integrated facilities; enhanced automated code generation system slightly coupled to specification and design documentation; modeling tools that support data flow analysis; and shared project data bases consisting of technical characteristics cast information, measurement parameters, and reusable software programs. Topics addressed include: advanced avionics development strategy; risk analysis and management; tool quality management; low cost avionics; cost estimation and benefits; computer aided software engineering; computer systems and software safety; system testability; and advanced avionics laboratories - and rapid prototyping. This presentation is represented by viewgraphs only.

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

PubMed

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

2016-08-30

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

Software systems for modeling articulated figures

NASA Technical Reports Server (NTRS)

Phillips, Cary B.

1989-01-01

Research in computer animation and simulation of human task performance requires sophisticated geometric modeling and user interface tools. The software for a research environment should present the programmer with a powerful but flexible substrate of facilities for displaying and manipulating geometric objects, yet insure that future tools have a consistent and friendly user interface. Jack is a system which provides a flexible and extensible programmer and user interface for displaying and manipulating complex geometric figures, particularly human figures in a 3D working environment. It is a basic software framework for high-performance Silicon Graphics IRIS workstations for modeling and manipulating geometric objects in a general but powerful way. It provides a consistent and user-friendly interface across various applications in computer animation and simulation of human task performance. Currently, Jack provides input and control for applications including lighting specification and image rendering, anthropometric modeling, figure positioning, inverse kinematics, dynamic simulation, and keyframe animation.

Citation and Recognition of contributions using Semantic Provenance Knowledge Captured in the OPeNDAP Software Framework

NASA Astrophysics Data System (ADS)

West, P.; Michaelis, J.; Lebot, T.; McGuinness, D. L.; Fox, P. A.

2014-12-01

Providing proper citation and attribution for published data, derived data products, and the software tools used to generate them, has always been an important aspect of scientific research. However, It is often the case that this type of detailed citation and attribution is lacking. This is in part because it often requires manual markup since dynamic generation of this type of provenance information is not typically done by the tools used to access, manipulate, transform, and visualize data. In addition, the tools themselves lack the information needed to be properly cited themselves. The OPeNDAP Hyrax Software Framework is a tool that provides access to and the ability to constrain, manipulate, and transform, different types of data from different data formats, into a common format, the DAP (Data Access Protocol), in order to derive new data products. A user, or another software client, specifies an HTTP URL in order to access a particular piece of data, and appropriately transform it to suit a specific purpose of use. The resulting data products, however, do not contain any information about what data was used to create it, or the software process used to generate it, let alone information that would allow the proper citing and attribution to down stream researchers and tool developers. We will present our approach to provenance capture in Hyrax including a mechanism that can be used to report back to the hosting site any derived products, such as publications and reports, using the W3C PROV recommendation pingback service. We will demonstrate our utilization of Semantic Web and Web standards, the development of an information model that extends the PROV model for provenance capture, and the development of the pingback service. We will present our findings, as well as our practices for providing provenance information, visualization of the provenance information, and the development of pingback services, to better enable scientists and tool developers to be recognized and properly cited for their contributions.

A New Look at NASA: Strategic Research In Information Technology

NASA Technical Reports Server (NTRS)

Alfano, David; Tu, Eugene (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on research undertaken by NASA to facilitate the development of information technologies. Specific ideas covered here include: 1) Bio/nano technologies: biomolecular and nanoscale systems and tools for assembly and computing; 2) Evolvable hardware: autonomous self-improving, self-repairing hardware and software for survivable space systems in extreme environments; 3) High Confidence Software Technologies: formal methods, high-assurance software design, and program synthesis; 4) Intelligent Controls and Diagnostics: Next generation machine learning, adaptive control, and health management technologies; 5) Revolutionary computing: New computational models to increase capability and robustness to enable future NASA space missions.

Software design by reusing architectures

NASA Technical Reports Server (NTRS)

Bhansali, Sanjay; Nii, H. Penny

1992-01-01

Abstraction fosters reuse by providing a class of artifacts that can be instantiated or customized to produce a set of artifacts meeting different specific requirements. It is proposed that significant leverage can be obtained by abstracting software system designs and the design process. The result of such an abstraction is a generic architecture and a set of knowledge-based, customization tools that can be used to instantiate the generic architecture. An approach for designing software systems based on the above idea are described. The approach is illustrated through an implemented example, and the advantages and limitations of the approach are discussed.

Instrument control software requirement specification for Extremely Large Telescopes

NASA Astrophysics Data System (ADS)

Young, Peter J.; Kiekebusch, Mario J.; Chiozzi, Gianluca

2010-07-01

Engineers in several observatories are now designing the next generation of optical telescopes, the Extremely Large Telescopes (ELT). These are very complex machines that will host sophisticated astronomical instruments to be used for a wide range of scientific studies. In order to carry out scientific observations, a software infrastructure is required to orchestrate the control of the multiple subsystems and functions. This paper will focus on describing the considerations, strategies and main issues related to the definition and analysis of the software requirements for the ELT's Instrument Control System using modern development processes and modelling tools like SysML.

Digital-flight-control-system software written in automated-engineering-design language: A user's guide of verification and validation tools

NASA Technical Reports Server (NTRS)

Saito, Jim

1987-01-01

The user guide of verification and validation (V&V) tools for the Automated Engineering Design (AED) language is specifically written to update the information found in several documents pertaining to the automated verification of flight software tools. The intent is to provide, in one document, all the information necessary to adequately prepare a run to use the AED V&V tools. No attempt is made to discuss the FORTRAN V&V tools since they were not updated and are not currently active. Additionally, the current descriptions of the AED V&V tools are contained and provides information to augment the NASA TM 84276. The AED V&V tools are accessed from the digital flight control systems verification laboratory (DFCSVL) via a PDP-11/60 digital computer. The AED V&V tool interface handlers on the PDP-11/60 generate a Univac run stream which is transmitted to the Univac via a Remote Job Entry (RJE) link. Job execution takes place on the Univac 1100 and the job output is transmitted back to the DFCSVL and stored as a PDP-11/60 printfile.

Undergraduate Planet Hunters: Tools and Results

NASA Astrophysics Data System (ADS)

Buzasi, Derek L.; Carboneau, Lindsey; Ferrell, Laura; Green, Gilbert; Kaiser, Maya; Kreke, Kira; Lundy, Samantha; Merritt, William; Passino, Matlin; Paxton, Harrison; Podaril, Alexandria; Stansfield, Alexis

2018-06-01

One student "Honors Experience" option at Florida Gulf Coast University is a research experience, and we have developed a "Planet Hunters" course to provide an astronomical research track that satisfies that requirement. Students spend the first semester learning astronomical background and exoplanet detection techniques, while the second semester is primarily devoted to planet searches in K2 data using student-oriented software tools developed specifically for the task. In this poster, we illustrate those tools and show results obtained by class participants during this years experience.

Development of a task analysis tool to facilitate user interface design

NASA Technical Reports Server (NTRS)

Scholtz, Jean C.

1992-01-01

A good user interface is one that facilitates the user in carrying out his task. Such interfaces are difficult and costly to produce. The most important aspect in producing a good interface is the ability to communicate to the software designers what the user's task is. The Task Analysis Tool is a system for cooperative task analysis and specification of the user interface requirements. This tool is intended to serve as a guide to development of initial prototypes for user feedback.

RSAT 2015: Regulatory Sequence Analysis Tools.

PubMed

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-07-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure and software tools of AIDA.

PubMed

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

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.

Software Innovation in a Mission Critical Environment

NASA Technical Reports Server (NTRS)

Fredrickson, Steven

2015-01-01

Operating in mission-critical environments requires trusted solutions, and the preference for "tried and true" approaches presents a potential barrier to infusing innovation into mission-critical systems. This presentation explores opportunities to overcome this barrier in the software domain. It outlines specific areas of innovation in software development achieved by the Johnson Space Center (JSC) Engineering Directorate in support of NASA's major human spaceflight programs, including International Space Station, Multi-Purpose Crew Vehicle (Orion), and Commercial Crew Programs. Software engineering teams at JSC work with hardware developers, mission planners, and system operators to integrate flight vehicles, habitats, robotics, and other spacecraft elements for genuinely mission critical applications. The innovations described, including the use of NASA Core Flight Software and its associated software tool chain, can lead to software that is more affordable, more reliable, better modelled, more flexible, more easily maintained, better tested, and enabling of automation.

[Research progress of probe design software of oligonucleotide microarrays].

PubMed

Chen, Xi; Wu, Zaoquan; Liu, Zhengchun

2014-02-01

DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (Tm). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software.

[The development and evaluation of software to verify diagnostic accuracy].

PubMed

Jensen, Rodrigo; de Moraes Lopes, Maria Helena Baena; Silveira, Paulo Sérgio Panse; Ortega, Neli Regina Siqueira

2012-02-01

This article describes the development and evaluation of software that verifies the accuracy of diagnoses made by nursing students. The software was based on a model that uses fuzzy logic concepts, including PERL, the MySQL database for Internet accessibility, and the NANDA-I 2007-2008 classification system. The software was evaluated in terms of its technical quality and usability through specific instruments. The activity proposed in the software involves four stages in which students establish the relationship values between nursing diagnoses, defining characteristics/risk factors and clinical cases. The relationship values determined by students are compared to those of specialists, generating performance scores for the students. In the evaluation, the software demonstrated satisfactory outcomes regarding the technical quality and, according to the students, helped in their learning and may become an educational tool to teach the process of nursing diagnosis.

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

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

Jette, M.; Caliga, D.

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

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

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example

PubMed Central

Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F.; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C.

2017-01-01

Background Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Objective Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Methods Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson’s disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Results Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Conclusion Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation. PMID:28441410

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.

Optimum-AIV: A planning and scheduling system for spacecraft AIV

NASA Technical Reports Server (NTRS)

Arentoft, M. M.; Fuchs, Jens J.; Parrod, Y.; Gasquet, Andre; Stader, J.; Stokes, I.; Vadon, H.

1991-01-01

A project undertaken for the European Space Agency (ESA) is presented. The project is developing a knowledge based software system for planning and scheduling of activities for spacecraft assembly, integration, and verification (AIV). The system extends into the monitoring of plan execution and the plan repair phase. The objectives are to develop an operational kernel of a planning, scheduling, and plan repair tool, called OPTIMUM-AIV, and to provide facilities which will allow individual projects to customize the kernel to suit its specific needs. The kernel shall consist of a set of software functionalities for assistance in initial specification of the AIV plan, in verification and generation of valid plans and schedules for the AIV activities, and in interactive monitoring and execution problem recovery for the detailed AIV plans. Embedded in OPTIMUM-AIV are external interfaces which allow integration with alternative scheduling systems and project databases. The current status of the OPTIMUM-AIV project, as of Jan. 1991, is that a further analysis of the AIV domain has taken place through interviews with satellite AIV experts, a software requirement document (SRD) for the full operational tool was approved, and an architectural design document (ADD) for the kernel excluding external interfaces is ready for review.

PyPWA: A partial-wave/amplitude analysis software framework

NASA Astrophysics Data System (ADS)

Salgado, Carlos

2016-05-01

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

High Performance Computing Software Applications for Space Situational Awareness

NASA Astrophysics Data System (ADS)

Giuliano, C.; Schumacher, P.; Matson, C.; Chun, F.; Duncan, B.; Borelli, K.; Desonia, R.; Gusciora, G.; Roe, K.

The High Performance Computing Software Applications Institute for Space Situational Awareness (HSAI-SSA) has completed its first full year of applications development. The emphasis of our work in this first year was in improving space surveillance sensor models and image enhancement software. These applications are the Space Surveillance Network Analysis Model (SSNAM), the Air Force Space Fence simulation (SimFence), and physically constrained iterative de-convolution (PCID) image enhancement software tool. Specifically, we have demonstrated order of magnitude speed-up in those codes running on the latest Cray XD-1 Linux supercomputer (Hoku) at the Maui High Performance Computing Center. The software applications improvements that HSAI-SSA has made, has had significant impact to the warfighter and has fundamentally changed the role of high performance computing in SSA.

Implementation of Biogas Stations into Smart Heating and Cooling Network

NASA Astrophysics Data System (ADS)

Milčák, P.; Konvička, J.; Jasenská, M.

2016-10-01

The paper is aimed at the description of implementation of a biogas station into software environment for the "Smart Heating and Cooling Networks". The aim of this project is creation of a software tool for preparation of operation and optimization of treatment of heat/cool in small regions. In this case, the biogas station represents a kind of renewable energy source, which, however, has its own operational specifics which need to be taken into account at the creation of an implementation project. For a specific biogas station, a detailed computational model was elaborated, which is parameterized in particular for an optimization of the total computational time.

Web-based interactive 2D/3D medical image processing and visualization software.

PubMed

Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

2010-05-01

There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

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.

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.

The software-cycle model for re-engineering and reuse

NASA Technical Reports Server (NTRS)

Bailey, John W.; Basili, Victor R.

1992-01-01

This paper reports on the progress of a study which will contribute to our ability to perform high-level, component-based programming by describing means to obtain useful components, methods for the configuration and integration of those components, and an underlying economic model of the costs and benefits associated with this approach to reuse. One goal of the study is to develop and demonstrate methods to recover reusable components from domain-specific software through a combination of tools, to perform the identification, extraction, and re-engineering of components, and domain experts, to direct the applications of those tools. A second goal of the study is to enable the reuse of those components by identifying techniques for configuring and recombining the re-engineered software. This component-recovery or software-cycle model addresses not only the selection and re-engineering of components, but also their recombination into new programs. Once a model of reuse activities has been developed, the quantification of the costs and benefits of various reuse options will enable the development of an adaptable economic model of reuse, which is the principal goal of the overall study. This paper reports on the conception of the software-cycle model and on several supporting techniques of software recovery, measurement, and reuse which will lead to the development of the desired economic model.

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.

Design and implementation of a privacy preserving electronic health record linkage tool in Chicago

PubMed Central

Cashy, John P; Jackson, Kathryn L; Pah, Adam R; Goel, Satyender; Boehnke, Jörn; Humphries, John Eric; Kominers, Scott Duke; Hota, Bala N; Sims, Shannon A; Malin, Bradley A; French, Dustin D; Walunas, Theresa L; Meltzer, David O; Kaleba, Erin O; Jones, Roderick C; Galanter, William L

2015-01-01

Objective To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research. Methods The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches. Results The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually reconciled set of 11 292 patients as a gold standard, the software achieved a sensitivity of 96% and a specificity of 100%, with a majority of the missed matches accounted for by patients with both a missing social security number and last name change. Using 3 disease examples, it is demonstrated that the software can reduce duplication of patient records across sites by as much as 28%. Conclusions Software that standardizes the assignment of a unique seeded hash identifier merged through an agreed upon third-party honest broker can enable large-scale secure linkage of EHR data for epidemiologic and public health research. The software algorithm can improve future epidemiologic research by providing more comprehensive data given that patients may make use of multiple healthcare systems. PMID:26104741

Design and implementation of a privacy preserving electronic health record linkage tool in Chicago.

PubMed

Kho, Abel N; Cashy, John P; Jackson, Kathryn L; Pah, Adam R; Goel, Satyender; Boehnke, Jörn; Humphries, John Eric; Kominers, Scott Duke; Hota, Bala N; Sims, Shannon A; Malin, Bradley A; French, Dustin D; Walunas, Theresa L; Meltzer, David O; Kaleba, Erin O; Jones, Roderick C; Galanter, William L

2015-09-01

To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research. The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches. The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually reconciled set of 11 292 patients as a gold standard, the software achieved a sensitivity of 96% and a specificity of 100%, with a majority of the missed matches accounted for by patients with both a missing social security number and last name change. Using 3 disease examples, it is demonstrated that the software can reduce duplication of patient records across sites by as much as 28%. Software that standardizes the assignment of a unique seeded hash identifier merged through an agreed upon third-party honest broker can enable large-scale secure linkage of EHR data for epidemiologic and public health research. The software algorithm can improve future epidemiologic research by providing more comprehensive data given that patients may make use of multiple healthcare systems. © 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.

A Software Tool for Quantitative Seismicity Analysis - ZMAP

NASA Astrophysics Data System (ADS)

Wiemer, S.; Gerstenberger, M.

2001-12-01

Earthquake catalogs are probably the most basic product of seismology, and remain arguably the most useful for tectonic studies. Modern seismograph networks can locate up to 100,000 earthquakes annually, providing a continuous and sometime overwhelming stream of data. ZMAP is a set of tools driven by a graphical user interface (GUI), designed to help seismologists analyze catalog data. ZMAP is primarily a research tool suited to the evaluation of catalog quality and to addressing specific hypotheses; however, it can also be useful in routine network operations. Examples of ZMAP features include catalog quality assessment (artifacts, completeness, explosion contamination), interactive data exploration, mapping transients in seismicity (rate changes, b-values, p-values), fractal dimension analysis and stress tensor inversions. Roughly 100 scientists worldwide have used the software at least occasionally. About 30 peer-reviewed publications have made use of ZMAP. ZMAP code is open source, written in the commercial software language Matlab by the Mathworks, a widely used software in the natural sciences. ZMAP was first published in 1994, and has continued to grow over the past 7 years. Recently, we released ZMAP v.6. The poster will introduce the features of ZMAP. We will specifically focus on ZMAP features related to time-dependent probabilistic hazard assessment. We are currently implementing a ZMAP based system that computes probabilistic hazard maps, which combine the stationary background hazard as well as aftershock and foreshock hazard into a comprehensive time dependent probabilistic hazard map. These maps will be displayed in near real time on the Internet. This poster is also intended as a forum for ZMAP users to provide feedback and discuss the future of ZMAP.

Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Christner, Martin; Dressler, Dirk; Andrian, Mark; Reule, Claudia; Petrini, Orlando

2017-01-01

The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e. g. for outbreak investigations, is often hampered by the complexity of data analysis. We have analysed publicly available MALDI-TOF mass spectra from a large outbreak of Shiga-Toxigenic Escherichia coli in northern Germany using a general purpose software tool for the analysis of complex biological data. The software was challenged with depauperate spectra and reduced learning group sizes to mimic poor spectrum quality and scarcity of reference spectra at the onset of an outbreak. With high quality formic acid extraction spectra, the software's built in classifier accurately identified outbreak related strains using as few as 10 reference spectra (99.8% sensitivity, 98.0% specificity). Selective variation of processing parameters showed impaired marker peak detection and reduced classification accuracy in samples with high background noise or artificially reduced peak counts. However, the software consistently identified mass signals suitable for a highly reliable marker peak based classification approach (100% sensitivity, 99.5% specificity) even from low quality direct deposition spectra. The study demonstrates that general purpose data analysis tools can effectively be used for the analysis of bacterial mass spectra.

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

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.

Rosetta CONSERT operations and data analysis preparation: simulation software tools.

NASA Astrophysics Data System (ADS)

Rogez, Yves; Hérique, Alain; Cardiet, Maël; Zine, Sonia; Westphal, Mathieu; Micallef, Mickael; Berquin, Yann; Kofman, Wlodek

2014-05-01

The CONSERT experiment onboard Rosetta and Philae will perform the tomography of the 67P/CG comet nucleus by measuring radio waves transmission from the Rosetta S/C to the Philae Lander. The accurate analysis of travel time measurements will deliver unique knowledge of the nucleus interior dielectric properties. The challenging complexity of CONSERT operations requirements, combining both Rosetta and Philae, allows only a few set of opportunities to acquire data. Thus, we need a fine analysis of the impact of Rosetta trajectory, Philae position and comet shape on CONSERT measurements, in order to take optimal decisions in a short time. The integration of simulation results and mission parameters provides synthetic information to evaluate performances and risks for each opportunity. The preparation of CONSERT measurements before space operations is a key to achieve the best science return of the experiment. In addition, during Rosetta space operations, these software tools will allow a "real-time" first analysis of the latest measurements to improve the next acquisition sequences. The software tools themselves are built around a 3D electromagnetic radio wave simulation, taking into account the signal polarization. It is based on ray-tracing algorithms specifically designed for quick orbit analysis and radar signal generation. This allows computation on big domains relatively to the wavelength. The extensive use of 3D visualization tools provides comprehensive and synthetic views of the results. The software suite is designed to be extended, after Rosetta operations, to the full 3D measurement data analysis using inversion methods.

Software Tools for Formal Specification and Verification of Distributed Real-Time Systems

DTIC Science & Technology

1994-07-29

time systems and to evaluate the design. The evaluation of the design includes investigation of both the capability and potential usefulness of the toolkit environment and the feasibility of its implementation....The goals of Phase 1 are to design in detail a toolkit environment based on formal methods for the specification and verification of distributed real

Maestro Workflow Conductor

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

Di Natale, Francesco

2017-06-01

MaestroWF is a Python tool and software package for loading YAML study specifications that represents a simulation campaign. The package is capable of parameterizing a study, pulling dependencies automatically, formatting output directories, and managing the flow and execution of the campaign. MaestroWF also provides a set of abstracted objects that can also be used to develop user specific scripts for launching simulation campaigns.

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.

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).

Process and information integration via hypermedia

NASA Technical Reports Server (NTRS)

Hammen, David G.; Labasse, Daniel L.; Myers, Robert M.

1990-01-01

Success stories for advanced automation prototypes abound in the literature but the deployments of practical large systems are few in number. There are several factors that militate against the maturation of such prototypes into products. Here, the integration of advanced automation software into large systems is discussed. Advanced automation systems tend to be specific applications that need to be integrated and aggregated into larger systems. Systems integration can be achieved by providing expert user-developers with verified tools to efficiently create small systems that interface to large systems through standard interfaces. The use of hypermedia as such a tool in the context of the ground control centers that support Shuttle and space station operations is explored. Hypermedia can be an integrating platform for data, conventional software, and advanced automation software, enabling data integration through the display of diverse types of information and through the creation of associative links between chunks of information. Further, hypermedia enables process integration through graphical invoking of system functions. Through analysis and examples, researchers illustrate how diverse information and processing paradigms can be integrated into a single software platform.

DAKOTA JAGUAR 3.0 user's manual.

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

Adams, Brian M.; Bauman, Lara E; Chan, Ethan

2013-05-01

JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the features necessary to use JAGUAR.

JAGUAR developer's manual.

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

Chan, Ethan

2011-06-01

JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the technical background necessary for a developer to understand JAGUAR.

Preparing Florida for deployment of SafetyAnalyst for all roads.

DOT National Transportation Integrated Search

2012-05-01

SafetyAnalyst is an advanced software system designed to provide the state and local highway agencies with a comprehensive set of tools to enhance their programming of site-specific highway safety improvements. As one of the 27 states that sponsored ...

Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis.

PubMed

Kalendar, Ruslan; Tselykh, Timofey V; Khassenov, Bekbolat; Ramanculov, Erlan M

2017-01-01

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine-pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html , and its online version is located at http://primerdigital.com/tools/pcr.html .

Reliability Analysis for AFTI-F16 SRFCS Using ASSIST and SURE

NASA Technical Reports Server (NTRS)

Wu, N. Eva

2001-01-01

This paper reports the results of a study on reliability analysis of an AFTI-16 Self-Repairing Flight Control System (SRFCS) using software tools SURE (Semi-Markov Unreliability Range Evaluator and ASSIST (Abstract Semi-Markov Specification Interface to the SURE Tool). The purpose of the study is to investigate the potential utility of the software tools in the ongoing effort of the NASA Aviation Safety Program, where the class of systems must be extended beyond the originally intended serving class of electronic digital processors. The study concludes that SURE and ASSIST are applicable to reliability, analysis of flight control systems. They are especially efficient for sensitivity analysis that quantifies the dependence of system reliability on model parameters. The study also confirms an earlier finding on the dominant role of a parameter called a failure coverage. The paper will remark on issues related to the improvement of coverage and the optimization of redundancy level.

Computer software tool REALM for sustainable water allocation and management.

PubMed

Perera, B J C; James, B; Kularathna, M D U

2005-12-01

REALM (REsource ALlocation Model) is a generalised computer simulation package that models harvesting and bulk distribution of water resources within a water supply system. It is a modeling tool, which can be applied to develop specific water allocation models. Like other water resource simulation software tools, REALM uses mass-balance accounting at nodes, while the movement of water within carriers is subject to capacity constraints. It uses a fast network linear programming algorithm to optimise the water allocation within the network during each simulation time step, in accordance with user-defined operating rules. This paper describes the main features of REALM and provides potential users with an appreciation of its capabilities. In particular, it describes two case studies covering major urban and rural water supply systems. These case studies illustrate REALM's capabilities in the use of stochastically generated data in water supply planning and management, modelling of environmental flows, and assessing security of supply issues.

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.

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

PubMed

Trinkaus, Hans L; Gaisser, Andrea E

2010-09-01

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

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

Small scale sequence automation pays big dividends

NASA Technical Reports Server (NTRS)

Nelson, Bill

1994-01-01

Galileo sequence design and integration are supported by a suite of formal software tools. Sequence review, however, is largely a manual process with reviewers scanning hundreds of pages of cryptic computer printouts to verify sequence correctness. Beginning in 1990, a series of small, PC based sequence review tools evolved. Each tool performs a specific task but all have a common 'look and feel'. The narrow focus of each tool means simpler operation, and easier creation, testing, and maintenance. Benefits from these tools are (1) decreased review time by factors of 5 to 20 or more with a concomitant reduction in staffing, (2) increased review accuracy, and (3) excellent returns on time invested.

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.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Software engineering for ESO's VLT project

NASA Astrophysics Data System (ADS)

Filippi, G.

1994-12-01

This paper reports on the experience at the European Southern Observatory on the application of software engineering techniques to a 200 man-year control software project for the Very Large Telescope (VLT). This shall provide astronomers, before the end of the century, with one of the most powerful telescopes in the world. From the definition of the general model, described in the software management plan, specific activities have been and will be defined: standards for documents and for code development, design approach using a CASE tool, the process of reviewing both documentation and code, quality assurance, test strategy, etc. The initial choices, the current implementation and the future planned activities are presented and, where feedback is already available, pros and cons are discussed.

Cross-platform validation and analysis environment for particle physics

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

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for onlinemore » validation of Monte Carlo event samples through a web interface.« less

Photogrammetric 3d Reconstruction in Matlab: Development of a Free Tool

NASA Astrophysics Data System (ADS)

Masiero, A.

2017-11-01

This paper presents the current state of development of a free Matlab tool for photogrammetric reconstruction developed at the University of Padova, Italy. The goal of this software is mostly educational, i.e. allowing students to have a close look to the specific steps which lead to the computation of a dense point cloud. As most of recently developed photogrammetric softwares, it is based on a Structure from Motion approach. Despite being mainly motivated by educational purposes, certain implementation details are clearly inspired by recent research works, e.g. limiting the computational burden of the feature matching by determining a suboptimal set of features to be considered, using information provided by external sensors to ease the matching process.

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.

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

Scrutinizing UML Activity Diagrams

NASA Astrophysics Data System (ADS)

Al-Fedaghi, Sabah

Building an information system involves two processes: conceptual modeling of the “real world domain” and designing the software system. Object-oriented methods and languages (e.g., UML) are typically used for describing the software system. For the system analysis process that produces the conceptual description, object-oriented techniques or semantics extensions are utilized. Specifically, UML activity diagrams are the “flow charts” of object-oriented conceptualization tools. This chapter proposes an alternative to UML activity diagrams through the development of a conceptual modeling methodology based on the notion of flow.

Software to Compare NPP HDF5 Data Files

NASA Technical Reports Server (NTRS)

Wiegand, Chiu P.; LeMoigne-Stewart, Jacqueline; Ruley, LaMont T.

2013-01-01

This software was developed for the NPOESS (National Polar-orbiting Operational Environmental Satellite System) Preparatory Project (NPP) Science Data Segment. The purpose of this software is to compare HDF5 (Hierarchical Data Format) files specific to NPP and report whether the HDF5 files are identical. If the HDF5 files are different, users have the option of printing out the list of differences in the HDF5 data files. The user provides paths to two directories containing a list of HDF5 files to compare. The tool would select matching HDF5 file names from the two directories and run the comparison on each file. The user can also select from three levels of detail. Level 0 is the basic level, which simply states whether the files match or not. Level 1 is the intermediate level, which lists the differences between the files. Level 2 lists all the details regarding the comparison, such as which objects were compared, and how and where they are different. The HDF5 tool is written specifically for the NPP project. As such, it ignores certain attributes (such as creation_date, creation_ time, etc.) in the HDF5 files. This is because even though two HDF5 files could represent exactly the same granule, if they are created at different times, the creation date and time would be different. This tool is smart enough to ignore differences that are not relevant to NPP users.

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.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

PubMed Central

Lutsik, Pavlo; Feuerbach, Lars; Arand, Julia; Lengauer, Thomas; Walter, Jörn; Bock, Christoph

2011-01-01

Bisulfite sequencing is a widely used method for measuring DNA methylation in eukaryotic genomes. The assay provides single-base pair resolution and, given sufficient sequencing depth, its quantitative accuracy is excellent. High-throughput sequencing of bisulfite-converted DNA can be applied either genome wide or targeted to a defined set of genomic loci (e.g. using locus-specific PCR primers or DNA capture probes). Here, we describe BiQ Analyzer HT (http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/), a user-friendly software tool that supports locus-specific analysis and visualization of high-throughput bisulfite sequencing data. The software facilitates the shift from time-consuming clonal bisulfite sequencing to the more quantitative and cost-efficient use of high-throughput sequencing for studying locus-specific DNA methylation patterns. In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data. PMID:21565797

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

Valassi, A.; Clemencic, M.; Dykstra, D.

The Persistency Framework consists of three software packages (CORAL, COOL and POOL) addressing the data access requirements of the LHC experiments in different areas. It is the result of the collaboration between the CERN IT Department and the three experiments (ATLAS, CMS and LHCb) that use this software to access their data. POOL is a hybrid technology store for C++ objects, metadata catalogs and collections. CORAL is a relational database abstraction layer with an SQL-free API. COOL provides specific software tools and components for the handling of conditions data. This paper reports on the status and outlook of the projectmore » and reviews in detail the usage of each package in the three experiments.« less

Seamless transitions from early prototypes to mature operational software - A technology that enables the process for planning and scheduling applications

NASA Technical Reports Server (NTRS)

Hornstein, Rhoda S.; Wunderlich, Dana A.; Willoughby, John K.

1992-01-01

New and innovative software technology is presented that provides a cost effective bridge for smoothly transitioning prototype software, in the field of planning and scheduling, into an operational environment. Specifically, this technology mixes the flexibility and human design efficiency of dynamic data typing with the rigor and run-time efficiencies of static data typing. This new technology provides a very valuable tool for conducting the extensive, up-front system prototyping that leads to specifying the correct system and producing a reliable, efficient version that will be operationally effective and will be accepted by the intended users.

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

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

PubMed Central

Easterly, Caleb; Gruening, Bjoern; Johnson, James; Kolmeder, Carolin A.; Kumar, Praveen; May, Damon; Mehta, Subina; Mesuere, Bart; Brown, Zachary; Elias, Joshua E.; Hervey, W. Judson; McGowan, Thomas; Muth, Thilo; Rudney, Joel; Griffin, Timothy J.

2018-01-01

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics “Contribution Fest“ undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software. PMID:29385081

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

PubMed

Blank, Clemens; Easterly, Caleb; Gruening, Bjoern; Johnson, James; Kolmeder, Carolin A; Kumar, Praveen; May, Damon; Mehta, Subina; Mesuere, Bart; Brown, Zachary; Elias, Joshua E; Hervey, W Judson; McGowan, Thomas; Muth, Thilo; Nunn, Brook; Rudney, Joel; Tanca, Alessandro; Griffin, Timothy J; Jagtap, Pratik D

2018-01-31

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

Hard Choices for Individual Situations.

ERIC Educational Resources Information Center

Landon, Bruce

This paper focuses on faculty use of a decision-making process for complex situations. The analysis part of the process describes and compares course management software focusing on: technical specifications, instructional design values,tools and features, ease of use, and standards compliance. The extensive comparisons provide faculty with…

Database & information tools for transportation research management : Connecticut transportation research peer exchange report of a thematic peer exchange.

DOT National Transportation Integrated Search

2006-05-01

Specific objectives of the Peer Exchange were: : Discuss and exchange information about databases and other software : used to support the program-cycles managed by state transportation : research offices. Elements of the program cycle include: :...

ExPASy: SIB bioinformatics resource portal.

PubMed

Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

2012-07-01

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

Screening_mgmt: a Python module for managing screening data.

PubMed

Helfenstein, Andreas; Tammela, Päivi

2015-02-01

High-throughput screening is an established technique in drug discovery and, as such, has also found its way into academia. High-throughput screening generates a considerable amount of data, which is why specific software is used for its analysis and management. The commercially available software packages are often beyond the financial limits of small-scale academic laboratories and, furthermore, lack the flexibility to fulfill certain user-specific requirements. We have developed a Python module, screening_mgmt, which is a lightweight tool for flexible data retrieval, analysis, and storage for different screening assays in one central database. The module reads custom-made analysis scripts and plotting instructions, and it offers a graphical user interface to import, modify, and display the data in a uniform manner. During the test phase, we used this module for the management of 10,000 data points of various origins. It has provided a practical, user-friendly tool for sharing and exchanging information between researchers. © 2014 Society for Laboratory Automation and Screening.

MapFactory - Towards a mapping design pattern for big geospatial data

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena

2018-05-01

With big geospatial data emerging, cartographers and geographic information scientists have to find new ways of dealing with the volume, variety, velocity, and veracity (4Vs) of the data. This requires the development of tools that allow processing, filtering, analysing, and visualising of big data through multidisciplinary collaboration. In this paper, we present the MapFactory design pattern that will be used for the creation of different maps according to the (input) design specification for big geospatial data. The design specification is based on elements from ISO19115-1:2014 Geographic information - Metadata - Part 1: Fundamentals that would guide the design and development of the map or set of maps to be produced. The results of the exploratory research suggest that the MapFactory design pattern will help with software reuse and communication. The MapFactory design pattern will aid software developers to build the tools that are required to automate map making with big geospatial data. The resulting maps would assist cartographers and others to make sense of big geospatial data.

Value Addition to Cartosat-I Imagery

NASA Astrophysics Data System (ADS)

Mohan, M.

2014-11-01

In the sector of remote sensing applications, the use of stereo data is on the steady rise. An attempt is hereby made to develop a software suite specifically for exploitation of Cartosat-I data. A few algorithms to enhance the quality of basic Cartosat-I products will be presented. The algorithms heavily exploit the Rational Function Coefficients (RPCs) that are associated with the image. The algorithms include improving the geometric positioning through Bundle Block Adjustment and producing refined RPCs; generating portable stereo views using raw / refined RPCs autonomously; orthorectification and mosaicing; registering a monoscopic image rapidly with a single seed point. The outputs of these modules (including the refined RPCs) are in standard formats for further exploitation in 3rd party software. The design focus has been on minimizing the user-interaction and to customize heavily to suit the Indian context. The core libraries are in C/C++ and some of the applications come with user-friendly GUI. Further customization to suit a specific workflow is feasible as the requisite photogrammetric tools are in place and are continuously upgraded. The paper discusses the algorithms and the design considerations of developing the tools. The value-added products so produced using these tools will also be presented.

Applying CASE Tools for On-Board Software Development

NASA Astrophysics Data System (ADS)

Brammer, U.; Hönle, A.

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

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

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.

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.

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

2016-01-01

Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

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.

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.

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

Reverse engineering tools can be used in satisfying the information needs of software maintainers. Especially in case of maintaining large-scale legacy systems tool support is essential. Reverse engineering tools provide various kinds of capabilities to provide the needed information to the tool user. In this paper we analyze the provided capabilities in terms of four aspects: provided data structures, visualization mechanisms, information request specification mechanisms, and navigation features. We provide a compact analysis of ten representative reverse engineering tools for supporting C, C++ or Java: Eclipse Java Development Tools, Wind River Workbench (for C and C++), Understand (for C++), Imagix 4D, Creole, Javadoc, Javasrc, Source Navigator, Doxygen, and HyperSoft. The results of the study supplement the earlier findings in this important area.

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.

ConfocalCheck - A Software Tool for the Automated Monitoring of Confocal Microscope Performance

PubMed Central

Hng, Keng Imm; Dormann, Dirk

2013-01-01

Laser scanning confocal microscopy has become an invaluable tool in biomedical research but regular quality testing is vital to maintain the system’s performance for diagnostic and research purposes. Although many methods have been devised over the years to characterise specific aspects of a confocal microscope like measuring the optical point spread function or the field illumination, only very few analysis tools are available. Our aim was to develop a comprehensive quality assurance framework ranging from image acquisition to automated analysis and documentation. We created standardised test data to assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation. The ConfocalCheck software presented here analyses the data fully automatically. It creates numerous visual outputs indicating potential issues requiring further investigation. By storing results in a web browser compatible file format the software greatly simplifies record keeping allowing the operator to quickly compare old and new data and to spot developing trends. We demonstrate that the systematic monitoring of confocal performance is essential in a core facility environment and how the quantitative measurements obtained can be used for the detailed characterisation of system components as well as for comparisons across multiple instruments. PMID:24224017

High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development.

PubMed

Clark, Randy T; Famoso, Adam N; Zhao, Keyan; Shaff, Jon E; Craft, Eric J; Bustamante, Carlos D; McCouch, Susan R; Aneshansley, Daniel J; Kochian, Leon V

2013-02-01

High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population. © 2012 Blackwell Publishing Ltd.

Development and Testing of Control Laws for the Active Aeroelastic Wing Program

NASA Technical Reports Server (NTRS)

Dibley, Ryan P.; Allen, Michael J.; Clarke, Robert; Gera, Joseph; Hodgkinson, John

2005-01-01

The Active Aeroelastic Wing research program was a joint program between the U.S. Air Force Research Laboratory and NASA established to investigate the characteristics of an aeroelastic wing and the technique of using wing twist for roll control. The flight test program employed the use of an F/A-18 aircraft modified by reducing the wing torsional stiffness and adding a custom research flight control system. The research flight control system was optimized to maximize roll rate using only wing surfaces to twist the wing while simultaneously maintaining design load limits, stability margins, and handling qualities. NASA Dryden Flight Research Center developed control laws using the software design tool called CONDUIT, which employs a multi-objective function optimization to tune selected control system design parameters. Modifications were made to the Active Aeroelastic Wing implementation in this new software design tool to incorporate the NASA Dryden Flight Research Center nonlinear F/A-18 simulation for time history analysis. This paper describes the design process, including how the control law requirements were incorporated into constraints for the optimization of this specific software design tool. Predicted performance is also compared to results from flight.

Evaluation of 3D Gamma index calculation implemented in two commercial dosimetry systems

NASA Astrophysics Data System (ADS)

Xing, Aitang; Arumugam, Sankar; Deshpande, Shrikant; George, Armia; Vial, Philip; Holloway, Lois; Goozee, Gary

2015-01-01

3D Gamma index is one of the metrics which have been widely used for clinical routine patient specific quality assurance for IMRT, Tomotherapy and VMAT. The algorithms for calculating the 3D Gamma index using global and local methods implemented in two software tools: PTW- VeriSoft® as a part of OCTIVIUS 4D dosimeter systems and 3DVHTM from Sun Nuclear were assessed. The Gamma index calculated by the two systems was compared with manual calculated for one data set. The Gamma pass rate calculated by the two systems was compared using 3%/3mm, 2%/2mm, 3%/2mm and 2%/3mm for two additional data sets. The Gamma indexes calculated by the two systems were accurate, but Gamma pass rates calculated by the two software tools for same data set with the same dose threshold were different due to the different interpolation of raw dose data by the two systems and different implementation of Gamma index calculation and other modules in the two software tools. The mean difference was -1.3%±3.38 (1SD) with a maximum difference of 11.7%.

Quality Improvement With Discrete Event Simulation: A Primer for Radiologists.

PubMed

Booker, Michael T; O'Connell, Ryan J; Desai, Bhushan; Duddalwar, Vinay A

2016-04-01

The application of simulation software in health care has transformed quality and process improvement. Specifically, software based on discrete-event simulation (DES) has shown the ability to improve radiology workflows and systems. Nevertheless, despite the successful application of DES in the medical literature, the power and value of simulation remains underutilized. For this reason, the basics of DES modeling are introduced, with specific attention to medical imaging. In an effort to provide readers with the tools necessary to begin their own DES analyses, the practical steps of choosing a software package and building a basic radiology model are discussed. In addition, three radiology system examples are presented, with accompanying DES models that assist in analysis and decision making. Through these simulations, we provide readers with an understanding of the theory, requirements, and benefits of implementing DES in their own radiology practices. Copyright © 2016 American College of Radiology. All rights reserved.

The Electronic View Box: a software tool for radiation therapy treatment verification.

PubMed

Bosch, W R; Low, D A; Gerber, R L; Michalski, J M; Graham, M V; Perez, C A; Harms, W B; Purdy, J A

1995-01-01

We have developed a software tool for interactively verifying treatment plan implementation. The Electronic View Box (EVB) tool copies the paradigm of current practice but does so electronically. A portal image (online portal image or digitized port film) is displayed side by side with a prescription image (digitized simulator film or digitally reconstructed radiograph). The user can measure distances between features in prescription and portal images and "write" on the display, either to approve the image or to indicate required corrective actions. The EVB tool also provides several features not available in conventional verification practice using a light box. The EVB tool has been written in ANSI C using the X window system. The tool makes use of the Virtual Machine Platform and Foundation Library specifications of the NCI-sponsored Radiation Therapy Planning Tools Collaborative Working Group for portability into an arbitrary treatment planning system that conforms to these specifications. The present EVB tool is based on an earlier Verification Image Review tool, but with a substantial redesign of the user interface. A graphical user interface prototyping system was used in iteratively refining the tool layout to allow rapid modifications of the interface in response to user comments. Features of the EVB tool include 1) hierarchical selection of digital portal images based on physician name, patient name, and field identifier; 2) side-by-side presentation of prescription and portal images at equal magnification and orientation, and with independent grayscale controls; 3) "trace" facility for outlining anatomical structures; 4) "ruler" facility for measuring distances; 5) zoomed display of corresponding regions in both images; 6) image contrast enhancement; and 7) communication of portal image evaluation results (approval, block modification, repeat image acquisition, etc.). The EVB tool facilitates the rapid comparison of prescription and portal images and permits electronic communication of corrections in port shape and positioning.

Friendly Extensible Transfer Tool Beta Version

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

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

2016-04-15

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

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

Vulnerabilities in GSM technology and feasibility of selected attacks

NASA Astrophysics Data System (ADS)

Voznak, M.; Prokes, M.; Sevcik, L.; Frnda, J.; Toral-Cruz, Homer; Jakovlev, Sergej; Fazio, Peppino; Mehic, M.; Mikulec, M.

2015-05-01

Global System for Mobile communication (GSM) is the most widespread technology for mobile communications in the world and serving over 7 billion users. Since first publication of system documentation there has been notified a potential safety problem's occurrence. Selected types of attacks, based on the analysis of the technical feasibility and the degree of risk of these weaknesses, were implemented and demonstrated in laboratory of the VSB-Technical University of Ostrava, Czech Republic. These vulnerabilities were analyzed and afterwards possible attacks were described. These attacks were implemented using open-source tools, software programmable radio USRP (Universal Software RadioPeripheral) and DVB-T (Digital Video Broadcasting - Terrestrial) receiver. GSM security architecture is being scrutinized since first public releases of its specification mainly pointing out weaknesses in authentication and ciphering mechanisms. This contribution also summarizes practically proofed and used scenarios that are performed using opensource software tools and variety of scripts mostly written in Python. Main goal of this paper is in analyzing security issues in GSM network and practical demonstration of selected attacks.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

PubMed Central

2013-01-01

Background Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. Results We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Conclusion Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. PMID:23953065

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.

Averting Denver Airports on a Chip

NASA Technical Reports Server (NTRS)

Sullivan, Kevin J.

1995-01-01

As a result of recent advances in software engineering capabilities, we are now in a more stable environment. De-facto hardware and software standards are emerging. Work on software architecture and design patterns signals a consensus on the importance of early system-level design decisions, and agreements on the uses of certain paradigmatic software structures. We now routinely build systems that would have been risky or infeasible a few years ago. Unfortunately, technological developments threaten to destabilize software design again. Systems designed around novel computing and peripheral devices will spark ambitious new projects that will stress current software design and engineering capabilities. Micro-electro-mechanical systems (MEMS) and related technologies provide the physical basis for new systems with the potential to produce this kind of destabilizing effect. One important response to anticipated software engineering and design difficulties is carefully directed engineering-scientific research. Two specific problems meriting substantial research attention are: A lack of sufficient means to build software systems by generating, extending, specializing, and integrating large-scale reusable components; and a lack of adequate computational and analytic tools to extend and aid engineers in maintaining intellectual control over complex software designs.

Improving the Agency's Software Acquisition Capability

NASA Technical Reports Server (NTRS)

Hankinson, Allen

2003-01-01

External development of software has oftc n led to unsatisfactory results and great frustration for the assurE 7ce community. Contracts frequently omit critical assuranc 4 processes or the right to oversee software development activitie: At a time when NASA depends more and more on software to in plement critical system functions, combination of three factors ex; cerbate this problem: I ) the ever-increasing trend to acquire rather than develop software in-house, 2) the trend toward performance based contracts, and 3) acquisition vehicles that only state softwar 2 requirements while leaving development standards and assur! ince methodologies up to the contractor. We propose to identify specific methods at d tools that NASA projects can use to mitigate the adverse el ects of the three problems. TWO broad classes of methoddt ols will be explored. The first will be those that provide NASA p ojects with insight and oversight into contractors' activities. The st cond will be those that help projects objectively assess, and thus i nprwe, their software acquisition capability. Of particular interest is the Software Engineering Institute's (SEI) Software Acqt isition Capability Maturity Model (SA-CMMO).

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.

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

PubMed

Strohalm, Martin; Kavan, Daniel; Novák, Petr; Volný, Michael; Havlícek, Vladimír

2010-06-01

While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the available software tools are often instrument-dependent. Here we present a new generation of mMass, a cross-platform environment for the precise analysis of individual mass spectra. The software covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration. Functions presented in the earlier versions such as in silico digestion and fragmentation were redesigned and improved. In addition to Mascot, an interface for ProFound has been implemented. A specific tool is available for isotopic pattern modeling to enable precise data validation. The largest available lipid database (from the LIPID MAPS Consortium) has been incorporated and together with the new compound search tool lipids can be rapidly identified. In addition, the user can define custom libraries of compounds and use them analogously. The new version of mMass is based on a stand-alone Python library, which provides the basic functionality for data processing and interpretation. This library can serve as a good starting point for other developers in their projects. Binary distributions of mMass, its source code, a detailed user's guide, and video tutorials are freely available from www.mmass.org .

Open environments to support systems engineering tool integration: A study using the Portable Common Tool Environment (PCTE)

NASA Technical Reports Server (NTRS)

Eckhardt, Dave E., Jr.; Jipping, Michael J.; Wild, Chris J.; Zeil, Steven J.; Roberts, Cathy C.

1993-01-01

A study of computer engineering tool integration using the Portable Common Tool Environment (PCTE) Public Interface Standard is presented. Over a 10-week time frame, three existing software products were encapsulated to work in the Emeraude environment, an implementation of the PCTE version 1.5 standard. The software products used were a computer-aided software engineering (CASE) design tool, a software reuse tool, and a computer architecture design and analysis tool. The tool set was then demonstrated to work in a coordinated design process in the Emeraude environment. The project and the features of PCTE used are described, experience with the use of Emeraude environment over the project time frame is summarized, and several related areas for future research are summarized.

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.

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...

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching.

PubMed

Kalendar, Ruslan; Muterko, Alexandr; Shamekova, Malika; Zhambakin, Kabyl

2017-01-01

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html .

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.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

PubMed

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Test and Evaluation of WiMAX Performance Using Open-Source Modeling and Simulation Software Tools

DTIC Science & Technology

2010-12-01

specific needs. For instance, one may seek to maximize the system throughput while maximizing the number of trans- mitted data packets with hard...seeking to maximize the throughput of the system (Yu 2008; Pishdad and Rabiee 2008; Piro et al. 2010; Wongthavarawat and Ganz 2003; Mohammadi, Akl, and...testing environment provides tools to allow for setting up and running test environments over multiple systems (buildbot) and provides classes to

GiA Roots: software for the high throughput analysis of plant root system architecture.

PubMed

Galkovskyi, Taras; Mileyko, Yuriy; Bucksch, Alexander; Moore, Brad; Symonova, Olga; Price, Charles A; Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Zurek, Paul R; Fang, Suqin; Harer, John; Benfey, Philip N; Weitz, Joshua S

2012-07-26

Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.

USER'S GUIDE FOR GLOED VERSION 1.0 - THE GLOBAL EMISSIONS DATABASE

EPA Science Inventory

The document is a user's guide for the EPA-developed, powerful software package, Global Emissions Database (GloED). GloED is a user-friendly, menu-driven tool for storing and retrieving emissions factors and activity data on a country-specific basis. Data can be selected from dat...

Technical Advances and Fifth Grade Reading Comprehension: Do Students Benefit?

ERIC Educational Resources Information Center

Fountaine, Drew

This paper takes a look at some recent studies on utilization of technical tools, primarily personal computers and software, for improving fifth-grade students' reading comprehension. Specifically, the paper asks what benefits an educator can expect students to derive from closed-captioning and computer-assisted reading comprehension products. It…

Teaching Visual Texts with the Multimodal Analysis Software

ERIC Educational Resources Information Center

Lim Fei, Victor; O'Halloran, Kay L.; Tan, Sabine; E., Marissa K. L.

2015-01-01

This exploratory study introduces the systemic approach and the explicit teaching of a meta-language to provide conceptual tools for students for the analysis and interpretation of multimodal texts. Equipping students with a set of specialised vocabulary with conventionalised meanings associated with specific choices in multimodal texts empowers…

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.

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

Moving Virtual Research Environments from high maintenance Stovepipes to Multi-purpose Sustainable Service-oriented Science Platforms

NASA Astrophysics Data System (ADS)

Klump, Jens; Fraser, Ryan; Wyborn, Lesley; Friedrich, Carsten; Squire, Geoffrey; Barker, Michelle; Moloney, Glenn

2017-04-01

The researcher of today is likely to be part of a team distributed over multiple sites that will access data from an external repository and then process the data on a public or private cloud or even on a large centralised supercomputer. They are increasingly likely to use a mixture of their own code, third party software and libraries, or even access global community codes. These components will be connected into a Virtual Research Environments (VREs) that will enable members of the research team who are not co-located to actively work together at various scales to share data, models, tools, software, workflows, best practices, infrastructures, etc. Many VRE's are built in isolation: designed to meet a specific research program with components tightly coupled and not capable of being repurposed for other use cases - they are becoming 'stovepipes'. The limited number of users of some VREs also means that the cost of maintenance per researcher can be unacceptably high. The alternative is to develop service-oriented Science Platforms that enable multiple communities to develop specialised solutions for specific research programs. The platforms can offer access to data, software tools and processing infrastructures (cloud, supercomputers) through globally distributed, interconnected modules. In Australia, the Virtual Geophysics Laboratory (VGL) was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools, that is now rapidly evolving into a multi-purpose Earth science platform with access to an increased variety of data, a broader range of tools, users from more sectors and a diversity of computational infrastructures. The expansion has been relatively easy, because of the architecture whereby data, tools and compute resources are loosely coupled via interfaces that are built on international standards and accessed as services wherever possible. In recent years, investments in discoverability and accessibility of data via online services in Australia mean that data resources can be easily added to the virtual environments as and when required. Another key to increasing to reusability and uptake of the VRE is the capability to capturing workflows so that they can be reused and repurposed both within and beyond the community that that defined the original use case. Unfortunately, Software-as-a-Service in the research sector is not yet mature. In response, we developed a Scientific Software solutions Center (SSSC) that enables researchers to discover, deploy and then share computational codes, code snippets or processes both in a human and machine-readable manner. Growth has come not only from within the Earth science community but from the Australian Virtual Laboratory community which is building VREs for a diversity of communities such as astronomy, genomics, environment, humanities, climate etc. Components such as access control, provenance, visualisation, accounting etc. are common to all scientific domains and sharing of these across multiple domains reduces costs, but more importantly increases the ability to undertake interdisciplinary science. These efforts are transitioning VREs to more sustainable Service-oriented Science Platforms that can be delivered in an agile, adaptable manner for broader community interests.

Developing medical device software in compliance with regulations.

PubMed

Zema, M; Rosati, S; Gioia, V; Knaflitz, M; Balestra, G

2015-08-01

In the last decade, the use of information technology (IT) in healthcare has taken a growing role. In fact, the adoption of an increasing number of computer tools has led to several benefits related to the process of patient care and allowed easier access to social and health care resources. At the same time this trend gave rise to new challenges related to the implementation of these new technologies. Software used in healthcare can be classified as medical devices depending on the way they are used and on their functional characteristics. If they are classified as medical devices they must satisfy specific regulations. The aim of this work is to present a software development framework that can allow the production of safe and high quality medical device software and to highlight the correspondence between each software development phase and the appropriate standard and/or regulation.

Enhancement of computer system for applications software branch

NASA Technical Reports Server (NTRS)

Bykat, Alex

1987-01-01

Presented is a compilation of the history of a two-month project concerned with a survey, evaluation, and specification of a new computer system for the Applications Software Branch of the Software and Data Management Division of Information and Electronic Systems Laboratory of Marshall Space Flight Center, NASA. Information gathering consisted of discussions and surveys of branch activities, evaluation of computer manufacturer literature, and presentations by vendors. Information gathering was followed by evaluation of their systems. The criteria of the latter were: the (tentative) architecture selected for the new system, type of network architecture supported, software tools, and to some extent the price. The information received from the vendors, as well as additional research, lead to detailed design of a suitable system. This design included considerations of hardware and software environments as well as personnel issues such as training. Design of the system culminated in a recommendation for a new computing system for the Branch.

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.'

Development of a patient-specific surgical simulator for pediatric laparoscopic procedures.

PubMed

Saber, Nikoo R; Menon, Vinay; St-Pierre, Jean C; Looi, Thomas; Drake, James M; Cyril, Xavier

2014-01-01

The purpose of this study is to develop and evaluate a pediatric patient-specific surgical simulator for the planning, practice, and validation of laparoscopic surgical procedures prior to intervention, initially focusing on the choledochal cyst resection and reconstruction scenario. The simulator is comprised of software elements including a deformable body physics engine, virtual surgical tools, and abdominal organs. Hardware components such as haptics-enabled hand controllers and a representative endoscopic tool have also been integrated. The prototype is able to perform a number of surgical tasks and further development work is under way to simulate the complete procedure with acceptable fidelity and accuracy.

LArSoft: toolkit for simulation, reconstruction and analysis of liquid argon TPC neutrino detectors

NASA Astrophysics Data System (ADS)

Snider, E. L.; Petrillo, G.

2017-10-01

LArSoft is a set of detector-independent software tools for the simulation, reconstruction and analysis of data from liquid argon (LAr) neutrino experiments The common features of LAr time projection chambers (TPCs) enable sharing of algorithm code across detectors of very different size and configuration. LArSoft is currently used in production simulation and reconstruction by the ArgoNeuT, DUNE, LArlAT, MicroBooNE, and SBND experiments. The software suite offers a wide selection of algorithms and utilities, including those for associated photo-detectors and the handling of auxiliary detectors outside the TPCs. Available algorithms cover the full range of simulation and reconstruction, from raw waveforms to high-level reconstructed objects, event topologies and classification. The common code within LArSoft is contributed by adopting experiments, which also provide detector-specific geometry descriptions, and code for the treatment of electronic signals. LArSoft is also a collaboration of experiments, Fermilab and associated software projects which cooperate in setting requirements, priorities, and schedules. In this talk, we outline the general architecture of the software and the interaction with external libraries and detector-specific code. We also describe the dynamics of LArSoft software development between the contributing experiments, the projects supporting the software infrastructure LArSoft relies on, and the core LArSoft support project.

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

Clinical results of HIS, RIS, PACS integration using data integration CASE tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Chan, Hing-Ming; Breant, Claudine M.; Huang, Lu J.; Valentino, Daniel J.

1995-05-01

Current infrastructure research in PACS is dominated by the development of communication networks (local area networks, teleradiology, ATM networks, etc.), multimedia display workstations, and hierarchical image storage architectures. However, limited work has been performed on developing flexible, expansible, and intelligent information processing architectures for the vast decentralized image and text data repositories prevalent in healthcare environments. Patient information is often distributed among multiple data management systems. Current large-scale efforts to integrate medical information and knowledge sources have been costly with limited retrieval functionality. Software integration strategies to unify distributed data and knowledge sources is still lacking commercially. Systems heterogeneity (i.e., differences in hardware platforms, communication protocols, database management software, nomenclature, etc.) is at the heart of the problem and is unlikely to be standardized in the near future. In this paper, we demonstrate the use of newly available CASE (computer- aided software engineering) tools to rapidly integrate HIS, RIS, and PACS information systems. The advantages of these tools include fast development time (low-level code is generated from graphical specifications), and easy system maintenance (excellent documentation, easy to perform changes, and centralized code repository in an object-oriented database). The CASE tools are used to develop and manage the `middle-ware' in our client- mediator-serve architecture for systems integration. Our architecture is scalable and can accommodate heterogeneous database and communication protocols.

Internet teleconferencing as a clinical tool for anesthesiologists.

PubMed

Ruskin, K J; Palmer, T E; Hagenouw, R R; Lack, A; Dunnill, R

1998-04-01

Internet teleconferencing software can be used to hold "virtual" meetings, during which participants around the world can share ideas. A core group of anesthetic medical practitioners, largely consisting of the Society for Advanced Telecommunications in Anesthesia (SATA), has begun to hold regularly scheduled "virtual grand rounds." This paper examines currently available software and offers impressions of our own early experiences with this technology. Two teleconferencing systems have been used: White Pine Software CU-SeeMe and Microsoft NetMeeting. While both provided acceptable results, each had specific advantages and disadvantages. CU-SeeMe is easier to use when conferences include more than two participants. NetMeeting provides higher quality audio and video signals under crowded network conditions, and is better for conferences with only two participants. While some effort is necessary to get these teleconferencing systems to work well, we have been using desktop conferencing for six months to hold virtual Internet meetings. The sound and video images produced by Internet teleconferencing software are inferior to dedicated point-to-point teleconferencing systems. However, low cost, wide availability, and ease of use make this technology a potentially valuable tool for clinicians and researchers.

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.

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.

IDL Object Oriented Software for Hinode/XRT Image Analysis

NASA Astrophysics Data System (ADS)

Higgins, P. A.; Gallagher, P. T.

2008-09-01

We have developed a set of object oriented IDL routines that enable users to search, download and analyse images from the X-Ray Telescope (XRT) on-board Hinode. In this paper, we give specific examples of how the object can be used and how multi-instrument data analysis can be performed. The XRT object is a highly versatile and powerful IDL object, which will prove to be a useful tool for solar researchers. This software utilizes the generic Framework object available within the GEN branch of SolarSoft.

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.

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.

Revel8or: Model Driven Capacity Planning Tool Suite

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

Zhu, Liming; Liu, Yan; Bui, Ngoc B.

2007-05-31

Designing complex multi-tier applications that must meet strict performance requirements is a challenging software engineering problem. Ideally, the application architect could derive accurate performance predictions early in the project life-cycle, leveraging initial application design-level models and a description of the target software and hardware platforms. To this end, we have developed a capacity planning tool suite for component-based applications, called Revel8tor. The tool adheres to the model driven development paradigm and supports benchmarking and performance prediction for J2EE, .Net and Web services platforms. The suite is composed of three different tools: MDAPerf, MDABench and DSLBench. MDAPerf allows annotation of designmore » diagrams and derives performance analysis models. MDABench allows a customized benchmark application to be modeled in the UML 2.0 Testing Profile and automatically generates a deployable application, with measurement automatically conducted. DSLBench allows the same benchmark modeling and generation to be conducted using a simple performance engineering Domain Specific Language (DSL) in Microsoft Visual Studio. DSLBench integrates with Visual Studio and reuses its load testing infrastructure. Together, the tool suite can assist capacity planning across platforms in an automated fashion.« less

Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN.

PubMed

Jug, Gregor; Anderluh, Marko; Tomašič, Tihomir

2015-06-01

Five docking tools, namely AutoDock, FRED, CDOCKER, FlexX and GOLD, have been critically examined, with the aim of selecting those most appropriate for use as docking tools for docking molecules to the lectin dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN). This lectin has been selected for its rather non-druggable binding site, which enables complex interactions that guide the binding of the core monosaccharide. Since optimal orientation is crucial for forming coordination bonds, it was important to assess whether the selected docking tools could reproduce the optimal binding conformation for several oligosaccharides that are known to bind DC-SIGN. Our results show that even widely used docking programs have certain limitations when faced with a rather shallow and featureless binding site, as is the case of DC-SIGN. The FRED docking software (OpenEye Scientific Software, Inc.) was found to score as the best tool for docking ligands to DC-SIGN. The performance of FRED was further assessed on another lectin, Langerin. We have demonstrated that this validated docking protocol could be used for docking to other lectins similar to DC-SIGN.

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.

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.

Our path to better science in less time using open data science tools.

PubMed

Lowndes, Julia S Stewart; Best, Benjamin D; Scarborough, Courtney; Afflerbach, Jamie C; Frazier, Melanie R; O'Hara, Casey C; Jiang, Ning; Halpern, Benjamin S

2017-05-23

Reproducibility has long been a tenet of science but has been challenging to achieve-we learned this the hard way when our old approaches proved inadequate to efficiently reproduce our own work. Here we describe how several free software tools have fundamentally upgraded our approach to collaborative research, making our entire workflow more transparent and streamlined. By describing specific tools and how we incrementally began using them for the Ocean Health Index project, we hope to encourage others in the scientific community to do the same-so we can all produce better science in less time.

Publishing Platform for Scientific Software - Lessons Learned

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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…

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.

Some issues related to simulation of the tracking and communications computer network

NASA Technical Reports Server (NTRS)

Lacovara, Robert C.

1989-01-01

The Communications Performance and Integration branch of the Tracking and Communications Division has an ongoing involvement in the simulation of its flight hardware for Space Station Freedom. Specifically, the communication process between central processor(s) and orbital replaceable units (ORU's) is simulated with varying degrees of fidelity. The results of investigations into three aspects of this simulation effort are given. The most general area involves the use of computer assisted software engineering (CASE) tools for this particular simulation. The second area of interest is simulation methods for systems of mixed hardware and software. The final area investigated is the application of simulation methods to one of the proposed computer network protocols for space station, specifically IEEE 802.4.

Some issues related to simulation of the tracking and communications computer network

NASA Astrophysics Data System (ADS)

Lacovara, Robert C.

1989-12-01

The Communications Performance and Integration branch of the Tracking and Communications Division has an ongoing involvement in the simulation of its flight hardware for Space Station Freedom. Specifically, the communication process between central processor(s) and orbital replaceable units (ORU's) is simulated with varying degrees of fidelity. The results of investigations into three aspects of this simulation effort are given. The most general area involves the use of computer assisted software engineering (CASE) tools for this particular simulation. The second area of interest is simulation methods for systems of mixed hardware and software. The final area investigated is the application of simulation methods to one of the proposed computer network protocols for space station, specifically IEEE 802.4.

Activity Catalog Tool (ACT) user manual, version 2.0

NASA Technical Reports Server (NTRS)

Segal, Leon D.; Andre, Anthony D.

1994-01-01

This report comprises the user manual for version 2.0 of the Activity Catalog Tool (ACT) software program, developed by Leon D. Segal and Anthony D. Andre in cooperation with NASA Ames Aerospace Human Factors Research Division, FLR branch. ACT is a software tool for recording and analyzing sequences of activity over time that runs on the Macintosh platform. It was designed as an aid for professionals who are interested in observing and understanding human behavior in field settings, or from video or audio recordings of the same. Specifically, the program is aimed at two primary areas of interest: human-machine interactions and interactions between humans. The program provides a means by which an observer can record an observed sequence of events, logging such parameters as frequency and duration of particular events. The program goes further by providing the user with a quantified description of the observed sequence, through application of a basic set of statistical routines, and enables merging and appending of several files and more extensive analysis of the resultant data.

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.

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.

Development approach to an enterprise-wide medication reconciliation tool in a free-standing pediatric hospital with commercial best-of-breed systems.

PubMed

Yu, Feliciano B; Leising, Scott; Turner, Scott

2007-10-11

Medication reconciliation is essential to providing a safer patient environment during transitions of care in the clinical setting. Current solutions include a mixed-bag of paper and electronic processes. Best-of-breed health information systems architecture poses a specific challenge to organizations that have limited software development resources. Using readily available service-oriented technology, a prototype for an integrated medication reconciliation tool is developed for use in an academic pediatric hospital with commercial systems.

An integrated set of UNIX based system tools at control room level

NASA Astrophysics Data System (ADS)

Potepan, F.; Scafuri, C.; Bortolotto, C.; Surace, G.

1994-12-01

The design effort of providing a simple point-and-click approach to the equipment access has led to the definition and realization of a modular set of software tools to be used at the ELETTRA control room level. Point-to-point equipment access requires neither programming nor specific knowledge of the control system architecture. The development and integration of communication, graphic, editing and global database modules are described in depth, followed by a report of their use in the first commissioning period.

Current and future trends in marine image annotation software

NASA Astrophysics Data System (ADS)

Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

2016-12-01

Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images. Integration into available MIAS is currently limited to semi-automated processes of pixel recognition through computer-vision modules that compile expert-based knowledge. Important topics aiding the choice of a specific software are outlined, the ideal software is discussed and future trends are presented.

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.

JAva GUi for Applied Research (JAGUAR) v 3.0

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

JAGUAR is a Java software tool for automatically rendering a graphical user interface (GUI) from a structured input specification. It is designed as a plug-in to the Eclipse workbench to enable users to create, edit, and externally execute analysis application input decks and then view the results. JAGUAR serves as a GUI for Sandia's DAKOTA software toolkit for optimization and uncertainty quantification. It will include problem (input deck)set-up, option specification, analysis execution, and results visualization. Through the use of wizards, templates, and views, JAGUAR helps uses navigate the complexity of DAKOTA's complete input specification. JAGUAR is implemented in Java, leveragingmore » Eclipse extension points and Eclipse user interface. JAGUAR parses a DAKOTA NIDR input specification and presents the user with linked graphical and plain text representations of problem set-up and option specification for DAKOTA studies. After the data has been input by the user, JAGUAR generates one or more input files for DAKOTA, executes DAKOTA, and captures and interprets the results« less

Comparison of quality control software tools for diffusion tensor imaging.

PubMed

Liu, Bilan; Zhu, Tong; Zhong, Jianhui

2015-04-01

Image quality of diffusion tensor imaging (DTI) is critical for image interpretation, diagnostic accuracy and efficiency. However, DTI is susceptible to numerous detrimental artifacts that may impair the reliability and validity of the obtained data. Although many quality control (QC) software tools are being developed and are widely used and each has its different tradeoffs, there is still no general agreement on an image quality control routine for DTIs, and the practical impact of these tradeoffs is not well studied. An objective comparison that identifies the pros and cons of each of the QC tools will be helpful for the users to make the best choice among tools for specific DTI applications. This study aims to quantitatively compare the effectiveness of three popular QC tools including DTI studio (Johns Hopkins University), DTIprep (University of North Carolina at Chapel Hill, University of Iowa and University of Utah) and TORTOISE (National Institute of Health). Both synthetic and in vivo human brain data were used to quantify adverse effects of major DTI artifacts to tensor calculation as well as the effectiveness of different QC tools in identifying and correcting these artifacts. The technical basis of each tool was discussed, and the ways in which particular techniques affect the output of each of the tools were analyzed. The different functions and I/O formats that three QC tools provide for building a general DTI processing pipeline and integration with other popular image processing tools were also discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

Bim and Gis: when Parametric Modeling Meets Geospatial Data

NASA Astrophysics Data System (ADS)

Barazzetti, L.; Banfi, F.

2017-12-01

Geospatial data have a crucial role in several projects related to infrastructures and land management. GIS software are able to perform advanced geospatial analyses, but they lack several instruments and tools for parametric modelling typically available in BIM. At the same time, BIM software designed for buildings have limited tools to handle geospatial data. As things stand at the moment, BIM and GIS could appear as complementary solutions, notwithstanding research work is currently under development to ensure a better level of interoperability, especially at the scale of the building. On the other hand, the transition from the local (building) scale to the infrastructure (where geospatial data cannot be neglected) has already demonstrated that parametric modelling integrated with geoinformation is a powerful tool to simplify and speed up some phases of the design workflow. This paper reviews such mixed approaches with both simulated and real examples, demonstrating that integration is already a reality at specific scales, which are not dominated by "pure" GIS or BIM. The paper will also demonstrate that some traditional operations carried out with GIS software are also available in parametric modelling software for BIM, such as transformation between reference systems, DEM generation, feature extraction, and geospatial queries. A real case study is illustrated and discussed to show the advantage of a combined use of both technologies. BIM and GIS integration can generate greater usage of geospatial data in the AECOO (Architecture, Engineering, Construction, Owner and Operator) industry, as well as new solutions for parametric modelling with additional geoinformation.

Integrated software environment based on COMKAT for analyzing tracer pharmacokinetics with molecular imaging.

PubMed

Fang, Yu-Hua Dean; Asthana, Pravesh; Salinas, Cristian; Huang, Hsuan-Ming; Muzic, Raymond F

2010-01-01

An integrated software package, Compartment Model Kinetic Analysis Tool (COMKAT), is presented in this report. COMKAT is an open-source software package with many functions for incorporating pharmacokinetic analysis in molecular imaging research and has both command-line and graphical user interfaces. With COMKAT, users may load and display images, draw regions of interest, load input functions, select kinetic models from a predefined list, or create a novel model and perform parameter estimation, all without having to write any computer code. For image analysis, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communications in Medicine (DICOM) standard. Image contrast, zoom, reslicing, display color table, and frame summation can be adjusted in COMKAT image tool. It also displays and automatically registers images from 2 modalities. Parametric imaging capability is provided and can be combined with the distributed computing support to enhance computation speeds. For users without MATLAB licenses, a compiled, executable version of COMKAT is available, although it currently has only a subset of the full COMKAT capability. Both the compiled and the noncompiled versions of COMKAT are free for academic research use. Extensive documentation, examples, and COMKAT itself are available on its wiki-based Web site, http://comkat.case.edu. Users are encouraged to contribute, sharing their experience, examples, and extensions of COMKAT. With integrated functionality specifically designed for imaging and kinetic modeling analysis, COMKAT can be used as a software environment for molecular imaging and pharmacokinetic analysis.

Bridging the Particle Physics and Big Data Worlds

NASA Astrophysics Data System (ADS)

Pivarski, James

2017-09-01

For decades, particle physicists have developed custom software because the scale and complexity of our problems were unique. In recent years, however, the ``big data'' industry has begun to tackle similar problems, and has developed some novel solutions. Incorporating scientific Python libraries, Spark, TensorFlow, and machine learning tools into the physics software stack can improve abstraction, reliability, and in some cases performance. Perhaps more importantly, it can free physicists to concentrate on domain-specific problems. Building bridges isn't always easy, however. Physics software and open-source software from industry differ in many incidental ways and a few fundamental ways. I will show work from the DIANA-HEP project to streamline data flow from ROOT to Numpy and Spark, to incorporate ideas of functional programming into histogram aggregation, and to develop real-time, query-style manipulations of particle data.

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

The State of Software for Evolutionary Biology.

PubMed

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-05-01

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.

Global Precipitation Measurement (GPM) Safety Inhibit Timeline Tool

NASA Technical Reports Server (NTRS)

Dion, Shirley

2012-01-01

The Global Precipitation Measurement (GPM) Observatory is a joint mission under the partnership by National Aeronautics and Space Administration (NASA) and the Japan Aerospace Exploration Agency (JAXA), Japan. The NASA Goddard Space Flight Center (GSFC) has the lead management responsibility for NASA on GPM. The GPM program will measure precipitation on a global basis with sufficient quality, Earth coverage, and sampling to improve prediction of the Earth's climate, weather, and specific components of the global water cycle. As part of the development process, NASA built the spacecraft (built in-house at GSFC) and provided one instrument (GPM Microwave Imager (GMI) developed by Ball Aerospace) JAXA provided the launch vehicle (H2-A by MHI) and provided one instrument (Dual-Frequency Precipitation Radar (DPR) developed by NTSpace). Each instrument developer provided a safety assessment which was incorporated into the NASA GPM Safety Hazard Assessment. Inhibit design was reviewed for hazardous subsystems which included the High Gain Antenna System (HGAS) deployment, solar array deployment, transmitter turn on, propulsion system release, GMI deployment, and DPR radar turn on. The safety inhibits for these listed hazards are controlled by software. GPM developed a "pathfinder" approach for reviewing software that controls the electrical inhibits. This is one of the first GSFC in-house programs that extensively used software controls. The GPM safety team developed a methodology to document software safety as part of the standard hazard report. As part of this process a new tool "safety inhibit time line" was created for management of inhibits and their controls during spacecraft buildup and testing during 1& Tat GSFC and at the Range in Japan. In addition to understanding inhibits and controls during 1& T the tool allows the safety analyst to better communicate with others the changes in inhibit states with each phase of hardware and software testing. The tool was very useful for communicating compliance with safety requirements especially when working with a foreign partner.

Rapid Prototyping of Hydrologic Model Interfaces with IPython

NASA Astrophysics Data System (ADS)

Farthing, M. W.; Winters, K. D.; Ahmadia, A. J.; Hesser, T.; Howington, S. E.; Johnson, B. D.; Tate, J.; Kees, C. E.

2014-12-01

A significant gulf still exists between the state of practice and state of the art in hydrologic modeling. Part of this gulf is due to the lack of adequate pre- and post-processing tools for newly developed computational models. The development of user interfaces has traditionally lagged several years behind the development of a particular computational model or suite of models. As a result, models with mature interfaces often lack key advancements in model formulation, solution methods, and/or software design and technology. Part of the problem has been a focus on developing monolithic tools to provide comprehensive interfaces for the entire suite of model capabilities. Such efforts require expertise in software libraries and frameworks for creating user interfaces (e.g., Tcl/Tk, Qt, and MFC). These tools are complex and require significant investment in project resources (time and/or money) to use. Moreover, providing the required features for the entire range of possible applications and analyses creates a cumbersome interface. For a particular site or application, the modeling requirements may be simplified or at least narrowed, which can greatly reduce the number and complexity of options that need to be accessible to the user. However, monolithic tools usually are not adept at dynamically exposing specific workflows. Our approach is to deliver highly tailored interfaces to users. These interfaces may be site and/or process specific. As a result, we end up with many, customized interfaces rather than a single, general-use tool. For this approach to be successful, it must be efficient to create these tailored interfaces. We need technology for creating quality user interfaces that is accessible and has a low barrier for integration into model development efforts. Here, we present efforts to leverage IPython notebooks as tools for rapid prototyping of site and application-specific user interfaces. We provide specific examples from applications in near-shore environments as well as levee analysis. We discuss our design decisions and methodology for developing customized interfaces, strategies for delivery of the interfaces to users in various computing environments, as well as implications for the design/implementation of simulation models.

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.

Analytical Utility of Mass Spectral Binning in Proteomic Experiments by SPectral Immonium Ion Detection (SPIID)*

PubMed Central

Kelstrup, Christian D.; Frese, Christian; Heck, Albert J. R.; Olsen, Jesper V.; Nielsen, Michael L.

2014-01-01

Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids. PMID:24895383

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.

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...

Leveraging Existing Mission Tools in a Re-Usable, Component-Based Software Environment

NASA Technical Reports Server (NTRS)

Greene, Kevin; Grenander, Sven; Kurien, James; z,s (fshir. z[orttr); z,scer; O'Reilly, Taifun

2006-01-01

Emerging methods in component-based software development offer significant advantages but may seem incompatible with existing mission operations applications. In this paper we relate our positive experiences integrating existing mission applications into component-based tools we are delivering to three missions. In most operations environments, a number of software applications have been integrated together to form the mission operations software. In contrast, with component-based software development chunks of related functionality and data structures, referred to as components, can be individually delivered, integrated and re-used. With the advent of powerful tools for managing component-based development, complex software systems can potentially see significant benefits in ease of integration, testability and reusability from these techniques. These benefits motivate us to ask how component-based development techniques can be relevant in a mission operations environment, where there is significant investment in software tools that are not component-based and may not be written in languages for which component-based tools even exist. Trusted and complex software tools for sequencing, validation, navigation, and other vital functions cannot simply be re-written or abandoned in order to gain the advantages offered by emerging component-based software techniques. Thus some middle ground must be found. We have faced exactly this issue, and have found several solutions. Ensemble is an open platform for development, integration, and deployment of mission operations software that we are developing. Ensemble itself is an extension of an open source, component-based software development platform called Eclipse. Due to the advantages of component-based development, we have been able to vary rapidly develop mission operations tools for three surface missions by mixing and matching from a common set of mission operation components. We have also had to determine how to integrate existing mission applications for sequence development, sequence validation, and high level activity planning, and other functions into a component-based environment. For each of these, we used a somewhat different technique based upon the structure and usage of the existing application.

Examining the Anatomy of a Screencast: Uncovering Common Elements and Instructional Strategies

ERIC Educational Resources Information Center

Sugar, William; Brown, Abbie; Luterbach, Kenneth

2010-01-01

The researchers engaged in cooperative inquiry in order to explore screencasts as online instructional tools. In total, each researcher analyzed 37 screencasts, which provided over two hours of instruction. The content area of these screencasts concentrated on teaching specific computing procedures (e.g., how to install web server software or how…

Adult Students' Perceptions of Automated Writing Assessment Software: Does It Foster Engagement?

ERIC Educational Resources Information Center

LaGuerre, Joselle L.

2013-01-01

Generally, this descriptive study endeavored to include the voice of adult learners to the scholarly body of research regarding automated writing assessment tools (AWATs). Specifically, the study sought to determine the extent to which students perceive that the AWAT named Criterion fosters learning and if students' opinions differ depending on…

Mutually Beneficial Foreign Language Learning: Creating Meaningful Interactions through Video-Synchronous Computer-Mediated Communication

ERIC Educational Resources Information Center

Kato, Fumie; Spring, Ryan; Mori, Chikako

2016-01-01

Providing learners of a foreign language with meaningful opportunities for interactions, specifically with native speakers, is especially challenging for instructors. One way to overcome this obstacle is through video-synchronous computer-mediated communication tools such as Skype software. This study reports quantitative and qualitative data from…

Library Signage: Applications for the Apple Macintosh and MacPaint.

ERIC Educational Resources Information Center

Diskin, Jill A.; FitzGerald, Patricia

1984-01-01

Describes specific applications of the Macintosh computer at Carnegie-Mellon University Libraries, where MacPaint was used as a flexible, easy to use, and powerful tool to produce informational, instructional, and promotional signage. Profiles of system hardware and software, an evaluation of the computer program MacPaint, and MacPaint signage…

Use of Data Visualisation in the Teaching of Statistics: A New Zealand Perspective

ERIC Educational Resources Information Center

Forbes, Sharleen; Chapman, Jeanette; Harraway, John; Stirling, Doug; Wild, Chris

2014-01-01

For many years, students have been taught to visualise data by drawing graphs. Recently, there has been a growing trend to teach statistics, particularly statistical concepts, using interactive and dynamic visualisation tools. Free down-loadable teaching and simulation software designed specifically for schools, and more general data visualisation…

Ada Adoption Handbook: A Program Manager’s Guide, Version 2.0

DTIC Science & Technology

1992-10-01

specifically Ada oriented: "* Compilation order tool: A capability that, when given a set of Ada units, determines the com- pilation order. "* Automatic...July 1992. 146. Knapper. R. J., Linn, C. J.. & Salasin, J. Guidelines for Tailoring DOD-S TD-2167A for SOS Software Development. IDA Paper P- 2018

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models.

PubMed

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)

PubMed Central

2013-01-01

Background The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. Results We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Conclusions Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools. PMID:24209455

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

PubMed

Sturgill, David; Malone, John H; Sun, Xia; Smith, Harold E; Rabinow, Leonard; Samson, Marie-Laure; Oliver, Brian

2013-11-09

The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splice-junction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools.

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models

PubMed Central

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A.

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients. PMID:25374542

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.

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

Teaching and assessment of mathematical principles for software correctness using a reasoning concept inventory

NASA Astrophysics Data System (ADS)

Drachova-Strang, Svetlana V.

As computing becomes ubiquitous, software correctness has a fundamental role in ensuring the safety and security of the systems we build. To design and develop software correctly according to their formal contracts, CS students, the future software practitioners, need to learn a critical set of skills that are necessary and sufficient for reasoning about software correctness. This dissertation presents a systematic approach to both introducing these reasoning skills into the curriculum, and assessing how well the students have learned them. Specifically, it introduces a comprehensive Reasoning Concept Inventory (RCI) that captures the fine details of basic reasoning skills that are ideally learned across the undergraduate curriculum to reason about software correctness, to develop high quality software, and to understand why software works as specified. The RCI forms the basis for developing learning outcomes that help educators to assess the adequacy of current techniques and pinpoint necessary improvements. This dissertation contains results from experimentation and assessment over the past few years in multiple CS courses. The results show that the finer principles of mathematical reasoning of software correctness can be taught effectively and continuously improved with the help of the RCI using suitable teaching practices, and supporting methods and tools.

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.

Diagnosis and Prognosis of Weapon Systems

NASA Technical Reports Server (NTRS)

Nolan, Mary; Catania, Rebecca; deMare, Gregory

2005-01-01

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

Software Certification - Coding, Code, and Coders

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Holzmann, Gerard J.

2011-01-01

We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

The Advanced Human Eye Model (AHEM): a personal binocular eye modeling system inclusive of refraction, diffraction, and scatter.

PubMed

Donnelly, William

2008-11-01

To present a commercially available software tool for creating eye models to assist the development of ophthalmic optics and instrumentation, simulate ailments or surgery-induced changes, explore vision research questions, and provide assistance to clinicians in planning treatment or analyzing clinical outcomes. A commercially available eye modeling system was developed, the Advanced Human Eye Model (AHEM). Two mainstream optical software engines, ZEMAX (ZEMAX Development Corp) and ASAP (Breault Research Organization), were used to construct a similar software eye model and compared. The method of using the AHEM is described and various eye modeling scenarios are created. These scenarios consist of retinal imaging of targets and sources; optimization capability; spectacles, contact lens, and intraocular lens insertion and correction; Zernike surface deformation on the cornea; cataract simulation and scattering; a gradient index lens; a binocular mode; a retinal implant; system import/export; and ray path exploration. Similarity of the two different optical software engines showed validity to the mechanism of the AHEM. Metrics and graphical data are generated from the various modeling scenarios particular to their input specifications. The AHEM is a user-friendly commercially available software tool from Breault Research Organization, which can assist the design of ophthalmic optics and instrumentation, simulate ailments or refractive surgery-induced changes, answer vision research questions, or assist clinicians in planning treatment or analyzing clinical outcomes.

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

Detilleux, Michel; Centner, Baudouin

The paper describes different methodologies and tools developed in-house by Tractebel Engineering to facilitate the engineering works to be carried out especially in the frame of decommissioning projects. Three examples of tools with their corresponding results are presented: - The LLWAA-DECOM code, a software developed for the radiological characterization of contaminated systems and equipment. The code constitutes a specific module of more general software that was originally developed to characterize radioactive waste streams in order to be able to declare the radiological inventory of critical nuclides, in particular difficult-to-measure radionuclides, to the Authorities. In the case of LLWAA-DECOM, deposited activitiesmore » inside contaminated equipment (piping, tanks, heat exchangers...) and scaling factors between nuclides, at any given time of the decommissioning time schedule, are calculated on the basis of physical characteristics of the systems and of operational parameters of the nuclear power plant. This methodology was applied to assess decommissioning costs of Belgian NPPs, to characterize the primary system of Trino NPP in Italy, to characterize the equipment of miscellaneous circuits of Ignalina NPP and of Kozloduy unit 1 and, to calculate remaining dose rates around equipment in the frame of the preparation of decommissioning activities; - The VISIMODELLER tool, a user friendly CAD interface developed to ease the introduction of lay-out areas in a software named VISIPLAN. VISIPLAN is a 3D dose rate assessment tool for ALARA work planning, developed by the Belgian Nuclear Research Centre SCK.CEN. Both softwares were used for projects such as the steam generators replacements in Belgian NPPs or the preparation of the decommissioning of units 1 and 2 of Kozloduy NPP; - The DBS software, a software developed to manage the different kinds of activities that are part of the general time schedule of a decommissioning project. For each activity, when relevant, algorithms allow to estimate, on the basis of local inputs, radiological exposures of the operators (collective and individual doses), production of primary, secondary and tertiary waste and their characterization, production of conditioned waste, release of effluents,... and enable the calculation and the presentation (histograms) of the global results for all activities together. An example of application in the frame of the Ignalina decommissioning project is given. (authors)« 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.

A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

PubMed

Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

2018-02-01

Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

BAM/DASS: Data Analysis Software for Sub-Microarcsecond Astrometry Device

NASA Astrophysics Data System (ADS)

Gardiol, D.; Bonino, D.; Lattanzi, M. G.; Riva, A.; Russo, F.

2010-12-01

The INAF - Osservatorio Astronomico di Torino is part of the Data Processing and Analysis Consortium (DPAC) for Gaia, a cornerstone mission of the European Space Agency. Gaia will perform global astrometry by means of two telescopes looking at the sky along two different lines of sight oriented at a fixed angle, also called basic angle. Knowledge of the basic angle fluctuations at the sub-microarcsecond level over periods of the order of the minute is crucial to reach the mission goals. A specific device, the Basic Angle Monitoring, will be dedicated to this purpose. We present here the software system we are developing to analyze the BAM data and recover the basic angle variations. This tool is integrated into the whole DPAC data analysis software.

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

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

Valassi, A.; /CERN; Clemencic, M.

2012-04-19

The Persistency Framework consists of three software packages (CORAL, COOL and POOL) addressing the data access requirements of the LHC experiments in different areas. It is the result of the collaboration between the CERN IT Department and the three experiments (ATLAS, CMS and LHCb) that use this software to access their data. POOL is a hybrid technology store for C++ objects, metadata catalogs and collections. CORAL is a relational database abstraction layer with an SQL-free API. COOL provides specific software tools and components for the handling of conditions data. This paper reports on the status and outlook of the projectmore » and reviews in detail the usage of each package in the three experiments.« less

Engineering specification and system design for CAD/CAM of custom shoes: UMC project effort

NASA Technical Reports Server (NTRS)

Bao, Han P.

1991-01-01

The goal of this project is to supplement the footwear design system of North Carolina State University (NCSU) with a software module to design and manufacture a combination sole. The four areas of concentration were: customization of NASCAD (NASA Computer Aided Design) to the footwear project; use of CENCIT data; computer aided manufacturing activities; and beginning work for the bottom elements of shoes. The task of generating a software module for producing a sole was completed with a demonstrated product realization. The software written in C was delivered to NCSU for inclusion in their design system for custom footwear known as LASTMOD. The machining process of the shoe last was improved using a spiral tool path approach.

Cluster tool solution for fabrication and qualification of advanced photomasks

NASA Astrophysics Data System (ADS)

Schaetz, Thomas; Hartmann, Hans; Peter, Kai; Lalanne, Frederic P.; Maurin, Olivier; Baracchi, Emanuele; Miramond, Corinne; Brueck, Hans-Juergen; Scheuring, Gerd; Engel, Thomas; Eran, Yair; Sommer, Karl

2000-07-01

The reduction of wavelength in optical lithography, phase shift technology and optical proximity correction (OPC), requires a rapid increase in cost effective qualification of photomasks. The knowledge about CD variation, loss of pattern fidelity especially for OPC pattern and mask defects concerning the impact on wafer level is becoming a key issue for mask quality assessment. As part of the European Community supported ESPRIT projection 'Q-CAP', a new cluster concept has been developed, which allows the combination of hardware tools as well as software tools via network communication. It is designed to be open for any tool manufacturer and mask hose. The bi-directional network access allows the exchange of all relevant mask data including grayscale images, measurement results, lithography parameters, defect coordinates, layout data, process data etc. and its storage to a SQL database. The system uses SEMI format descriptions as well as standard network hardware and software components for the client server communication. Each tool is used mainly to perform its specific application without using expensive time to perform optional analysis, but the availability of the database allows each component to share the full data ste gathered by all components. Therefore, the cluster can be considered as one single virtual tool. The paper shows the advantage of the cluster approach, the benefits of the tools linked together already, and a vision of a mask house in the near future.

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.

Man-machine Integration Design and Analysis System (MIDAS) Task Loading Model (TLM) experimental and software detailed design report

NASA Technical Reports Server (NTRS)

Staveland, Lowell

1994-01-01

This is the experimental and software detailed design report for the prototype task loading model (TLM) developed as part of the man-machine integration design and analysis system (MIDAS), as implemented and tested in phase 6 of the Army-NASA Aircrew/Aircraft Integration (A3I) Program. The A3I program is an exploratory development effort to advance the capabilities and use of computational representations of human performance and behavior in the design, synthesis, and analysis of manned systems. The MIDAS TLM computationally models the demands designs impose on operators to aide engineers in the conceptual design of aircraft crewstations. This report describes TLM and the results of a series of experiments which were run this phase to test its capabilities as a predictive task demand modeling tool. Specifically, it includes discussions of: the inputs and outputs of TLM, the theories underlying it, the results of the test experiments, the use of the TLM as both stand alone tool and part of a complete human operator simulation, and a brief introduction to the TLM software design.

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

Sattison, M.B.; Schroeder, J.A.; Russell, K.D.

The Idaho National Engineering Laboratory (INEL) over the past year has created 75 plant-specific Accident Sequence Precursor (ASP) models using the SAPHIRE suite of PRA codes. Along with the new models, the INEL has also developed a new module for SAPHIRE which is tailored specifically to the unique needs of ASP evaluations. These models and software will be the next generation of risk tools for the evaluation of accident precursors by both NRR and AEOD. This paper presents an overview of the models and software. Key characteristics include: (1) classification of the plant models according to plant response with amore » unique set of event trees for each plant class, (2) plant-specific fault trees using supercomponents, (3) generation and retention of all system and sequence cutsets, (4) full flexibility in modifying logic, regenerating cutsets, and requantifying results, and (5) user interface for streamlined evaluation of ASP events.« less

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

Sattison, M.B.; Schroeder, J.A.; Russell, K.D.

The Idaho National Engineering Laboratory (INEL) over the past year has created 75 plant-specific Accident Sequence Precursor (ASP) models using the SAPHIRE suite of PRA codes. Along with the new models, the INEL has also developed a new module for SAPHIRE which is tailored specifically to the unique needs of conditional core damage probability (CCDP) evaluations. These models and software will be the next generation of risk tools for the evaluation of accident precursors by both NRR and AEOD. This paper presents an overview of the models and software. Key characteristics include: (1) classification of the plant models according tomore » plant response with a unique set of event trees for each plant class, (2) plant-specific fault trees using supercomponents, (3) generation and retention of all system and sequence cutsets, (4) full flexibility in modifying logic, regenerating cutsets, and requantifying results, and (5) user interface for streamlined evaluation of ASP events.« less

PT-SAFE: a software tool for development and annunciation of medical audible alarms.

PubMed

Bennett, Christopher L; McNeer, Richard R

2012-03-01

Recent reports by The Joint Commission as well as the Anesthesia Patient Safety Foundation have indicated that medical audible alarm effectiveness needs to be improved. Several recent studies have explored various approaches to improving the audible alarms, motivating the authors to develop real-time software capable of comparing such alarms. We sought to devise software that would allow for the development of a variety of audible alarm designs that could also integrate into existing operating room equipment configurations. The software is meant to be used as a tool for alarm researchers to quickly evaluate novel alarm designs. A software tool was developed for the purpose of creating and annunciating audible alarms. The alarms consisted of annunciators that were mapped to vital sign data received from a patient monitor. An object-oriented approach to software design was used to create a tool that is flexible and modular at run-time, can annunciate wave-files from disk, and can be programmed with MATLAB by the user to create custom alarm algorithms. The software was tested in a simulated operating room to measure technical performance and to validate the time-to-annunciation against existing equipment alarms. The software tool showed efficacy in a simulated operating room environment by providing alarm annunciation in response to physiologic and ventilator signals generated by a human patient simulator, on average 6.2 seconds faster than existing equipment alarms. Performance analysis showed that the software was capable of supporting up to 15 audible alarms on a mid-grade laptop computer before audio dropouts occurred. These results suggest that this software tool provides a foundation for rapidly staging multiple audible alarm sets from the laboratory to a simulation environment for the purpose of evaluating novel alarm designs, thus producing valuable findings for medical audible alarm standardization.

World Workshop on Oral Medicine VI: Utilization of Oral Medicine-specific software for support of clinical care, research, and education: current status and strategy for broader implementation.

PubMed

Brailo, Vlaho; Firriolo, Francis John; Tanaka, Takako Imai; Varoni, Elena; Sykes, Rosemary; McCullough, Michael; Hua, Hong; Sklavounou, Alexandra; Jensen, Siri Beier; Lockhart, Peter B; Mattsson, Ulf; Jontell, Mats

2015-08-01

To assess the current scope and status of Oral Medicine-specific software (OMSS) utilized to support clinical care, research, and education in Oral Medicine and to propose a strategy for broader implementation of OMSS within the global Oral Medicine community. An invitation letter explaining the objectives was sent to the global Oral Medicine community. Respondents were interviewed to obtain information about different aspects of OMSS functionality. Ten OMSS tools were identified. Four were being used for clinical care, one was being used for research, two were being used for education, and three were multipurpose. Clinical software was being utilized as databases developed to integrate of different type of clinical information. Research software was designed to facilitate multicenter research. Educational software represented interactive, case-orientated technology designed for clinical training in Oral Medicine. Easy access to patient data was the most commonly reported advantage. Difficulty of use and poor integration with other software was the most commonly reported disadvantage. The OMSS presented in this paper demonstrate how information technology (IT) can have an impact on the quality of patient care, research, and education in the field of Oral Medicine. A strategy for broader implementation of OMSS is proposed. Copyright © 2015 Elsevier Inc. All rights reserved.

Development of a Software Tool to Automate ADCO Flight Controller Console Planning Tasks

NASA Technical Reports Server (NTRS)

Anderson, Mark G.

2011-01-01

This independent study project covers the development of the International Space Station (ISS) Attitude Determination and Control Officer (ADCO) Planning Exchange APEX Tool. The primary goal of the tool is to streamline existing manual and time-intensive planning tools into a more automated, user-friendly application that interfaces with existing products and allows the ADCO to produce accurate products and timelines more effectively. This paper will survey the current ISS attitude planning process and its associated requirements, goals, documentation and software tools and how a software tool could simplify and automate many of the planning actions which occur at the ADCO console. The project will be covered from inception through the initial prototype delivery in November 2011 and will include development of design requirements and software as well as design verification and testing.

The State of Software for Evolutionary Biology

PubMed Central

Darriba, Diego; Flouri, Tomáš; Stamatakis, Alexandros

2018-01-01

Abstract With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C++ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development. PMID:29385525

The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale

PubMed Central

2011-01-01

Background Computational models play an increasingly important role in the assessment and control of public health crises, as demonstrated during the 2009 H1N1 influenza pandemic. Much research has been done in recent years in the development of sophisticated data-driven models for realistic computer-based simulations of infectious disease spreading. However, only a few computational tools are presently available for assessing scenarios, predicting epidemic evolutions, and managing health emergencies that can benefit a broad audience of users including policy makers and health institutions. Results We present "GLEaMviz", a publicly available software system that simulates the spread of emerging human-to-human infectious diseases across the world. The GLEaMviz tool comprises three components: the client application, the proxy middleware, and the simulation engine. The latter two components constitute the GLEaMviz server. The simulation engine leverages on the Global Epidemic and Mobility (GLEaM) framework, a stochastic computational scheme that integrates worldwide high-resolution demographic and mobility data to simulate disease spread on the global scale. The GLEaMviz design aims at maximizing flexibility in defining the disease compartmental model and configuring the simulation scenario; it allows the user to set a variety of parameters including: compartment-specific features, transition values, and environmental effects. The output is a dynamic map and a corresponding set of charts that quantitatively describe the geo-temporal evolution of the disease. The software is designed as a client-server system. The multi-platform client, which can be installed on the user's local machine, is used to set up simulations that will be executed on the server, thus avoiding specific requirements for large computational capabilities on the user side. Conclusions The user-friendly graphical interface of the GLEaMviz tool, along with its high level of detail and the realism of its embedded modeling approach, opens up the platform to simulate realistic epidemic scenarios. These features make the GLEaMviz computational tool a convenient teaching/training tool as well as a first step toward the development of a computational tool aimed at facilitating the use and exploitation of computational models for the policy making and scenario analysis of infectious disease outbreaks. PMID:21288355

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

NASA Technical Reports Server (NTRS)

Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

2004-01-01

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

NASA Astrophysics Data System (ADS)

Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

2004-09-01

This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

CosmoQuest: A Glance at Citizen Science Building

NASA Astrophysics Data System (ADS)

Richardson, Matthew; Grier, Jennifer; Gay, Pamela; Lehan, Cory; Buxner, Sanlyn; CosmoQuest Team

2018-01-01

CosmoQuest is a virtual research facility focused on engaging people - citizen scientists - from across the world in authentic research projects designed to enhance our knowledge of the cosmos around us. Using image data acquired by NASA missions, our citizen scientists are first trained to identify specific features within the data and then requested to identify those features across large datasets. Responses submitted by the citizen scientists are then stored in our database where they await for analysis and eventual publication by CosmoQuest staff and collaborating professional research scientists.While it is clear that the driving power behind our projects are the eyes and minds of our citizen scientists, it is CosmoQuest’s custom software, Citizen Science Builder (CSB), that enables citizen science to be accomplished. On the front end, CosmoQuest’s CSB software allows for the creation of web-interfaces that users can access to perform image annotation through both drawing tools and questions that can accompany images. These tools include: using geometric shapes to identify regions within an image, tracing image attributes using freeform line tools, and flagging features within images. Additionally, checkboxes, dropdowns, and free response boxes may be used to collect information. On the back end, this software is responsible for the proper storage of all data, which allows project staff to perform periodic data quality checks and track the progress of each project. In this poster we present these available tools and resources and seek potential collaborations.

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.

HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software.

PubMed

Sauter, Jürgen; Schäfer, Christian; Schmidt, Alexander H

2018-01-01

HLA haplotype frequencies are of use in a variety of settings. Such data is typically derived either from family pedigree data by targeted typing or statistical analysis of large population-specific genotype samples. As established tools for the latter approach lacked ability to treat the amount, ambiguity, and inhomogeneity found in genotype data in hematopoietic stem cell donor registries, we developed Hapl-o-Mat to alleviate these specific shortcomings.

Using open source software for the supervision and management of the water resources system of Athens

NASA Astrophysics Data System (ADS)

Kozanis, S.; Christofides, A.; Efstratiadis, A.; Koukouvinos, A.; Karavokiros, G.; Mamassis, N.; Koutsoyiannis, D.; Nikolopoulos, D.

2012-04-01

The water supply of Athens, Greece, is implemented through a complex water resource system, extending over an area of around 4 000 km2 and including surface water and groundwater resources. It incorporates four reservoirs, 350 km of main aqueducts, 15 pumping stations, more than 100 boreholes and 5 small hydropower plants. The system is run by the Athens Water Supply and Sewerage Company (EYDAP) Over more than 10 years we have developed, information technology tools such as GIS, database and decision support systems, to assist the management of the system. Among the software components, "Enhydris", a web application for the visualization and management of geographical and hydrometeorological data, and "Hydrognomon", a data analysis and processing tool, are now free software. Enhydris is entirely based on free software technologies such as Python, Django, PostgreSQL, and JQuery. We also created http://openmeteo.org/, a web site hosting our free software products as well as a free database system devoted to the dissemination of free data. In particular, "Enhydris" is used for the management of the hydrometeorological stations and the major hydraulic structures (aqueducts, reservoirs, boreholes, etc.), as well as for the retrieval of time series, online graphs etc. For the specific needs of EYDAP, additional GIS functionality was introduced for the display and monitoring of the water supply network. This functionality is also implemented as free software and can be reused in similar projects. Except for "Hydrognomon" and "Enhydris", we have developed a number of advanced modeling applications, which are also generic-purpose tools that have been used for a long time to provide decision support for the water resource system of Athens. These are "Hydronomeas", which optimizes the operation of complex water resource systems, based on a stochastic simulation framework, "Castalia", which implements the generation of synthetic time series, and "Hydrogeios", which employs conjunctive hydrological and hydrogeological simulation, with emphasis to human-modified river basins. These tools are currently available as executable files that are free for download though the ITIA web site (http://itia.ntua.gr/). Currently, we are working towards releasing their source code as well, through making them free software, after some licensing issues are resolved.

Virtual facebow technique.

PubMed

Solaberrieta, Eneko; Garmendia, Asier; Minguez, Rikardo; Brizuela, Aritza; Pradies, Guillermo

2015-12-01

This article describes a virtual technique for transferring the location of a digitized cast from the patient to a virtual articulator (virtual facebow transfer). Using a virtual procedure, the maxillary digital cast is transferred to a virtual articulator by means of reverse engineering devices. The following devices necessary to carry out this protocol are available in many contemporary practices: an intraoral scanner, a digital camera, and specific software. Results prove the viability of integrating different tools and software and of completely integrating this procedure into a dental digital workflow. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Enhancing participatory approach in water resources management: development of a survey to evaluate stakeholders needs and priorities related to software capabilities

NASA Astrophysics Data System (ADS)

Foglia, L.; Rossetto, R.; Borsi, I.; Josef, S.; Boukalova, Z.; Triana, F.; Ghetta, M.; Sabbatini, T.; Bonari, E.; Cannata, M.; De Filippis, G.

2016-12-01

The EU H2020 FREEWAT project (FREE and open source software tools for WATer resource management) aims at simplifying the application of EU-water related Directives, by developing an open source and public domain, GIS-integrated platform for planning and management of ground- and surface-water resources. The FREEWAT platform is conceived as a canvas, where several distributed and physically-based simulation codes are virtually integrated. The choice of such codes was supported by the result of a survey performed by means of questionnaires distributed to 14 case study FREEWAT project partners and several stakeholders. This was performed in the first phase of the project within the WP 6 (Enhanced science and participatory approach evidence-based decision making), Task 6.1 (Definition of a "needs/tools" evaluation grid). About 30% among all the invited entities and institutions from several EU and non-EU Countries expressed their interest in contributing to the survey. Most of them were research institutions, government and geoenvironmental companies and river basin authorities.The result of the questionnaire provided a spectrum of needs and priorities of partners/stakeholders, which were addressed during the development phase of the FREEWAT platform. The main needs identified were related to ground- and surface-water quality, sustainable water management, interaction between groundwater/surface-water bodies, and design and management of Managed Aquifer Recharge schemes. Needs and priorities were then connected to the specific EU Directives and Regulations to be addressed.One of the main goals of the questionnaires was to collect information and suggestions regarding the use of existing commercial/open-source software tools to address needs and priorities, and regarding the needs to address specific water-related processes/problems.

Avionics System Architecture Tool

NASA Technical Reports Server (NTRS)

Chau, Savio; Hall, Ronald; Traylor, marcus; Whitfield, Adrian

2005-01-01

Avionics System Architecture Tool (ASAT) is a computer program intended for use during the avionics-system-architecture- design phase of the process of designing a spacecraft for a specific mission. ASAT enables simulation of the dynamics of the command-and-data-handling functions of the spacecraft avionics in the scenarios in which the spacecraft is expected to operate. ASAT is built upon I-Logix Statemate MAGNUM, providing a complement of dynamic system modeling tools, including a graphical user interface (GUI), modeling checking capabilities, and a simulation engine. ASAT augments this with a library of predefined avionics components and additional software to support building and analyzing avionics hardware architectures using these components.

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.

The Value of Open Source Software Tools in Qualitative Research

ERIC Educational Resources Information Center

Greenberg, Gary

2011-01-01

In an era of global networks, researchers using qualitative methods must consider the impact of any software they use on the sharing of data and findings. In this essay, I identify researchers' main areas of concern regarding the use of qualitative software packages for research. I then examine how open source software tools, wherein the publisher…

Rapid Development of Custom Software Architecture Design Environments

DTIC Science & Technology

1999-08-01

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

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

A self-referential HOWTO on release engineering

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

Galassi, Mark C.

Release engineering is a fundamental part of the software development cycle: it is the point at which quality control is exercised and bug fixes are integrated. The way in which software is released also gives the end user her first experience of a software package, while in scientific computing release engineering can guarantee reproducibility. For these reasons and others, the release process is a good indicator of the maturity and organization of a development team. Software teams often do not put in place a release process at the beginning. This is unfortunate because the team does not have early andmore » continuous execution of test suites, and it does not exercise the software in the same conditions as the end users. I describe an approach to release engineering based on the software tools developed and used by the GNU project, together with several specific proposals related to packaging and distribution. I do this in a step-by-step manner, demonstrating how this very paper is written and built using proper release engineering methods. Because many aspects of release engineering are not exercised in the building of the paper, the accompanying software repository also contains examples of software libraries.« less

Identifying Dyscalculia Symptoms Related to Magnocellular Reasoning Using Smartphones.

PubMed

Knudsen, Greger Siem; Babic, Ankica

2016-01-01

This paper presents a study that has developed a mobile software application for assisting diagnosis of learning disabilities in mathematics, called dyscalculia, and measuring correlations between dyscalculia symptoms and magnocellular reasoning. Usually, software aids for dyscalculic individuals are focused on both assisting diagnosis and teaching the material. The software developed in this study however maintains a specific focus on the former, and in the process attempts to capture alleged correlations between dyscalculia symptoms and possible underlying causes of the condition. Classification of symptoms is performed by k-Nearest Neighbor algorithm classifying five parameters evaluating user's skills, returning calculated performance in each category as well as correlation strength between detected symptoms and magnocellular reasoning abilities. Expert evaluations has found the application to be appropriate and productive for its intended purpose, proving that mobile software is a suitable and valuable tool for assisting dyscalculia diagnosis and identifying root causes of developing the condition.

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.

Supporting Development of Satellite's Guidance Navigation and Control Software: A Product Line Approach

NASA Technical Reports Server (NTRS)

McComas, David; Stark, Michael; Leake, Stephen; White, Michael; Morisio, Maurizio; Travassos, Guilherme H.; Powers, Edward I. (Technical Monitor)

2000-01-01

The NASA Goddard Space Flight Center Flight Software Branch (FSB) is developing a Guidance, Navigation, and Control (GNC) Flight Software (FSW) product line. The demand for increasingly more complex flight software in less time while maintaining the same level of quality has motivated us to look for better FSW development strategies. The GNC FSW product line has been planned to address the core GNC FSW functionality very similar on many recent low/near Earth missions in the last ten years. Unfortunately these missions have not accomplished significant drops in development cost since a systematic approach towards reuse has not been adopted. In addition, new demands are continually being placed upon the FSW which means the FSB must become more adept at providing GNC FSW functionality's core so it can accommodate additional requirements. These domain features together with engineering concepts are influencing the specification, description and evaluation of FSW product line. Domain engineering is the foundation for emerging product line software development approaches. A product line is 'A family of products designed to take advantage of their common aspects and predicted variabilities'. In our product line approach, domain engineering includes the engineering activities needed to produce reusable artifacts for a domain. Application engineering refers to developing an application in the domain starting from reusable artifacts. The focus of this paper is regarding the software process, lessons learned and on how the GNC FSW product line manages variability. Existing domain engineering approaches do not enforce any specific notation for domain analysis or commonality and variability analysis. Usually, natural language text is the preferred tool. The advantage is the flexibility and adapt ability of natural language. However, one has to be ready to accept also its well-known drawbacks, such as ambiguity, inconsistency, and contradictions. While most domain analysis approaches are functionally oriented, the idea of applying the object-oriented approach in domain analysis is not new. Some authors propose to use UML as the notation underlying domain analysis. Our work is based on the same idea of merging UML and domain analysis. Further, we propose a few extensions to UML in order to express variability, and we define precisely their semantics so that a tool can support them. The extensions are designed to be implemented on the API of a popular industrial CASE tool, with obvious advantages in cost and availability of tool support. The paper outlines the product line processes and identifies where variability must be addressed. Then it describes the product line products with respect to how they accommodate variability. The Celestial Body subdomain is used as a working example. Our results to date are summarized and plans for the future are described.

BH-ShaDe: A Software Tool That Assists Architecture Students in the III-Structured Task of Housing Design

ERIC Educational Resources Information Center

Millan, Eva; Belmonte, Maria-Victoria; Ruiz-Montiel, Manuela; Gavilanes, Juan; Perez-de-la-Cruz, Jose-Luis

2016-01-01

In this paper, we present BH-ShaDe, a new software tool to assist architecture students learning the ill-structured domain/task of housing design. The software tool provides students with automatic or interactively generated floor plan schemas for basic houses. The students can then use the generated schemas as initial seeds to develop complete…

Toward domain-specific design environments: Some representation ideas from the telecommunications domain

NASA Technical Reports Server (NTRS)

Greenspan, Sol; Feblowitz, Mark

1992-01-01

ACME is an experimental environment for investigating new approaches to modeling and analysis of system requirements and designs. ACME is built on and extends object-oriented conceptual modeling techniques and knowledge representation and reasoning (KRR) tools. The most immediate intended use for ACME is to help represent, understand, and communicate system designs during the early stages of system planning and requirements engineering. While our research is ostensibly aimed at software systems in general, we are particularly motivated to make an impact in the telecommunications domain, especially in the area referred to as Intelligent Networks (IN's). IN systems contain the software to provide services to users of a telecommunications network (e.g., call processing services, information services, etc.) as well as the software that provides the internal infrastructure for providing the services (e.g., resource management, billing, etc.). The software includes not only systems developed by the network proprietors but also by a growing group of independent service software providers.

Guided Assessment or Open Discourse: A Comparative Analysis of Students Interaction on Facebook Groups

ERIC Educational Resources Information Center

Singh, Lenandlar

2013-01-01

Web 2.0 and specifically Social Networking Software have become ubiquitous tools for communication over the last five years. Across many disciplines, practitioners and researchers have been exploring these technologies with the hope of tapping into their perceived potential. Not least in this endeavor is the field of Education. Educators and…

A Guide to Analyzing Message-Response Sequences and Group Interaction Patterns in Computer-Mediated Communication

ERIC Educational Resources Information Center

Jeong, Allan

2005-01-01

This paper proposes a set of methods and a framework for evaluating, modeling, and predicting group interactions in computer-mediated communication. The method of sequential analysis is described along with specific software tools and techniques to facilitate the analysis of message-response sequences. In addition, the Dialogic Theory and its…

Data Analysis Tools and Methods for Improving the Interaction Design in E-Learning

ERIC Educational Resources Information Center

Popescu, Paul Stefan

2015-01-01

In this digital era, learning from data gathered from different software systems may have a great impact on the quality of the interaction experience. There are two main directions that come to enhance this emerging research domain, Intelligent Data Analysis (IDA) and Human Computer Interaction (HCI). HCI specific research methodologies can be…

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

PubMed Central

2015-01-01

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

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

PubMed

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

2015-02-06

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

Advanced techniques in reliability model representation and solution

NASA Technical Reports Server (NTRS)

Palumbo, Daniel L.; Nicol, David M.

1992-01-01

The current tendency of flight control system designs is towards increased integration of applications and increased distribution of computational elements. The reliability analysis of such systems is difficult because subsystem interactions are increasingly interdependent. Researchers at NASA Langley Research Center have been working for several years to extend the capability of Markov modeling techniques to address these problems. This effort has been focused in the areas of increased model abstraction and increased computational capability. The reliability model generator (RMG) is a software tool that uses as input a graphical object-oriented block diagram of the system. RMG uses a failure-effects algorithm to produce the reliability model from the graphical description. The ASSURE software tool is a parallel processing program that uses the semi-Markov unreliability range evaluator (SURE) solution technique and the abstract semi-Markov specification interface to the SURE tool (ASSIST) modeling language. A failure modes-effects simulation is used by ASSURE. These tools were used to analyze a significant portion of a complex flight control system. The successful combination of the power of graphical representation, automated model generation, and parallel computation leads to the conclusion that distributed fault-tolerant system architectures can now be analyzed.

Intelligent systems and advanced user interfaces for design, operation, and maintenance of command management systems

NASA Technical Reports Server (NTRS)

Potter, William J.; Mitchell, Christine M.

1993-01-01

Historically, command management systems (CMS) have been large and expensive spacecraft-specific software systems that were costly to build, operate, and maintain. Current and emerging hardware, software, and user interface technologies may offer an opportunity to facilitate the initial formulation and design of a spacecraft-specific CMS as well as to develop a more generic CMS system. New technologies, in addition to a core CMS common to a range of spacecraft, may facilitate the training and enhance the efficiency of CMS operations. Current mission operations center (MOC) hardware and software include Unix workstations, the C/C++ programming languages, and an X window interface. This configuration provides the power and flexibility to support sophisticated and intelligent user interfaces that exploit state-of-the-art technologies in human-machine interaction, artificial intelligence, and software engineering. One of the goals of this research is to explore the extent to which technologies developed in the research laboratory can be productively applied in a complex system such as spacecraft command management. Initial examination of some of these issues in CMS design and operation suggests that application of technologies such as intelligent planning, case-based reasoning, human-machine systems design and analysis tools (e.g., operator and designer models), and human-computer interaction tools (e.g., graphics, visualization, and animation) may provide significant savings in the design, operation, and maintenance of the CMS for a specific spacecraft as well as continuity for CMS design and development across spacecraft. The first six months of this research saw a broad investigation by Georgia Tech researchers into the function, design, and operation of current and planned command management systems at Goddard Space Flight Center. As the first step, the researchers attempted to understand the current and anticipated horizons of command management systems at Goddard. Preliminary results are given on CMS commonalities and causes of low re-use, and methods are proposed to facilitate increased re-use.

VSO For Dummies

NASA Astrophysics Data System (ADS)

Schwartz, Richard A.; Zarro, D.; Csillaghy, A.; Dennis, B.; Tolbert, A. K.; Etesi, L.

2009-05-01

We report on our activities to integrate VSO search and retrieval capabilities into standard data access, display, and analysis tools. In addition to its standard Web-based search form, the VSO provides an Interactive Data Language (IDL) client (vso_search) that is available through the Solar Software (SSW) package. We have incorporated this client into an IDL-widget interface program (show_synop) that allows for more simplified searching and downloading of VSO datasets directly into a user's IDL data analysis environment. In particular, we have provided the capability to read VSO datasets into a general purpose IDL package (plotman) that can display different datatypes (lightcurves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. Currently, the show_synop tool supports access to ground-based and space-based (SOHO, STEREO, and Hinode) observations, and has the capability to include new datasets as they become available. A user encounters two major hurdles when using the VSO: (1) Instrument-specific software (such as level-0 file readers and data-prepping procedures) may not be available in the user's local SSW distribution. (2) Recent calibration files (such as flat-fields) are not automatically distributed with the analysis software. To address these issues, we have developed a dedicated server (prepserver) that incorporates all the latest instrument-specific software libraries and calibration files. The prepserver uses an IDL-Java bridge to read and implement data processing requests from a client and return a processed data file that can be readily displayed with the show_synop/plotman package. The advantage of the prepserver is that the user is only required to install the general branch (gen) of the SSW tree, and is freed from the more onerous task of installing instrument-specific libraries and calibration files. We will demonstrate how the prepserver can be used to read, process, and overlay SOHO/EIT, TRACE, SECCHI/EUVI, and RHESSI images.

GPM Timeline Inhibits For IT Processing

NASA Technical Reports Server (NTRS)

Dion, Shirley K.

2014-01-01

The Safety Inhibit Timeline Tool was created as one approach to capturing and understanding inhibits and controls from IT through launch. Global Precipitation Measurement (GPM) Mission, which launched from Japan in March 2014, was a joint mission under a partnership between the National Aeronautics and Space Administration (NASA) and the Japan Aerospace Exploration Agency (JAXA). GPM was one of the first NASA Goddard in-house programs that extensively used software controls. Using this tool during the GPM buildup allowed a thorough review of inhibit and safety critical software design for hazardous subsystems such as the high gain antenna boom, solar array, and instrument deployments, transmitter turn-on, propulsion system release, and instrument radar turn-on. The GPM safety team developed a methodology to document software safety as part of the standard hazard report. As a result of this process, a new tool safety inhibit timeline was created for management of inhibits and their controls during spacecraft buildup and testing during IT at GSFC and at the launch range in Japan. The Safety Inhibit Timeline Tool was a pathfinder approach for reviewing software that controls the electrical inhibits. The Safety Inhibit Timeline Tool strengthens the Safety Analysts understanding of the removal of inhibits during the IT process with safety critical software. With this tool, the Safety Analyst can confirm proper safe configuration of a spacecraft during each IT test, track inhibit and software configuration changes, and assess software criticality. In addition to understanding inhibits and controls during IT, the tool allows the Safety Analyst to better communicate to engineers and management the changes in inhibit states with each phase of hardware and software testing and the impact of safety risks. Lessons learned from participating in the GPM campaign at NASA and JAXA will be discussed during this session.

Three Software Tools for Viewing Sectional Planes, Volume Models, and Surface Models of a Cadaver Hand.

PubMed

Chung, Beom Sun; Chung, Min Suk; Shin, Byeong Seok; Kwon, Koojoo

2018-02-19

The hand anatomy, including the complicated hand muscles, can be grasped by using computer-assisted learning tools with high quality two-dimensional images and three-dimensional models. The purpose of this study was to present up-to-date software tools that promote learning of stereoscopic morphology of the hand. On the basis of horizontal sectioned images and outlined images of a male cadaver, vertical planes, volume models, and surface models were elaborated. Software to browse pairs of the sectioned and outlined images in orthogonal planes and software to peel and rotate the volume models, as well as a portable document format (PDF) file to select and rotate the surface models, were produced. All of the software tools were downloadable free of charge and usable off-line. The three types of tools for viewing multiple aspects of the hand could be adequately employed according to individual needs. These new tools involving the realistic images of a cadaver and the diverse functions are expected to improve comprehensive knowledge of the hand shape. © 2018 The Korean Academy of Medical Sciences.

Three Software Tools for Viewing Sectional Planes, Volume Models, and Surface Models of a Cadaver Hand

PubMed Central

2018-01-01

Background The hand anatomy, including the complicated hand muscles, can be grasped by using computer-assisted learning tools with high quality two-dimensional images and three-dimensional models. The purpose of this study was to present up-to-date software tools that promote learning of stereoscopic morphology of the hand. Methods On the basis of horizontal sectioned images and outlined images of a male cadaver, vertical planes, volume models, and surface models were elaborated. Software to browse pairs of the sectioned and outlined images in orthogonal planes and software to peel and rotate the volume models, as well as a portable document format (PDF) file to select and rotate the surface models, were produced. Results All of the software tools were downloadable free of charge and usable off-line. The three types of tools for viewing multiple aspects of the hand could be adequately employed according to individual needs. Conclusion These new tools involving the realistic images of a cadaver and the diverse functions are expected to improve comprehensive knowledge of the hand shape. PMID:29441756

Raising Virtual Laboratories in Australia onto global platforms

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Barker, M.; Fraser, R.; Evans, B. J. K.; Moloney, G.; Proctor, R.; Moise, A. F.; Hamish, H.

2016-12-01

Across the globe, Virtual Laboratories (VLs), Science Gateways (SGs), and Virtual Research Environments (VREs) are being developed that enable users who are not co-located to actively work together at various scales to share data, models, tools, software, workflows, best practices, etc. Outcomes range from enabling `long tail' researchers to more easily access specific data collections, to facilitating complex workflows on powerful supercomputers. In Australia, government funding has facilitated the development of a range of VLs through the National eResearch Collaborative Tools and Resources (NeCTAR) program. The VLs provide highly collaborative, research-domain oriented, integrated software infrastructures that meet user community needs. Twelve VLs have been funded since 2012, including the Virtual Geophysics Laboratory (VGL); Virtual Hazards, Impact and Risk Laboratory (VHIRL); Climate and Weather Science Laboratory (CWSLab); Marine Virtual Laboratory (MarVL); and Biodiversity and Climate Change Virtual Laboratory (BCCVL). These VLs share similar technical challenges, with common issues emerging on integration of tools, applications and access data collections via both cloud-based environments and other distributed resources. While each VL began with a focus on a specific research domain, communities of practice have now formed across the VLs around common issues, and facilitate identification of best practice case studies, and new standards. As a result, tools are now being shared where the VLs access data via data services using international standards such as ISO, OGC, W3C. The sharing of these approaches is starting to facilitate re-usability of infrastructure and is a step towards supporting interdisciplinary research. Whilst the focus of the VLs are Australia-centric, by using standards, these environments are able to be extended to analysis on other international datasets. Many VL datasets are subsets of global datasets and so extension to global is a small (and often requested) step. Similarly, most of the tools, software, and other technologies could be shared across infrastructures globally. Therefore, it is now time to better connect the Australian VLs with similar initiatives elsewhere to create international platforms that can contribute to global research challenges.

Building a Generic Virtual Research Environment Framework for Multiple Earth and Space Science Domains and a Diversity of Users.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Fraser, R.; Evans, B. J. K.; Friedrich, C.; Klump, J. F.; Lescinsky, D. T.

2017-12-01

Virtual Research Environments (VREs) are now part of academic infrastructures. Online research workflows can be orchestrated whereby data can be accessed from multiple external repositories with processing taking place on public or private clouds, and centralised supercomputers using a mixture of user codes, and well-used community software and libraries. VREs enable distributed members of research teams to actively work together to share data, models, tools, software, workflows, best practices, infrastructures, etc. These environments and their components are increasingly able to support the needs of undergraduate teaching. External to the research sector, they can also be reused by citizen scientists, and be repurposed for industry users to help accelerate the diffusion and hence enable the translation of research innovations. The Virtual Geophysics Laboratory (VGL) in Australia was started in 2012, built using a collaboration between CSIRO, the National Computational Infrastructure (NCI) and Geoscience Australia, with support funding from the Australian Government Department of Education. VGL comprises three main modules that provide an interface to enable users to first select their required data; to choose a tool to process that data; and then access compute infrastructure for execution. VGL was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools. Over the years it has evolved into a multi-purpose Earth science platform with access to an increased variety of data (e.g., Natural Hazards, Geochemistry), a broader range of software packages, and an increasing diversity of compute infrastructures. This expansion has been possible because of the approach to loosely couple data, tools and compute resources via interfaces that are built on international standards and accessed as network-enabled services wherever possible. Built originally for researchers that were not fussy about general usability, increasing emphasis on User Interfaces (UIs) and stability will lead to increased uptake in the education and industry sectors. Simultaneously, improvements are being added to facilitate access to data and tools by experienced researchers who want direct access to both data and flexible workflows.

Software Management Environment (SME) concepts and architecture, revision 1

NASA Technical Reports Server (NTRS)

Hendrick, Robert; Kistler, David; Valett, Jon

1992-01-01

This document presents the concepts and architecture of the Software Management Environment (SME), developed for the Software Engineering Branch of the Flight Dynamic Division (FDD) of GSFC. The SME provides an integrated set of experience-based management tools that can assist software development managers in managing and planning flight dynamics software development projects. This document provides a high-level description of the types of information required to implement such an automated management tool.

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

PubMed

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

2007-10-11

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

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

Keszei, András P; Berkels, Benjamin; Deserno, Thomas M

2017-02-01

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n = 22). Exclusions are due to unavailability or inappropriateness. The remaining (n = 18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.

An evaluation of software tools for the design and development of cockpit displays

NASA Technical Reports Server (NTRS)

Ellis, Thomas D., Jr.

1993-01-01

The use of all-glass cockpits at the NASA Langley Research Center (LaRC) simulation facility has changed the means of design, development, and maintenance of instrument displays. The human-machine interface has evolved from a physical hardware device to a software-generated electronic display system. This has subsequently caused an increased workload at the facility. As computer processing power increases and the glass cockpit becomes predominant in facilities, software tools used in the design and development of cockpit displays are becoming both feasible and necessary for a more productive simulation environment. This paper defines LaRC requirements of a display software development tool and compares two available applications against these requirements. As a part of the software engineering process, these tools reduce development time, provide a common platform for display development, and produce exceptional real-time results.

Global GIS database; digital atlas of Central and South America

USGS Publications Warehouse

Hearn,, Paul P.; Hare, T.; Schruben, P.; Sherrill, D.; LaMar, C.; Tsushima, P.

2000-01-01

This CD-ROM contains a digital atlas of the countries of Central and South America. This atlas is part of a global database compiled from USGS and other data sources at the nominal scale of 1:1 million and is intended to be used as a regional-scale reference and analytical tool by government officials, researchers, the private sector, and the general public. The atlas includes free GIS software or may also be used with ESRI's ArcView software. Customized ArcView tools, specifically designed to make the atlas easier to use, are also included. The atlas contains the following datasets: country political boundaries, digital shaded relief map, elevation, slope, hydrology, locations of cities and towns, airfields, roads, railroads, utility lines, population density, geology, ecological regions, historical seismicity, volcanoes, ore deposits, oil and gas fields, climate data, landcover, vegetation index, and lights at night.

Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications

NASA Technical Reports Server (NTRS)

Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.

2017-01-01

Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.

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.

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. PMID:24833336

Application of Architectural Patterns and Lightweight Formal Method for the Validation and Verification of Safety Critical Systems

DTIC Science & Technology

2013-09-01

to a XML file, a code that Bonine in [21] developed for a similar purpose. Using the StateRover XML log file import tool, we are able to generate a...C. Bonine , M. Shing, T.W. Otani, “Computer-aided process and tools for mobile software acquisition,” NPS, Monterey, CA, Tech. Rep. NPS-SE-13...C10P07R05– 075, 2013. [21] C. Bonine , “Specification, validation and verification of mobile application behavior,” M.S. thesis, Dept. Comp. Science, NPS

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

PubMed

Schreiber, Fabian; Pick, Kerstin; Erpenbeck, Dirk; Wörheide, Gert; Morgenstern, Burkhard

2009-07-16

Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from different species. A first crucial step in EST-based phylogeny reconstruction is to identify groups of orthologous sequences. From these data sets, appropriate target genes are selected, and redundant sequences are eliminated to obtain suitable sequence sets as input data for tree-reconstruction software. Generating such data sets manually can be very time consuming. Thus, software tools are needed that carry out these steps automatically. We developed a flexible and user-friendly software pipeline, running on desktop machines or computer clusters, that constructs data sets for phylogenomic analyses. It automatically searches assembled EST sequences against databases of orthologous groups (OG), assigns ESTs to these predefined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified orthologous sequences and offers the possibility to further process this alignment in a last step by excluding potentially homoplastic sites and selecting sufficiently conserved parts. Our software pipeline can be used as it is, but it can also be adapted by integrating additional external programs. This makes the pipeline useful for non-bioinformaticians as well as to bioinformatic experts. The software pipeline is especially designed for ESTs, but it can also handle protein sequences. OrthoSelect is a tool that produces orthologous gene alignments from assembled ESTs. Our tests show that OrthoSelect detects orthologs in EST libraries with high accuracy. In the absence of a gold standard for orthology prediction, we compared predictions by OrthoSelect to a manually created and published phylogenomic data set. Our tool was not only able to rebuild the data set with a specificity of 98%, but it detected four percent more orthologous sequences. Furthermore, the results OrthoSelect produces are in absolut agreement with the results of other programs, but our tool offers a significant speedup and additional functionality, e.g. handling of ESTs, computing sequence alignments, and refining them. To our knowledge, there is currently no fully automated and freely available tool for this purpose. Thus, OrthoSelect is a valuable tool for researchers in the field of phylogenomics who deal with large quantities of EST sequences. OrthoSelect is written in Perl and runs on Linux/Mac OS X. The tool can be downloaded at (http://gobics.de/fabian/orthoselect.php).

Ensemble: an Architecture for Mission-Operations Software

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Powell, Mark; Fox, Jason; Rabe, Kenneth; Shu, IHsiang; McCurdy, Michael; Vera, Alonso

2008-01-01

Ensemble is the name of an open architecture for, and a methodology for the development of, spacecraft mission operations software. Ensemble is also potentially applicable to the development of non-spacecraft mission-operations- type software. Ensemble capitalizes on the strengths of the open-source Eclipse software and its architecture to address several issues that have arisen repeatedly in the development of mission-operations software: Heretofore, mission-operations application programs have been developed in disparate programming environments and integrated during the final stages of development of missions. The programs have been poorly integrated, and it has been costly to develop, test, and deploy them. Users of each program have been forced to interact with several different graphical user interfaces (GUIs). Also, the strategy typically used in integrating the programs has yielded serial chains of operational software tools of such a nature that during use of a given tool, it has not been possible to gain access to the capabilities afforded by other tools. In contrast, the Ensemble approach offers a low-risk path towards tighter integration of mission-operations software tools.

Taking advantage of ground data systems attributes to achieve quality results in testing software

NASA Technical Reports Server (NTRS)

Sigman, Clayton B.; Koslosky, John T.; Hageman, Barbara H.

1994-01-01

During the software development life cycle process, basic testing starts with the development team. At the end of the development process, an acceptance test is performed for the user to ensure that the deliverable is acceptable. Ideally, the delivery is an operational product with zero defects. However, the goal of zero defects is normally not achieved but is successful to various degrees. With the emphasis on building low cost ground support systems while maintaining a quality product, a key element in the test process is simulator capability. This paper reviews the Transportable Payload Operations Control Center (TPOCC) Advanced Spacecraft Simulator (TASS) test tool that is used in the acceptance test process for unmanned satellite operations control centers. The TASS is designed to support the development, test and operational environments of the Goddard Space Flight Center (GSFC) operations control centers. The TASS uses the same basic architecture as the operations control center. This architecture is characterized by its use of distributed processing, industry standards, commercial off-the-shelf (COTS) hardware and software components, and reusable software. The TASS uses much of the same TPOCC architecture and reusable software that the operations control center developer uses. The TASS also makes use of reusable simulator software in the mission specific versions of the TASS. Very little new software needs to be developed, mainly mission specific telemetry communication and command processing software. By taking advantage of the ground data system attributes, successful software reuse for operational systems provides the opportunity to extend the reuse concept into the test area. Consistency in test approach is a major step in achieving quality results.

Experience with case tools in the design of process-oriented software

NASA Astrophysics Data System (ADS)

Novakov, Ognian; Sicard, Claude-Henri

1994-12-01

In Accelerator systems such as the CERN PS complex, process equipment has a life time which may exceed the typical life cycle of its related software. Taking into account the variety of such equipment, it is important to keep the analysis and design of the software in a system-independent form. This paper discusses the experience gathered in using commercial CASE tools for analysis, design and reverse engineering of different process-oriented software modules, with a principal emphasis on maintaining the initial analysis in a standardized form. Such tools have been in existence for several years, but this paper shows that they are not fully adapted to our needs. In particular, the paper stresses the problems of integrating such a tool into an existing data-base-dependent development chain, the lack of real-time simulation tools and of Object-Oriented concepts in existing commercial packages. Finally, the paper gives a broader view of software engineering needs in our particular context.

Automating Risk Analysis of Software Design Models

PubMed Central

Ruiz, Guifré; Heymann, Elisa; César, Eduardo; Miller, Barton P.

2014-01-01

The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance. PMID:25136688

Automating risk analysis of software design models.

PubMed

Frydman, Maxime; Ruiz, Guifré; Heymann, Elisa; César, Eduardo; Miller, Barton P

2014-01-01

The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance.

Estimating Computer-Based Training Development Times

DTIC Science & Technology

1987-10-14

beginners , must be sure they interpret terms correctly. As a result of this informal validation, the authors suggest refinements in the tool which...Productivity tools available: automated design tools, text processor interfaces, flowcharting software, software interfaces a Multimedia interfaces e

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

Svetlana Shasharina

The goal of the Center for Technology for Advanced Scientific Component Software is to fundamentally changing the way scientific software is developed and used by bringing component-based software development technologies to high-performance scientific and engineering computing. The role of Tech-X work in TASCS project is to provide an outreach to accelerator physics and fusion applications by introducing TASCS tools into applications, testing tools in the applications and modifying the tools to be more usable.

Software Analysis of New Space Gravity Data for Geophysics and Climate Research

NASA Technical Reports Server (NTRS)

Deese, Rupert; Ivins, Erik R.; Fielding, Eric J.

2012-01-01

Both the Gravity Recovery and Climate Experiment (GRACE) and Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellites are returning rich data for the study of the solid earth, the oceans, and the climate. Current software analysis tools do not provide researchers with the ease and flexibility required to make full use of this data. We evaluate the capabilities and shortcomings of existing software tools including Mathematica, the GOCE User Toolbox, the ICGEM's (International Center for Global Earth Models) web server, and Tesseroids. Using existing tools as necessary, we design and implement software with the capability to produce gridded data and publication quality renderings from raw gravity data. The straight forward software interface marks an improvement over previously existing tools and makes new space gravity data more useful to researchers. Using the software we calculate Bouguer anomalies of the gravity tensor's vertical component in the Gulf of Mexico, Antarctica, and the 2010 Maule earthquake region. These maps identify promising areas of future research.