Using Statistical Analysis Software to Advance Nitro Plasticizer Wettability

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

Shear, Trevor Allan

Statistical analysis in science is an extremely powerful tool that is often underutilized. Additionally, it is frequently the case that data is misinterpreted or not used to its fullest extent. Utilizing the advanced software JMP®, many aspects of experimental design and data analysis can be evaluated and improved. This overview will detail the features of JMP® and how they were used to advance a project, resulting in time and cost savings, as well as the collection of scientifically sound data. The project analyzed in this report addresses the inability of a nitro plasticizer to coat a gold coated quartz crystalmore » sensor used in a quartz crystal microbalance. Through the use of the JMP® software, the wettability of the nitro plasticizer was increased by over 200% using an atmospheric plasma pen, ensuring good sample preparation and reliable results.« less

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.

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

Regional Sediment Management (RSM) Modeling Tools: Integration of Advanced Sediment Transport Tools into HEC-RAS

DTIC Science & Technology

2014-06-01

Integration of Advanced Sediment Transport Tools into HEC-RAS by Paul M. Boyd and Stanford A. Gibson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) summarizes the development and initial testing of new sediment transport and modeling tools developed by the U.S. Army Corps...sediment transport within the USACE HEC River Analysis System (HEC-RAS) software package and to determine its applicability to Regional Sediment

A Visual Basic simulation software tool for performance analysis of a membrane-based advanced water treatment plant.

PubMed

Pal, P; Kumar, R; Srivastava, N; Chaudhuri, J

2014-02-01

A Visual Basic simulation software (WATTPPA) has been developed to analyse the performance of an advanced wastewater treatment plant. This user-friendly and menu-driven software is based on the dynamic mathematical model for an industrial wastewater treatment scheme that integrates chemical, biological and membrane-based unit operations. The software-predicted results corroborate very well with the experimental findings as indicated in the overall correlation coefficient of the order of 0.99. The software permits pre-analysis and manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. It allows quick performance analysis of the whole system as well as the individual units. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for hazardous wastewater.

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

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

Software Framework for Advanced Power Plant Simulations

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

John Widmann; Sorin Munteanu; Aseem Jain

2010-08-01

This report summarizes the work accomplished during the Phase II development effort of the Advanced Process Engineering Co-Simulator (APECS). The objective of the project is to develop the tools to efficiently combine high-fidelity computational fluid dynamics (CFD) models with process modeling software. During the course of the project, a robust integration controller was developed that can be used in any CAPE-OPEN compliant process modeling environment. The controller mediates the exchange of information between the process modeling software and the CFD software. Several approaches to reducing the time disparity between CFD simulations and process modeling have been investigated and implemented. Thesemore » include enabling the CFD models to be run on a remote cluster and enabling multiple CFD models to be run simultaneously. Furthermore, computationally fast reduced-order models (ROMs) have been developed that can be 'trained' using the results from CFD simulations and then used directly within flowsheets. Unit operation models (both CFD and ROMs) can be uploaded to a model database and shared between multiple users.« less

A software tool for advanced MRgFUS prostate therapy planning and follow up

NASA Astrophysics Data System (ADS)

van Straaten, Dörte; Hoogenboom, Martijn; van Amerongen, Martinus J.; Weiler, Florian; Issawi, Jumana Al; Günther, Matthias; Fütterer, Jurgen; Jenne, Jürgen W.

2017-03-01

US guided HIFU/FUS ablation for the therapy of prostate cancer is a clinical established method, while MR guided HIFU/FUS applications for prostate recently started clinical evaluation. Even if MRI examination is an excellent diagnostic tool for prostate cancer, it is a time consuming procedure and not practicable within an MRgFUS therapy session. The aim of our ongoing work is to develop software to support therapy planning and post-therapy follow-up for MRgFUS on localized prostate cancer, based on multi-parametric MR protocols. The clinical workflow of diagnosis, therapy and follow-up of MR guided FUS on prostate cancer was deeply analyzed. Based on this, the image processing workflow was designed and all necessary components, e.g. GUI, viewer, registration tools etc. were defined and implemented. The software bases on MeVisLab with several implemented C++ modules for the image processing tasks. The developed software, called LTC (Local Therapy Control) will register and visualize automatically all images (T1w, T2w, DWI etc.) and ADC or perfusion maps gained from the diagnostic MRI session. This maximum of diagnostic information helps to segment all necessary ROIs, e.g. the tumor, for therapy planning. Final therapy planning will be performed based on these segmentation data in the following MRgFUS therapy session. In addition, the developed software should help to evaluate the therapy success, by synchronization and display of pre-therapeutic, therapy and follow-up image data including the therapy plan and thermal dose information. In this ongoing project, the first stand-alone prototype was completed and will be clinically evaluated.

Software tool for physics chart checks.

PubMed

Li, H Harold; Wu, Yu; Yang, Deshan; Mutic, Sasa

2014-01-01

Physics chart check has long been a central quality assurance (QC) measure in radiation oncology. The purpose of this work is to describe a software tool that aims to accomplish simplification, standardization, automation, and forced functions in the process. Nationally recognized guidelines, including American College of Radiology and American Society for Radiation Oncology guidelines and technical standards, and the American Association of Physicists in Medicine Task Group reports were identified, studied, and summarized. Meanwhile, the reported events related to physics chart check service were analyzed using an event reporting and learning system. A number of shortfalls in the chart check process were identified. To address these problems, a software tool was designed and developed under Microsoft. Net in C# to hardwire as many components as possible at each stage of the process. The software consists of the following 4 independent modules: (1) chart check management; (2) pretreatment and during treatment chart check assistant; (3) posttreatment chart check assistant; and (4) quarterly peer-review management. The users were a large group of physicists in the author's radiation oncology clinic. During over 1 year of use the tool has proven very helpful in chart checking management, communication, documentation, and maintaining consistency. The software tool presented in this work aims to assist physicists at each stage of the physics chart check process. The software tool is potentially useful for any radiation oncology clinics that are either in the process of pursuing or maintaining the American College of Radiology accreditation.

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.

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.

Software Tool Issues

NASA Astrophysics Data System (ADS)

Hennell, Michael

This chapter relies on experience with tool development gained over the last thirty years. It shows that there are a large number of techniques that contribute to any successful project, and that formality is always the key: a modern software test tool is based on a firm mathematical foundation. After a brief introduction, Section 2 recalls and extends the terminology of Chapter 1. Section 3 discusses the the design of different sorts of static and dynamic analysis tools. Nine important issues to be taken into consideration when evaluating such tools are presented in Section 4. Section 5 investigates the interplay between testing and proof. In Section 6, we call for developers to take their own medicine and verify their tools. Finally, we conclude in Section 7 with a summary of our main messages, emphasising the important role of testing.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

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

Experimental Evaluation of Verification and Validation Tools on Martian Rover Software

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Giannakopoulou, Dimitra; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareanu, Corina; Venet, Arnaud; Visser, Willem

2003-01-01

To achieve its science objectives in deep space exploration, NASA has a need for science platform vehicles to autonomously make control decisions in a time frame that excludes intervention from Earth-based controllers. Round-trip light-time is one significant factor motivating autonomy capability, another factor is the need to reduce ground support operations cost. An unsolved problem potentially impeding the adoption of autonomy capability is the verification and validation of such software systems, which exhibit far more behaviors (and hence distinct execution paths in the software) than is typical in current deepspace platforms. Hence the need for a study to benchmark advanced Verification and Validation (V&V) tools on representative autonomy software. The objective of the study was to access the maturity of different technologies, to provide data indicative of potential synergies between them, and to identify gaps in the technologies with respect to the challenge of autonomy V&V. The study consisted of two parts: first, a set of relatively independent case studies of different tools on the same autonomy code, second a carefully controlled experiment with human participants on a subset of these technologies. This paper describes the second part of the study. Overall, nearly four hundred hours of data on human use of three different advanced V&V tools were accumulated, with a control group that used conventional testing methods. The experiment simulated four independent V&V teams debugging three successive versions of an executive controller for a Martian Rover. Defects were carefully seeded into the three versions based on a profile of defects from CVS logs that occurred in the actual development of the executive controller. The rest of the document is structured a s follows. In section 2 and 3, we respectively describe the tools used in the study and the rover software that was analyzed. In section 4 the methodology for the experiment is described; this

Towards early software reliability prediction for computer forensic tools (case study).

PubMed

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

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

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

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...

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.

Software Tools Streamline Project Management

NASA Technical Reports Server (NTRS)

2009-01-01

Three innovative software inventions from Ames Research Center (NETMARK, Program Management Tool, and Query-Based Document Management) are finding their way into NASA missions as well as industry applications. The first, NETMARK, is a program that enables integrated searching of data stored in a variety of databases and documents, meaning that users no longer have to look in several places for related information. NETMARK allows users to search and query information across all of these sources in one step. This cross-cutting capability in information analysis has exponentially reduced the amount of time needed to mine data from days or weeks to mere seconds. NETMARK has been used widely throughout NASA, enabling this automatic integration of information across many documents and databases. NASA projects that use NETMARK include the internal reporting system and project performance dashboard, Erasmus, NASA s enterprise management tool, which enhances organizational collaboration and information sharing through document routing and review; the Integrated Financial Management Program; International Space Station Knowledge Management; Mishap and Anomaly Information Reporting System; and management of the Mars Exploration Rovers. Approximately $1 billion worth of NASA s projects are currently managed using Program Management Tool (PMT), which is based on NETMARK. PMT is a comprehensive, Web-enabled application tool used to assist program and project managers within NASA enterprises in monitoring, disseminating, and tracking the progress of program and project milestones and other relevant resources. The PMT consists of an integrated knowledge repository built upon advanced enterprise-wide database integration techniques and the latest Web-enabled technologies. The current system is in a pilot operational mode allowing users to automatically manage, track, define, update, and view customizable milestone objectives and goals. The third software invention, Query

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.

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

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

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.

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

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PubMed Central

Latendresse, Mario; Paley, Suzanne M.; Krummenacker, Markus; Ong, Quang D.; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M.; Caspi, Ron

2016-01-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. PMID:26454094

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.

GeMS: an advanced software package for designing synthetic genes.

PubMed

Jayaraj, Sebastian; Reid, Ralph; Santi, Daniel V

2005-01-01

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

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.

Designing a Software Tool for Fuzzy Logic Programming

NASA Astrophysics Data System (ADS)

Abietar, José M.; Morcillo, Pedro J.; Moreno, Ginés

2007-12-01

Fuzzy Logic Programming is an interesting and still growing research area that agglutinates the efforts for introducing fuzzy logic into logic programming (LP), in order to incorporate more expressive resources on such languages for dealing with uncertainty and approximated reasoning. The multi-adjoint logic programming approach is a recent and extremely flexible fuzzy logic paradigm for which, unfortunately, we have not found practical tools implemented so far. In this work, we describe a prototype system which is able to directly translate fuzzy logic programs into Prolog code in order to safely execute these residual programs inside any standard Prolog interpreter in a completely transparent way for the final user. We think that the development of such fuzzy languages and programing tools might play an important role in the design of advanced software applications for computational physics, chemistry, mathematics, medicine, industrial control and so on.

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.

Real time software tools and methodologies

NASA Technical Reports Server (NTRS)

Christofferson, M. J.

1981-01-01

Real time systems are characterized by high speed processing and throughput as well as asynchronous event processing requirements. These requirements give rise to particular implementations of parallel or pipeline multitasking structures, of intertask or interprocess communications mechanisms, and finally of message (buffer) routing or switching mechanisms. These mechanisms or structures, along with the data structue, describe the essential character of the system. These common structural elements and mechanisms are identified, their implementation in the form of routines, tasks or macros - in other words, tools are formalized. The tools developed support or make available the following: reentrant task creation, generalized message routing techniques, generalized task structures/task families, standardized intertask communications mechanisms, and pipeline and parallel processing architectures in a multitasking environment. Tools development raise some interesting prospects in the areas of software instrumentation and software portability. These issues are discussed following the description of the tools themselves.

Exploiting Software Tool Towards Easier Use And Higher Efficiency

NASA Astrophysics Data System (ADS)

Lin, G. H.; Su, J. T.; Deng, Y. Y.

2006-08-01

In developing countries, using data based on instrument made by themselves in maximum extent is very important. It is not only related to maximizing science returns upon prophase investment -- deep accumulations in every aspects but also science output. Based on the idea, we are exploiting a software (called THDP: Tool of Huairou Data Processing). It is used for processing a series of issues, which is met necessary in processing data. This paper discusses its designed purpose, functions, method and specialities. The primary vehicle for general data interpretation is through various techniques of data visualization, techniques of interactive. In the software, we employed Object Oriented approach. It is appropriate to the vehicle. it is imperative that the approach provide not only function, but do so in as convenient a fashion as possible. As result of the software exploiting, it is not only easier to learn data processing for beginner and more convenienter to need further improvement for senior but also increase greatly efficiency in every phrases include analyse, parameter adjusting, result display. Under frame of virtual observatory, for developing countries, we should study more and newer related technologies, which can advance ability and efficiency in science research, like the software we are developing

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.

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

PubMed

Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

2016-09-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

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

Caesy: A software tool for computer-aided engineering

NASA Technical Reports Server (NTRS)

Wette, Matt

1993-01-01

A new software tool, Caesy, is described. This tool provides a strongly typed programming environment for research in the development of algorithms and software for computer-aided control system design. A description of the user language and its implementation as they currently stand are presented along with a description of work in progress and areas of future work.

Software Tools for Battery Design | Transportation Research | NREL

Science.gov Websites

battery designers, developers, and manufacturers create affordable, high-performance lithium-ion (Li-ion Software Tools for Battery Design Software Tools for Battery Design Under the Computer-Aided ) batteries for next-generation electric-drive vehicles (EDVs). An image of a simulation of a battery pack

Using CONFIG for Simulation of Operation of Water Recovery Subsystems for Advanced Control Software Evaluation

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Flores, Luis; Fleming, Land; Throop, Daiv

2002-01-01

A hybrid discrete/continuous simulation tool, CONFIG, has been developed to support evaluation of the operability life support systems. CON FIG simulates operations scenarios in which flows and pressures change continuously while system reconfigurations occur as discrete events. In simulations, intelligent control software can interact dynamically with hardware system models. CONFIG simulations have been used to evaluate control software and intelligent agents for automating life support systems operations. A CON FIG model of an advanced biological water recovery system has been developed to interact with intelligent control software that is being used in a water system test at NASA Johnson Space Center

Toxicity Estimation Software Tool (TEST)

EPA Science Inventory

The Toxicity Estimation Software Tool (TEST) was developed to allow users to easily estimate the toxicity of chemicals using Quantitative Structure Activity Relationships (QSARs) methodologies. QSARs are mathematical models used to predict measures of toxicity from the physical c...

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

PubMed Central

Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.; Chen, Albert J.; Ayaz-Guner, Serife; Peng, Ying; Valeja, Santosh G.; Liu, Xiaowen; Ge, Ying

2016-01-01

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics. PMID:26598644

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert; LeCompte, Tom

2015-10-29

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

The Utility of Free Software for Gravity and Magnetic Advanced Data Processing

NASA Astrophysics Data System (ADS)

Grandis, Hendra; Dahrin, Darharta

2017-04-01

The lack of computational tools, i.e. software, often hinders the proper teaching and application of geophysical data processing in academic institutions in Indonesia. Although there are academic licensing options for commercial software, such options are still way beyond the financial capability of some academic institutions. Academic community members (both lecturers and students) are supposed to be creative and resourceful to overcome such situation. Therefore, capability for writing computer programs or codes is a necessity. However, there are also many computer programs and even software that are freely available on the internet. Generally, the utility of the freely distributed software is limited for demonstration only or for visualizing and exchanging data. The paper discusses the utility of Geosoft’s Oasis Montaj Viewer along with USGS GX programs that are available for free. Useful gravity and magnetic advanced data processing (i.e. gradient calculation, spectral analysis etc.) can be performed “correctly” without any approximation that sometimes leads to dubious results and interpretation.

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.

Runtime Performance Monitoring Tool for RTEMS System Software

NASA Astrophysics Data System (ADS)

Cho, B.; Kim, S.; Park, H.; Kim, H.; Choi, J.; Chae, D.; Lee, J.

2007-08-01

RTEMS is a commercial-grade real-time operating system that supports multi-processor computers. However, there are not many development tools for RTEMS. In this paper, we report new RTEMS-based runtime performance monitoring tool. We have implemented a light weight runtime monitoring task with an extension to the RTEMS APIs. Using our tool, software developers can verify various performance- related parameters during runtime. Our tool can be used during software development phase and in-orbit operation as well. Our implemented target agent is light weight and has small overhead using SpaceWire interface. Efforts to reduce overhead and to add other monitoring parameters are currently under research.

FFI: A software tool for ecological monitoring

Treesearch

Duncan C. Lutes; Nathan C. Benson; MaryBeth Keifer; John F. Caratti; S. Austin Streetman

2009-01-01

A new monitoring tool called FFI (FEAT/FIREMON Integrated) has been developed to assist managers with collection, storage and analysis of ecological information. The tool was developed through the complementary integration of two fire effects monitoring systems commonly used in the United States: FIREMON and the Fire Ecology Assessment Tool. FFI provides software...

Software tool for data mining and its applications

NASA Astrophysics Data System (ADS)

Yang, Jie; Ye, Chenzhou; Chen, Nianyi

2002-03-01

A software tool for data mining is introduced, which integrates pattern recognition (PCA, Fisher, clustering, hyperenvelop, regression), artificial intelligence (knowledge representation, decision trees), statistical learning (rough set, support vector machine), computational intelligence (neural network, genetic algorithm, fuzzy systems). It consists of nine function models: pattern recognition, decision trees, association rule, fuzzy rule, neural network, genetic algorithm, Hyper Envelop, support vector machine, visualization. The principle and knowledge representation of some function models of data mining are described. The software tool of data mining is realized by Visual C++ under Windows 2000. Nonmonotony in data mining is dealt with by concept hierarchy and layered mining. The software tool of data mining has satisfactorily applied in the prediction of regularities of the formation of ternary intermetallic compounds in alloy systems, and diagnosis of brain glioma.

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

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...

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.…

Modeling Tool Advances Rotorcraft Design

NASA Technical Reports Server (NTRS)

2007-01-01

Continuum Dynamics Inc. (CDI), founded in 1979, specializes in advanced engineering services, including fluid dynamic modeling and analysis for aeronautics research. The company has completed a number of SBIR research projects with NASA, including early rotorcraft work done through Langley Research Center, but more recently, out of Ames Research Center. NASA Small Business Innovation Research (SBIR) grants on helicopter wake modeling resulted in the Comprehensive Hierarchical Aeromechanics Rotorcraft Model (CHARM), a tool for studying helicopter and tiltrotor unsteady free wake modeling, including distributed and integrated loads, and performance prediction. Application of the software code in a blade redesign program for Carson Helicopters, of Perkasie, Pennsylvania, increased the payload and cruise speeds of its S-61 helicopter. Follow-on development resulted in a $24 million revenue increase for Sikorsky Aircraft Corporation, of Stratford, Connecticut, as part of the company's rotor design efforts. Now under continuous development for more than 25 years, CHARM models the complete aerodynamics and dynamics of rotorcraft in general flight conditions. CHARM has been used to model a broad spectrum of rotorcraft attributes, including performance, blade loading, blade-vortex interaction noise, air flow fields, and hub loads. The highly accurate software is currently in use by all major rotorcraft manufacturers, NASA, the U.S. Army, and the U.S. Navy.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

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

Advanced Prosthetic Gait Training Tool

DTIC Science & Technology

2014-10-01

AWARD NUMBER: W81XWH-10-1-0870 TITLE: Advanced Prosthetic Gait Training Tool...October 2014 2. REPORT TYPE Annual Report 3. DATES COVERED 20 Sep 2013 to 19 Sep 2014 4. TITLE AND SUBTITLE Advanced Prosthetic Gait Training...produce a computer-based Advanced Prosthetic Gait Training Tool to aid in the training of clinicians at military treatment facilities providing care

Advanced Software Development Workstation Project

NASA Technical Reports Server (NTRS)

Lee, Daniel

1989-01-01

The Advanced Software Development Workstation Project, funded by Johnson Space Center, is investigating knowledge-based techniques for software reuse in NASA software development projects. Two prototypes have been demonstrated and a third is now in development. The approach is to build a foundation that provides passive reuse support, add a layer that uses domain-independent programming knowledge, add a layer that supports the acquisition of domain-specific programming knowledge to provide active support, and enhance maintainability and modifiability through an object-oriented approach. The development of new application software would use specification-by-reformulation, based on a cognitive theory of retrieval from very long-term memory in humans, and using an Ada code library and an object base. Current tasks include enhancements to the knowledge representation of Ada packages and abstract data types, extensions to support Ada package instantiation knowledge acquisition, integration with Ada compilers and relational databases, enhancements to the graphical user interface, and demonstration of the system with a NASA contractor-developed trajectory simulation package. Future work will focus on investigating issues involving scale-up and integration.

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.

A software communication tool for the tele-ICU.

PubMed

Pimintel, Denise M; Wei, Shang Heng; Odor, Alberto

2013-01-01

The Tele Intensive Care Unit (tele-ICU) supports a high volume, high acuity population of patients. There is a high-volume of incoming and outgoing calls, especially during the evening and night hours, through the tele-ICU hubs. The tele-ICU clinicians must be able to communicate effectively to team members in order to support the care of complex and critically ill patients while supporting and maintaining a standard to improve time to intervention. This study describes a software communication tool that will improve the time to intervention, over the paper-driven communication format presently used in the tele-ICU. The software provides a multi-relational database of message instances to mine information for evaluation and quality improvement for all entities that touch the tele-ICU. The software design incorporates years of critical care and software design experience combined with new skills acquired in an applied Health Informatics program. This software tool will function in the tele-ICU environment and perform as a front-end application that gathers, routes, and displays internal communication messages for intervention by priority and provider.

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…

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

Advanced Software V&V for Civil Aviation and Autonomy

NASA Technical Reports Server (NTRS)

Brat, Guillaume P.

2017-01-01

With the advances in high-computing platform (e.g., advanced graphical processing units or multi-core processors), computationally-intensive software techniques such as the ones used in artificial intelligence or formal methods have provided us with an opportunity to further increase safety in the aviation industry. Some of these techniques have facilitated building safety at design time, like in aircraft engines or software verification and validation, and others can introduce safety benefits during operations as long as we adapt our processes. In this talk, I will present how NASA is taking advantage of these new software techniques to build in safety at design time through advanced software verification and validation, which can be applied earlier and earlier in the design life cycle and thus help also reduce the cost of aviation assurance. I will then show how run-time techniques (such as runtime assurance or data analytics) offer us a chance to catch even more complex problems, even in the face of changing and unpredictable environments. These new techniques will be extremely useful as our aviation systems become more complex and more autonomous.

Software tools for interactive instruction in radiologic anatomy.

PubMed

Alvarez, Antonio; Gold, Garry E; Tobin, Brian; Desser, Terry S

2006-04-01

To promote active learning in an introductory Radiologic Anatomy course through the use of computer-based exercises. DICOM datasets from our hospital PACS system were transferred to a networked cluster of desktop computers in a medical school classroom. Medical students in the Radiologic Anatomy course were divided into four small groups and assigned to work on a clinical case for 45 minutes. The groups used iPACS viewer software, a free DICOM viewer, to view images and annotate anatomic structures. The classroom instructor monitored and displayed each group's work sequentially on the master screen by running SynchronEyes, a software tool for controlling PC desktops remotely. Students were able to execute the assigned tasks using the iPACS software with minimal oversight or instruction. Course instructors displayed each group's work on the main display screen of the classroom as the students presented the rationale for their decisions. The interactive component of the course received high ratings from the students and overall course ratings were higher than in prior years when the course was given solely in lecture format. DICOM viewing software is an excellent tool for enabling students to learn radiologic anatomy from real-life clinical datasets. Interactive exercises performed in groups can be powerful tools for stimulating students to learn radiologic anatomy.

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

PubMed Central

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

2011-01-01

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

Advanced transport operating system software upgrade: Flight management/flight controls software description

NASA Technical Reports Server (NTRS)

Clinedinst, Winston C.; Debure, Kelly R.; Dickson, Richard W.; Heaphy, William J.; Parks, Mark A.; Slominski, Christopher J.; Wolverton, David A.

1988-01-01

The Flight Management/Flight Controls (FM/FC) software for the Norden 2 (PDP-11/70M) computer installed on the NASA 737 aircraft is described. The software computes the navigation position estimates, guidance commands, those commands to be issued to the control surfaces to direct the aircraft in flight based on the modes selected on the Advanced Guidance Control System (AGSC) mode panel, and the flight path selected via the Navigation Control/Display Unit (NCDU).

A software tool for ecosystem services assessments

NASA Astrophysics Data System (ADS)

Riegels, Niels; Klinting, Anders; Butts, Michael; Middelboe, Anne Lise; Mark, Ole

2017-04-01

The EU FP7 DESSIN project is developing methods and tools for assessment of ecosystem services (ESS) and associated economic values, with a focus on freshwater ESS in urban settings. Although the ESS approach has gained considerable visibility over the past ten years, operationalizing the approach remains a challenge. Therefore, DESSSIN is also supporting development of a free software tool to support users implementing the DESSIN ESS evaluation framework. The DESSIN ESS evaluation framework is a structured approach to measuring changes in ecosystem services. The main purpose of the framework is to facilitate the application of the ESS approach in the appraisal of projects that have impacts on freshwater ecosystems and their services. The DESSIN framework helps users evaluate changes in ESS by linking biophysical, economic, and sustainability assessments sequentially. It was developed using the Common International Classification of Ecosystem Services (CICES) and the DPSIR (Drivers, Pressures, States, Impacts, Responses) adaptive management cycle. The former is a standardized system for the classification of ESS developed by the European Union to enhance the consistency and comparability of ESS assessments. The latter is a well-known concept to disentangle the biophysical and social aspects of a system under study. As part of its analytical component, the DESSIN framework also integrates elements of the Final Ecosystem Goods and Services-Classification System (FEGS-CS) of the US Environmental Protection Agency (USEPA). As implemented in the software tool, the DESSIN framework consists of five parts: • In part I of the evaluation, the ecosystem is defined and described and the local stakeholders are identified. In addition, administrative details and objectives of the assessment are defined. • In part II, drivers and pressures are identified. Once these first two elements of the DPSIR scheme have been characterized, the claimed/expected capabilities of a

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.

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.

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

CSAM Metrology Software Tool

NASA Technical Reports Server (NTRS)

Vu, Duc; Sandor, Michael; Agarwal, Shri

2005-01-01

CSAM Metrology Software Tool (CMeST) is a computer program for analysis of false-color CSAM images of plastic-encapsulated microcircuits. (CSAM signifies C-mode scanning acoustic microscopy.) The colors in the images indicate areas of delamination within the plastic packages. Heretofore, the images have been interpreted by human examiners. Hence, interpretations have not been entirely consistent and objective. CMeST processes the color information in image-data files to detect areas of delamination without incurring inconsistencies of subjective judgement. CMeST can be used to create a database of baseline images of packages acquired at given times for comparison with images of the same packages acquired at later times. Any area within an image can be selected for analysis, which can include examination of different delamination types by location. CMeST can also be used to perform statistical analyses of image data. Results of analyses are available in a spreadsheet format for further processing. The results can be exported to any data-base-processing software.

Artificial intelligence and expert systems in-flight software testing

NASA Technical Reports Server (NTRS)

Demasie, M. P.; Muratore, J. F.

1991-01-01

The authors discuss the introduction of advanced information systems technologies such as artificial intelligence, expert systems, and advanced human-computer interfaces directly into Space Shuttle software engineering. The reconfiguration automation project (RAP) was initiated to coordinate this move towards 1990s software technology. The idea behind RAP is to automate several phases of the flight software testing procedure and to introduce AI and ES into space shuttle flight software testing. In the first phase of RAP, conventional tools to automate regression testing have already been developed or acquired. There are currently three tools in use.

Lessons learned applying CASE methods/tools to Ada software development projects

NASA Technical Reports Server (NTRS)

Blumberg, Maurice H.; Randall, Richard L.

1993-01-01

This paper describes the lessons learned from introducing CASE methods/tools into organizations and applying them to actual Ada software development projects. This paper will be useful to any organization planning to introduce a software engineering environment (SEE) or evolving an existing one. It contains management level lessons learned, as well as lessons learned in using specific SEE tools/methods. The experiences presented are from Alpha Test projects established under the STARS (Software Technology for Adaptable and Reliable Systems) project. They reflect the front end efforts by those projects to understand the tools/methods, initial experiences in their introduction and use, and later experiences in the use of specific tools/methods and the introduction of new ones.

Software Engineering Tools for Scientific Models

NASA Technical Reports Server (NTRS)

Abrams, Marc; Saboo, Pallabi; Sonsini, Mike

2013-01-01

Software tools were constructed to address issues the NASA Fortran development community faces, and they were tested on real models currently in use at NASA. These proof-of-concept tools address the High-End Computing Program and the Modeling, Analysis, and Prediction Program. Two examples are the NASA Goddard Earth Observing System Model, Version 5 (GEOS-5) atmospheric model in Cell Fortran on the Cell Broadband Engine, and the Goddard Institute for Space Studies (GISS) coupled atmosphere- ocean model called ModelE, written in fixed format Fortran.

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.

Computer-Aided Process and Tools for Mobile Software Acquisition

DTIC Science & Technology

2013-04-01

Software Acquisition Christopher Bonine , Man-Tak Shing, and Thomas W. Otani Naval Postgraduate School Published April 1, 2013 Approved for public...ManTech International Corporation Computer-Aided Process and Tools for Mobile Software Acquisition Christopher Bonine , Man-Tak Shing, and Thomas W. Otani...Mobile Software Acquisition Christopher Bonine — Bonine is a lieutenant in the United States Navy. He is currently assigned to the Navy Cyber Defense

Software development tools: A bibliography, appendix C.

NASA Technical Reports Server (NTRS)

Riddle, W. E.

1980-01-01

A bibliography containing approximately 200 citations on tools which help software developers perform some development task (such as text manipulation, testing, etc.), and which would not necessarily be found as part of a computing facility is given. The bibliography comes from a relatively random sampling of the literature and is not complete. But it is indicative of the nature and range of tools currently being prepared or currently available.

Advanced software integration: The case for ITV facilities

NASA Technical Reports Server (NTRS)

Garman, John R.

1990-01-01

The array of technologies and methodologies involved in the development and integration of avionics software has moved almost as rapidly as computer technology itself. Future avionics systems involve major advances and risks in the following areas: (1) Complexity; (2) Connectivity; (3) Security; (4) Duration; and (5) Software engineering. From an architectural standpoint, the systems will be much more distributed, involve session-based user interfaces, and have the layered architectures typified in the layers of abstraction concepts popular in networking. Typified in the NASA Space Station Freedom will be the highly distributed nature of software development itself. Systems composed of independent components developed in parallel must be bound by rigid standards and interfaces, the clean requirements and specifications. Avionics software provides a challenge in that it can not be flight tested until the first time it literally flies. It is the binding of requirements for such an integration environment into the advances and risks of future avionics systems that form the basis of the presented concept and the basic Integration, Test, and Verification concept within the development and integration life cycle of Space Station Mission and Avionics systems.

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.

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.

Framework Support For Knowledge-Based Software Development

NASA Astrophysics Data System (ADS)

Huseth, Steve

1988-03-01

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

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

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

Software Certification for Temporal Properties With Affordable Tool Qualification

NASA Technical Reports Server (NTRS)

Xia, Songtao; DiVito, Benedetto L.

2005-01-01

It has been recognized that a framework based on proof-carrying code (also called semantic-based software certification in its community) could be used as a candidate software certification process for the avionics industry. To meet this goal, tools in the "trust base" of a proof-carrying code system must be qualified by regulatory authorities. A family of semantic-based software certification approaches is described, each different in expressive power, level of automation and trust base. Of particular interest is the so-called abstraction-carrying code, which can certify temporal properties. When a pure abstraction-carrying code method is used in the context of industrial software certification, the fact that the trust base includes a model checker would incur a high qualification cost. This position paper proposes a hybrid of abstraction-based and proof-based certification methods so that the model checker used by a client can be significantly simplified, thereby leading to lower cost in tool qualification.

NASA's Advanced Multimission Operations System: A Case Study in Formalizing Software Architecture Evolution

NASA Technical Reports Server (NTRS)

Barnes, Jeffrey M.

2011-01-01

All software systems of significant size and longevity eventually undergo changes to their basic architectural structure. Such changes may be prompted by evolving requirements, changing technology, or other reasons. Whatever the cause, software architecture evolution is commonplace in real world software projects. Recently, software architecture researchers have begun to study this phenomenon in depth. However, this work has suffered from problems of validation; research in this area has tended to make heavy use of toy examples and hypothetical scenarios and has not been well supported by real world examples. To help address this problem, I describe an ongoing effort at the Jet Propulsion Laboratory to re-architect the Advanced Multimission Operations System (AMMOS), which is used to operate NASA's deep-space and astrophysics missions. Based on examination of project documents and interviews with project personnel, I describe the goals and approach of this evolution effort and then present models that capture some of the key architectural changes. Finally, I demonstrate how approaches and formal methods from my previous research in architecture evolution may be applied to this evolution, while using languages and tools already in place at the Jet Propulsion Laboratory.

Knickpoint finder: A software tool that improves neotectonic analysis

NASA Astrophysics Data System (ADS)

Queiroz, G. L.; Salamuni, E.; Nascimento, E. R.

2015-03-01

This work presents a new software tool for morphometric analysis of drainage networks based on the methods of Hack (1973) and Etchebehere et al. (2004). This tool is applicable to studies of morphotectonics and neotectonics. The software used a digital elevation model (DEM) to identify the relief breakpoints along drainage profiles (knickpoints). The program was coded in Python for use on the ArcGIS platform and is called Knickpoint Finder. A study area was selected to test and evaluate the software's ability to analyze and identify neotectonic morphostructures based on the morphology of the terrain. For an assessment of its validity, we chose an area of the James River basin, which covers most of the Piedmont area of Virginia (USA), which is an area of constant intraplate seismicity and non-orogenic active tectonics and exhibits a relatively homogeneous geodesic surface currently being altered by the seismogenic features of the region. After using the tool in the chosen area, we found that the knickpoint locations are associated with the geologic structures, epicenters of recent earthquakes, and drainages with rectilinear anomalies. The regional analysis demanded the use of a spatial representation of the data after processing using Knickpoint Finder. The results were satisfactory in terms of the correlation of dense areas of knickpoints with active lineaments and the rapidity of the identification of deformed areas. Therefore, this software tool may be considered useful in neotectonic analyses of large areas and may be applied to any area where there is DEM coverage.

The Perfect Neuroimaging-Genetics-Computation Storm: Collision of Petabytes of Data, Millions of Hardware Devices and Thousands of Software Tools

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Zamanyan, Alen; Torri, Federica; Macciardi, Fabio; Hobel, Sam; Moon, Seok Woo; Sung, Young Hee; Jiang, Zhiguo; Labus, Jennifer; Kurth, Florian; Ashe-McNalley, Cody; Mayer, Emeran; Vespa, Paul M.; Van Horn, John D.; Toga, Arthur W.

2013-01-01

The volume, diversity and velocity of biomedical data are exponentially increasing providing petabytes of new neuroimaging and genetics data every year. At the same time, tens-of-thousands of computational algorithms are developed and reported in the literature along with thousands of software tools and services. Users demand intuitive, quick and platform-agnostic access to data, software tools, and infrastructure from millions of hardware devices. This explosion of information, scientific techniques, computational models, and technological advances leads to enormous challenges in data analysis, evidence-based biomedical inference and reproducibility of findings. The Pipeline workflow environment provides a crowd-based distributed solution for consistent management of these heterogeneous resources. The Pipeline allows multiple (local) clients and (remote) servers to connect, exchange protocols, control the execution, monitor the states of different tools or hardware, and share complete protocols as portable XML workflows. In this paper, we demonstrate several advanced computational neuroimaging and genetics case-studies, and end-to-end pipeline solutions. These are implemented as graphical workflow protocols in the context of analyzing imaging (sMRI, fMRI, DTI), phenotypic (demographic, clinical), and genetic (SNP) data. PMID:23975276

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…

A Software Tool for Integrated Optical Design Analysis

NASA Technical Reports Server (NTRS)

Moore, Jim; Troy, Ed; DePlachett, Charles; Montgomery, Edward (Technical Monitor)

2001-01-01

Design of large precision optical systems requires multi-disciplinary analysis, modeling, and design. Thermal, structural and optical characteristics of the hardware must be accurately understood in order to design a system capable of accomplishing the performance requirements. The interactions between each of the disciplines become stronger as systems are designed lighter weight for space applications. This coupling dictates a concurrent engineering design approach. In the past, integrated modeling tools have been developed that attempt to integrate all of the complex analysis within the framework of a single model. This often results in modeling simplifications and it requires engineering specialist to learn new applications. The software described in this presentation addresses the concurrent engineering task using a different approach. The software tool, Integrated Optical Design Analysis (IODA), uses data fusion technology to enable a cross discipline team of engineering experts to concurrently design an optical system using their standard validated engineering design tools.

Advanced Spacesuit Informatics Software Design for Power, Avionics and Software Version 2.0

NASA Technical Reports Server (NTRS)

Wright, Theodore W.

2016-01-01

A description of the software design for the 2016 edition of the Informatics computer assembly of the NASAs Advanced Extravehicular Mobility Unit (AEMU), also called the Advanced Spacesuit. The Informatics system is an optional part of the spacesuit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and warning information. It also provides an interface to the suit mounted camera for recording still images, video, and audio field notes.

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.

Advanced information processing system: Input/output network management software

NASA Technical Reports Server (NTRS)

Nagle, Gail; Alger, Linda; Kemp, Alexander

1988-01-01

The purpose of this document is to provide the software requirements and specifications for the Input/Output Network Management Services for the Advanced Information Processing System. This introduction and overview section is provided to briefly outline the overall architecture and software requirements of the AIPS system before discussing the details of the design requirements and specifications of the AIPS I/O Network Management software. A brief overview of the AIPS architecture followed by a more detailed description of the network architecture.

Software modifications to the Demonstration Advanced Avionics Systems (DAAS)

NASA Technical Reports Server (NTRS)

Nedell, B. F.; Hardy, G. H.

1984-01-01

Critical information required for the design of integrated avionics suitable for generation aviation is applied towards software modifications for the Demonstration Advanced Avionics System (DAAS). The program emphasizes the use of data busing, distributed microprocessors, shared electronic displays and data entry devices, and improved functional capability. A demonstration advanced avionics system (DAAS) is designed, built, and flight tested in a Cessna 402, twin engine, general aviation aircraft. Software modifications are made to DAAS at Ames concurrent with the flight test program. The changes are the result of the experience obtained with the system at Ames, and the comments of the pilots who evaluated the system.

Advanced Tools for River Science: EAARL and MD_SWMS: Chapter 3

USGS Publications Warehouse

Kinzel, Paul J.

2009-01-01

Disruption of flow regimes and sediment supplies, induced by anthropogenic or climatic factors, can produce dramatic alterations in river form, vegetation patterns, and associated habitat conditions. To improve habitat in these fluvial systems, resource managers may choose from a variety of treatments including flow and/or sediment prescriptions, vegetation management, or engineered approaches. Monitoring protocols developed to assess the morphologic response of these treatments require techniques that can measure topographic changes above and below the water surface efficiently, accurately, and in a standardized, cost-effective manner. Similarly, modeling of flow, sediment transport, habitat, and channel evolution requires characterization of river morphology for model input and verification. Recent developments by the U.S. Geological Survey with regard to both remotely sensed methods (the Experimental Advanced Airborne Research LiDAR; EAARL) and computational modeling software (the Multi-Dimensional Surface-Water Modeling System; MD_SWMS) have produced advanced tools for spatially explicit monitoring and modeling in aquatic environments. In this paper, we present a pilot study conducted along the Platte River, Nebraska, that demonstrates the combined use of these river science tools.

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

PAnalyzer: a software tool for protein inference in shotgun proteomics.

PubMed

Prieto, Gorka; Aloria, Kerman; Osinalde, Nerea; Fullaondo, Asier; Arizmendi, Jesus M; Matthiesen, Rune

2012-11-05

Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and

PAnalyzer: A software tool for protein inference in shotgun proteomics

PubMed Central

2012-01-01

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an

GenePRIMP: A software quality control tool

ScienceCinema

Amrita Pati

2017-12-09

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

Meta-tools for software development and knowledge acquisition

NASA Technical Reports Server (NTRS)

Eriksson, Henrik; Musen, Mark A.

1992-01-01

The effectiveness of tools that provide support for software development is highly dependent on the match between the tools and their task. Knowledge-acquisition (KA) tools constitute a class of development tools targeted at knowledge-based systems. Generally, KA tools that are custom-tailored for particular application domains are more effective than are general KA tools that cover a large class of domains. The high cost of custom-tailoring KA tools manually has encouraged researchers to develop meta-tools for KA tools. Current research issues in meta-tools for knowledge acquisition are the specification styles, or meta-views, for target KA tools used, and the relationships between the specification entered in the meta-tool and other specifications for the target program under development. We examine different types of meta-views and meta-tools. Our current project is to provide meta-tools that produce KA tools from multiple specification sources--for instance, from a task analysis of the target application.

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

The IHMC CmapTools software in research and education: a multi-level use case in Space Meteorology

NASA Astrophysics Data System (ADS)

Messerotti, Mauro

2010-05-01

The IHMC (Institute for Human and Machine Cognition, Florida University System, USA) CmapTools software is a powerful multi-platform tool for knowledge modelling in graphical form based on concept maps. In this work we present its application for the high-level development of a set of multi-level concept maps in the framework of Space Meteorology to act as the kernel of a space meteorology domain ontology. This is an example of a research use case, as a domain ontology coded in machine-readable form via e.g. OWL (Web Ontology Language) is suitable to be an active layer of any knowledge management system embedded in a Virtual Observatory (VO). Apart from being manageable at machine level, concept maps developed via CmapTools are intrinsically human-readable and can embed hyperlinks and objects of many kinds. Therefore they are suitable to be published on the web: the coded knowledge can be exploited for educational purposes by the students and the public, as the level of information can be naturally organized among linked concept maps in progressively increasing complexity levels. Hence CmapTools and its advanced version COE (Concept-map Ontology Editor) represent effective and user-friendly software tools for high-level knowledge represention in research and education.

Modernizing Systems and Software: How Evolving Trends in Future Trends in Systems and Software Technology Bode Well for Advancing the Precision of Technology

DTIC Science & Technology

2009-04-23

of Code Need for increased functionality will be a forcing function to bring the fields of software and systems engineering... of Software-Intensive Systems is Increasing 3 How Evolving Trends in Systems and Software Technologies Bode Well for Advancing the Precision of ...Engineering in Continued Partnership 4 How Evolving Trends in Systems and Software Technologies Bode Well for Advancing the

Economic Consequence Analysis of Disasters: The ECAT Software Tool

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

Rose, Adam; Prager, Fynn; Chen, Zhenhua

This study develops a methodology for rapidly obtaining approximate estimates of the economic consequences from numerous natural, man-made and technological threats. This software tool is intended for use by various decision makers and analysts to obtain estimates rapidly. It is programmed in Excel and Visual Basic for Applications (VBA) to facilitate its use. This tool is called E-CAT (Economic Consequence Analysis Tool) and accounts for the cumulative direct and indirect impacts (including resilience and behavioral factors that significantly affect base estimates) on the U.S. economy. E-CAT is intended to be a major step toward advancing the current state of economicmore » consequence analysis (ECA) and also contributing to and developing interest in further research into complex but rapid turnaround approaches. The essence of the methodology involves running numerous simulations in a computable general equilibrium (CGE) model for each threat, yielding synthetic data for the estimation of a single regression equation based on the identification of key explanatory variables (threat characteristics and background conditions). This transforms the results of a complex model, which is beyond the reach of most users, into a "reduced form" model that is readily comprehensible. Functionality has been built into E-CAT so that its users can switch various consequence categories on and off in order to create customized profiles of economic consequences of numerous risk events. E-CAT incorporates uncertainty on both the input and output side in the course of the analysis.« less

Software engineering techniques and CASE tools in RD13

NASA Astrophysics Data System (ADS)

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

1994-12-01

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

Control Software for Advanced Video Guidance Sensor

NASA Technical Reports Server (NTRS)

Howard, Richard T.; Book, Michael L.; Bryan, Thomas C.

2006-01-01

Embedded software has been developed specifically for controlling an Advanced Video Guidance Sensor (AVGS). A Video Guidance Sensor is an optoelectronic system that provides guidance for automated docking of two vehicles. Such a system includes pulsed laser diodes and a video camera, the output of which is digitized. From the positions of digitized target images and known geometric relationships, the relative position and orientation of the vehicles are computed. The present software consists of two subprograms running in two processors that are parts of the AVGS. The subprogram in the first processor receives commands from an external source, checks the commands for correctness, performs commanded non-image-data-processing control functions, and sends image data processing parts of commands to the second processor. The subprogram in the second processor processes image data as commanded. Upon power-up, the software performs basic tests of functionality, then effects a transition to a standby mode. When a command is received, the software goes into one of several operational modes (e.g. acquisition or tracking). The software then returns, to the external source, the data appropriate to the command.

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.

A Symphony of Software.

ERIC Educational Resources Information Center

Currents, 2002

2002-01-01

Offers a descriptive table of databases that help higher education institutions orchestrate advancement operations. Information includes vendor, contact, software, price, database engine/server platform, recommended reporting tools, record capacity, and client type. (EV)

COSTMODL: An automated software development cost estimation tool

NASA Technical Reports Server (NTRS)

Roush, George B.

1991-01-01

The cost of developing computer software continues to consume an increasing portion of many organizations' total budgets, both in the public and private sector. As this trend develops, the capability to produce reliable estimates of the effort and schedule required to develop a candidate software product takes on increasing importance. The COSTMODL program was developed to provide an in-house capability to perform development cost estimates for NASA software projects. COSTMODL is an automated software development cost estimation tool which incorporates five cost estimation algorithms including the latest models for the Ada language and incrementally developed products. The principal characteristic which sets COSTMODL apart from other software cost estimation programs is its capacity to be completely customized to a particular environment. The estimation equations can be recalibrated to reflect the programmer productivity characteristics demonstrated by the user's organization, and the set of significant factors which effect software development costs can be customized to reflect any unique properties of the user's development environment. Careful use of a capability such as COSTMODL can significantly reduce the risk of cost overruns and failed projects.

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

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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.

Experimental Evaluation of Verification and Validation Tools on Martian Rover Software

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Giannakopoulou, Dimitra; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareani, Corina; Venet, Arnaud; Visser, Willem; Washington, Rich

2003-01-01

We report on a study to determine the maturity of different verification and validation technologies (V&V) on a representative example of NASA flight software. The study consisted of a controlled experiment where three technologies (static analysis, runtime analysis and model checking) were compared to traditional testing with respect to their ability to find seeded errors in a prototype Mars Rover. What makes this study unique is that it is the first (to the best of our knowledge) to do a controlled experiment to compare formal methods based tools to testing on a realistic industrial-size example where the emphasis was on collecting as much data on the performance of the tools and the participants as possible. The paper includes a description of the Rover code that was analyzed, the tools used as well as a detailed description of the experimental setup and the results. Due to the complexity of setting up the experiment, our results can not be generalized, but we believe it can still serve as a valuable point of reference for future studies of this kind. It did confirm the belief we had that advanced tools can outperform testing when trying to locate concurrency errors. Furthermore the results of the experiment inspired a novel framework for testing the next generation of the Rover.

Atrioventricular junction (AVJ) motion tracking: a software tool with ITK/VTK/Qt.

PubMed

Pengdong Xiao; Shuang Leng; Xiaodan Zhao; Hua Zou; Ru San Tan; Wong, Philip; Liang Zhong

2016-08-01

The quantitative measurement of the Atrioventricular Junction (AVJ) motion is an important index for ventricular functions of one cardiac cycle including systole and diastole. In this paper, a software tool that can conduct AVJ motion tracking from cardiovascular magnetic resonance (CMR) images is presented by using Insight Segmentation and Registration Toolkit (ITK), The Visualization Toolkit (VTK) and Qt. The software tool is written in C++ by using Visual Studio Community 2013 integrated development environment (IDE) containing both an editor and a Microsoft complier. The software package has been successfully implemented. From the software engineering practice, it is concluded that ITK, VTK, and Qt are very handy software systems to implement automatic image analysis functions for CMR images such as quantitative measure of motion by visual tracking.

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.

New software tools for enhanced precision in robot-assisted laser phonomicrosurgery.

PubMed

Dagnino, Giulio; Mattos, Leonardo S; Caldwell, Darwin G

2012-01-01

This paper describes a new software package created to enhance precision during robot-assisted laser phonomicrosurgery procedures. The new software is composed of three tools for camera calibration, automatic tumor segmentation, and laser tracking. These were designed and developed to improve the outcome of this demanding microsurgical technique, and were tested herein to produce quantitative performance data. The experimental setup was based on the motorized laser micromanipulator created by Istituto Italiano di Tecnologia and the experimental protocols followed are fully described in this paper. The results show the new tools are robust and effective: The camera calibration tool reduced residual errors (RMSE) to 0.009 ± 0.002 mm under 40× microscope magnification; the automatic tumor segmentation tool resulted in deep lesion segmentations comparable to manual segmentations (RMSE= 0.160 ± 0.028 mm under 40× magnification); and the laser tracker tool proved to be reliable even during cutting procedures (RMSE= 0.073 ± 0.023 mm under 40× magnification). These results demonstrate the new software package can provide excellent improvements to the previous microsurgical system, leading to important enhancements in surgical outcome.

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

X-ray system simulation software tools for radiology and radiography education.

PubMed

Kengyelics, Stephen M; Treadgold, Laura A; Davies, Andrew G

2018-02-01

To develop x-ray simulation software tools to support delivery of radiological science education for a range of learning environments and audiences including individual study, lectures, and tutorials. Two software tools were developed; one simulated x-ray production for a simple two dimensional radiographic system geometry comprising an x-ray source, beam filter, test object and detector. The other simulated the acquisition and display of two dimensional radiographic images of complex three dimensional objects using a ray casting algorithm through three dimensional mesh objects. Both tools were intended to be simple to use, produce results accurate enough to be useful for educational purposes, and have an acceptable simulation time on modest computer hardware. The radiographic factors and acquisition geometry could be altered in both tools via their graphical user interfaces. A comparison of radiographic contrast measurements of the simulators to a real system was performed. The contrast output of the simulators had excellent agreement with measured results. The software simulators were deployed to 120 computers on campus. The software tools developed are easy-to-use, clearly demonstrate important x-ray physics and imaging principles, are accessible within a standard University setting and could be used to enhance the teaching of x-ray physics to undergraduate students. Current approaches to teaching x-ray physics in radiological science lack immediacy when linking theory with practice. This method of delivery allows students to engage with the subject in an experiential learning environment. Copyright © 2017. Published by Elsevier Ltd.

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.

Software Tools on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

Debugger or performance analysis Tool for understanding the behavior of MPI applications. Intel VTune environment for statistical computing and graphics. VirtualGL/TurboVNC Visualization and analytics Remote Tools on the Peregrine System Software Tools on the Peregrine System NREL has a variety of

Management of an affiliated Physics Residency Program using a commercial software tool.

PubMed

Zacarias, Albert S; Mills, Michael D

2010-06-01

A review of commercially available allied health educational management software tools was performed to evaluate their capacity to manage program data associated with a CAMPEP-accredited Therapy Physics Residency Program. Features of these software tools include: a) didactic course reporting and organization, b) competency reporting by topic, category and didactic course, c) student time management and accounting, and d) student patient case reporting by topic, category and course. The software package includes features for recording school administrative information; setting up lists of courses, faculty, clinical sites, categories, competencies, and time logs; and the inclusion of standardized external documents. There are provisions for developing evaluation and survey instruments. The mentors and program may be evaluated by residents, and residents may be evaluated by faculty members using this feature. Competency documentation includes the time spent on the problem or with the patient, time spent with the mentor, date of the competency, and approval by the mentor and program director. Course documentation includes course and lecture title, lecturer, topic information, date of lecture and approval by the Program Director. These software tools have the facility to include multiple clinical sites, with local subadministrators having the ability to approve competencies and attendance at clinical conferences. In total, these software tools have the capability of managing all components of a CAMPEP-accredited residency program. The application database lends the software to the support of multiple affiliated clinical sites within a single residency program. Such tools are a critical and necessary component if the medical physics profession is to meet the projected needs for qualified medical physicists in future years.

Advanced software development workstation project: Engineering scripting language. Graphical editor

NASA Technical Reports Server (NTRS)

1992-01-01

Software development is widely considered to be a bottleneck in the development of complex systems, both in terms of development and in terms of maintenance of deployed systems. Cost of software development and maintenance can also be very high. One approach to reducing costs and relieving this bottleneck is increasing the reuse of software designs and software components. A method for achieving such reuse is a software parts composition system. Such a system consists of a language for modeling software parts and their interfaces, a catalog of existing parts, an editor for combining parts, and a code generator that takes a specification and generates code for that application in the target language. The Advanced Software Development Workstation is intended to be an expert system shell designed to provide the capabilities of a software part composition system.

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.

COSTMODL - AN AUTOMATED SOFTWARE DEVELOPMENT COST ESTIMATION TOOL

NASA Technical Reports Server (NTRS)

Roush, G. B.

1994-01-01

The cost of developing computer software consumes an increasing portion of many organizations' budgets. As this trend continues, the capability to estimate the effort and schedule required to develop a candidate software product becomes increasingly important. COSTMODL is an automated software development estimation tool which fulfills this need. Assimilating COSTMODL to any organization's particular environment can yield significant reduction in the risk of cost overruns and failed projects. This user-customization capability is unmatched by any other available estimation tool. COSTMODL accepts a description of a software product to be developed and computes estimates of the effort required to produce it, the calendar schedule required, and the distribution of effort and staffing as a function of the defined set of development life-cycle phases. This is accomplished by the five cost estimation algorithms incorporated into COSTMODL: the NASA-developed KISS model; the Basic, Intermediate, and Ada COCOMO models; and the Incremental Development model. This choice affords the user the ability to handle project complexities ranging from small, relatively simple projects to very large projects. Unique to COSTMODL is the ability to redefine the life-cycle phases of development and the capability to display a graphic representation of the optimum organizational structure required to develop the subject project, along with required staffing levels and skills. The program is menu-driven and mouse sensitive with an extensive context-sensitive help system that makes it possible for a new user to easily install and operate the program and to learn the fundamentals of cost estimation without having prior training or separate documentation. The implementation of these functions, along with the customization feature, into one program makes COSTMODL unique within the industry. COSTMODL was written for IBM PC compatibles, and it requires Turbo Pascal 5.0 or later and Turbo

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.

Exoskeletons, Robots and System Software: Tools for the Warfighter

DTIC Science & Technology

2012-04-24

Exoskeletons , Robots and System Software: Tools for the Warfighter? Paul Flanagan, Tuesday, April 24, 2012 11:15 am– 12:00 pm 1 “The views...Emerging technologies such as exoskeletons , robots , drones, and the underlying software are and will change the face of the battlefield. Warfighters will...global hub for educating, informing, and connecting Information Age leaders.” What is an exoskeleton ? An exoskeleton is a wearable robot suit that

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 .

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

PubMed

Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

2017-06-28

High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

Recent Advances in Algal Genetic Tool Development

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

R. Dahlin, Lukas; T. Guarnieri, Michael

The goal of achieving cost-effective biofuels and bioproducts derived from algal biomass will require improvements along the entire value chain, including identification of robust, high-productivity strains and development of advanced genetic tools. Though there have been modest advances in development of genetic systems for the model alga Chlamydomonas reinhardtii, progress in development of algal genetic tools, especially as applied to non-model algae, has generally lagged behind that of more commonly utilized laboratory and industrial microbes. This is in part due to the complex organellar structure of algae, including robust cell walls and intricate compartmentalization of target loci, as well asmore » prevalent gene silencing mechanisms, which hinder facile utilization of conventional genetic engineering tools and methodologies. However, recent progress in global tool development has opened the door for implementation of strain-engineering strategies in industrially-relevant algal strains. Here, we review recent advances in algal genetic tool development and applications in eukaryotic microalgae.« less

Recent Advances in Algal Genetic Tool Development

DOE PAGES

R. Dahlin, Lukas; T. Guarnieri, Michael

2016-06-24

The goal of achieving cost-effective biofuels and bioproducts derived from algal biomass will require improvements along the entire value chain, including identification of robust, high-productivity strains and development of advanced genetic tools. Though there have been modest advances in development of genetic systems for the model alga Chlamydomonas reinhardtii, progress in development of algal genetic tools, especially as applied to non-model algae, has generally lagged behind that of more commonly utilized laboratory and industrial microbes. This is in part due to the complex organellar structure of algae, including robust cell walls and intricate compartmentalization of target loci, as well asmore » prevalent gene silencing mechanisms, which hinder facile utilization of conventional genetic engineering tools and methodologies. However, recent progress in global tool development has opened the door for implementation of strain-engineering strategies in industrially-relevant algal strains. Here, we review recent advances in algal genetic tool development and applications in eukaryotic microalgae.« less

A software tool for analyzing multichannel cochlear implant signals.

PubMed

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

2003-10-01

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

Data-Driven Decision Making as a Tool to Improve Software Development Productivity

ERIC Educational Resources Information Center

Brown, Mary Erin

2013-01-01

The worldwide software project failure rate, based on a survey of information technology software manager's view of user satisfaction, product quality, and staff productivity, is estimated to be between 24% and 36% and software project success has not kept pace with the advances in hardware. The problem addressed by this study was the limited…

ISWHM: Tools and Techniques for Software and System Health Management

NASA Technical Reports Server (NTRS)

Schumann, Johann; Mengshoel, Ole J.; Darwiche, Adnan

2010-01-01

This presentation presents status and results of research on Software Health Management done within the NRA "ISWHM: Tools and Techniques for Software and System Health Management." Topics include: Ingredients of a Guidance, Navigation, and Control System (GN and C); Selected GN and C Testbed example; Health Management of major ingredients; ISWHM testbed architecture; and Conclusions and next Steps.

IUWare and Computing Tools: Indiana University's Approach to Low-Cost Software.

ERIC Educational Resources Information Center

Sheehan, Mark C.; Williams, James G.

1987-01-01

Describes strategies for providing low-cost microcomputer-based software for classroom use on college campuses. Highlights include descriptions of the software (IUWare and Computing Tools); computing center support; license policies; documentation; promotion; distribution; staff, faculty, and user training; problems; and future plans. (LRW)

Advanced program development management software system. Software description and user's manual

NASA Technical Reports Server (NTRS)

1990-01-01

The objectives of this project were to apply emerging techniques and tools from the computer science discipline of paperless management to the activities of the Space Transportation and Exploration Office (PT01) in Marshall Space Flight Center (MSFC) Program Development, thereby enhancing the productivity of the workforce, the quality of the data products, and the collection, dissemination, and storage of information. The approach used to accomplish the objectives emphasized the utilization of finished form (off-the-shelf) software products to the greatest extent possible without impacting the performance of the end product, to pursue developments when necessary in the rapid prototyping environment to provide a mechanism for frequent feedback from the users, and to provide a full range of user support functions during the development process to promote testing of the software.

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer.

PubMed

Bigler, Don C; Aksu, Yaman; Miller, David J; Yang, Qing X

2009-08-01

This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

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.

Anvil Tool in the Advanced Weather Interactive Processing System

NASA Technical Reports Server (NTRS)

Barrett, Joe, III; Bauman, William, III; Keen, Jeremy

2007-01-01

Meteorologists from the 45th Weather Squadron (45 WS) and Spaceflight Meteorology Group (SMG) have identified anvil forecasting as one of their most challenging tasks when predicting the probability of violations of the lightning Launch Commit Criteria and Space Shuttle Flight Rules. As a result, the Applied Meteorology Unit (AMU) created a graphical overlay tool for the Meteorological Interactive Data Display Systems (MIDDS) to indicate the threat of thunderstorm anvil clouds, using either observed or model forecast winds as input. In order for the Anvil Tool to remain available to the meteorologists, the AMU was tasked to transition the tool to the Advanced Weather interactive Processing System (AWIPS). This report describes the work done by the AMU to develop the Anvil Tool for AWIPS to create a graphical overlay depicting the threat from thunderstorm anvil clouds. The AWIPS Anvil Tool is based on the previously deployed AMU MIDDS Anvil Tool. SMG and 45 WS forecasters have used the MIDDS Anvil Tool during launch and landing operations. SMG's primary weather analysis and display system is now AWIPS and the 45 WS has plans to replace MIDDS with AWIPS. The Anvil Tool creates a graphic that users can overlay on satellite or radar imagery to depict the potential location of thunderstorm anvils one, two, and three hours into the future. The locations are based on an average of the upper-level observed or forecasted winds. The graphic includes 10 and 20 nm standoff circles centered at the location of interest, in addition to one-, two-, and three-hour arcs in the upwind direction. The arcs extend outward across a 30 degree sector width based on a previous AMU study which determined thunderstorm anvils move in a direction plus or minus 15 degrees of the upper-level (300- to 150-mb) wind direction. This report briefly describes the history of the MIDDS Anvil Tool and then explains how the initial development of the AWIPS Anvil Tool was carried out. After testing was

The Toxicity Estimation Software Tool (T.E.S.T.)

EPA Science Inventory

The Toxicity Estimation Software Tool (T.E.S.T.) has been developed to estimate toxicological values for aquatic and mammalian species considering acute and chronic endpoints for screening purposes within TSCA and REACH programs.

Benchmarking of software tools for optical proximity correction

NASA Astrophysics Data System (ADS)

Jungmann, Angelika; Thiele, Joerg; Friedrich, Christoph M.; Pforr, Rainer; Maurer, Wilhelm

1998-06-01

The point when optical proximity correction (OPC) will become a routine procedure for every design is not far away. For such a daily use the requirements for an OPC tool go far beyond the principal functionality of OPC that was proven by a number of approaches and is documented well in literature. In this paper we first discuss the requirements for a productive OPC tool. Against these requirements a benchmarking was performed with three different OPC tools available on market (OPRX from TVT, OPTISSIMO from aiss and PROTEUS from TMA). Each of these tools uses a different approach to perform the correction (rules, simulation or model). To assess the accuracy of the correction, a test chip was fabricated, which contains corrections done by each software tool. The advantages and weakness of the several solutions are discussed.

Comparison of software tools for kinetic evaluation of chemical degradation data.

PubMed

Ranke, Johannes; Wöltjen, Janina; Meinecke, Stefan

2018-01-01

For evaluating the fate of xenobiotics in the environment, a variety of degradation or environmental metabolism experiments are routinely conducted. The data generated in such experiments are evaluated by optimizing the parameters of kinetic models in a way that the model simulation fits the data. No comparison of the main software tools currently in use has been published to date. This article shows a comparison of numerical results as well as an overall, somewhat subjective comparison based on a scoring system using a set of criteria. The scoring was separately performed for two types of uses. Uses of type I are routine evaluations involving standard kinetic models and up to three metabolites in a single compartment. Evaluations involving non-standard model components, more than three metabolites or more than a single compartment belong to use type II. For use type I, usability is most important, while the flexibility of the model definition is most important for use type II. Test datasets were assembled that can be used to compare the numerical results for different software tools. These datasets can also be used to ensure that no unintended or erroneous behaviour is introduced in newer versions. In the comparison of numerical results, good agreement between the parameter estimates was observed for datasets with up to three metabolites. For the now unmaintained reference software DegKinManager/ModelMaker, and for OpenModel which is still under development, user options were identified that should be taken care of in order to obtain results that are as reliable as possible. Based on the scoring system mentioned above, the software tools gmkin, KinGUII and CAKE received the best scores for use type I. Out of the 15 software packages compared with respect to use type II, again gmkin and KinGUII were the first two, followed by the script based tool mkin, which is the technical basis for gmkin, and by OpenModel. Based on the evaluation using the system of criteria

TEST (Toxicity Estimation Software Tool) Ver 4.1

EPA Science Inventory

The Toxicity Estimation Software Tool (T.E.S.T.) has been developed to allow users to easily estimate toxicity and physical properties using a variety of QSAR methodologies. T.E.S.T allows a user to estimate toxicity without requiring any external programs. Users can input a chem...

Reliability, Safety and Error Recovery for Advanced Control Software

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2003-01-01

For long-duration automated operation of regenerative life support systems in space environments, there is a need for advanced integration and control systems that are significantly more reliable and safe, and that support error recovery and minimization of operational failures. This presentation outlines some challenges of hazardous space environments and complex system interactions that can lead to system accidents. It discusses approaches to hazard analysis and error recovery for control software and challenges of supporting effective intervention by safety software and the crew.

Software Tools for Developing and Simulating the NASA LaRC CMF Motion Base

NASA Technical Reports Server (NTRS)

Bryant, Richard B., Jr.; Carrelli, David J.

2006-01-01

The NASA Langley Research Center (LaRC) Cockpit Motion Facility (CMF) motion base has provided many design and analysis challenges. In the process of addressing these challenges, a comprehensive suite of software tools was developed. The software tools development began with a detailed MATLAB/Simulink model of the motion base which was used primarily for safety loads prediction, design of the closed loop compensator and development of the motion base safety systems1. A Simulink model of the digital control law, from which a portion of the embedded code is directly generated, was later added to this model to form a closed loop system model. Concurrently, software that runs on a PC was created to display and record motion base parameters. It includes a user interface for controlling time history displays, strip chart displays, data storage, and initializing of function generators used during motion base testing. Finally, a software tool was developed for kinematic analysis and prediction of mechanical clearances for the motion system. These tools work together in an integrated package to support normal operations of the motion base, simulate the end to end operation of the motion base system providing facilities for software-in-the-loop testing, mechanical geometry and sensor data visualizations, and function generator setup and evaluation.

Proceedings, Conference on the Computing Environment for Mathematical Software

NASA Technical Reports Server (NTRS)

1981-01-01

Recent advances in software and hardware technology which make it economical to create computing environments appropriate for specialized applications are addressed. Topics included software tools, FORTRAN standards activity, and features of languages, operating systems, and hardware that are important for the development, testing, and maintenance of mathematical software.

An online database for plant image analysis software tools.

PubMed

Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

2013-10-09

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

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

Classroom Live: a software-assisted gamification tool

NASA Astrophysics Data System (ADS)

de Freitas, Adrian A.; de Freitas, Michelle M.

2013-06-01

Teachers have come to rely on a variety of approaches in order to elicit and sustain student interest in the classroom. One particular approach, known as gamification, seeks to improve student engagement by transforming the traditional classroom experience into a competitive multiplayer game. Initial attempts at classroom gamification relied on the teacher manually tracking student progress. At the US Air Force Academy, we wanted to experiment with a software gamification tool. Our client/server suite, dubbed Classroom Live, streamlines the gamification process for the teacher by simplifying common tasks. Simultaneously, the tool provides students with an esthetically pleasing user interface that offers in game rewards in exchange for their participation. Classroom Live is still in development, but our initial experience using the tool has been extremely positive and confirms our belief that students respond positively to gamification, even at the undergraduate level.

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 .

Chips: A Tool for Developing Software Interfaces Interactively.

ERIC Educational Resources Information Center

Cunningham, Robert E.; And Others

This report provides a detailed description of Chips, an interactive tool for developing software employing graphical/computer interfaces on Xerox Lisp machines. It is noted that Chips, which is implemented as a collection of customizable classes, provides the programmer with a rich graphical interface for the creation of rich graphical…

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by UAH and provide versions of the software in a Macintosh and Windows compatible format.

Advanced Extravehicular Mobility Unit Informatics Software Design

NASA Technical Reports Server (NTRS)

Wright, Theodore

2014-01-01

This is a description of the software design for the 2013 edition of the Advanced Extravehicular Mobility Unit (AEMU) Informatics computer assembly. The Informatics system is an optional part of the space suit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and caution and warning information. In the future it will display maps with GPS position data, and video and still images captured by the astronaut.

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

Creating an automated tool for measuring software cohesion

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

Tutton, J.M.; Zucconi, L.

1994-05-06

Program modules with high complexity tend to be more error prone and more difficult to understand. These factors increase maintenance and enhancement costs. Hence, a tool that can help programmers determine a key factor in module complexity should be very useful. Our goal is to create a software tool that will automatically give a quantitative measure of the cohesiveness of a given module, and hence give us an estimate of the {open_quotes}maintainability{close_quotes} of that module. The Tool will use a metric developed by Professors Linda M. Ott and James M. Bieman. The Ott/Bieman metric gives quantitative measures that indicate themore » degree of functional cohesion using abstract data slices.« less

Advances in Games Technology: Software, Models, and Intelligence

ERIC Educational Resources Information Center

Prakash, Edmond; Brindle, Geoff; Jones, Kevin; Zhou, Suiping; Chaudhari, Narendra S.; Wong, Kok-Wai

2009-01-01

Games technology has undergone tremendous development. In this article, the authors report the rapid advancement that has been observed in the way games software is being developed, as well as in the development of games content using game engines. One area that has gained special attention is modeling the game environment such as terrain and…

An Overview of Public Access Computer Software Management Tools for Libraries

ERIC Educational Resources Information Center

Wayne, Richard

2004-01-01

An IT decision maker gives an overview of public access PC software that's useful in controlling session length and scheduling, Internet access, print output, security, and the latest headaches: spyware and adware. In this article, the author describes a representative sample of software tools in several important categories such as setup…

Development, Implementation and Application of Micromechanical Analysis Tools for Advanced High Temperature Composites

NASA Technical Reports Server (NTRS)

2005-01-01

This document contains the final report to the NASA Glenn Research Center (GRC) for the research project entitled Development, Implementation, and Application of Micromechanical Analysis Tools for Advanced High-Temperature Composites. The research supporting this initiative has been conducted by Dr. Brett A. Bednarcyk, a Senior Scientist at OM in Brookpark, Ohio from the period of August 1998 to March 2005. Most of the work summarized herein involved development, implementation, and application of enhancements and new capabilities for NASA GRC's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package. When the project began, this software was at a low TRL (3-4) and at release version 2.0. Due to this project, the TRL of MAC/GMC has been raised to 7 and two new versions (3.0 and 4.0) have been released. The most important accomplishments with respect to MAC/GMC are: (1) A multi-scale framework has been built around the software, enabling coupled design and analysis from the global structure scale down to the micro fiber-matrix scale; (2) The software has been expanded to analyze smart materials; (3) State-of-the-art micromechanics theories have been implemented and validated within the code; (4) The damage, failure, and lifing capabilities of the code have been expanded from a very limited state to a vast degree of functionality and utility; and (5) The user flexibility of the code has been significantly enhanced. MAC/GMC is now the premier code for design and analysis of advanced composite and smart materials. It is a candidate for the 2005 NASA Software of the Year Award. The work completed over the course of the project is summarized below on a year by year basis. All publications resulting from the project are listed at the end of this report.

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.

Tool for Sizing Analysis of the Advanced Life Support System

NASA Technical Reports Server (NTRS)

Yeh, Hue-Hsie Jannivine; Brown, Cheryl B.; Jeng, Frank J.

2005-01-01

Advanced Life Support Sizing Analysis Tool (ALSSAT) is a computer model for sizing and analyzing designs of environmental-control and life support systems (ECLSS) for spacecraft and surface habitats involved in the exploration of Mars and Moon. It performs conceptual designs of advanced life support (ALS) subsystems that utilize physicochemical and biological processes to recycle air and water, and process wastes in order to reduce the need of resource resupply. By assuming steady-state operations, ALSSAT is a means of investigating combinations of such subsystems technologies and thereby assisting in determining the most cost-effective technology combination available. In fact, ALSSAT can perform sizing analysis of the ALS subsystems that are operated dynamically or steady in nature. Using the Microsoft Excel spreadsheet software with Visual Basic programming language, ALSSAT has been developed to perform multiple-case trade studies based on the calculated ECLSS mass, volume, power, and Equivalent System Mass, as well as parametric studies by varying the input parameters. ALSSAT s modular format is specifically designed for the ease of future maintenance and upgrades.

Sandia Advanced MEMS Design Tools v. 3.0

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

Yarberry, Victor R.; Allen, James J.; Lantz, Jeffrey W.

This is a major revision to the Sandia Advanced MEMS Design Tools. It replaces all previous versions. New features in this version: Revised to support AutoCAD 2014 and 2015 This CD contains an integrated set of electronic files that: a) Describe the SUMMiT V fabrication process b) Provide enabling educational information (including pictures, videos, technical information) c) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) d) Facilitate the process of having MEMS fabricated at Sandia National Laboratories e) Facilitate the process of having post-fabrication services performed. While there exists somemore » files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« 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.

User Driven Development of Software Tools for Open Data Discovery and Exploration

NASA Astrophysics Data System (ADS)

Schlobinski, Sascha; Keppel, Frank; Dihe, Pascal; Boot, Gerben; Falkenroth, Esa

2016-04-01

The use of open data in research faces challenges not restricted to inherent properties such as data quality, resolution of open data sets. Often Open data is catalogued insufficiently or fragmented. Software tools that support the effective discovery including the assessment of the data's appropriateness for research have shortcomings such as the lack of essential functionalities like support for data provenance. We believe that one of the reasons is the neglect of real end users requirements in the development process of aforementioned software tools. In the context of the FP7 Switch-On project we have pro-actively engaged the relevant user user community to collaboratively develop a means to publish, find and bind open data relevant for hydrologic research. Implementing key concepts of data discovery and exploration we have used state of the art web technologies to provide an interactive software tool that is easy to use yet powerful enough to satisfy the data discovery and access requirements of the hydrological research community.

Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan. Part 1: ASC software quality engineering practices, Version 2.0.

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

Sturtevant, Judith E.; Heaphy, Robert; Hodges, Ann Louise

2006-09-01

The purpose of the Sandia National Laboratories Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. The plan defines the ASC program software quality practices and provides mappings of these practices to Sandia Corporate Requirements CPR 1.3.2 and 1.3.6 and to a Department of Energy document, ASCI Software Quality Engineering: Goals, Principles, and Guidelines. This document also identifies ASC management and software project teams responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals.

Learn by Yourself: The Self-Learning Tools for Qualitative Analysis Software Packages

ERIC Educational Resources Information Center

Freitas, Fábio; Ribeiro, Jaime; Brandão, Catarina; Reis, Luís Paulo; de Souza, Francislê Neri; Costa, António Pedro

2017-01-01

Computer Assisted Qualitative Data Analysis Software (CAQDAS) are tools that help researchers to develop qualitative research projects. These software packages help the users with tasks such as transcription analysis, coding and text interpretation, writing and annotation, content search and analysis, recursive abstraction, grounded theory…

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

A software tool for dataflow graph scheduling

NASA Technical Reports Server (NTRS)

Jones, Robert L., III

1994-01-01

A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on multiple processors. The dataflow paradigm is very useful in exposing the parallelism inherent in algorithms. It provides a graphical and mathematical model which describes a partial ordering of algorithm tasks based on data precedence.

System and Software Reliability (C103)

NASA Technical Reports Server (NTRS)

Wallace, Dolores

2003-01-01

Within the last decade better reliability models (hardware. software, system) than those currently used have been theorized and developed but not implemented in practice. Previous research on software reliability has shown that while some existing software reliability models are practical, they are no accurate enough. New paradigms of development (e.g. OO) have appeared and associated reliability models have been proposed posed but not investigated. Hardware models have been extensively investigated but not integrated into a system framework. System reliability modeling is the weakest of the three. NASA engineers need better methods and tools to demonstrate that the products meet NASA requirements for reliability measurement. For the new models for the software component of the last decade, there is a great need to bring them into a form that they can be used on software intensive systems. The Statistical Modeling and Estimation of Reliability Functions for Systems (SMERFS'3) tool is an existing vehicle that may be used to incorporate these new modeling advances. Adapting some existing software reliability modeling changes to accommodate major changes in software development technology may also show substantial improvement in prediction accuracy. With some additional research, the next step is to identify and investigate system reliability. System reliability models could then be incorporated in a tool such as SMERFS'3. This tool with better models would greatly add value in assess in GSFC projects.

Software engineering and data management for automated payload experiment tool

NASA Technical Reports Server (NTRS)

Maddux, Gary A.; Provancha, Anna; Chattam, David

1994-01-01

The Microgravity Projects Office identified a need to develop a software package that will lead experiment developers through the development planning process, obtain necessary information, establish an electronic data exchange avenue, and allow easier manipulation/reformatting of the collected information. An MS-DOS compatible software package called the Automated Payload Experiment Tool (APET) has been developed and delivered. The objective of this task is to expand on the results of the APET work previously performed by University of Alabama in Huntsville (UAH) and provide versions of the software in a Macintosh and Windows compatible format. Appendix 1 science requirements document (SRD) Users Manual is attached.

Designing and Using Software Tools for Educational Purposes: FLAT, a Case Study

ERIC Educational Resources Information Center

Castro-Schez, J. J.; del Castillo, E.; Hortolano, J.; Rodriguez, A.

2009-01-01

Educational software tools are considered to enrich teaching strategies, providing a more compelling means of exploration and feedback than traditional blackboard methods. Moreover, software simulators provide a more motivating link between theory and practice than pencil-paper methods, encouraging active and discovery learning in the students.…

A Vision on the Status and Evolution of HEP Physics Software Tools

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

Canal, P.; Elvira, D.; Hatcher, R.

2013-07-28

This paper represents the vision of the members of the Fermilab Scientific Computing Division's Computational Physics Department (SCD-CPD) on the status and the evolution of various HEP software tools such as the Geant4 detector simulation toolkit, the Pythia and GENIE physics generators, and the ROOT data analysis framework. The goal of this paper is to contribute ideas to the Snowmass 2013 process toward the composition of a unified document on the current status and potential evolution of the physics software tools which are essential to HEP.

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.

Understanding Computation of Impulse Response in Microwave Software Tools

ERIC Educational Resources Information Center

Potrebic, Milka M.; Tosic, Dejan V.; Pejovic, Predrag V.

2010-01-01

In modern microwave engineering curricula, the introduction of the many new topics in microwave industrial development, or of software tools for design and simulation, sometimes results in students having an inadequate understanding of the fundamental theory. The terminology for and the explanation of algorithms for calculating impulse response in…

Award-Winning CARES/Life Ceramics Durability Evaluation Software Is Making Advanced Technology Accessible

NASA Technical Reports Server (NTRS)

1997-01-01

Products made from advanced ceramics show great promise for revolutionizing aerospace and terrestrial propulsion and power generation. However, ceramic components are difficult to design because brittle materials in general have widely varying strength values. The CARES/Life software developed at the NASA Lewis Research Center eases this by providing a tool that uses probabilistic reliability analysis techniques to optimize the design and manufacture of brittle material components. CARES/Life is an integrated package that predicts the probability of a monolithic ceramic component's failure as a function of its time in service. It couples commercial finite element programs--which resolve a component's temperature and stress distribution - with reliability evaluation and fracture mechanics routines for modeling strength - limiting defects. These routines are based on calculations of the probabilistic nature of the brittle material's strength.

Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan : ASC software quality engineering practices Version 3.0.

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

Turgeon, Jennifer L.; Minana, Molly A.; Hackney, Patricia

2009-01-01

The purpose of the Sandia National Laboratories (SNL) Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. Quality is defined in the US Department of Energy/National Nuclear Security Agency (DOE/NNSA) Quality Criteria, Revision 10 (QC-1) as 'conformance to customer requirements and expectations'. This quality plan defines the SNL ASC Program software quality engineering (SQE) practices and provides a mapping of these practices to the SNL Corporate Process Requirement (CPR) 001.3.6; 'Corporate Software Engineering Excellence'. This plan also identifies ASC management's and themore » software project teams responsibilities in implementing the software quality practices and in assessing progress towards achieving their software quality goals. This SNL ASC Software Quality Plan establishes the signatories commitments to improving software products by applying cost-effective SQE practices. This plan enumerates the SQE practices that comprise the development of SNL ASC's software products and explains the project teams opportunities for tailoring and implementing the practices.« less

CmapTools: A Software Environment for Knowledge Modeling and Sharing

NASA Technical Reports Server (NTRS)

Canas, Alberto J.

2004-01-01

In an ongoing collaborative effort between a group of NASA Ames scientists and researchers at the Institute for Human and Machine Cognition (IHMC) of the University of West Florida, a new version of CmapTools has been developed that enable scientists to construct knowledge models of their domain of expertise, share them with other scientists, make them available to anybody on the Internet with access to a Web browser, and peer-review other scientists models. These software tools have been successfully used at NASA to build a large-scale multimedia on Mars and in knowledge model on Habitability Assessment. The new version of the software places emphasis on greater usability for experts constructing their own knowledge models, and support for the creation of large knowledge models with large number of supporting resources in the forms of images, videos, web pages, and other media. Additionally, the software currently allows scientists to cooperate with each other in the construction, sharing and criticizing of knowledge models. Scientists collaborating from remote distances, for example researchers at the Astrobiology Institute, can concurrently manipulate the knowledge models they are viewing without having to do this at a special videoconferencing facility.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Research flight software engineering and MUST, an integrated system of support tools

NASA Technical Reports Server (NTRS)

Straeter, T. A.; Foudriat, E. C.; Will, R. W.

1977-01-01

Consideration is given to software development to support NASA flight research. The Multipurpose User-Oriented Software Technology (MUST) program, designed to integrate digital systems into flight research, is discussed. Particular attention is given to the program's special interactive user interface, subroutine library, assemblers, compiler, automatic documentation tools, and test and simulation subsystems.

Software Tools: A One-Semester Secondary School Computer Course.

ERIC Educational Resources Information Center

Bromley, John; Lakatos, John

1985-01-01

Provides a course outline, describes equipment and teacher requirements, discusses student evaluation and course outcomes, and details the computer programs used in a high school course. The course is designed to teach students use of the microcomputer as a tool through hands-on experience with a variety of commercial software programs. (MBR)

Proposing a Mathematical Software Tool in Physics Secondary Education

ERIC Educational Resources Information Center

Baltzis, Konstantinos B.

2009-01-01

MathCad® is a very popular software tool for mathematical and statistical analysis in science and engineering. Its low cost, ease of use, extensive function library, and worksheet-like user interface distinguish it among other commercial packages. Its features are also well suited to educational process. The use of natural mathematical notation…

Overview of T.E.S.T. (Toxicity Estimation Software Tool)

EPA Science Inventory

This talk provides an overview of T.E.S.T. (Toxicity Estimation Software Tool). T.E.S.T. predicts toxicity values and physical properties using a variety of different QSAR (quantitative structure activity relationship) approaches including hierarchical clustering, group contribut...

Visualization and Analytics Software Tools for Peregrine System |

Science.gov Websites

R is a language and environment for statistical computing and graphics. Go to the R web site for System Visualization and Analytics Software Tools for Peregrine System Learn about the available visualization for OpenGL-based applications. For more information, please go to the FastX page. ParaView An open

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.

Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

van Beek, J; Haanperä, M; Smit, P W; Mentula, S; Soini, H

2018-04-11

Culture-based assays are currently the reference standard for drug susceptibility testing for Mycobacterium tuberculosis. They provide good sensitivity and specificity but are time consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture-based assays for drug susceptibility testing of M. tuberculosis. M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n = 211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first-line drug susceptibilities. WGS was performed for all isolates using the Illumina MiSeq system, and data were analysed using five software tools (PhyResSE, Mykrobe Predictor, TB Profiler, TGS-TB and KvarQ). Diagnostic time and reagent costs were estimated for both methods. The sensitivity of the five software tools to predict any resistance among strains was almost identical, ranging from 74% to 80%, and specificity was more than 95% for all software tools except for TGS-TB. The sensitivity and specificity to predict resistance to individual drugs varied considerably among the software tools. Reagent costs for MGIT and WGS were €26 and €143 per isolate respectively. Turnaround time for MGIT was 19 days (range 10-50 days) for first-line drugs, and turnaround time for WGS was estimated to be 5 days (range 3-7 days). WGS could be used as a prescreening assay for drug susceptibility testing with confirmation of resistant strains by MGIT. The functionality and ease of use of the software tools need to be improved. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

A SOFTWARE TOOL TO COMPARE MEASURED AND SIMULATED BUILDING ENERGY PERFORMANCE DATA

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

Maile, Tobias; Bazjanac, Vladimir; O'Donnell, James

2011-11-01

Building energy performance is often inadequate when compared to design goals. To link design goals to actual operation one can compare measured with simulated energy performance data. Our previously developed comparison approach is the Energy Performance Comparison Methodology (EPCM), which enables the identification of performance problems based on a comparison of measured and simulated performance data. In context of this method, we developed a software tool that provides graphing and data processing capabilities of the two performance data sets. The software tool called SEE IT (Stanford Energy Efficiency Information Tool) eliminates the need for manual generation of data plots andmore » data reformatting. SEE IT makes the generation of time series, scatter and carpet plots independent of the source of data (measured or simulated) and provides a valuable tool for comparing measurements with simulation results. SEE IT also allows assigning data points on a predefined building object hierarchy and supports different versions of simulated performance data. This paper briefly introduces the EPCM, describes the SEE IT tool and illustrates its use in the context of a building case study.« less

Advanced Transport Operating System (ATOPS) control display unit software description

NASA Technical Reports Server (NTRS)

Slominski, Christopher J.; Parks, Mark A.; Debure, Kelly R.; Heaphy, William J.

1992-01-01

The software created for the Control Display Units (CDUs), used for the Advanced Transport Operating Systems (ATOPS) project, on the Transport Systems Research Vehicle (TSRV) is described. Module descriptions are presented in a standardized format which contains module purpose, calling sequence, a detailed description, and global references. The global reference section includes subroutines, functions, and common variables referenced by a particular module. The CDUs, one for the pilot and one for the copilot, are used for flight management purposes. Operations performed with the CDU affects the aircraft's guidance, navigation, and display software.

Case Studies of Software Development Tools for Parallel Architectures

DTIC Science & Technology

1993-06-01

Simulation ............................................. 29 4.7.3 Visualization...autonomous entities, each with its own state and set of behaviors, as in simulation , tracking, or Battle Management. Because C2 applications are often... simulation , that is used to help the developer solve the problems. The new tool/problem solution matrix is structured in terms of the software development

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.

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

Center for Center for Technology for Advanced Scientific Component Software (TASCS)

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

Kostadin, Damevski

A resounding success of the Scientific Discovery through Advanced Computing (SciDAC) program is that high-performance computational science is now universally recognized as a critical aspect of scientific discovery [71], complementing both theoretical and experimental research. As scientific communities prepare to exploit unprecedented computing capabilities of emerging leadership-class machines for multi-model simulations at the extreme scale [72], it is more important than ever to address the technical and social challenges of geographically distributed teams that combine expertise in domain science, applied mathematics, and computer science to build robust and flexible codes that can incorporate changes over time. The Center for Technologymore » for Advanced Scientific Component Software (TASCS)1 tackles these these issues by exploiting component-based software development to facilitate collaborative high-performance scientific computing.« less

Tools Automate Spacecraft Testing, Operation

NASA Technical Reports Server (NTRS)

2010-01-01

"NASA began the Small Explorer (SMEX) program to develop spacecraft to advance astrophysics and space physics. As one of the entities supporting software development at Goddard Space Flight Center, the Hammers Company Inc. (tHC Inc.), of Greenbelt, Maryland, developed the Integrated Test and Operations System to support SMEX. Later, the company received additional Small Business Innovation Research (SBIR) funding from Goddard for a tool to facilitate the development of flight software called VirtualSat. NASA uses the tools to support 15 satellites, and the aerospace industry is using them to develop science instruments, spacecraft computer systems, and navigation and control software."

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.

Advanced software development workstation. OOPSLA 1992 Conference. Trip report

NASA Technical Reports Server (NTRS)

Izygon, Michel E.

1992-01-01

This report summarizes the main trends observed at the Object Oriented Programming Systems, Languages, and Applications Conference held in Vancouver, British Columbia. This conference is the main object-oriented event that allows us to assess the dynamism of the technology and to meet the main actors of the field. It is an invaluable source of information for the advanced software development project.

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.

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

Software Tools for In-Situ Documentation of Built Heritage

NASA Astrophysics Data System (ADS)

Smars, P.

2013-07-01

The paper presents open source software tools developed by the author to facilitate in-situ documentation of architectural and archæological heritage. The design choices are exposed and related to a general issue in conservation and documentation: taking decisions about a valuable object under threat . The questions of level of objectivity is central to the three steps of this process. It is our belief that in-situ documentation has to be favoured in this demanding context, full of potential discoveries. The very powerful surveying techniques in rapid development nowadays enhance our vision but often tend to bring back a critical part of the documentation process to the office. The software presented facilitate a direct treatment of the data on the site. Emphasis is given to flexibility, interoperability and simplicity. Key features of the software are listed and illustrated with examples (3D model of Gothic vaults, analysis of the shape of a column, deformation of a wall, direct interaction with AutoCAD).

Data Visualization: An Exploratory Study into the Software Tools Used by Businesses

ERIC Educational Resources Information Center

Diamond, Michael; Mattia, Angela

2017-01-01

Data visualization is a key component to business and data analytics, allowing analysts in businesses to create tools such as dashboards for business executives. Various software packages allow businesses to create these tools in order to manipulate data for making informed business decisions. The focus is to examine what skills employers are…

Data Visualization: An Exploratory Study into the Software Tools Used by Businesses

ERIC Educational Resources Information Center

Diamond, Michael; Mattia, Angela

2015-01-01

Data visualization is a key component to business and data analytics, allowing analysts in businesses to create tools such as dashboards for business executives. Various software packages allow businesses to create these tools in order to manipulate data for making informed business decisions. The focus is to examine what skills employers are…

The Environmental Control and Life Support System (ECLSS) advanced automation project

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, Ray

1990-01-01

The objective of the environmental control and life support system (ECLSS) Advanced Automation Project is to influence the design of the initial and evolutionary Space Station Freedom Program (SSFP) ECLSS toward a man-made closed environment in which minimal flight and ground manpower is needed. Another objective includes capturing ECLSS design and development knowledge future missions. Our approach has been to (1) analyze the SSFP ECLSS, (2) envision as our goal a fully automated evolutionary environmental control system - an augmentation of the baseline, and (3) document the advanced software systems, hooks, and scars which will be necessary to achieve this goal. From this analysis, prototype software is being developed, and will be tested using air and water recovery simulations and hardware subsystems. In addition, the advanced software is being designed, developed, and tested using automation software management plan and lifecycle tools. Automated knowledge acquisition, engineering, verification and testing tools are being used to develop the software. In this way, we can capture ECLSS development knowledge for future use develop more robust and complex software, provide feedback to the knowledge based system tool community, and ensure proper visibility of our efforts.

HITCal: a software tool for analysis of video head impulse test responses.

PubMed

Rey-Martinez, Jorge; Batuecas-Caletrio, Angel; Matiño, Eusebi; Perez Fernandez, Nicolás

2015-09-01

The developed software (HITCal) may be a useful tool in the analysis and measurement of the saccadic video head impulse test (vHIT) responses and with the experience obtained during its use the authors suggest that HITCal is an excellent method for enhanced exploration of vHIT outputs. To develop a (software) method to analyze and explore the vHIT responses, mainly saccades. HITCal was written using a computational development program; the function to access a vHIT file was programmed; extended head impulse exploration and measurement tools were created and an automated saccade analysis was developed using an experimental algorithm. For pre-release HITCal laboratory tests, a database of head impulse tests (HITs) was created with the data collected retrospectively in three reference centers. This HITs database was evaluated by humans and was also computed with HITCal. The authors have successfully built HITCal and it has been released as open source software; the developed software was fully operative and all the proposed characteristics were incorporated in the released version. The automated saccades algorithm implemented in HITCal has good concordance with the assessment by human observers (Cohen's kappa coefficient = 0.7).

DAISY: a new software tool to test global identifiability of biological and physiological systems.

PubMed

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D'Angiò, Leontina

2007-10-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

DAISY: a new software tool to test global identifiability of biological and physiological systems

PubMed Central

Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D’Angiò, Leontina

2009-01-01

A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/. PMID:17707944

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.

Data management system advanced development

NASA Technical Reports Server (NTRS)

Douglas, Katherine; Humphries, Terry

1990-01-01

The Data Management System (DMS) Advanced Development task provides for the development of concepts, new tools, DMS services, and for the testing of the Space Station DMS hardware and software. It also provides for the development of techniques capable of determining the effects of system changes/enhancements, additions of new technology, and/or hardware and software growth on system performance. This paper will address the built-in characteristics which will support network monitoring requirements in the design of the evolving DMS network implementation, functional and performance requirements for a real-time, multiprogramming, multiprocessor operating system, and the possible use of advanced development techniques such as expert systems and artificial intelligence tools in the DMS design.

ICE: An Automated Tool for Teaching Advanced C Programming

ERIC Educational Resources Information Center

Gonzalez, Ruben

2017-01-01

There are many difficulties with learning and teaching programming that can be alleviated with the use of software tools. Most of these tools have focused on the teaching of introductory programming concepts where commonly code fragments or small user programs are run in a sandbox or virtual machine, often in the cloud. These do not permit user…

Self-advancing step-tap tool

NASA Technical Reports Server (NTRS)

Pettit, Donald R. (Inventor); Penner, Ronald K. (Inventor); Franklin, Larry D. (Inventor); Camarda, Charles J. (Inventor)

2008-01-01

Methods and tool for simultaneously forming a bore in a work piece and forming a series of threads in said bore. In an embodiment, the tool has a predetermined axial length, a proximal end, and a distal end, said tool comprising: a shank located at said proximal end; a pilot drill portion located at said distal end; and a mill portion intermediately disposed between said shank and said pilot drill portion. The mill portion is comprised of at least two drill-tap sections of predetermined axial lengths and at least one transition section of predetermined axial length, wherein each of said at least one transition section is sandwiched between a distinct set of two of said at least two drill-tap sections. The at least two drill-tap sections are formed of one or more drill-tap cutting teeth spirally increasing along said at least two drill-tap sections, wherein said tool is self-advanced in said work piece along said formed threads, and wherein said tool simultaneously forms said bore and said series of threads along a substantially similar longitudinal axis.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

A Business Analytics Software Tool for Monitoring and Predicting Radiology Throughput Performance.

PubMed

Jones, Stephen; Cournane, Seán; Sheehy, Niall; Hederman, Lucy

2016-12-01

Business analytics (BA) is increasingly being utilised by radiology departments to analyse and present data. It encompasses statistical analysis, forecasting and predictive modelling and is used as an umbrella term for decision support and business intelligence systems. The primary aim of this study was to determine whether utilising BA technologies could contribute towards improved decision support and resource management within radiology departments. A set of information technology requirements were identified with key stakeholders, and a prototype BA software tool was designed, developed and implemented. A qualitative evaluation of the tool was carried out through a series of semi-structured interviews with key stakeholders. Feedback was collated, and emergent themes were identified. The results indicated that BA software applications can provide visibility of radiology performance data across all time horizons. The study demonstrated that the tool could potentially assist with improving operational efficiencies and management of radiology resources.

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

ATLAS software code base is over 6 million lines organised in about 2000 packages. It makes use of some 100 external software packages, is developed by more than 400 developers and used by more than 2500 physicists from over 200 universities and laboratories in 6 continents. To meet the challenge of configuration and building of this software, the Configuration Management Tool (CMT) is used. CMT expects each package to describe its build targets, build and environment setup parameters, dependencies on other packages in a text file called requirements, and each project (group of packages) to describe its policies and dependencies on other projects in a text project file. Based on the effective set of configuration parameters read from the requirements files of dependent packages and project files, CMT commands build the packages, generate the environment for their use, or query the packages. The main focus was on build time performance that was optimised within several approaches: reduction of the number of reads of requirements files that are now read once per package by a CMT build command that generates cached requirements files for subsequent CMT build commands; introduction of more fine-grained build parallelism at package task level, i.e., dependent applications and libraries are compiled in parallel; code optimisation of CMT commands used for build; introduction of package level build parallelism, i. e., parallelise the build of independent packages. By default, CMT launches NUMBER-OF-PROCESSORS build commands in parallel. The other focus was on CMT commands optimisation in general that made them approximately 2 times faster. CMT can generate a cached requirements file for the environment setup command, which is especially useful for deployment on distributed file systems like AFS or CERN VMFS. The use of parallelism, caching and code optimisation significantly-by several times-reduced software build time, environment setup time, increased the efficiency of

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.

Using Software Tools to Automate the Assessment of Student Programs.

ERIC Educational Resources Information Center

Jackson, David

1991-01-01

Argues that advent of computer-aided instruction (CAI) systems for teaching introductory computer programing makes it imperative that software be developed to automate assessment and grading of student programs. Examples of typical student programing problems are given, and application of the Unix tools Lex and Yacc to the automatic assessment of…

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.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

A NEO population generation and observation simulation software tool

NASA Astrophysics Data System (ADS)

Müller, Sven; Gelhaus, Johannes; Hahn, Gerhard; Franco, Raffaella

One of the main targets of ESA's Space Situational Awareness (SSA) program is to build a wide knowledge base about objects that can potentially harm Earth (Near-Earth Objects, NEOs). An important part of this effort is to create the Small Bodies Data Centre (SBDC) which is going to aggregate measurement data from a fully-integrated NEO observation sensor network. Until this network is developed, artificial NEO measurement data is needed in order to validate SBDC algorithms. Moreover, to establish a functioning NEO observation sensor network, it has to be determined where to place sensors, what technical requirements have to be met in order to be able to detect NEOs and which observation strategies work the best. Because of this, a sensor simulation software was needed. This paper presents a software tool which allows users to create and analyse NEO populations and to simulate and analyse population observations. It is a console program written in Fortran and comes with a Graphical User Interface (GUI) written in Java and C. The tool can be distinguished into the components ``Population Generator'' and ``Observation Simulator''. The Population Generator component is responsible for generating and analysing a NEO population. Users can choose between creating fictitious (random) and synthetic populations. The latter are based on one of two models describing the orbital and size distribution of observed NEOs: The existing socalled ``Bottke Model'' (Bottke et al. 2000, 2002) and the new ``Granvik Model'' (Granvik et al. 2014, in preparation) which has been developed in parallel to the tool. Generated populations can be analysed by defining 2D, 3D and scatter plots using various NEO attributes. As a result, the tool creates the appropiate files for the plotting tool ``gnuplot''. The tool's Observation Simulator component yields the Observation Simulation and Observation Analysis functions. Users can define sensor systems using ground- or space-based locations as well as

SafetyAnalyst : software tools for safety management of specific highway sites

DOT National Transportation Integrated Search

2010-07-01

SafetyAnalyst provides a set of software tools for use by state and local highway agencies for highway safety management. SafetyAnalyst can be used by highway agencies to improve their programming of site-specific highway safety improvements. SafetyA...

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Treesearch

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Evaluation of the Red Blood Cell Advanced Software Application on the CellaVision DM96.

PubMed

Criel, M; Godefroid, M; Deckers, B; Devos, H; Cauwelier, B; Emmerechts, J

2016-08-01

The CellaVision Advanced Red Blood Cell (RBC) Software Application is a new software for advanced morphological analysis of RBCs on a digital microscopy system. Upon automated precharacterization into 21 categories, the software offers the possibility of reclassification of RBCs by the operator. We aimed to define the optimal cut-off to detect morphological RBC abnormalities and to evaluate the precharacterization performance of this software. Thirty-eight blood samples of healthy donors and sixty-eight samples of hospitalized patients were analyzed. Different methodologies to define a cut-off between negativity and positivity were used. Sensitivity and specificity were calculated according to these different cut-offs using the manual microscopic method as the gold standard. Imprecision was assessed by measuring analytical within-run and between-run variability and by measuring between-observer variability. By optimizing the cut-off between negativity and positivity, sensitivities exceeded 80% for 'critical' RBC categories (target cells, tear drop cells, spherocytes, sickle cells, and parasites), while specificities exceeded 80% for the other RBC morphological categories. Results of within-run, between-run, and between-observer variabilities were all clinically acceptable. The CellaVision Advanced RBC Software Application is an easy-to-use software that helps to detect most RBC morphological abnormalities in a sensitive and specific way without increasing work load, provided the proper cut-offs are chosen. However, evaluation of the images by an experienced observer remains necessary. © 2016 John Wiley & Sons Ltd.

Learning Photogrammetry with Interactive Software Tool PhoX

NASA Astrophysics Data System (ADS)

Luhmann, T.

2016-06-01

Photogrammetry is a complex topic in high-level university teaching, especially in the fields of geodesy, geoinformatics and metrology where high quality results are demanded. In addition, more and more black-box solutions for 3D image processing and point cloud generation are available that generate nice results easily, e.g. by structure-from-motion approaches. Within this context, the classical approach of teaching photogrammetry (e.g. focusing on aerial stereophotogrammetry) has to be reformed in order to educate students and professionals with new topics and provide them with more information behind the scene. Since around 20 years photogrammetry courses at the Jade University of Applied Sciences in Oldenburg, Germany, include the use of digital photogrammetry software that provide individual exercises, deep analysis of calculation results and a wide range of visualization tools for almost all standard tasks in photogrammetry. During the last years the software package PhoX has been developed that is part of a new didactic concept in photogrammetry and related subjects. It also serves as analysis tool in recent research projects. PhoX consists of a project-oriented data structure for images, image data, measured points and features and 3D objects. It allows for almost all basic photogrammetric measurement tools, image processing, calculation methods, graphical analysis functions, simulations and much more. Students use the program in order to conduct predefined exercises where they have the opportunity to analyse results in a high level of detail. This includes the analysis of statistical quality parameters but also the meaning of transformation parameters, rotation matrices, calibration and orientation data. As one specific advantage, PhoX allows for the interactive modification of single parameters and the direct view of the resulting effect in image or object space.

Software attribute visualization for high integrity software

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

Pollock, G.M.

1998-03-01

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

Advanced genetic tools for plant biotechnology.

PubMed

Liu, Wusheng; Yuan, Joshua S; Stewart, C Neal

2013-11-01

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

Computerized assessment of placental calcification post-ultrasound: a novel software tool.

PubMed

Moran, M; Higgins, M; Zombori, G; Ryan, J; McAuliffe, F M

2013-05-01

Placental calcification is associated with an increased risk of perinatal morbidity and mortality. The subjectivity of current ultrasound methods of assessment of placental calcification indicates that a more objective method is required. The aim of this study was to correlate the percentage of calcification defined by the clinician using a new software tool for calculating the extent of placental calcification with traditional ultrasound methods and with pregnancy outcome. Ninety placental images were individually assessed. An upper threshold was defined, based on high intensity, to quantify calcification within the placenta. Output metrics were then produced including the overall percentage of calcification with respect to the total number of pixels within the region of interest. The results were correlated with traditional ultrasound methods of assessment of placental calcification and with pregnancy outcome. The results demonstrate a significant correlation between placental calcification, as defined using the software, and traditional methods of Grannum grading of placental calcification. Whilst correlation with perinatal outcome and cord pH was not significant as a result of small numbers, patients with placental calcification assessed using the computerized software at the upper quartile had higher rates of poor perinatal outcome when compared with those at the lower quartile (8/22 (36%) vs 3/23 (13%); P = 0.069). These results suggest that this computerized software tool has the potential to become an alternative method of assessing placental calcification. Copyright © 2012 ISUOG. Published by John Wiley & Sons Ltd.

Software Tools | Office of Cancer Clinical Proteomics Research

Cancer.gov

The CPTAC program develops new approaches to elucidate aspects of the molecular complexity of cancer made from large-scale proteogenomic datasets, and advance them toward precision medicine.  Part of the CPTAC mission is to make data and tools available and accessible to the greater research community to accelerate the discovery process.

The Business Case for Automated Software Engineering

NASA Technical Reports Server (NTRS)

Menzies, Tim; Elrawas, Oussama; Hihn, Jairus M.; Feather, Martin S.; Madachy, Ray; Boehm, Barry

2007-01-01

Adoption of advanced automated SE (ASE) tools would be more favored if a business case could be made that these tools are more valuable than alternate methods. In theory, software prediction models can be used to make that case. In practice, this is complicated by the 'local tuning' problem. Normally. predictors for software effort and defects and threat use local data to tune their predictions. Such local tuning data is often unavailable. This paper shows that assessing the relative merits of different SE methods need not require precise local tunings. STAR 1 is a simulated annealer plus a Bayesian post-processor that explores the space of possible local tunings within software prediction models. STAR 1 ranks project decisions by their effects on effort and defects and threats. In experiments with NASA systems. STARI found one project where ASE were essential for minimizing effort/ defect/ threats; and another project were ASE tools were merely optional.

Computer-Aided Process and Tools for Mobile Software Acquisition

DTIC Science & Technology

2013-07-30

moldo^j= pmlkploba=obmloq=pbofbp= Computer-Aided Process and Tools for Mobile Software Acquisition 30 July 2013 LT Christopher Bonine , USN, Dr...Christopher Bonine is a lieutenant in the United States Navy. He is currently assigned to the Navy Cyber Defense Operations Command in Norfolk, VA. He has...interests are in development and implementation of cyber security policy. Bonine has a master’s in computer science from the Naval Postgraduate School

Use of software tools in the development of real time software systems

NASA Technical Reports Server (NTRS)

Garvey, R. C.

1981-01-01

The transformation of a preexisting software system into a larger and more versatile system with different mission requirements is discussed. The history of this transformation is used to illustrate the use of structured real time programming techniques and tools to produce maintainable and somewhat transportable systems. The predecessor system is a single ground diagnostic system; its purpose is to exercise a computer controlled hardware set prior to its deployment in its functional environment, as well as test the equipment set by supplying certain well known stimulas. The successor system (FTE) is required to perform certain testing and control functions while this hardware set is in its functional environment. Both systems must deal with heavy user input/output loads and a new I/O requirement is included in the design of the FTF system. Human factors are enhanced by adding an improved console interface and special function keyboard handler. The additional features require the inclusion of much new software to the original set from which FTF was developed. As a result, it is necessary to split the system into a duel programming configuration with high rates of interground communications. A generalized information routing mechanism is used to support this configuration.

Recent advances in systems metabolic engineering tools and strategies.

PubMed

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of Cloud-Based Graphic Narrative Software in Medical Ethics Teaching

ERIC Educational Resources Information Center

Weber, Alan S.

2015-01-01

Although used as a common pedagogical tool in K-12 education, online graphic narrative ("comics") software has not generally been incorporated into advanced professional or technical education. This contribution reports preliminary data from a study on the use of cloud-based graphics software Pixton.com to teach basic medical ethics…

WILDFIRE IGNITION RESISTANCE ESTIMATOR WIZARD SOFTWARE DEVELOPMENT REPORT

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

Phillips, M.; Robinson, C.; Gupta, N.

2012-10-10

This report describes the development of a software tool, entitled “WildFire Ignition Resistance Estimator Wizard” (WildFIRE Wizard, Version 2.10). This software was developed within the Wildfire Ignition Resistant Home Design (WIRHD) program, sponsored by the U. S. Department of Homeland Security, Science and Technology Directorate, Infrastructure Protection & Disaster Management Division. WildFIRE Wizard is a tool that enables homeowners to take preventive actions that will reduce their home’s vulnerability to wildfire ignition sources (i.e., embers, radiant heat, and direct flame impingement) well in advance of a wildfire event. This report describes the development of the software, its operation, its technicalmore » basis and calculations, and steps taken to verify its performance.« less

Recent development in software and automation tools for high-throughput discovery bioanalysis.

PubMed

Shou, Wilson Z; Zhang, Jun

2012-05-01

Bioanalysis with LC-MS/MS has been established as the method of choice for quantitative determination of drug candidates in biological matrices in drug discovery and development. The LC-MS/MS bioanalytical support for drug discovery, especially for early discovery, often requires high-throughput (HT) analysis of large numbers of samples (hundreds to thousands per day) generated from many structurally diverse compounds (tens to hundreds per day) with a very quick turnaround time, in order to provide important activity and liability data to move discovery projects forward. Another important consideration for discovery bioanalysis is its fit-for-purpose quality requirement depending on the particular experiments being conducted at this stage, and it is usually not as stringent as those required in bioanalysis supporting drug development. These aforementioned attributes of HT discovery bioanalysis made it an ideal candidate for using software and automation tools to eliminate manual steps, remove bottlenecks, improve efficiency and reduce turnaround time while maintaining adequate quality. In this article we will review various recent developments that facilitate automation of individual bioanalytical procedures, such as sample preparation, MS/MS method development, sample analysis and data review, as well as fully integrated software tools that manage the entire bioanalytical workflow in HT discovery bioanalysis. In addition, software tools supporting the emerging high-resolution accurate MS bioanalytical approach are also discussed.

Advanced fingerprint verification software

NASA Astrophysics Data System (ADS)

Baradarani, A.; Taylor, J. R. B.; Severin, F.; Maev, R. Gr.

2016-05-01

We have developed a fingerprint software package that can be used in a wide range of applications from law enforcement to public and private security systems, and to personal devices such as laptops, vehicles, and door- locks. The software and processing units are a unique implementation of new and sophisticated algorithms that compete with the current best systems in the world. Development of the software package has been in line with the third generation of our ultrasonic fingerprinting machine1. Solid and robust performance is achieved in the presence of misplaced and low quality fingerprints.

Role of Social Software Tools in Education: A Literature Review

ERIC Educational Resources Information Center

Minocha, Shailey

2009-01-01

Purpose: The purpose of this paper is to provide a review of literature on the role of Web 2.0 or social software tools in education. Design/methodology/approach: This paper is a critical and comprehensive review of a range of literature sources (until January 2009) addressing the various issues related to the educator's perspective of pedagogical…

Proceedings of the Eighteenth Annual Software Engineering Workshop

NASA Technical Reports Server (NTRS)

1993-01-01

The workshop provided a forum for software practitioners from around the world to exchange information on the measurement, use, and evaluation of software methods, models, and tools. This year, approximately 450 people attended the workshop, which consisted of six sessions on the following topics: the Software Engineering Laboratory, measurement, technology assessment, advanced concepts, process, and software engineering issues in NASA. Three presentations were given in each of the topic areas. The content of those presentations and the research papers detailing the work reported are included in these proceedings. The workshop concluded with a tutorial session on how to start an Experience Factory.

Software tool for mining liquid chromatography/multi-stage mass spectrometry data for comprehensive glycerophospholipid profiling.

PubMed

Hein, Eva-Maria; Bödeker, Bertram; Nolte, Jürgen; Hayen, Heiko

2010-07-30

Electrospray ionization mass spectrometry (ESI-MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler-Merger-Viewer tool is a software package for automatic processing of raw-data from data-dependent experiments, measured by high-performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR-MS and Orbitrap) in single and multi-stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black-box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso-glycerophospholipids and free fatty acids. Copyright 2010 John Wiley & Sons, Ltd.

Advanced genetic tools for plant biotechnology

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

Liu, WS; Yuan, JS; Stewart, CN

2013-10-09

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis ofmore » large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.« less

A tool to include gamma analysis software into a quality assurance program.

PubMed

Agnew, Christina E; McGarry, Conor K

2016-03-01

To provide a tool to enable gamma analysis software algorithms to be included in a quality assurance (QA) program. Four image sets were created comprising two geometric images to independently test the distance to agreement (DTA) and dose difference (DD) elements of the gamma algorithm, a clinical step and shoot IMRT field and a clinical VMAT arc. The images were analysed using global and local gamma analysis with 2 in-house and 8 commercially available software encompassing 15 software versions. The effect of image resolution on gamma pass rates was also investigated. All but one software accurately calculated the gamma passing rate for the geometric images. Variation in global gamma passing rates of 1% at 3%/3mm and over 2% at 1%/1mm was measured between software and software versions with analysis of appropriately sampled images. This study provides a suite of test images and the gamma pass rates achieved for a selection of commercially available software. This image suite will enable validation of gamma analysis software within a QA program and provide a frame of reference by which to compare results reported in the literature from various manufacturers and software versions. Copyright © 2015. Published by Elsevier Ireland Ltd.

Using Academia-Industry Partnerships to Enhance Software Verification & Validation Education via Active Learning Tools

ERIC Educational Resources Information Center

Acharya, Sushil; Manohar, Priyadarshan; Wu, Peter; Schilling, Walter

2017-01-01

Imparting real world experiences in a software verification and validation (SV&V) course is often a challenge due to the lack of effective active learning tools. This pedagogical requirement is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains. Realizing the…

Sandia National Laboratories Advanced Simulation and Computing (ASC) software quality plan. Part 1 : ASC software quality engineering practices version 1.0.

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

Minana, Molly A.; Sturtevant, Judith E.; Heaphy, Robert

2005-01-01

The purpose of the Sandia National Laboratories (SNL) Advanced Simulation and Computing (ASC) Software Quality Plan is to clearly identify the practices that are the basis for continually improving the quality of ASC software products. Quality is defined in DOE/AL Quality Criteria (QC-1) as conformance to customer requirements and expectations. This quality plan defines the ASC program software quality practices and provides mappings of these practices to the SNL Corporate Process Requirements (CPR 1.3.2 and CPR 1.3.6) and the Department of Energy (DOE) document, ASCI Software Quality Engineering: Goals, Principles, and Guidelines (GP&G). This quality plan identifies ASC management andmore » software project teams' responsibilities for cost-effective software engineering quality practices. The SNL ASC Software Quality Plan establishes the signatories commitment to improving software products by applying cost-effective software engineering quality practices. This document explains the project teams opportunities for tailoring and implementing the practices; enumerates the practices that compose the development of SNL ASC's software products; and includes a sample assessment checklist that was developed based upon the practices in this document.« less

The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.

PubMed

Ceroni, Alessio; Dell, Anne; Haslam, Stuart M

2007-08-07

Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics. The branched nature of carbohydrates, the great diversity of their constituents and the numerous alternative symbolic notations, make the input and display of glycans not as straightforward as for example the amino-acid sequence of a protein. Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format. A software tool for building and displaying glycan structures using a chosen symbolic notation is described here. The "GlycanBuilder" uses an automatic rendering algorithm to draw the saccharide symbols and to place them on the drawing board. The information about the symbolic notation is derived from a configurable graphical model as a set of rules governing the aspect and placement of residues and linkages. The algorithm is able to represent a structure using only few traversals of the tree and is inherently fast. The tool uses an XML format for import and export of encoded structures. The rendering algorithm described here is able to produce high-quality representations of glycan structures in a chosen symbolic notation. The automated rendering process enables the "GlycanBuilder" to be used both as a user-independent component for displaying glycans and as an easy-to-use drawing tool. The "GlycanBuilder" can be integrated in web pages as a Java applet for the visual editing of glycans. The same component is available as a web service to render an encoded structure into a graphical format. Finally, the "GlycanBuilder" can be integrated into other applications to create intuitive and appealing user

MemAxes Visualization Software

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

Hardware advancements such as Intel's PEBS and AMD's IBS, as well as software developments such as the perf_event API in Linux have made available the acquisition of memory access samples with performance information. MemAxes is a visualization and analysis tool for memory access sample data. By mapping the samples to their associated code, variables, node topology, and application dataset, MemAxes provides intuitive views of the data.

Software Schedules Missions, Aids Project Management

NASA Technical Reports Server (NTRS)

2008-01-01

NASA missions require advanced planning, scheduling, and management, and the Space Agency has worked extensively to develop the programs and software suites necessary to facilitate these complex missions. These enormously intricate undertakings have hundreds of active components that need constant management and monitoring. It is no surprise, then, that the software developed for these tasks is often applicable in other high-stress, complex environments, like in government or industrial settings. NASA work over the past few years has resulted in a handful of new scheduling, knowledge-management, and research tools developed under contract with one of NASA s partners. These tools have the unique responsibility of supporting NASA missions, but they are also finding uses outside of the Space Program.

Computer-assisted learning in medicine. How to create a novel software for immunology.

PubMed

Colsman, Andreas; Sticherling, Michael; Stöpel, Claus; Emmrich, Frank

2006-06-01

Teaching medical issues is increasingly demanding due to the permanent progress in medical sciences. Simultaneously, software applications are rapidly advancing with regard to their availability and easy use. Here a novel teaching program is presented for immunology, which is one of the fastest expanding topics in medical sciences. The requirements of media didactics were transferred to this e-learning tool for German students. After implementation, medical students evaluated the software and the different learning approaches showed acceptance. Altogether this novel software compares favourably to other English e-learning tools available in the Internet.

Splash: a software tool for stereotactic planning of recording chamber placement and electrode trajectories.

PubMed

Sperka, Daniel J; Ditterich, Jochen

2011-01-01

While computer-aided planning of human neurosurgeries is becoming more and more common, animal researchers still largely rely on paper atlases for planning their approach before implanting recording chambers to perform invasive recordings of neural activity, which makes this planning process tedious and error-prone. Here we present SPLASh (Stereotactic PLAnning Software), an interactive software tool for the stereotactic planning of recording chamber placement and electrode trajectories. SPLASh has been developed for monkey cortical recordings and relies on a combination of structural MRIs and electronic brain atlases. Since SPLASh is based on the neuroanatomy software Caret, it should also be possible to use it for other parts of the brain or other species for which Caret atlases are available. The tool allows the user to interactively evaluate different possible placements of recording chambers and to simulate electrode trajectories.

Splash: A Software Tool for Stereotactic Planning of Recording Chamber Placement and Electrode Trajectories

PubMed Central

Sperka, Daniel J.; Ditterich, Jochen

2011-01-01

While computer-aided planning of human neurosurgeries is becoming more and more common, animal researchers still largely rely on paper atlases for planning their approach before implanting recording chambers to perform invasive recordings of neural activity, which makes this planning process tedious and error-prone. Here we present SPLASh (Stereotactic PLAnning Software), an interactive software tool for the stereotactic planning of recording chamber placement and electrode trajectories. SPLASh has been developed for monkey cortical recordings and relies on a combination of structural MRIs and electronic brain atlases. Since SPLASh is based on the neuroanatomy software Caret, it should also be possible to use it for other parts of the brain or other species for which Caret atlases are available. The tool allows the user to interactively evaluate different possible placements of recording chambers and to simulate electrode trajectories. PMID:21472085

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

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.

"SABER": A new software tool for radiotherapy treatment plan evaluation.

PubMed

Zhao, Bo; Joiner, Michael C; Orton, Colin G; Burmeister, Jay

2010-11-01

Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information. A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper-radiosensitivity using the induced-repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash-out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions (gEUD2) and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control (P+). TCP, NTCP, and P+ are provided as a function of prescribed dose and multivariable TCP, NTCP, and P+ plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software. By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined

Contingency Contractor Optimization Phase 3 Sustainment Software Design Document - Contingency Contractor Optimization Tool - Prototype

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

Durfee, Justin David; Frazier, Christopher Rawls; Bandlow, Alisa

This document describes the final software design of the Contingency Contractor Optimization Tool - Prototype. Its purpose is to provide the overall architecture of the software and the logic behind this architecture. Documentation for the individual classes is provided in the application Javadoc. The Contingency Contractor Optimization project is intended to address Department of Defense mandates by delivering a centralized strategic planning tool that allows senior decision makers to quickly and accurately assess the impacts, risks, and mitigation strategies associated with utilizing contract support. The Contingency Contractor Optimization Tool - Prototype was developed in Phase 3 of the OSD ATLmore » Contingency Contractor Optimization project to support strategic planning for contingency contractors. The planning tool uses a model to optimize the Total Force mix by minimizing the combined total costs for selected mission scenarios. The model optimizes the match of personnel types (military, DoD civilian, and contractors) and capabilities to meet mission requirements as effectively as possible, based on risk, cost, and other requirements.« less

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.

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.

The Advanced Software Development and Commercialization Project

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

Gallopoulos, E.; Canfield, T.R.; Minkoff, M.

1990-09-01

This is the first of a series of reports pertaining to progress in the Advanced Software Development and Commercialization Project, a joint collaborative effort between the Center for Supercomputing Research and Development of the University of Illinois and the Computing and Telecommunications Division of Argonne National Laboratory. The purpose of this work is to apply techniques of parallel computing that were pioneered by University of Illinois researchers to mature computational fluid dynamics (CFD) and structural dynamics (SD) computer codes developed at Argonne. The collaboration in this project will bring this unique combination of expertise to bear, for the first time,more » on industrially important problems. By so doing, it will expose the strengths and weaknesses of existing techniques for parallelizing programs and will identify those problems that need to be solved in order to enable wide spread production use of parallel computers. Secondly, the increased efficiency of the CFD and SD codes themselves will enable the simulation of larger, more accurate engineering models that involve fluid and structural dynamics. In order to realize the above two goals, we are considering two production codes that have been developed at ANL and are widely used by both industry and Universities. These are COMMIX and WHAMS-3D. The first is a computational fluid dynamics code that is used for both nuclear reactor design and safety and as a design tool for the casting industry. The second is a three-dimensional structural dynamics code used in nuclear reactor safety as well as crashworthiness studies. These codes are currently available for both sequential and vector computers only. Our main goal is to port and optimize these two codes on shared memory multiprocessors. In so doing, we shall establish a process that can be followed in optimizing other sequential or vector engineering codes for parallel processors.« less

Oxygen octahedra picker: A software tool to extract quantitative information from STEM images.

PubMed

Wang, Yi; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y; van Aken, Peter A

2016-09-01

In perovskite oxide based materials and hetero-structures there are often strong correlations between oxygen octahedral distortions and functionality. Thus, atomistic understanding of the octahedral distortion, which requires accurate measurements of atomic column positions, will greatly help to engineer their properties. Here, we report the development of a software tool to extract quantitative information of the lattice and of BO6 octahedral distortions from STEM images. Center-of-mass and 2D Gaussian fitting methods are implemented to locate positions of individual atom columns. The precision of atomic column distance measurements is evaluated on both simulated and experimental images. The application of the software tool is demonstrated using practical examples. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Software analysis handbook: Software complexity analysis and software reliability estimation and prediction

NASA Technical Reports Server (NTRS)

Lee, Alice T.; Gunn, Todd; Pham, Tuan; Ricaldi, Ron

1994-01-01

This handbook documents the three software analysis processes the Space Station Software Analysis team uses to assess space station software, including their backgrounds, theories, tools, and analysis procedures. Potential applications of these analysis results are also presented. The first section describes how software complexity analysis provides quantitative information on code, such as code structure and risk areas, throughout the software life cycle. Software complexity analysis allows an analyst to understand the software structure, identify critical software components, assess risk areas within a software system, identify testing deficiencies, and recommend program improvements. Performing this type of analysis during the early design phases of software development can positively affect the process, and may prevent later, much larger, difficulties. The second section describes how software reliability estimation and prediction analysis, or software reliability, provides a quantitative means to measure the probability of failure-free operation of a computer program, and describes the two tools used by JSC to determine failure rates and design tradeoffs between reliability, costs, performance, and schedule.

APT - NASA ENHANCED VERSION OF AUTOMATICALLY PROGRAMMED TOOL SOFTWARE - STAND-ALONE VERSION

NASA Technical Reports Server (NTRS)

Premo, D. A.

1994-01-01

The APT code is one of the most widely used software tools for complex numerically controlled (N/C) machining. APT is an acronym for Automatically Programmed Tools and is used to denote both a language and the computer software that processes that language. Development of the APT language and software system was begun over twenty years ago as a U. S. government sponsored industry and university research effort. APT is a "problem oriented" language that was developed for the explicit purpose of aiding the N/C machine tools. Machine-tool instructions and geometry definitions are written in the APT language to constitute a "part program." The APT part program is processed by the APT software to produce a cutter location (CL) file. This CL file may then be processed by user supplied post processors to convert the CL data into a form suitable for a particular N/C machine tool. This June, 1989 offering of the APT system represents an adaptation, with enhancements, of the public domain version of APT IV/SSX8 to the DEC VAX-11/780 for use by the Engineering Services Division of the NASA Goddard Space Flight Center. Enhancements include the super pocket feature which allows concave and convex polygon shapes of up to 40 points including shapes that overlap, that leave islands of material within the pocket, and that have one or more arcs as part of the pocket boundary. Recent modifications to APT include a rework of the POCKET subroutine and correction of an error that prevented the use within a macro of a macro variable cutter move statement combined with macro variable double check surfaces. Former modifications included the expansion of array and buffer sizes to accommodate larger part programs, and the insertion of a few user friendly error messages. The APT system software on the DEC VAX-11/780 is organized into two separate programs: the load complex and the APT processor. The load complex handles the table initiation phase and is usually only run when changes to the

Sandia Advanced MEMS Design Tools, Version 2.2.5

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

Yarberry, Victor; Allen, James; Lantz, Jeffery

2010-01-19

The Sandia National Laboratories Advanced MEMS Design Tools, Version 2.2.5, is a collection of menus, prototype drawings, and executables that provide significant productivity enhancements when using AutoCAD to design MEMS components. This release is designed for AutoCAD 2000i, 2002, or 2004 and is supported under Windows NT 4.0, Windows 2000, or XP. SUMMiT V (Sandia Ultra planar Multi level MEMS Technology) is a 5 level surface micromachine fabrication technology, which customers internal and external to Sandia can access to fabricate prototype MEMS devices. This CD contains an integrated set of electronic files that: a) Describe the SUMMiT V fabrication processmore » b) Facilitate the process of designing MEMS with the SUMMiT process (prototype file, Design Rule Checker, Standard Parts Library) New features in this version: AutoCAD 2004 support has been added. SafeExplode ? a new feature that explodes blocks without affecting polylines (avoids exploding polylines into objects that are ignored by the DRC and Visualization tools). Layer control menu ? a pull-down menu for selecting layers to isolate, freeze, or thaw. Updated tools: A check has been added to catch invalid block names. DRC features: Added username/password validation, added a method to update the user?s password. SNL_DRC_WIDTH ? a value to control the width of the DRC error lines. SNL_BIAS_VALUE ? a value use to offset selected geometry SNL_PROCESS_NAME ? a value to specify the process name Documentation changes: The documentation has been updated to include the new features. While there exist some files on the CD that are used in conjunction with software package AutoCAD, these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.« less

Advanced Transport Operating System (ATOPS) Flight Management/Flight Controls (FM/FC) software description

NASA Technical Reports Server (NTRS)

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

1993-01-01

The flight software developed for the Flight Management/Flight Controls (FM/FC) MicroVAX computer used on the Transport Systems Research Vehicle for Advanced Transport Operating Systems (ATOPS) research is described. The FM/FC software computes navigation position estimates, guidance commands, and those commands issued to the control surfaces to direct the aircraft in flight. Various modes of flight are provided for, ranging from computer assisted manual modes to fully automatic modes including automatic landing. A high-level system overview as well as a description of each software module comprising the system is provided. Digital systems diagrams are included for each major flight control component and selected flight management functions.

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

PubMed

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

2013-08-30

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

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

PubMed

Chen, Yi-Bu; Chattopadhyay, Ansuman; Bergen, Phillip; Gadd, Cynthia; Tannery, Nancy

2007-01-01

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

Advances in molecular labeling, high throughput imaging and machine intelligence portend powerful functional cellular biochemistry tools.

PubMed

Price, Jeffrey H; Goodacre, Angela; Hahn, Klaus; Hodgson, Louis; Hunter, Edward A; Krajewski, Stanislaw; Murphy, Robert F; Rabinovich, Andrew; Reed, John C; Heynen, Susanne

2002-01-01

Cellular behavior is complex. Successfully understanding systems at ever-increasing complexity is fundamental to advances in modern science and unraveling the functional details of cellular behavior is no exception. We present a collection of prospectives to provide a glimpse of the techniques that will aid in collecting, managing and utilizing information on complex cellular processes via molecular imaging tools. These include: 1) visualizing intracellular protein activity with fluorescent markers, 2) high throughput (and automated) imaging of multilabeled cells in statistically significant numbers, and 3) machine intelligence to analyze subcellular image localization and pattern. Although not addressed here, the importance of combining cell-image-based information with detailed molecular structure and ligand-receptor binding models cannot be overlooked. Advanced molecular imaging techniques have the potential to impact cellular diagnostics for cancer screening, clinical correlations of tissue molecular patterns for cancer biology, and cellular molecular interactions for accelerating drug discovery. The goal of finally understanding all cellular components and behaviors will be achieved by advances in both instrumentation engineering (software and hardware) and molecular biochemistry. Copyright 2002 Wiley-Liss, Inc.

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…

Software/hardware distributed processing network supporting the Ada environment

NASA Astrophysics Data System (ADS)

Wood, Richard J.; Pryk, Zen

1993-09-01

A high-performance, fault-tolerant, distributed network has been developed, tested, and demonstrated. The network is based on the MIPS Computer Systems, Inc. R3000 Risc for processing, VHSIC ASICs for high speed, reliable, inter-node communications and compatible commercial memory and I/O boards. The network is an evolution of the Advanced Onboard Signal Processor (AOSP) architecture. It supports Ada application software with an Ada- implemented operating system. A six-node implementation (capable of expansion up to 256 nodes) of the RISC multiprocessor architecture provides 120 MIPS of scalar throughput, 96 Mbytes of RAM and 24 Mbytes of non-volatile memory. The network provides for all ground processing applications, has merit for space-qualified RISC-based network, and interfaces to advanced Computer Aided Software Engineering (CASE) tools for application software development.

Assess/Mitigate Risk through the Use of Computer-Aided Software Engineering (CASE) Tools

NASA Technical Reports Server (NTRS)

Aguilar, Michael L.

2013-01-01

The NASA Engineering and Safety Center (NESC) was requested to perform an independent assessment of the mitigation of the Constellation Program (CxP) Risk 4421 through the use of computer-aided software engineering (CASE) tools. With the cancellation of the CxP, the assessment goals were modified to capture lessons learned and best practices in the use of CASE tools. The assessment goal was to prepare the next program for the use of these CASE tools. The outcome of the assessment is contained in this document.

A software tool of digital tomosynthesis application for patient positioning in radiotherapy.

PubMed

Yan, Hui; Dai, Jian-Rong

2016-03-08

Digital Tomosynthesis (DTS) is an image modality in reconstructing tomographic images from two-dimensional kV projections covering a narrow scan angles. Comparing with conventional cone-beam CT (CBCT), it requires less time and radiation dose in data acquisition. It is feasible to apply this technique in patient positioning in radiotherapy. To facilitate its clinical application, a software tool was developed and the reconstruction processes were accelerated by graphic process-ing unit (GPU). Two reconstruction and two registration processes are required for DTS application which is different from conventional CBCT application which requires one image reconstruction process and one image registration process. The reconstruction stage consists of productions of two types of DTS. One type of DTS is reconstructed from cone-beam (CB) projections covering a narrow scan angle and is named onboard DTS (ODTS), which represents the real patient position in treatment room. Another type of DTS is reconstructed from digitally reconstructed radiography (DRR) and is named reference DTS (RDTS), which represents the ideal patient position in treatment room. Prior to the reconstruction of RDTS, The DRRs are reconstructed from planning CT using the same acquisition setting of CB projections. The registration stage consists of two matching processes between ODTS and RDTS. The target shift in lateral and longitudinal axes are obtained from the matching between ODTS and RDTS in coronal view, while the target shift in longitudinal and vertical axes are obtained from the matching between ODTS and RDTS in sagittal view. In this software, both DRR and DTS reconstruction algorithms were implemented on GPU environments for acceleration purpose. The comprehensive evaluation of this software tool was performed including geometric accuracy, image quality, registration accuracy, and reconstruction efficiency. The average correlation coefficient between DRR/DTS generated by GPU-based algorithm

A software tool of digital tomosynthesis application for patient positioning in radiotherapy

PubMed Central

Dai, Jian‐Rong

2016-01-01

Digital Tomosynthesis (DTS) is an image modality in reconstructing tomographic images from two‐dimensional kV projections covering a narrow scan angles. Comparing with conventional cone‐beam CT (CBCT), it requires less time and radiation dose in data acquisition. It is feasible to apply this technique in patient positioning in radiotherapy. To facilitate its clinical application, a software tool was developed and the reconstruction processes were accelerated by graphic processing unit (GPU). Two reconstruction and two registration processes are required for DTS application which is different from conventional CBCT application which requires one image reconstruction process and one image registration process. The reconstruction stage consists of productions of two types of DTS. One type of DTS is reconstructed from cone‐beam (CB) projections covering a narrow scan angle and is named onboard DTS (ODTS), which represents the real patient position in treatment room. Another type of DTS is reconstructed from digitally reconstructed radiography (DRR) and is named reference DTS (RDTS), which represents the ideal patient position in treatment room. Prior to the reconstruction of RDTS, The DRRs are reconstructed from planning CT using the same acquisition setting of CB projections. The registration stage consists of two matching processes between ODTS and RDTS. The target shift in lateral and longitudinal axes are obtained from the matching between ODTS and RDTS in coronal view, while the target shift in longitudinal and vertical axes are obtained from the matching between ODTS and RDTS in sagittal view. In this software, both DRR and DTS reconstruction algorithms were implemented on GPU environments for acceleration purpose. The comprehensive evaluation of this software tool was performed including geometric accuracy, image quality, registration accuracy, and reconstruction efficiency. The average correlation coefficient between DRR/DTS generated by GPU�

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

cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.

PubMed

Cianfrocco, Michael A; Lahiri, Indrajit; DiMaio, Frank; Leschziner, Andres E

2018-06-01

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud. Copyright © 2018. Published by Elsevier Inc.

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.

SAMPA: A free software tool for skin and membrane permeation data analysis.

PubMed

Bezrouk, Aleš; Fiala, Zdeněk; Kotingová, Lenka; Krulichová, Iva Selke; Kopečná, Monika; Vávrová, Kateřina

2017-10-01

Skin and membrane permeation experiments comprise an important step in the development of a transdermal or topical formulation or toxicological risk assessment. The standard method for analyzing these data relies on the linear part of a permeation profile. However, it is difficult to objectively determine when the profile becomes linear, or the experiment duration may be insufficient to reach a maximum or steady state. Here, we present a software tool for Skin And Membrane Permeation data Analysis, SAMPA, that is easy to use and overcomes several of these difficulties. The SAMPA method and software have been validated on in vitro and in vivo permeation data on human, pig and rat skin and model stratum corneum lipid membranes using compounds that range from highly lipophilic polycyclic aromatic hydrocarbons to highly hydrophilic antiviral drug, with and without two permeation enhancers. The SAMPA performance was compared with the standard method using a linear part of the permeation profile and a complex mathematical model. SAMPA is a user-friendly, open-source software tool for analyzing the data obtained from skin and membrane permeation experiments. It runs on a Microsoft Windows platform and is freely available as a Supporting file to this article. Copyright © 2017 Elsevier Ltd. All rights reserved.

The anatomy of E-Learning tools: Does software usability influence learning outcomes?

PubMed

Van Nuland, Sonya E; Rogers, Kem A

2016-07-08

Reductions in laboratory hours have increased the popularity of commercial anatomy e-learning tools. It is critical to understand how the functionality of such tools can influence the mental effort required during the learning process, also known as cognitive load. Using dual-task methodology, two anatomical e-learning tools were examined to determine the effect of their design on cognitive load during two joint learning exercises. A.D.A.M. Interactive Anatomy is a simplistic, two-dimensional tool that presents like a textbook, whereas Netter's 3D Interactive Anatomy has a more complex three-dimensional usability that allows structures to be rotated. It was hypothesized that longer reaction times on an observation task would be associated with the more complex anatomical software (Netter's 3D Interactive Anatomy), indicating a higher cognitive load imposed by the anatomy software, which would result in lower post-test scores. Undergraduate anatomy students from Western University, Canada (n = 70) were assessed using a baseline knowledge test, Stroop observation task response times (a measure of cognitive load), mental rotation test scores, and an anatomy post-test. Results showed that reaction times and post-test outcomes were similar for both tools, whereas mental rotation test scores were positively correlated with post-test values when students used Netter's 3D Interactive Anatomy (P = 0.007), but not when they used A.D.A.M. Interactive Anatomy. This suggests that a simple e-learning tool, such as A.D.A.M. Interactive Anatomy, is as effective as more complicated tools, such as Netter's 3D Interactive Anatomy, and does not academically disadvantage those with poor spatial ability. Anat Sci Educ 9: 378-390. © 2015 American Association of Anatomists. © 2015 American Association of Anatomists.

Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

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

Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

2007-01-01

The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

Accelerating Project and Process Improvement using Advanced Software Simulation Technology: From the Office to the Enterprise

DTIC Science & Technology

2010-04-29

Technology: From the Office Larry Smith Software Technology Support Center to the Enterprise 517 SMXS/MXDEA 6022 Fir Avenue Hill AFB, UT 84056 801...2010 to 00-00-2010 4. TITLE AND SUBTITLE Accelerating Project and Process Improvement using Advanced Software Simulation Technology: From the Office to

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

DTIC Science & Technology

1997-09-30

set of software tools for specification and verification of distributed real time systems using formal methods. The task of this SBIR Phase II effort...to be used by designers of real - time systems for early detection of errors. The mathematical complexity of formal specification and verification has

Using a Self-Administered Visual Basic Software Tool To Teach Psychological Concepts.

ERIC Educational Resources Information Center

Strang, Harold R.; Sullivan, Amie K.; Schoeny, Zahrl G.

2002-01-01

Introduces LearningLinks, a Visual Basic software tool that allows teachers to create individualized learning modules that use constructivist and behavioral learning principles. Describes field testing of undergraduates at the University of Virginia that tested a module designed to improve understanding of the psychological concepts of…

Utility of the advanced chronic kidney disease patient management tools: case studies.

PubMed

Patwardhan, Meenal B; Matchar, David B; Samsa, Gregory P; Haley, William E

2008-01-01

Appropriate management of advanced chronic kidney disease (CKD) delays or limits its progression. The Advanced CKD Patient Management Toolkit was developed using a process-improvement technique to assist patient management and address CKD-specific management issues. We pilot tested the toolkit in 2 community nephrology practices, assessed the utility of individual tools, and evaluated the impact on conformance to an advanced CKD guideline through patient chart abstraction. Tool use was distinct in the 2 sites and depended on the site champion's involvement, the extent of process reconfiguration demanded by a tool, and its perceived value. Baseline conformance varied across guideline recommendations (averaged 54%). Posttrial conformance increased in all clinical areas (averaged 59%). Valuable features of the toolkit in real-world settings were its ability to: facilitate tool selection, direct implementation efforts in response to a baseline performance audit, and allow selection of tool versions and customizing them. Our results suggest that systematically created, multifaceted, and customizable tools can promote guideline conformance.

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.

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

PubMed

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

2017-03-22

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

76 FR 5832 - International Business Machines (IBM), Software Group Business Unit, Optim Data Studio Tools QA...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-02

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,554] International Business Machines (IBM), Software Group Business Unit, Optim Data Studio Tools QA, San Jose, CA; Notice of... determination of the TAA petition filed on behalf of workers at International Business Machines (IBM), Software...

QCScreen: a software tool for data quality control in LC-HRMS based metabolomics.

PubMed

Simader, Alexandra Maria; Kluger, Bernhard; Neumann, Nora Katharina Nicole; Bueschl, Christoph; Lemmens, Marc; Lirk, Gerald; Krska, Rudolf; Schuhmacher, Rainer

2015-10-24

Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources of error e.g. retention time or mass accuracy shifts. Especially in liquid chromatography-high resolution mass spectrometry (LC-HRMS) based metabolomics research, proper quality control checks (e.g. for precision, signal drifts or offsets) are crucial prerequisites to achieve reliable and comparable results within and across experimental measurement sequences. Software tools can support this process. The software tool QCScreen was developed to offer a quick and easy data quality check of LC-HRMS derived data. It allows a flexible investigation and comparison of basic quality-related parameters within user-defined target features and the possibility to automatically evaluate multiple sample types within or across different measurement sequences in a short time. It offers a user-friendly interface that allows an easy selection of processing steps and parameter settings. The generated results include a coloured overview plot of data quality across all analysed samples and targets and, in addition, detailed illustrations of the stability and precision of the chromatographic separation, the mass accuracy and the detector sensitivity. The use of QCScreen is demonstrated with experimental data from metabolomics experiments using selected standard compounds in pure solvent. The application of the software identified problematic features, samples and analytical parameters and suggested which data files or compounds required closer manual inspection. QCScreen is an open source software tool which provides a useful basis for assessing the suitability of LC-HRMS data prior to time consuming, detailed data processing and subsequent statistical analysis. It accepts the generic mzXML format and thus can be used with many different LC-HRMS platforms to process both multiple

Data and Tools | Integrated Energy Solutions | NREL

Science.gov Websites

for a research campus eQUEST. Detailed analysis of today's state-of-the-art building design source software tools to support whole building energy modeling and advanced daylight analysis BESTEST-EX

Data and software tools for gamma radiation spectral threat detection and nuclide identification algorithm development and evaluation

NASA Astrophysics Data System (ADS)

Portnoy, David; Fisher, Brian; Phifer, Daniel

2015-06-01

The detection of radiological and nuclear threats is extremely important to national security. The federal government is spending significant resources developing new detection systems and attempting to increase the performance of existing ones. The detection of illicit radionuclides that may pose a radiological or nuclear threat is a challenging problem complicated by benign radiation sources (e.g., cat litter and medical treatments), shielding, and large variations in background radiation. Although there is a growing acceptance within the community that concentrating efforts on algorithm development (independent of the specifics of fully assembled systems) has the potential for significant overall system performance gains, there are two major hindrances to advancements in gamma spectral analysis algorithms under the current paradigm: access to data and common performance metrics along with baseline performance measures. Because many of the signatures collected during performance measurement campaigns are classified, dissemination to algorithm developers is extremely limited. This leaves developers no choice but to collect their own data if they are lucky enough to have access to material and sensors. This is often combined with their own definition of metrics for measuring performance. These two conditions make it all but impossible for developers and external reviewers to make meaningful comparisons between algorithms. Without meaningful comparisons, performance advancements become very hard to achieve and (more importantly) recognize. The objective of this work is to overcome these obstacles by developing and freely distributing real and synthetically generated gamma-spectra data sets as well as software tools for performance evaluation with associated performance baselines to national labs, academic institutions, government agencies, and industry. At present, datasets for two tracks, or application domains, have been developed: one that includes temporal

Training, Quality Assurance Factors, and Tools Investigation: a Work Report and Suggestions on Software Quality Assurance

NASA Technical Reports Server (NTRS)

Lee, Pen-Nan

1991-01-01

Previously, several research tasks have been conducted, some observations were obtained, and several possible suggestions have been contemplated involving software quality assurance engineering at NASA Johnson. These research tasks are briefly described. Also, a brief discussion is given on the role of software quality assurance in software engineering along with some observations and suggestions. A brief discussion on a training program for software quality assurance engineers is provided. A list of assurance factors as well as quality factors are also included. Finally, a process model which can be used for searching and collecting software quality assurance tools is presented.

New technologies for supporting real-time on-board software development

NASA Astrophysics Data System (ADS)

Kerridge, D.

1995-03-01

The next generation of on-board data management systems will be significantly more complex than current designs, and will be required to perform more complex and demanding tasks in software. Improved hardware technology, in the form of the MA31750 radiation hard processor, is one key component in addressing the needs of future embedded systems. However, to complement these hardware advances, improved support for the design and implementation of real-time data management software is now needed. This will help to control the cost and risk assoicated with developing data management software development as it becomes an increasingly significant element within embedded systems. One particular problem with developing embedded software is managing the non-functional requirements in a systematic way. This paper identifies how Logica has exploited recent developments in hard real-time theory to address this problem through the use of new hard real-time analysis and design methods which can be supported by specialized tools. The first stage in transferring this technology from the research domain to industrial application has already been completed. The MA37150 Hard Real-Time Embedded Software Support Environment (HESSE) is a loosely integrated set of hardware and software tools which directly support the process of hard real-time analysis for software targeting the MA31750 processor. With further development, this HESSE promises to provide embedded system developers with software tools which can reduce the risks associated with developing complex hard real-time software. Supported in this way by more sophisticated software methods and tools, it is foreseen that MA31750 based embedded systems can meet the processing needs for the next generation of on-board data management systems.

Virtual Beach: Decision Support Tools for Beach Pathogen Prediction

EPA Science Inventory

The Virtual Beach Managers Tool (VB) is decision-making software developed to help local beach managers make decisions as to when beaches should be closed due to predicted high levels of water borne pathogens. The tool is being developed under the umbrella of EPA's Advanced Monit...

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.

Clinical software development for the Web: lessons learned from the BOADICEA project.

PubMed

Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web

Clinical software development for the Web: lessons learned from the BOADICEA project

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers

Microsoft Producer: A Software Tool for Creating Multimedia PowerPoint[R] Presentations

ERIC Educational Resources Information Center

Leffingwell, Thad R.; Thomas, David G.; Elliott, William H.

2007-01-01

Microsoft[R] Producer[R] is a powerful yet user-friendly PowerPoint companion tool for creating on-demand multimedia presentations. Instructors can easily distribute these presentations via compact disc or streaming media over the Internet. We describe the features of the software, system requirements, and other required hardware. We also describe…

Conceptual Assessment Tool for Advanced Undergraduate Electrodynamics

ERIC Educational Resources Information Center

Baily, Charles; Ryan, Qing X.; Astolfi, Cecilia; Pollock, Steven J.

2017-01-01

As part of ongoing investigations into student learning in advanced undergraduate courses, we have developed a conceptual assessment tool for upper-division electrodynamics (E&M II): the Colorado UppeR-division ElectrodyNamics Test (CURrENT). This is a free response, postinstruction diagnostic with 6 multipart questions, an optional 3-question…

Advanced Transport Operating System (ATOPS) color displays software description microprocessor system

NASA Technical Reports Server (NTRS)

Slominski, Christopher J.; Plyler, Valerie E.; Dickson, Richard W.

1992-01-01

This document describes the software created for the Sperry Microprocessor Color Display System used for the Advanced Transport Operating Systems (ATOPS) project on the Transport Systems Research Vehicle (TSRV). The software delivery known as the 'baseline display system', is the one described in this document. Throughout this publication, module descriptions are presented in a standardized format which contains module purpose, calling sequence, detailed description, and global references. The global reference section includes procedures and common variables referenced by a particular module. The system described supports the Research Flight Deck (RFD) of the TSRV. The RFD contains eight cathode ray tubes (CRTs) which depict a Primary Flight Display, Navigation Display, System Warning Display, Takeoff Performance Monitoring System Display, and Engine Display.

Software Tools for Emittance Measurement and Matching for 12 GeV CEBAF

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

Turner, Dennis L.

2016-05-01

This paper discusses model-driven setup of the Continuous Electron Beam Accelerator Facility (CEBAF) for the 12GeV era, focusing on qsUtility. qsUtility is a set of software tools created to perform emittance measurements, analyze those measurements, and compute optics corrections based upon the measurements.qsUtility was developed as a toolset to facilitate reducing machine configuration time and reproducibility by way of an accurate accelerator model, and to provide Operations staff with tools to measure and correct machine optics with little or no assistance from optics experts.

Accuracy of Dolphin visual treatment objective (VTO) prediction software on class III patients treated with maxillary advancement and mandibular setback.

PubMed

Peterman, Robert J; Jiang, Shuying; Johe, Rene; Mukherjee, Padma M

2016-12-01

Dolphin® visual treatment objective (VTO) prediction software is routinely utilized by orthodontists during the treatment planning of orthognathic cases to help predict post-surgical soft tissue changes. Although surgical soft tissue prediction is considered to be a vital tool, its accuracy is not well understood in tow-jaw surgical procedures. The objective of this study was to quantify the accuracy of Dolphin Imaging's VTO soft tissue prediction software on class III patients treated with maxillary advancement and mandibular setback and to validate the efficacy of the software in such complex cases. This retrospective study analyzed the records of 14 patients treated with comprehensive orthodontics in conjunction with two-jaw orthognathic surgery. Pre- and post-treatment radiographs were traced and superimposed to determine the actual skeletal movements achieved in surgery. This information was then used to simulate surgery in the software and generate a final soft tissue patient profile prediction. Prediction images were then compared to the actual post-treatment profile photos to determine differences. Dolphin Imaging's software was determined to be accurate within an error range of +/- 2 mm in the X-axis at most landmarks. The lower lip predictions were most inaccurate. Clinically, the observed error suggests that the VTO may be used for demonstration and communication with a patient or consulting practitioner. However, Dolphin should not be useful for precise treatment planning of surgical movements. This program should be used with caution to prevent unrealistic patient expectations and dissatisfaction.

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

Space Flight Software Development Software for Intelligent System Health Management

NASA Technical Reports Server (NTRS)

Trevino, Luis C.; Crumbley, Tim

2004-01-01

The slide presentation examines the Marshall Space Flight Center Flight Software Branch, including software development projects, mission critical space flight software development, software technical insight, advanced software development technologies, and continuous improvement in the software development processes and methods.

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

PubMed

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

2015-10-01

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

Tools Ensure Reliability of Critical Software

NASA Technical Reports Server (NTRS)

2012-01-01

In November 2006, after attempting to make a routine maneuver, NASA's Mars Global Surveyor (MGS) reported unexpected errors. The onboard software switched to backup resources, and a 2-day lapse in communication took place between the spacecraft and Earth. When a signal was finally received, it indicated that MGS had entered safe mode, a state of restricted activity in which the computer awaits instructions from Earth. After more than 9 years of successful operation gathering data and snapping pictures of Mars to characterize the planet's land and weather communication between MGS and Earth suddenly stopped. Months later, a report from NASA's internal review board found the spacecraft's battery failed due to an unfortunate sequence of events. Updates to the spacecraft's software, which had taken place months earlier, were written to the wrong memory address in the spacecraft's computer. In short, the mission ended because of a software defect. Over the last decade, spacecraft have become increasingly reliant on software to carry out mission operations. In fact, the next mission to Mars, the Mars Science Laboratory, will rely on more software than all earlier missions to Mars combined. According to Gerard Holzmann, manager at the Laboratory for Reliable Software (LaRS) at NASA's Jet Propulsion Laboratory (JPL), even the fault protection systems on a spacecraft are mostly software-based. For reasons like these, well-functioning software is critical for NASA. In the same year as the failure of MGS, Holzmann presented a new approach to critical software development to help reduce risk and provide consistency. He proposed The Power of 10: Rules for Developing Safety-Critical Code, which is a small set of rules that can easily be remembered, clearly relate to risk, and allow compliance to be verified. The reaction at JPL was positive, and developers in the private sector embraced Holzmann's ideas.

A Structural Health Monitoring Software Tool for Optimization, Diagnostics and Prognostics

DTIC Science & Technology

2011-01-01

A Structural Health Monitoring Software Tool for Optimization, Diagnostics and Prognostics Seth S . Kessler1, Eric B. Flynn2, Christopher T...technology more accessible, and commercially practical. 1. INTRODUCTION Currently successful laboratory non- destructive testing and monitoring...PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES

A software tool for determination of breast cancer treatment methods using data mining approach.

PubMed

Cakır, Abdülkadir; Demirel, Burçin

2011-12-01

In this work, breast cancer treatment methods are determined using data mining. For this purpose, software is developed to help to oncology doctor for the suggestion of application of the treatment methods about breast cancer patients. 462 breast cancer patient data, obtained from Ankara Oncology Hospital, are used to determine treatment methods for new patients. This dataset is processed with Weka data mining tool. Classification algorithms are applied one by one for this dataset and results are compared to find proper treatment method. Developed software program called as "Treatment Assistant" uses different algorithms (IB1, Multilayer Perception and Decision Table) to find out which one is giving better result for each attribute to predict and by using Java Net beans interface. Treatment methods are determined for the post surgical operation of breast cancer patients using this developed software tool. At modeling step of data mining process, different Weka algorithms are used for output attributes. For hormonotherapy output IB1, for tamoxifen and radiotherapy outputs Multilayer Perceptron and for the chemotherapy output decision table algorithm shows best accuracy performance compare to each other. In conclusion, this work shows that data mining approach can be a useful tool for medical applications particularly at the treatment decision step. Data mining helps to the doctor to decide in a short time.

A practical overview and comparison of certain commercial forensic software tools for processing large-scale digital investigations

NASA Astrophysics Data System (ADS)

Kröger, Knut; Creutzburg, Reiner

2013-05-01

The aim of this paper is to show the usefulness of modern forensic software tools for processing large-scale digital investigations. In particular, we focus on the new version of Nuix 4.2 and compare it with AccessData FTK 4.2, X-Ways Forensics 16.9 and Guidance Encase Forensic 7 regarding its performance, functionality, usability and capability. We will show how these software tools work with large forensic images and how capable they are in examining complex and big data scenarios.

[Assessment of a software application tool for managing nursing care processes in the period 2005-2010].

PubMed

Medina-Valverde, M José; Rodríguez-Borrego, M Aurora; Luque-Alcaraz, Olga; de la Torre-Barbero, M José; Parra-Perea, Julia; Moros-Molina, M del Pilar

2012-01-01

To identify problems and critical points in the software application. Assessment of the implementation of the software tool "Azahar" used to manage nursing care processes. The monitored population consisted of nurses who were users of the tool, at the Hospital and those who benefited from it in Primary Care. Each group was selected randomly and the number was determined by data saturation. A qualitative approach was employed using in-depth interviews and group discussion as data collection techniques. The nurses considered that the most beneficial and useful application of the tool was the initial assessment and the continuity of care release forms, as well as the recording of all data on the nursing process to ensure quality. The disadvantages and weaknesses identified were associated with the continuous variability in their daily care. The nurses related an increase in workload with the impossibility of entering the records into the computer, making paper records, thus duplicating the recording process. Likewise, they consider that the operating system of the software should be improved in terms of simplicity and functionality. The simplicity of the tool and the adjustment of workloads would favour its use and as a result, continuity of care. Copyright © 2010 Elsevier España, S.L. All rights reserved.

Advances in the production of freeform optical surfaces

NASA Astrophysics Data System (ADS)

Tohme, Yazid E.; Luniya, Suneet S.

2007-05-01

Recent market demands for free-form optics have challenged the industry to find new methods and techniques to manufacture free-form optical surfaces with a high level of accuracy and reliability. Production techniques are becoming a mix of multi-axis single point diamond machining centers or deterministic ultra precision grinding centers coupled with capable measurement systems to accomplish the task. It has been determined that a complex software tool is required to seamlessly integrate all aspects of the manufacturing process chain. Advances in computational power and improved performance of computer controlled precision machinery have driven the use of such software programs to measure, visualize, analyze, produce and re-validate the 3D free-form design thus making the process of manufacturing such complex surfaces a viable task. Consolidation of the entire production cycle in a comprehensive software tool that can interact with all systems in design, production and measurement phase will enable manufacturers to solve these complex challenges providing improved product quality, simplified processes, and enhanced performance. The work being presented describes the latest advancements in developing such software package for the entire fabrication process chain for aspheric and free-form shapes. It applies a rational B-spline based kernel to transform an optical design in the form of parametrical definition (optical equation), standard CAD format, or a cloud of points to a central format that drives the simulation. This software tool creates a closed loop for the fabrication process chain. It integrates surface analysis and compensation, tool path generation, and measurement analysis in one package.

CrossTalk. The Journal of Defense Software Engineering. Volume 13, Number 6, June 2000

DTIC Science & Technology

2000-06-01

Techniques for Efficiently Generating and Testing Software This paper presents a proven process that uses advanced tools to design, develop and test... optimal software. by Keith R. Wegner Large Software Systems—Back to Basics Development methods that work on small problems seem to not scale well to...Ability Requirements for Teamwork: Implications for Human Resource Management, Journal of Management, Vol. 20, No. 2, 1994. 11. Ferguson, Pat, Watts S

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

PubMed

Sarpe, Vladimir; Schriemer, David C

2017-02-01

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

Hosted Services for Advanced V and V Technologies: An Approach to Achieving Adoption without the Woes of Usage

NASA Technical Reports Server (NTRS)

Koga, Dennis (Technical Monitor); Penix, John; Markosian, Lawrence Z.; OMalley, Owen; Brew, William A.

2003-01-01

Attempts to achieve widespread use of software verification tools have been notably unsuccessful. Even 'straightforward', classic, and potentially effective verification tools such as lint-like tools face limits on their acceptance. These limits are imposed by the expertise required applying the tools and interpreting the results, the high false positive rate of many verification tools, and the need to integrate the tools into development environments. The barriers are even greater for more complex advanced technologies such as model checking. Web-hosted services for advanced verification technologies may mitigate these problems by centralizing tool expertise. The possible benefits of this approach include eliminating the need for software developer expertise in tool application and results filtering, and improving integration with other development tools.

Advance reservation access control using software-defined networking and tokens

DOE PAGES

Chung, Joaquin; Jung, Eun-Sung; Kettimuthu, Rajkumar; ...

2017-03-09

Advance reservation systems allow users to reserve dedicated bandwidth connection resources from advanced high-speed networks. A common use case for such systems is data transfers in distributed science environments in which a user wants exclusive access to the reservation. However, current advance network reservation methods cannot ensure exclusive access of a network reservation to the specific flow for which the user made the reservation. We present in this paper a novel network architecture that addresses this limitation and ensures that a reservation is used only by the intended flow. We achieve this by leveraging software-defined networking (SDN) and token-based authorization.more » We use SDN to orchestrate and automate the reservation of networking resources, end-to-end and across multiple administrative domains, and tokens to create a strong binding between the user or application that requested the reservation and the flows provisioned by SDN. Finally, we conducted experiments on the ESNet 100G SDN testbed, and demonstrated that our system effectively protects authorized flows from competing traffic in the network.« less

Advance reservation access control using software-defined networking and tokens

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

Chung, Joaquin; Jung, Eun-Sung; Kettimuthu, Rajkumar

Advance reservation systems allow users to reserve dedicated bandwidth connection resources from advanced high-speed networks. A common use case for such systems is data transfers in distributed science environments in which a user wants exclusive access to the reservation. However, current advance network reservation methods cannot ensure exclusive access of a network reservation to the specific flow for which the user made the reservation. We present in this paper a novel network architecture that addresses this limitation and ensures that a reservation is used only by the intended flow. We achieve this by leveraging software-defined networking (SDN) and token-based authorization.more » We use SDN to orchestrate and automate the reservation of networking resources, end-to-end and across multiple administrative domains, and tokens to create a strong binding between the user or application that requested the reservation and the flows provisioned by SDN. Finally, we conducted experiments on the ESNet 100G SDN testbed, and demonstrated that our system effectively protects authorized flows from competing traffic in the network.« less

Advance reservation access control using software-defined networking and tokens

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

Chung, Joaquin; Jung, Eun-Sung; Kettimuthu, Rajkumar

Advance reservation systems allow users to reserve dedicated bandwidth connection resources from advanced high-speed networks. A common use case for such systems is data transfers in distributed science environments in which a user wants exclusive access to the reservation. However, current advance network reservation methods cannot ensure exclusive access of a network reservation to the specific flow for which the user made the reservation. We present here a novel network architecture that addresses this limitation and ensures that a reservation is used only by the intended flow. We achieve this by leveraging software-defined networking (SDN) and token-based authorization. We usemore » SDN to orchestrate and automate the reservation of networking resources, end-to-end and across multiple administrative domains, and tokens to create a strong binding between the user or application that requested the reservation and the flows provisioned by SDN. We conducted experiments on the ESNet 100G SDN testbed, and demonstrated that our system effectively protects authorized flows from competing traffic in the network. (C) 2017 Elsevier B.V. All rights reserved.« less

Wiki as a Corporate Learning Tool: Case Study for Software Development Company

ERIC Educational Resources Information Center

Milovanovic, Milos; Minovic, Miroslav; Stavljanin, Velimir; Savkovic, Marko; Starcevic, Dusan

2012-01-01

In our study, we attempted to further investigate how Web 2.0 technologies influence workplace learning. Our particular interest was on using Wiki as a tool for corporate exchange of knowledge with the focus on informal learning. In this study, we collaborated with a multinational software development company that uses Wiki as a corporate tool…

Software applications for flux balance analysis.

PubMed

Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

2014-01-01

Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers.

Users' manual for the Hydroecological Integrity Assessment Process software (including the New Jersey Assessment Tools)

USGS Publications Warehouse

Henriksen, James A.; Heasley, John; Kennen, Jonathan G.; Nieswand, Steven

2006-01-01

Applying the Hydroecological Integrity Assessment Process involves four steps: (1) a hydrologic classification of relatively unmodified streams in a geographic area using long-term gage records and 171 ecologically relevant indices; (2) the identification of statistically significant, nonredundant, hydroecologically relevant indices associated with the five major flow components for each stream class; and (3) the development of a stream-classification tool and a hydrologic assessment tool. Four computer software tools have been developed.

MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.

PubMed

Martín-Campos, Trinidad; Mylonas, Roman; Masselot, Alexandre; Waridel, Patrice; Petricevic, Tanja; Xenarios, Ioannis; Quadroni, Manfredo

2017-08-04

Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTMs of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation. Software tools for large scale analyses are highly efficient but are rarely conceived for interactive, in-depth exploration of data on individual proteins. We here describe MsViz, a web-based and interactive software tool that supports manual validation of PTMs and their relative quantitation in small- and medium-size experiments. The tool displays sequence coverage information, peptide-spectrum matches, tandem MS spectra and extracted ion chromatograms through a single, highly intuitive interface. We found that MsViz greatly facilitates manual data inspection to validate PTM location and quantitate modified species across multiple samples.

The development procedures and tools applied for the attitude control software of the Italian satellite SAX

NASA Astrophysics Data System (ADS)

Hameetman, G. J.; Dekker, G. J.

1993-11-01

The Italian satellite (with a large Dutch contribution) SAX is a scientific satellite which has the mission to study roentgen sources. One main requirement for the Attitude and Orbit Control Subsystem (AOCS) is to achieve and maintain a stable pointing accuracy with a limit cycle of less than 90 arcsec during pointings of maximal 28 hours. The main SAX instrument, the Narrow Field Instrument, is highly sensitive to (indirect) radiation coming from the Sun. This sensitivity leads to another main requirement that under no circumstances the safe attitude domain may be left. The paper describes the application software in relation with the overall SAX AOCS subsystem, the CASE tools that have been used during the development, some advantages and disadvantages of the use of these tools, the measures taken to meet the more or less conflicting requirements of reliability and flexibility, and the lessons learned during development. The quality of the approach to the development has proven the (separately executed) hardware/software integration tests. During these tests, a neglectible number of software errors has been detected in the application software.

Virtual Power Electronics: Novel Software Tools for Design, Modeling and Education

NASA Astrophysics Data System (ADS)

Hamar, Janos; Nagy, István; Funato, Hirohito; Ogasawara, Satoshi; Dranga, Octavian; Nishida, Yasuyuki

The current paper is dedicated to present browser-based multimedia-rich software tools and e-learning curriculum to support the design and modeling process of power electronics circuits and to explain sometimes rather sophisticated phenomena. Two projects will be discussed. The so-called Inetele project is financed by the Leonardo da Vinci program of the European Union (EU). It is a collaborative project between numerous EU universities and institutes to develop state-of-the art curriculum in Electrical Engineering. Another cooperative project with participation of Japanese, European and Australian institutes focuses especially on developing e-learning curriculum, interactive design and modeling tools, furthermore on development of a virtual laboratory. Snapshots from these two projects will be presented.

Tool Support for Software Lookup Table Optimization

DOE PAGES

Wilcox, Chris; Strout, Michelle Mills; Bieman, James M.

2011-01-01

A number of scientific applications are performance-limited by expressions that repeatedly call costly elementary functions. Lookup table (LUT) optimization accelerates the evaluation of such functions by reusing previously computed results. LUT methods can speed up applications that tolerate an approximation of function results, thereby achieving a high level of fuzzy reuse. One problem with LUT optimization is the difficulty of controlling the tradeoff between performance and accuracy. The current practice of manual LUT optimization adds programming effort by requiring extensive experimentation to make this tradeoff, and such hand tuning can obfuscate algorithms. In this paper we describe a methodology andmore » tool implementation to improve the application of software LUT optimization. Our Mesa tool implements source-to-source transformations for C or C++ code to automate the tedious and error-prone aspects of LUT generation such as domain profiling, error analysis, and code generation. We evaluate Mesa with five scientific applications. Our results show a performance improvement of 3.0× and 6.9× for two molecular biology algorithms, 1.4× for a molecular dynamics program, 2.1× to 2.8× for a neural network application, and 4.6× for a hydrology calculation. We find that Mesa enables LUT optimization with more control over accuracy and less effort than manual approaches.« less

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

NASA Technical Reports Server (NTRS)

Walker, Carrie K.; Turkovich, John J.

1989-01-01

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

Using McIDAS-V data analysis and visualization software as an educational tool for understanding the atmosphere

NASA Astrophysics Data System (ADS)

Achtor, T. H.; Rink, T.

2010-12-01

The University of Wisconsin’s Space Science and Engineering Center (SSEC) has been at the forefront in developing data analysis and visualization tools for environmental satellites and other geophysical data. The fifth generation of the Man-computer Interactive Data Access System (McIDAS-V) is Java-based, open-source, freely available software that operates on Linux, Macintosh and Windows systems. The software tools provide powerful new data manipulation and visualization capabilities that work with geophysical data in research, operational and educational environments. McIDAS-V provides unique capabilities to support innovative techniques for evaluating research results, teaching and training. McIDAS-V is based on three powerful software elements. VisAD is a Java library for building interactive, collaborative, 4 dimensional visualization and analysis tools. The Integrated Data Viewer (IDV) is a reference application based on the VisAD system and developed by the Unidata program that demonstrates the flexibility that is needed in this evolving environment, using a modern, object-oriented software design approach. The third tool, HYDRA, allows users to build, display and interrogate multi and hyperspectral environmental satellite data in powerful ways. The McIDAS-V software is being used for training and education in several settings. The McIDAS User Group provides training workshops at its annual meeting. Numerous online tutorials with training data sets have been developed to aid users in learning simple and more complex operations in McIDAS-V, all are available online. In a University of Wisconsin-Madison undergraduate course in Radar and Satellite Meteorology, McIDAS-V is used to create and deliver laboratory exercises using case study and real time data. At the high school level, McIDAS-V is used in several exercises in our annual Summer Workshop in Earth and Atmospheric Sciences to provide young scientists the opportunity to examine data with friendly and

Software engineering

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Toolkit of Available EPA Green Infrastructure Modeling Software: Watershed Management Optimization Support Tool (WMOST)

EPA Science Inventory

Watershed Management Optimization Support Tool (WMOST) is a software application designed tofacilitate integrated water resources management across wet and dry climate regions. It allows waterresources managers and planners to screen a wide range of practices across their watersh...

Distributed and Collaborative Software Analysis

NASA Astrophysics Data System (ADS)

Ghezzi, Giacomo; Gall, Harald C.

Throughout the years software engineers have come up with a myriad of specialized tools and techniques that focus on a certain type of software analysissoftware analysis such as source code analysis, co-change analysis or bug prediction. However, easy and straight forward synergies between these analyses and tools rarely exist because of their stand-alone nature, their platform dependence, their different input and output formats and the variety of data to analyze. As a consequence, distributed and collaborative software analysiscollaborative software analysis scenarios and in particular interoperability are severely limited. We describe a distributed and collaborative software analysis platform that allows for a seamless interoperability of software analysis tools across platform, geographical and organizational boundaries. We realize software analysis tools as services that can be accessed and composed over the Internet. These distributed analysis services shall be widely accessible in our incrementally augmented Software Analysis Broker software analysis broker where organizations and tool providers can register and share their tools. To allow (semi-) automatic use and composition of these tools, they are classified and mapped into a software analysis taxonomy and adhere to specific meta-models and ontologiesontologies for their category of analysis.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Software reengineering

NASA Technical Reports Server (NTRS)

Fridge, Ernest M., III

1991-01-01

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

Design, Development and Delivery of Active Learning Tools in Software Verification & Validation Education

ERIC Educational Resources Information Center

Acharya, Sushil; Manohar, Priyadarshan Anant; Wu, Peter; Maxim, Bruce; Hansen, Mary

2018-01-01

Active learning tools are critical in imparting real world experiences to the students within a classroom environment. This is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains with little to no training. However, there is a well-recognized need for the…

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.

Development and Evaluation of Computer-Based Laboratory Practical Learning Tool

ERIC Educational Resources Information Center

Gandole, Y. B.

2006-01-01

Effective evaluation of educational software is a key issue for successful introduction of advanced tools in the curriculum. This paper details to developing and evaluating a tool for computer assisted learning of science laboratory courses. The process was based on the generic instructional system design model. Various categories of educational…

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

PubMed

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

2013-12-01

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

Development of Usability Criteria for E-Learning Content Development Software

ERIC Educational Resources Information Center

Celik, Serkan

2012-01-01

Revolutionary advancements have been observed in e-learning technologies though an amalgamated evaluation methodology for new generation e-learning content development tools is not available. The evaluation of educational software for online use must consider its usability and as well as its pedagogic effectiveness. This study is a first step…

Advanced Transport Operating System (ATOPS) color displays software description: MicroVAX system

NASA Technical Reports Server (NTRS)

Slominski, Christopher J.; Plyler, Valerie E.; Dickson, Richard W.

1992-01-01

This document describes the software created for the Display MicroVAX computer used for the Advanced Transport Operating Systems (ATOPS) project on the Transport Systems Research Vehicle (TSRV). The software delivery of February 27, 1991, known as the 'baseline display system', is the one described in this document. Throughout this publication, module descriptions are presented in a standardized format which contains module purpose, calling sequence, detailed description, and global references. The global references section includes subroutines, functions, and common variables referenced by a particular module. The system described supports the Research Flight Deck (RFD) of the TSRV. The RFD contains eight Cathode Ray Tubes (CRTs) which depict a Primary Flight Display, Navigation Display, System Warning Display, Takeoff Performance Monitoring System Display, and Engine Display.

Interoperability of Neuroscience Modeling Software

PubMed Central

Cannon, Robert C.; Gewaltig, Marc-Oliver; Gleeson, Padraig; Bhalla, Upinder S.; Cornelis, Hugo; Hines, Michael L.; Howell, Fredrick W.; Muller, Eilif; Stiles, Joel R.; Wils, Stefan; De Schutter, Erik

2009-01-01

Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena. As a result, considerable effort is invested in the development of software tools and technologies for numerical simulations and for the creation and publication of models. The diversity of related tools leads to the duplication of effort and hinders model reuse. Development practices and technologies that support interoperability between software systems therefore play an important role in making the modeling process more efficient and in ensuring that published models can be reliably and easily reused. Various forms of interoperability are possible including the development of portable model description standards, the adoption of common simulation languages or the use of standardized middleware. Each of these approaches finds applications within the broad range of current modeling activity. However more effort is required in many areas to enable new scientific questions to be addressed. Here we present the conclusions of the “Neuro-IT Interoperability of Simulators” workshop, held at the 11th computational neuroscience meeting in Edinburgh (July 19-20 2006; http://www.cnsorg.org). We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance. PMID:17873374

A software tool for rapid flood inundation mapping

USGS Publications Warehouse

Verdin, James; Verdin, Kristine; Mathis, Melissa L.; Magadzire, Tamuka; Kabuchanga, Eric; Woodbury, Mark; Gadain, Hussein

2016-06-02

The GIS Flood Tool (GFT) was developed by the U.S. Geological Survey with support from the U.S. Agency for International Development’s Office of U.S. Foreign Disaster Assistance to provide a means for production of reconnaissance-level flood inundation mapping for data-sparse and resource-limited areas of the world. The GFT has also attracted interest as a tool for rapid assessment flood inundation mapping for the Flood Inundation Mapping Program of the U.S. Geological Survey. The GFT can fill an important gap for communities that lack flood inundation mapping by providing a first-estimate of inundation zones, pending availability of resources to complete an engineering study. The tool can also help identify priority areas for application of scarce flood inundation mapping resources. The technical basis of the GFT is an application of the Manning equation for steady flow in an open channel, operating on specially processed digital elevation data. The GFT is implemented as a software extension in ArcGIS. Output maps from the GFT were validated at 11 sites with inundation maps produced previously by the Flood Inundation Mapping Program using standard one-dimensional hydraulic modeling techniques. In 80 percent of the cases, the GFT inundation patterns matched 75 percent or more of the one-dimensional hydraulic model inundation patterns. Lower rates of pattern agreement were seen at sites with low relief and subtle surface water divides. Although the GFT is simple to use, it should be applied with the oversight or review of a qualified hydraulic engineer who understands the simplifying assumptions of the approach.

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.

Advanced Computing Tools and Models for Accelerator Physics

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

Ryne, Robert; Ryne, Robert D.

2008-06-11

This paper is based on a transcript of my EPAC'08 presentation on advanced computing tools for accelerator physics. Following an introduction I present several examples, provide a history of the development of beam dynamics capabilities, and conclude with thoughts on the future of large scale computing in accelerator physics.

Review of free software tools for image analysis of fluorescence cell micrographs.

PubMed

Wiesmann, V; Franz, D; Held, C; Münzenmayer, C; Palmisano, R; Wittenberg, T

2015-01-01

An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand-alone, Matlab-based, ImageJ-based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure-ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure-ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well-structured menu and intuitive graphical user interface. © 2014 Fraunhofer-Institute for Integrated Circuits IIS Journal of Microscopy © 2014 Royal Microscopical Society.

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.

Advances in knowledge-based software engineering

NASA Technical Reports Server (NTRS)

Truszkowski, Walt

1991-01-01

The underlying hypothesis of this work is that a rigorous and comprehensive software reuse methodology can bring about a more effective and efficient utilization of constrained resources in the development of large-scale software systems by both government and industry. It is also believed that correct use of this type of software engineering methodology can significantly contribute to the higher levels of reliability that will be required of future operational systems. An overview and discussion of current research in the development and application of two systems that support a rigorous reuse paradigm are presented: the Knowledge-Based Software Engineering Environment (KBSEE) and the Knowledge Acquisition fo the Preservation of Tradeoffs and Underlying Rationales (KAPTUR) systems. Emphasis is on a presentation of operational scenarios which highlight the major functional capabilities of the two systems.

Contingency Contractor Optimization Phase 3 Sustainment Third-Party Software List - Contingency Contractor Optimization Tool - Prototype

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

Durfee, Justin David; Frazier, Christopher Rawls; Bandlow, Alisa

2016-05-01

The Contingency Contractor Optimization Tool - Prototype (CCOT-P) requires several third-party software packages. These are documented below for each of the CCOT-P elements: client, web server, database server, solver, web application and polling application.

Integrated Design Tools Reduce Risk, Cost

NASA Technical Reports Server (NTRS)

2012-01-01

Thanks in part to a SBIR award with Langley Research Center, Phoenix Integration Inc., based in Wayne, Pennsylvania, modified and advanced software for process integration and design automation. For NASA, the tool has resulted in lower project costs and reductions in design time; clients of Phoenix Integration are experiencing the same rewards.

An integrated modeling and design tool for advanced optical spacecraft

NASA Technical Reports Server (NTRS)

Briggs, Hugh C.

1992-01-01

Consideration is given to the design and status of the Integrated Modeling of Optical Systems (IMOS) tool and to critical design issues. A multidisciplinary spacecraft design and analysis tool with support for structural dynamics, controls, thermal analysis, and optics, IMOS provides rapid and accurate end-to-end performance analysis, simulations, and optimization of advanced space-based optical systems. The requirements for IMOS-supported numerical arrays, user defined data structures, and a hierarchical data base are outlined, and initial experience with the tool is summarized. A simulation of a flexible telescope illustrates the integrated nature of the tools.

An open source software tool to assign the material properties of bone for ABAQUS finite element simulations.

PubMed

Pegg, Elise C; Gill, Harinderjit S

2016-09-06

A new software tool to assign the material properties of bone to an ABAQUS finite element mesh was created and compared with Bonemat, a similar tool originally designed to work with Ansys finite element models. Our software tool (py_bonemat_abaqus) was written in Python, which is the chosen scripting language for ABAQUS. The purpose of this study was to compare the software packages in terms of the material assignment calculation and processing speed. Three element types were compared (linear hexahedral (C3D8), linear tetrahedral (C3D4) and quadratic tetrahedral elements (C3D10)), both individually and as part of a mesh. Comparisons were made using a CT scan of a hemi-pelvis as a test case. A small difference, of -0.05kPa on average, was found between Bonemat version 3.1 (the current version) and our Python package. Errors were found in the previous release of Bonemat (version 3.0 downloaded from www.biomedtown.org) during calculation of the quadratic tetrahedron Jacobian, and conversion of the apparent density to modulus when integrating over the Young׳s modulus field. These issues caused up to 2GPa error in the modulus assignment. For these reasons, we recommend users upgrade to the most recent release of Bonemat. Processing speeds were assessed for the three different element types. Our Python package took significantly longer (110s on average) to perform the calculations compared with the Bonemat software (10s). Nevertheless, the workflow advantages of the package and added functionality makes 'py_bonemat_abaqus' a useful tool for ABAQUS users. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evidence synthesis software.

PubMed

Park, Sophie Elizabeth; Thomas, James

2018-06-07

It can be challenging to decide which evidence synthesis software to choose when doing a systematic review. This article discusses some of the important questions to consider in relation to the chosen method and synthesis approach. Software can support researchers in a range of ways. Here, a range of review conditions and software solutions. For example, facilitating contemporaneous collaboration across time and geographical space; in-built bias assessment tools; and line-by-line coding for qualitative textual analysis. EPPI-Reviewer is a review software for research synthesis managed by the EPPI-centre, UCL Institute of Education. EPPI-Reviewer has text mining automation technologies. Version 5 supports data sharing and re-use across the systematic review community. Open source software will soon be released. EPPI-Centre will continue to offer the software as a cloud-based service. The software is offered via a subscription with a one-month (extendible) trial available and volume discounts for 'site licences'. It is free to use for Cochrane and Campbell reviews. The next EPPI-Reviewer version is being built in collaboration with National Institute for Health and Care Excellence using 'surveillance' of newly published research to support 'living' iterative reviews. This is achieved using a combination of machine learning and traditional information retrieval technologies to identify the type of research each new publication describes and determine its relevance for a particular review, domain or guideline. While the amount of available knowledge and research is constantly increasing, the ways in which software can support the focus and relevance of data identification are also developing fast. Software advances are maximising the opportunities for the production of relevant and timely reviews. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise

A taxonomy and discussion of software attack technologies

NASA Astrophysics Data System (ADS)

Banks, Sheila B.; Stytz, Martin R.

2005-03-01

Software is a complex thing. It is not an engineering artifact that springs forth from a design by simply following software coding rules; creativity and the human element are at the heart of the process. Software development is part science, part art, and part craft. Design, architecture, and coding are equally important activities and in each of these activities, errors may be introduced that lead to security vulnerabilities. Therefore, inevitably, errors enter into the code. Some of these errors are discovered during testing; however, some are not. The best way to find security errors, whether they are introduced as part of the architecture development effort or coding effort, is to automate the security testing process to the maximum extent possible and add this class of tools to the tools available, which aids in the compilation process, testing, test analysis, and software distribution. Recent technological advances, improvements in computer-generated forces (CGFs), and results in research in information assurance and software protection indicate that we can build a semi-intelligent software security testing tool. However, before we can undertake the security testing automation effort, we must understand the scope of the required testing, the security failures that need to be uncovered during testing, and the characteristics of the failures. Therefore, we undertook the research reported in the paper, which is the development of a taxonomy and a discussion of software attacks generated from the point of view of the security tester with the goal of using the taxonomy to guide the development of the knowledge base for the automated security testing tool. The representation for attacks and threat cases yielded by this research captures the strategies, tactics, and other considerations that come into play during the planning and execution of attacks upon application software. The paper is organized as follows. Section one contains an introduction to our research

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.

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.

Payload software technology: Software technology development plan

NASA Technical Reports Server (NTRS)

1977-01-01

Programmatic requirements for the advancement of software technology are identified for meeting the space flight requirements in the 1980 to 1990 time period. The development items are described, and software technology item derivation worksheets are presented along with the cost/time/priority assessments.

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.

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

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

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

PubMed

Helt, Gregg A; Nicol, John W; Erwin, Ed; Blossom, Eric; Blanchard, Steven G; Chervitz, Stephen A; Harmon, Cyrus; Loraine, Ann E

2009-08-25

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities. Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/.

Review of Ground Systems Development and Operations (GSDO) Tools for Verifying Command and Control Software

NASA Technical Reports Server (NTRS)

Aguilar, Michael L.; Bonanne, Kevin H.; Favretto, Jeffrey A.; Jackson, Maddalena M.; Jones, Stephanie L.; Mackey, Ryan M.; Sarrel, Marc A.; Simpson, Kimberly A.

2014-01-01

The Exploration Systems Development (ESD) Standing Review Board (SRB) requested the NASA Engineering and Safety Center (NESC) conduct an independent review of the plan developed by Ground Systems Development and Operations (GSDO) for identifying models and emulators to create a tool(s) to verify their command and control software. The NESC was requested to identify any issues or weaknesses in the GSDO plan. This document contains the outcome of the NESC review.

Michigan Department of Transportation statewide advanced traffic management system (ATMS) procurement evaluation - phase I : software procurement.

DOT National Transportation Integrated Search

2009-04-01

This project evaluates the process that was followed by MDOT and other stakeholders for the acquisition : of new Advanced Traffic Management System (ATMS) software aiming to integrate and facilitate the : management of various Intelligent Transportat...

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.

ACTS (Advanced Communications Technology Satellite) Propagation Experiment: Preprocessing Software User's Manual

NASA Technical Reports Server (NTRS)

Crane, Robert K.; Wang, Xuhe; Westenhaver, David

1996-01-01

The preprocessing software manual describes the Actspp program originally developed to observe and diagnose Advanced Communications Technology Satellite (ACTS) propagation terminal/receiver problems. However, it has been quite useful for automating the preprocessing functions needed to convert the terminal output to useful attenuation estimates. Prior to having data acceptable for archival functions, the individual receiver system must be calibrated and the power level shifts caused by ranging tone modulation must be received. Actspp provides three output files: the daylog, the diurnal coefficient file, and the file that contains calibration information.

Development of the software tool for generation and visualization of the finite element head model with bone conduction sounds

NASA Astrophysics Data System (ADS)

Nikolić, Dalibor; Milošević, Žarko; Saveljić, Igor; Filipović, Nenad

2015-12-01

Vibration of the skull causes a hearing sensation. We call it Bone Conduction (BC) sound. There are several investigations about transmission properties of bone conducted sound. The aim of this study was to develop a software tool for easy generation of the finite element (FE) model of the human head with different materials based on human head anatomy and to calculate sound conduction through the head. Developed software tool generates a model in a few steps. The first step is to do segmentation of CT medical images (DICOM) and to generate a surface mesh files (STL). Each STL file presents a different layer of human head with different material properties (brain, CSF, different layers of the skull bone, skin, etc.). The next steps are to make tetrahedral mesh from obtained STL files, to define FE model boundary conditions and to solve FE equations. This tool uses PAK solver, which is the open source software implemented in SIFEM FP7 project, for calculations of the head vibration. Purpose of this tool is to show impact of the bone conduction sound of the head on the hearing system and to estimate matching of obtained results with experimental measurements.

Landscape analysis software tools

Treesearch

Don Vandendriesche

2008-01-01

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

Kubios HRV--heart rate variability analysis software.

PubMed

Tarvainen, Mika P; Niskanen, Juha-Pekka; Lipponen, Jukka A; Ranta-Aho, Perttu O; Karjalainen, Pasi A

2014-01-01

Kubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data. It includes an adaptive QRS detection algorithm and tools for artifact correction, trend removal and analysis sample selection. The software computes all the commonly used time-domain and frequency-domain HRV parameters and several nonlinear parameters. There are several adjustable analysis settings through which the analysis methods can be optimized for different data. The ECG derived respiratory frequency is also computed, which is important for reliable interpretation of the analysis results. The analysis results can be saved as an ASCII text file (easy to import into MS Excel or SPSS), Matlab MAT-file, or as a PDF report. The software is easy to use through its compact graphical user interface. The software is available free of charge for Windows and Linux operating systems at http://kubios.uef.fi. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A PICKSC Science Gateway for enabling the common plasma physicist to run kinetic software

NASA Astrophysics Data System (ADS)

Hu, Q.; Winjum, B. J.; Zonca, A.; Youn, C.; Tsung, F. S.; Mori, W. B.

2017-10-01

Computer simulations offer tremendous opportunities for studying plasmas, ranging from simulations for students that illuminate fundamental educational concepts to research-level simulations that advance scientific knowledge. Nevertheless, there is a significant hurdle to using simulation tools. Users must navigate codes and software libraries, determine how to wrangle output into meaningful plots, and oftentimes confront a significant cyberinfrastructure with powerful computational resources. Science gateways offer a Web-based environment to run simulations without needing to learn or manage the underlying software and computing cyberinfrastructure. We discuss our progress on creating a Science Gateway for the Particle-in-Cell and Kinetic Simulation Software Center that enables users to easily run and analyze kinetic simulations with our software. We envision that this technology could benefit a wide range of plasma physicists, both in the use of our simulation tools as well as in its adaptation for running other plasma simulation software. Supported by NSF under Grant ACI-1339893 and by the UCLA Institute for Digital Research and Education.

In-depth evaluation of software tools for data-independent acquisition based label-free quantification.

PubMed

Kuharev, Jörg; Navarro, Pedro; Distler, Ute; Jahn, Olaf; Tenzer, Stefan

2015-09-01

Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and downregulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on quantification results. Analysis of technical reproducibility revealed median coefficients of variation of reported protein abundances below 5% for MS(E) data for Progenesis and ISOQuant. Regarding accuracy of LFQ, evaluation with synapter and ISOQuant yielded superior results compared to Progenesis. In addition, we discuss reporting formats and user friendliness of the software packages. The data generated in this study have been deposited to the ProteomeXchange Consortium with identifier PXD001240 (http://proteomecentral.proteomexchange.org/dataset/PXD001240). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Evaluation of reliability modeling tools for advanced fault tolerant systems

NASA Technical Reports Server (NTRS)

Baker, Robert; Scheper, Charlotte

1986-01-01

The Computer Aided Reliability Estimation (CARE III) and Automated Reliability Interactice Estimation System (ARIES 82) reliability tools for application to advanced fault tolerance aerospace systems were evaluated. To determine reliability modeling requirements, the evaluation focused on the Draper Laboratories' Advanced Information Processing System (AIPS) architecture as an example architecture for fault tolerance aerospace systems. Advantages and limitations were identified for each reliability evaluation tool. The CARE III program was designed primarily for analyzing ultrareliable flight control systems. The ARIES 82 program's primary use was to support university research and teaching. Both CARE III and ARIES 82 were not suited for determining the reliability of complex nodal networks of the type used to interconnect processing sites in the AIPS architecture. It was concluded that ARIES was not suitable for modeling advanced fault tolerant systems. It was further concluded that subject to some limitations (the difficulty in modeling systems with unpowered spare modules, systems where equipment maintenance must be considered, systems where failure depends on the sequence in which faults occurred, and systems where multiple faults greater than a double near coincident faults must be considered), CARE III is best suited for evaluating the reliability of advanced tolerant systems for air transport.

Towards a publicly available, map-based regional software tool to estimate unregulated daily streamflow at ungauged rivers

USGS Publications Warehouse

Archfield, Stacey A.; Steeves, Peter A.; Guthrie, John D.; Ries, Kernell G.

2013-01-01

Streamflow information is critical for addressing any number of hydrologic problems. Often, streamflow information is needed at locations that are ungauged and, therefore, have no observations on which to base water management decisions. Furthermore, there has been increasing need for daily streamflow time series to manage rivers for both human and ecological functions. To facilitate negotiation between human and ecological demands for water, this paper presents the first publicly available, map-based, regional software tool to estimate historical, unregulated, daily streamflow time series (streamflow not affected by human alteration such as dams or water withdrawals) at any user-selected ungauged river location. The map interface allows users to locate and click on a river location, which then links to a spreadsheet-based program that computes estimates of daily streamflow for the river location selected. For a demonstration region in the northeast United States, daily streamflow was, in general, shown to be reliably estimated by the software tool. Estimating the highest and lowest streamflows that occurred in the demonstration region over the period from 1960 through 2004 also was accomplished but with more difficulty and limitations. The software tool provides a general framework that can be applied to other regions for which daily streamflow estimates are needed.

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules.

PubMed

Solernou, Albert; Hanson, Benjamin S; Richardson, Robin A; Welch, Robert; Read, Daniel J; Harlen, Oliver G; Harris, Sarah A

2018-03-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package.

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

PubMed Central

Solernou, Albert

2018-01-01

Fluctuating Finite Element Analysis (FFEA) is a software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools. It requires 3D volumetric information as input, which can be low resolution structural information such as cryo-electron tomography (cryo-ET) maps or much higher resolution atomistic co-ordinates from which volumetric information can be extracted. In this article we introduce our open source software package for performing FFEA simulations which we have released under a GPLv3 license. The software package includes a C ++ implementation of FFEA, together with tools to assist the user to set up the system from Electron Microscopy Data Bank (EMDB) or Protein Data Bank (PDB) data files. We also provide a PyMOL plugin to perform basic visualisation and additional Python tools for the analysis of FFEA simulation trajectories. This manuscript provides a basic background to the FFEA method, describing the implementation of the core mechanical model and how intermolecular interactions and the solvent environment are included within this framework. We provide prospective FFEA users with a practical overview of how to set up an FFEA simulation with reference to our publicly available online tutorials and manuals that accompany this first release of the package. PMID:29570700

Cost benefits of advanced software: A review of methodology used at Kennedy Space Center

NASA Technical Reports Server (NTRS)

Joglekar, Prafulla N.

1993-01-01

To assist rational investments in advanced software, a formal, explicit, and multi-perspective cost-benefit analysis methodology is proposed. The methodology can be implemented through a six-stage process which is described and explained. The current practice of cost-benefit analysis at KSC is reviewed in the light of this methodology. The review finds that there is a vicious circle operating. Unsound methods lead to unreliable cost-benefit estimates. Unreliable estimates convince management that cost-benefit studies should not be taken seriously. Then, given external demands for cost-benefit estimates, management encourages software enginees to somehow come up with the numbers for their projects. Lacking the expertise needed to do a proper study, courageous software engineers with vested interests use ad hoc and unsound methods to generate some estimates. In turn, these estimates are unreliable, and the cycle continues. The proposed methodology should help KSC to break out of this cycle.

PsychoPy--Psychophysics software in Python.

PubMed

Peirce, Jonathan W

2007-05-15

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

PsychoPy—Psychophysics software in Python

PubMed Central

Peirce, Jonathan W.

2007-01-01

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

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.

Software system safety

NASA Technical Reports Server (NTRS)

Uber, James G.

1988-01-01

Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

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

DTIC Science & Technology

2011-05-10

concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility...existing surveillance applications or the SAGES tools may be used en masse for an end–to-end biosurveillance capability. doi:10.1371/journal.pone...health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular

TaxI: a software tool for DNA barcoding using distance methods

PubMed Central

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

2005-01-01

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

S2O - A software tool for integrating research data from general purpose statistic software into electronic data capture systems.

PubMed

Bruland, Philipp; Dugas, Martin

2017-01-07

Data capture for clinical registries or pilot studies is often performed in spreadsheet-based applications like Microsoft Excel or IBM SPSS. Usually, data is transferred into statistic software, such as SAS, R or IBM SPSS Statistics, for analyses afterwards. Spreadsheet-based solutions suffer from several drawbacks: It is generally not possible to ensure a sufficient right and role management; it is not traced who has changed data when and why. Therefore, such systems are not able to comply with regulatory requirements for electronic data capture in clinical trials. In contrast, Electronic Data Capture (EDC) software enables a reliable, secure and auditable collection of data. In this regard, most EDC vendors support the CDISC ODM standard to define, communicate and archive clinical trial meta- and patient data. Advantages of EDC systems are support for multi-user and multicenter clinical trials as well as auditable data. Migration from spreadsheet based data collection to EDC systems is labor-intensive and time-consuming at present. Hence, the objectives of this research work are to develop a mapping model and implement a converter between the IBM SPSS and CDISC ODM standard and to evaluate this approach regarding syntactic and semantic correctness. A mapping model between IBM SPSS and CDISC ODM data structures was developed. SPSS variables and patient values can be mapped and converted into ODM. Statistical and display attributes from SPSS are not corresponding to any ODM elements; study related ODM elements are not available in SPSS. The S2O converting tool was implemented as command-line-tool using the SPSS internal Java plugin. Syntactic and semantic correctness was validated with different ODM tools and reverse transformation from ODM into SPSS format. Clinical data values were also successfully transformed into the ODM structure. Transformation between the spreadsheet format IBM SPSS and the ODM standard for definition and exchange of trial data is feasible

Toolpack mathematical software development environment

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

Osterweil, L.

1982-07-21

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

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

LevRad software as a tool to learn how to proceed with an evaluation of barriers.

PubMed

Ferreira, C C; Souza, S O

2011-05-30

We developed the software LevRad with the objective of teaching how to proceed in an analysis of barriers shielding against x-rays to minimize the contact of the professional or the student with x-rays and also to prevent wearing out of the x-ray equipment. Some tests of the software were made, and preliminary results indicate that LevRad is efficient as a complementary tool for the development of professionals related to diagnostic radiology. In the case of education, an advantage is gained when the beginner uses the software before his or her first contact with x-ray equipment in locu. The software introduces a basic knowledge about evaluation of barriers, prevents wearing out of the x—ray tube, reinforces teaching of evaluation of barriers, and reduces the collective effective dose by avoiding unnecessary exposures when possible.

OsiriX software as a preoperative planning tool in cranial neurosurgery: A step-by-step guide for neurosurgical residents

PubMed Central

Spiriev, Toma; Nakov, Vladimir; Laleva, Lili; Tzekov, Christo

2017-01-01

Background: OsiriX (Pixmeo, Switzerland) is an open-source Digital Imaging and Communications in Medicine (DICOM) viewer that is gaining more and more attention in the neurosurgical community because of its user-friendly interface, powerful three-dimensional (3D) volumetric rendering capabilities, and various options for data integration. This paper presents in detail the use of OsiriX software as a preoperative planning tool in cranial neurosurgery. Methods: In January 2013, OsiriX software was introduced into our clinical practice as a preoperative planning tool. Its capabilities are being evaluated on an ongoing basis in routine elective cranial cases. Results: The program has proven to be highly effective at volumetrically representing data from radiological examinations in 3D. Among its benefits in preoperative planning are simulating the position and exact location of the lesion in 3D, tailoring the skin incision and craniotomy bone flap, enhancing the representation of normal and pathological anatomy, and aiding in planning the reconstruction of the affected area. Conclusion: OsiriX is a useful tool for preoperative planning and visualization in neurosurgery. The software greatly facilitates the surgeon's understanding of the relationship between normal and pathological anatomy and can be used as a teaching tool. PMID:29119039

Tools and Methods for Teaching Informatics at School: An Advanced Logo Course.

ERIC Educational Resources Information Center

Nikolov, Rumen

1992-01-01

Describes a course in educational informatics for preservice teachers and students in educational software development that emphasizes the use of LOGO, and summarizes course modules that cover tools and methods for teaching informatics, informatics curriculum design, introducing the basic notions of informatics, integrating informatics into the…

Proofreading using an assistive software homophone tool: compensatory and remedial effects on the literacy skills of students with reading difficulties.

PubMed

Lange, Alissa A; Mulhern, Gerry; Wylie, Judith

2009-01-01

The present study investigated the effects of using an assistive software homophone tool on the assisted proofreading performance and unassisted basic skills of secondary-level students with reading difficulties. Students aged 13 to 15 years proofread passages for homophonic errors under three conditions: with the homophone tool, with homophones highlighted only, or with no help. The group using the homophone tool significantly outperformed the other two groups on assisted proofreading and outperformed the others on unassisted spelling, although not significantly. Remedial (unassisted) improvements in automaticity of word recognition, homophone proofreading, and basic reading were found over all groups. Results elucidate the differential contributions of each function of the homophone tool and suggest that with the proper training, assistive software can help not only students with diagnosed disabilities but also those with generally weak reading skills.

Semantic integration of gene expression analysis tools and data sources using software connectors

PubMed Central

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

Semantic integration of gene expression analysis tools and data sources using software connectors.

PubMed

Miyazaki, Flávia A; Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

2013-10-25

The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The

Autonomy Software: V&V Challenges and Characteristics

NASA Technical Reports Server (NTRS)

Schumann, Johann; Visser, Willem

2006-01-01

The successful operation of unmanned air vehicles requires software with a high degree of autonomy. Only if high level functions can be carried out without human control and intervention, complex missions in a changing and potentially unknown environment can be carried out successfully. Autonomy software is highly mission and safety critical: failures, caused by flaws in the software cannot only jeopardize the mission, but could also endanger human life (e.g., a crash of an UAV in a densely populated area). Due to its large size, high complexity, and use of specialized algorithms (planner, constraint-solver, etc.), autonomy software poses specific challenges for its verification, validation, and certification. -- - we have carried out a survey among researchers aid scientists at NASA to study these issues. In this paper, we will present major results of this study, discussing the broad spectrum. of notions and characteristics of autonomy software and its challenges for design and development. A main focus of this survey was to evaluate verification and validation (V&V) issues and challenges, compared to the development of "traditional" safety-critical software. We will discuss important issues in V&V of autonomous software and advanced V&V tools which can help to mitigate software risks. Results of this survey will help to identify and understand safety concerns in autonomy software and will lead to improved strategies for mitigation of these risks.

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical

Software Testing and Verification in Climate Model Development

NASA Technical Reports Server (NTRS)

Clune, Thomas L.; Rood, RIchard B.

2011-01-01

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

Advanced Flow Control as a Management Tool in the National Airspace System

NASA Technical Reports Server (NTRS)

Wugalter, S.

1974-01-01

Advanced Flow Control is closely related to Air Traffic Control. Air Traffic Control is the business of the Federal Aviation Administration. To formulate an understanding of advanced flow control and its use as a management tool in the National Airspace System, it becomes necessary to speak somewhat of air traffic control, the role of FAA, and their relationship to advanced flow control. Also, this should dispell forever, any notion that advanced flow control is the inspirational master valve scheme to be used on the Alaskan Oil Pipeline.

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

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

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

Material Protection, Accounting, and Control Technologies (MPACT) Advanced Integration Roadmap

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

Miller, Mike; Cipiti, Ben; Demuth, Scott Francis

2017-01-30

The development of sustainable advanced nuclear fuel cycles is a long-term goal of the Office of Nuclear Energy’s (DOE-NE) Fuel Cycle Technologies program. The Material Protection, Accounting, and Control Technologies (MPACT) campaign is supporting research and development (R&D) of advanced instrumentation, analysis tools, and integration methodologies to meet this goal (Miller, 2015). This advanced R&D is intended to facilitate safeguards and security by design of fuel cycle facilities. The lab-scale demonstration of a virtual facility, distributed test bed, that connects the individual tools being developed at National Laboratories and university research establishments, is a key program milestone for 2020. Thesemore » tools will consist of instrumentation and devices as well as computer software for modeling, simulation and integration.« less

Material Protection, Accounting, and Control Technologies (MPACT) Advanced Integration Roadmap

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

Durkee, Joe W.; Cipiti, Ben; Demuth, Scott Francis

The development of sustainable advanced nuclear fuel cycles is a long-term goal of the Office of Nuclear Energy’s (DOE-NE) Fuel Cycle Technologies program. The Material Protection, Accounting, and Control Technologies (MPACT) campaign is supporting research and development (R&D) of advanced instrumentation, analysis tools, and integration methodologies to meet this goal (Miller, 2015). This advanced R&D is intended to facilitate safeguards and security by design of fuel cycle facilities. The lab-scale demonstration of a virtual facility, distributed test bed, that connects the individual tools being developed at National Laboratories and university research establishments, is a key program milestone for 2020. Thesemore » tools will consist of instrumentation and devices as well as computer software for modeling, simulation and integration.« less

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

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

Effectiveness and usability of Scanning Wizard software: a tool for enhancing switch scanning.

PubMed

Koester, Heidi Horstmann; Simpson, Richard C

2017-11-24

Scanning Wizard software helps scanning users improve the setup of their switch and scanning system. This study evaluated Scanning Wizard's effectiveness and usability. Ten people who use switch scanning and ten practitioners used Scanning Wizard in the initial session. Usability was high, based on survey responses averaging over 4.5 out of 5, and qualitative feedback was very positive. Five switch users were able to complete the multi-week protocol, using settings on their own scanning system that were recommended from the Scanning Wizard session. Using these revised settings, text entry rates improved by an average of 71%, ranging from 29% to 172% improvement. Results suggest that Scanning Wizard is a useful tool for improving the configuration of scanning systems for people who use switch scanning to communicate. Implications for Rehabilitation Some individuals with severe physical impairments use switch scanning for spoken and written communication. Scanning Wizard software helps scanning users improve the setup of their switch and scanning system. This study demonstrated high usability of Scanning Wizard (with 10 switch userpractitioner teams) and increased text entry rate by an average of 71% (for five switch users). Results suggest that Scanning Wizard is a useful tool for improving the configuration of scanning systems for people who use switch scanning to communicate.

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.

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

New software for statistical analysis of Cambridge Structural Database data